void
nco_dmn_dfn /* [fnc] Define dimensions in output file */
(const char * const fl_nm, /* I [sng] Name of output file */
const int nc_id, /* I [id] netCDF output file ID */
dmn_sct ** const dmn, /* I [sct] Dimension structures to define in output file */
const int nbr_dmn) /* I [nbr] Number of dimension structures in structure list */
{
/* Purpose: Define dimensions in output file */
int idx;
int rcd=NC_NOERR; /* [rcd] Return code */
for(idx=0;idx<nbr_dmn;idx++){
/* Has dimension already been defined? */
rcd=nco_inq_dimid_flg(nc_id,dmn[idx]->nm,&dmn[idx]->id);
/* If dimension has not been defined yet, define it */
if(rcd != NC_NOERR){
if(dmn[idx]->is_rec_dmn){
(void)nco_def_dim(nc_id,dmn[idx]->nm,NC_UNLIMITED,&(dmn[idx]->id));
}else{
(void)nco_def_dim(nc_id,dmn[idx]->nm,dmn[idx]->cnt,&(dmn[idx]->id));
} /* end else */
}else{
(void)fprintf(stderr,"%s: WARNING dimension \"%s\" is already defined in %s\n",nco_prg_nm_get(),dmn[idx]->nm,fl_nm);
} /* end if */
} /* end loop over idx */
} /* end nco_dmn_dfn() */
nco_bool /* O [flg] File obeys CCM/CCSM/CF conventions */
nco_cnv_ccm_ccsm_cf_inq /* O [fnc] Check if file obeys CCM/CCSM/CF conventions */
(const int nc_id) /* I [id] netCDF file ID */
{
/* Purpose: Check if file adheres to CCM/CCSM/CF history tape format */
nco_bool CNV_CCM_CCSM_CF=False;
char *att_val;
char *cnv_sng=NULL_CEWI;
/* netCDF standard is uppercase Conventions, though some models user lowercase */
char cnv_sng_UC[]="Conventions"; /* Unidata standard string (uppercase) */
char cnv_sng_LC[]="conventions"; /* Unidata non-standard string (lowercase) */
int rcd; /* [rcd] Return code */
long att_sz;
nc_type att_typ;
/* Look for signature of a CCM/CCSM/CF-format file */
cnv_sng=cnv_sng_UC;
rcd=nco_inq_att_flg(nc_id,NC_GLOBAL,cnv_sng,&att_typ,&att_sz);
if(rcd != NC_NOERR){
/* Re-try with lowercase string because some models, e.g., CLM, user lowercase "conventions" */
cnv_sng=cnv_sng_LC;
rcd=nco_inq_att_flg(nc_id,NC_GLOBAL,cnv_sng,&att_typ,&att_sz);
} /* endif lowercase */
if(rcd == NC_NOERR && att_typ == NC_CHAR){
/* Add one for NUL byte */
att_val=(char *)nco_malloc(att_sz*nco_typ_lng(att_typ)+1L);
(void)nco_get_att(nc_id,NC_GLOBAL,cnv_sng,att_val,att_typ);
/* NUL-terminate convention attribute before using strcmp() */
att_val[att_sz]='\0';
/* CCM3, CCSM1 conventions */
if(strstr(att_val,"NCAR-CSM")) CNV_CCM_CCSM_CF=True; /* Backwards compatibility */
/* Climate-Forecast conventions */
if(strstr(att_val,"CF-1.")) CNV_CCM_CCSM_CF=True; /* NB: Not fully implemented TODO nco145 */
/* As of 20060514, CLM 3.0 uses CF1.0 not CF-1.0 (CAM gets it right) */
if(strstr(att_val,"CF1.")) CNV_CCM_CCSM_CF=True; /* NB: Not fully implemented TODO nco145 */
if(CNV_CCM_CCSM_CF && nco_dbg_lvl_get() >= nco_dbg_std){
(void)fprintf(stderr,"%s: CONVENTION File \"%s\" attribute is \"%s\"\n",nco_prg_nm_get(),cnv_sng,att_val);
if(cnv_sng == cnv_sng_LC) (void)fprintf(stderr,"%s: WARNING: This file uses a non-standard attribute (\"%s\") to indicate the netCDF convention. The correct attribute is \"%s\".\n",nco_prg_nm_get(),cnv_sng_LC,cnv_sng_UC);
/* Only warn in arithmetic operators where conventions change behavior */
if(nco_dbg_lvl_get() >= nco_dbg_fl && nco_dbg_lvl_get() != nco_dbg_dev && nco_is_rth_opr(nco_prg_id_get())) (void)fprintf(stderr,"%s: INFO NCO attempts to abide by many official and unofficial metadata conventions including ARM, CCM, CCSM, and CF. To adhere to these conventions, NCO implements variable-specific exceptions in certain operators, e.g., ncbo will not subtract variables named \"date\" or \"gw\", and many operators will always leave coordinate variables unchanged. The full list of exceptions is in the manual http://nco.sf.net/nco.html#CF\n",nco_prg_nm_get());
} /* endif dbg */
att_val=(char *)nco_free(att_val);
} /* endif */
return CNV_CCM_CCSM_CF;
} /* end nco_cnv_ccm_ccsm_cf_inq */
int /* [rcd] Successful conversion returns NCO_NOERR */
nco_cln_prs_tm /* UDUnits2 Extract time stamp from parsed UDUnits string */
(const char *unt_sng, /* I [ptr] units attribute string */
tm_cln_sct *tm_in) /* O [sct] Time structure to be populated */
{
const char fnc_nm[]="nco_cln_prs_tm()"; /* [sng] Function name */
/* 20141230: fxm figure out a better length */
char bfr[200];
char *dt_sng;
int ut_rcd; /* [enm] UDUnits2 status */
ut_system *ut_sys;
ut_unit *ut_sct_in; /* UDUnits structure, input units */
/* When empty, ut_read_xml() uses environment variable UDUNITS2_XML_PATH, if any
Otherwise it uses default initial location hardcoded when library was built */
if(nco_dbg_lvl_get() >= nco_dbg_vrb) ut_set_error_message_handler(ut_write_to_stderr); else ut_set_error_message_handler(ut_ignore);
ut_sys=ut_read_xml(NULL);
if(ut_sys == NULL){
(void)fprintf(stdout,"%s: %s failed to initialize UDUnits2 library\n",nco_prg_nm_get(),fnc_nm);
return NCO_ERR; /* Failure */
} /* end if err */
/* Units string to convert from */
ut_sct_in=ut_parse(ut_sys,unt_sng,UT_ASCII);
if(ut_sct_in == NULL){ /* Problem with 'units' attribute */
ut_rcd=ut_get_status(); /* [enm] UDUnits2 status */
if(ut_rcd == UT_BAD_ARG) (void)fprintf(stderr,"ERROR: empty units attribute string\n");
if(ut_rcd == UT_SYNTAX) (void)fprintf(stderr,"ERROR: units attribute \"%s\" has a syntax error\n",unt_sng);
if(ut_rcd == UT_UNKNOWN) (void)fprintf(stderr,"ERROR: units attribute \"%s\" is not listed in UDUnits2 SI system database\n",unt_sng);
return NCO_ERR; /* Failure */
} /* endif coordinate on disk has no units attribute */
/* Print timestamp to buffer in standard, dependable format */
ut_format(ut_sct_in,bfr,sizeof(bfr),UT_ASCII|UT_NAMES);
/* Extract parsed time units from print string (kludgy)
20141230 change to using ut_decode_time() instead? */
dt_sng=strstr(bfr,"since");
sscanf(dt_sng,"%*s %d-%d-%d %d:%d:%f",&tm_in->year,&tm_in->month,&tm_in->day,&tm_in->hour,&tm_in->min,&tm_in->sec);
ut_free_system(ut_sys); /* Free memory taken by UDUnits library */
ut_free(ut_sct_in);
return NCO_NOERR;
} /* end UDUnits2 nco_cln_prs_tm() */
void
err_prn /* [fnc] Print formatted error messages */
(char *err_msg) /* I [sng] Formatted error message to print */
{
/* Purpose: Print error message (currently only to stdout) approximately in GNU style, i.e., "program_name: ERROR error message....\n".
Routine is intended to make error messages convenient to use in routines without routine itself needing access to copy of program.
Therefore a copy of this routine should be placed in each main.c file, just like the program's nco_usg_prn() routine. */
/* Routine is more difficult to implement practically than it first seemed, because
it assumes all calling routines have their error messages in a single string, when
in reality, they often utilize var_args capabilities of fprintf() themselves and
have multiple formatted inputs. Hold off for now. */
(void)fprintf(stdout,"%s: %s",nco_prg_nm_get(),err_msg);
} /* end err_prn() */
FILE * /* O [fl] Unformatted binary file handle */
nco_bnr_open /* [fnc] Open unformatted binary data file */
(const char * const fl_bnr, /* [sng] Unformatted binary file */
const char * const fl_mode) /* [sng] Open-mode ("r", "w", ...) */
{
/* Purpose: Open unformatted binary data file for writing */
FILE *fp_bnr; /* [fl] Unformatted binary output file handle */
/* Open output file */
if((fp_bnr=fopen(fl_bnr,fl_mode)) == NULL){
(void)fprintf(stderr,"%s: ERROR unable to open binary output file %s\n",nco_prg_nm_get(),fl_bnr);
nco_exit(EXIT_FAILURE);
} /* end if */
if(nco_dbg_lvl_get() >= nco_dbg_fl) (void)fprintf(stdout,"%s: Opened binary file %s\n",nco_prg_nm_get(),fl_bnr);
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"Variable(s): Name (native type, # elements x bytes per element):\n");
return fp_bnr; /* O [fl] Unformatted binary output file handle */
} /* end nco_bnr_open() */
int /* [rcd] Successful conversion returns NCO_NOERR */
nco_cln_prs_tm /* UDUnits1 Extract time stamp from a parsed udunits string */
(const char *unt_sng, /* I [ptr] units attribute string */
tm_cln_sct *tm_in) /* O [sct] Time structure to be populated */
{
const char fnc_nm[]="nco_cln_prs_tm()"; /* [sng] Function name */
int rcd;
utUnit udu_sct_in; /* UDUnits structure, input units */
#ifdef UDUNITS_PATH
/* UDUNITS_PATH macro expands to where autoconf found database file */
rcd=utInit(UDUNITS_PATH);
#else /* !UDUNITS_PATH */
/* When empty, utInit() uses environment variable UDUNITS_PATH, if any
Otherwise it uses default initial location hardcoded when library was built */
rcd=utInit("");
#endif /* !UDUNITS_PATH */
if(rcd != UDUNITS_NOERR){
(void)fprintf(stdout,"%s: %s failed to initialize UDUnits library\n",nco_prg_nm_get(),fnc_nm);
return NCO_ERR;
} /* end if err */
/* Units string to convert from */
rcd=utScan(unt_sng,&udu_sct_in);
if(rcd != UDUNITS_NOERR){
if(rcd == UT_EINVALID) (void)fprintf(stderr,"ERROR: units attribute \"%s\" is invalid \n",unt_sng);
if(rcd == UT_ESYNTAX) (void)fprintf(stderr,"ERROR units attribute \"%s\" contains a syntax error",unt_sng);
if(rcd == UT_EUNKNOWN) (void)fprintf(stderr,"ERROR units attribute \"%s\" is not in udunits database",unt_sng);
(void)utTerm(); /* Free memory taken by UDUnits library */
return NCO_ERR;
} /* endif unkown type */
/* Extract time origin */
if(utIsTime(&udu_sct_in)){
utCalendar(0.0,&udu_sct_in,&tm_in->year,&tm_in->month,&tm_in->day,&tm_in->hour,&tm_in->min,&tm_in->sec);
rcd=NCO_NOERR;
}else{
rcd=NCO_ERR;
} /* endelse */
(void)utTerm(); /* Free memory taken by UDUnits library */
return rcd;
} /* end UDUnits1 nco_cln_prs_tm() */
int /* O [enm] Return code */
nco_var_prc_crr_prn /* [fnc] Print name of current variable */
(const int idx, /* I [idx] Index of current variable */
const char * const var_nm) /* I [sng] Variable name */
{
/* Purpose: Print name of current variable */
int rcd=0; /* [rcd] Return code */
#ifdef _OPENMP
(void)fprintf(stderr,"%s: INFO main loop thread #%d processing var_prc[%d] = \"%s\"\n",nco_prg_nm_get(),omp_get_thread_num(),idx,var_nm);
#else /* !_OPENMP */
rcd+=idx*0; /* CEWI */
(void)fprintf(stderr,"%s: INFO main loop processing var_prc[%d] = \"%s\"\n",nco_prg_nm_get(),idx,var_nm);
#endif /* !_OPENMP */
return rcd;
} /* end nco_var_prc_crr_prn() */
int /* [rcd] Return code */
nco_bnr_close /* [fnc] Close unformatted binary data file for writing */
(FILE *fp_bnr, /* I [fl] Unformatted binary output file handle */
const char * const fl_bnr) /* [sng] Unformatted binary output file */
{
/* Purpose: Close unformatted binary data file for writing */
int rcd; /* [rcd] Return code */
/* Close output file */
rcd=fclose(fp_bnr);
if(rcd != 0){
(void)fprintf(stderr,"%s: ERROR unable to close binary output file %s\n",nco_prg_nm_get(),fl_bnr);
nco_exit(EXIT_FAILURE);
} /* end if */
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"\n");
if(nco_dbg_lvl_get() >= nco_dbg_fl) (void)fprintf(stdout,"%s: Closed binary file %s\n",nco_prg_nm_get(),fl_bnr);
return rcd; /* O [rcd] Return code */
} /* end nco_bnr_close() */
int /* O [nbr] Number of days to end of month */
nco_nd2endm /* [fnc] Compute number of days to end of month */
(const int mth, /* I [mth] Month */
const int day) /* I [day] Current day */
{
/* Purpose: Returns number of days to end of month
This number added to the input argument day gives last day of month mth
Original fortran: Brian Eaton cal_util.F:nd2endm()
C version: Charlie Zender */
const int mdays[]={31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31};
int nbr_day_2_mth_end;
if(mth < 1 || mth > 12 || day < 0){
(void)fprintf(stdout,"%s: ERROR nco_nd2endm() reports mth = %d, day = %d\n",nco_prg_nm_get(),mth,day);
nco_exit(EXIT_FAILURE);
} /* end if */
nbr_day_2_mth_end=mdays[mth-1]-day;
return nbr_day_2_mth_end;
} /* nco_nd2endm */
int
main(int argc,char **argv)
{
aed_sct *aed_lst_add_fst=NULL_CEWI;
aed_sct *aed_lst_scl_fct=NULL_CEWI;
char **dmn_rdr_lst_in=NULL_CEWI; /* Option a */
char **fl_lst_abb=NULL; /* Option n */
char **fl_lst_in=NULL_CEWI;
char **gaa_arg=NULL; /* [sng] Global attribute arguments */
char **var_lst_in=NULL_CEWI;
char **grp_lst_in=NULL_CEWI;
char *aux_arg[NC_MAX_DIMS];
char *cmd_ln;
char *cnk_arg[NC_MAX_DIMS];
char *cnk_map_sng=NULL_CEWI; /* [sng] Chunking map */
char *cnk_plc_sng=NULL_CEWI; /* [sng] Chunking policy */
char *fl_in=NULL;
char *fl_out=NULL; /* Option o */
char *fl_out_tmp=NULL_CEWI;
char *fl_pth=NULL; /* Option p */
char *fl_pth_lcl=NULL; /* Option l */
char *lmt_arg[NC_MAX_DIMS];
char *nco_pck_plc_sng=NULL_CEWI; /* [sng] Packing policy Option P */
char *nco_pck_map_sng=NULL_CEWI; /* [sng] Packing map Option M */
char *opt_crr=NULL; /* [sng] String representation of current long-option name */
char *optarg_lcl; /* [sng] Local copy of system optarg */
char *ppc_arg[NC_MAX_VARS]; /* [sng] PPC arguments */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
char add_fst_sng[]="add_offset"; /* [sng] Unidata standard string for add offset */
char scl_fct_sng[]="scale_factor"; /* [sng] Unidata standard string for scale factor */
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
const char * const CVS_Id="$Id$";
const char * const CVS_Revision="$Revision$";
const char * const opt_sht_lst="3467Aa:CcD:d:Fg:G:hL:l:M:Oo:P:p:Rrt:v:UxZ-:";
cnk_sct cnk; /* [sct] Chunking structure */
#if defined(__cplusplus) || defined(PGI_CC)
ddra_info_sct ddra_info;
ddra_info.flg_ddra=False;
#else /* !__cplusplus */
ddra_info_sct ddra_info={.flg_ddra=False};
#endif /* !__cplusplus */
dmn_sct **dmn_rdr_trv=NULL; /* [sct] Dimension structures to be re-ordered (from global table) */
extern char *optarg;
extern int optind;
/* Using naked stdin/stdout/stderr in parallel region generates warning
Copy appropriate filehandle to variable scoped shared in parallel clause */
FILE * const fp_stderr=stderr; /* [fl] stderr filehandle CEWI */
FILE * const fp_stdout=stdout; /* [fl] stdout filehandle CEWI */
gpe_sct *gpe=NULL; /* [sng] Group Path Editing (GPE) structure */
int *in_id_arr;
int abb_arg_nbr=0;
int aux_nbr=0; /* [nbr] Number of auxiliary coordinate hyperslabs specified */
int cnk_map=nco_cnk_map_nil; /* [enm] Chunking map */
int cnk_nbr=0; /* [nbr] Number of chunk sizes */
int cnk_plc=nco_cnk_plc_nil; /* [enm] Chunking policy */
int dfl_lvl=NCO_DFL_LVL_UNDEFINED; /* [enm] Deflate level */
int dmn_rdr_nbr=0; /* [nbr] Number of dimension to re-order */
int dmn_rdr_nbr_trv=0; /* [nbr] Number of dimension to re-order (from global table) */
int dmn_rdr_nbr_in=0; /* [nbr] Original number of dimension to re-order */
int fl_idx=int_CEWI;
int fl_nbr=0;
int fl_in_fmt; /* [enm] Input file format */
int fl_out_fmt=NCO_FORMAT_UNDEFINED; /* [enm] Output file format */
int fll_md_old; /* [enm] Old fill mode */
int gaa_nbr=0; /* [nbr] Number of global attributes to add */
int idx=int_CEWI;
int idx_rdr=int_CEWI;
int in_id;
int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */
int md_open; /* [enm] Mode flag for nc_open() call */
int nbr_dmn_fl;
int nbr_var_fix; /* nbr_var_fix gets incremented */
int nbr_var_fl;
int nbr_var_prc; /* nbr_var_prc gets incremented */
int nco_pck_map=nco_pck_map_flt_sht; /* [enm] Packing map */
int nco_pck_plc=nco_pck_plc_nil; /* [enm] Packing policy */
int opt;
int out_id;
int ppc_nbr=0; /* [nbr] Number of PPC arguments */
int rcd=NC_NOERR; /* [rcd] Return code */
int thr_idx; /* [idx] Index of current thread */
int thr_nbr=int_CEWI; /* [nbr] Thread number Option t */
int xtr_nbr=0; /* xtr_nbr won't otherwise be set for -c with no -v */
int var_lst_in_nbr=0;
int grp_lst_in_nbr=0; /* [nbr] Number of groups explicitly specified by user */
md5_sct *md5=NULL; /* [sct] MD5 configuration */
nco_bool *dmn_rvr_rdr=NULL; /* [flg] Reverse dimensions */
nco_bool CNV_CCM_CCSM_CF;
nco_bool EXCLUDE_INPUT_LIST=False; /* Option c */
nco_bool EXTRACT_ALL_COORDINATES=False; /* Option c */
nco_bool EXTRACT_ASSOCIATED_COORDINATES=True; /* Option C */
nco_bool FL_RTR_RMT_LCN;
nco_bool FL_LST_IN_FROM_STDIN=False; /* [flg] fl_lst_in comes from stdin */
nco_bool FORCE_APPEND=False; /* Option A */
nco_bool FORCE_OVERWRITE=False; /* Option O */
nco_bool FORTRAN_IDX_CNV=False; /* Option F */
nco_bool GRP_VAR_UNN=False; /* [flg] Select union of specified groups and variables */
nco_bool HISTORY_APPEND=True; /* Option h */
nco_bool IS_REORDER=False; /* Re-order mode */
nco_bool MSA_USR_RDR=False; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order*/
nco_bool RAM_CREATE=False; /* [flg] Create file in RAM */
nco_bool RAM_OPEN=False; /* [flg] Open (netCDF3-only) file(s) in RAM */
nco_bool RM_RMT_FL_PST_PRC=True; /* Option R */
nco_bool WRT_TMP_FL=True; /* [flg] Write output to temporary file */
nco_bool flg_cln=True; /* [flg] Clean memory prior to exit */
nco_bool flg_dmn_prc_usr_spc=False; /* [flg] Processed dimensions specified on command line */
size_t bfr_sz_hnt=NC_SIZEHINT_DEFAULT; /* [B] Buffer size hint */
size_t cnk_min_byt=NCO_CNK_SZ_MIN_BYT_DFL; /* [B] Minimize size of variable to chunk */
size_t cnk_sz_byt=0UL; /* [B] Chunk size in bytes */
size_t cnk_sz_scl=0UL; /* [nbr] Chunk size scalar */
size_t hdr_pad=0UL; /* [B] Pad at end of header section */
var_sct **var;
var_sct **var_fix;
var_sct **var_fix_out;
var_sct **var_out;
var_sct **var_prc;
var_sct **var_prc_out;
trv_tbl_sct *trv_tbl=NULL; /* [lst] Traversal table */
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
#ifdef ENABLE_MPI
/* Declare all MPI-specific variables here */
MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
int prc_rnk; /* [idx] Process rank */
int prc_nbr=0; /* [nbr] Number of MPI processes */
#endif /* !ENABLE_MPI */
static struct option opt_lng[]={ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
{"cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"clean",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"mmr_cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"dirty",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"mmr_drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"hdf4",no_argument,0,0}, /* [flg] Treat file as HDF4 */
{"hdf_upk",no_argument,0,0}, /* [flg] HDF unpack convention: unpacked=scale_factor*(packed-add_offset) */
{"hdf_unpack",no_argument,0,0}, /* [flg] HDF unpack convention: unpacked=scale_factor*(packed-add_offset) */
{"mrd",no_argument,0,0}, /* [enm] Multiple Record Dimension convention */
{"multiple_record_dimension",no_argument,0,0}, /* [enm] Multiple Record Dimension convention */
{"msa_usr_rdr",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"msa_user_order",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"ram_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"create_ram",no_argument,0,0}, /* [flg] Create file in RAM */
{"open_ram",no_argument,0,0}, /* [flg] Open (netCDF3) file(s) in RAM */
{"diskless_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"wrt_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"write_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"no_tmp_fl",no_argument,0,0}, /* [flg] Do not write output to temporary file */
{"intersection",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"nsx",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"union",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"unn",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"version",no_argument,0,0},
{"vrs",no_argument,0,0},
/* Long options with argument, no short option counterpart */
{"bfr_sz_hnt",required_argument,0,0}, /* [B] Buffer size hint */
{"buffer_size_hint",required_argument,0,0}, /* [B] Buffer size hint */
{"cnk_byt",required_argument,0,0}, /* [B] Chunk size in bytes */
{"chunk_byte",required_argument,0,0}, /* [B] Chunk size in bytes */
{"cnk_dmn",required_argument,0,0}, /* [nbr] Chunk size */
{"chunk_dimension",required_argument,0,0}, /* [nbr] Chunk size */
{"cnk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"chunk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"cnk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"chunk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"cnk_plc",required_argument,0,0}, /* [nbr] Chunking policy */
{"chunk_policy",required_argument,0,0}, /* [nbr] Chunking policy */
{"cnk_scl",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"chunk_scalar",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"fl_fmt",required_argument,0,0},
{"file_format",required_argument,0,0},
{"gaa",required_argument,0,0}, /* [sng] Global attribute add */
{"glb_att_add",required_argument,0,0}, /* [sng] Global attribute add */
{"hdr_pad",required_argument,0,0},
{"header_pad",required_argument,0,0},
{"ppc",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"precision_preserving_compression",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"quantize",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"upk",required_argument,0,0}, /* [enm] Unpacking convention to utilize */
/* Long options with short counterparts */
{"3",no_argument,0,'3'},
{"4",no_argument,0,'4'},
{"64bit",no_argument,0,'4'},
{"netcdf4",no_argument,0,'4'},
{"append",no_argument,0,'A'},
{"arrange",required_argument,0,'a'},
{"permute",required_argument,0,'a'},
{"reorder",required_argument,0,'a'},
{"rdr",required_argument,0,'a'},
{"no-coords",no_argument,0,'C'},
{"no-crd",no_argument,0,'C'},
{"coords",no_argument,0,'c'},
{"crd",no_argument,0,'c'},
{"debug",required_argument,0,'D'},
{"nco_dbg_lvl",required_argument,0,'D'},
{"dimension",required_argument,0,'d'},
{"dmn",required_argument,0,'d'},
{"fortran",no_argument,0,'F'},
{"ftn",no_argument,0,'F'},
{"gpe",required_argument,0,'G'}, /* [sng] Group Path Edit (GPE) */
{"grp",required_argument,0,'g'},
{"group",required_argument,0,'g'},
{"history",no_argument,0,'h'},
{"hst",no_argument,0,'h'},
{"dfl_lvl",required_argument,0,'L'}, /* [enm] Deflate level */
{"deflate",required_argument,0,'L'}, /* [enm] Deflate level */
{"local",required_argument,0,'l'},
{"lcl",required_argument,0,'l'},
{"pack_map",required_argument,0,'M'},
{"pck_map",required_argument,0,'M'},
{"map",required_argument,0,'M'},
{"overwrite",no_argument,0,'O'},
{"ovr",no_argument,0,'O'},
{"output",required_argument,0,'o'},
{"fl_out",required_argument,0,'o'},
{"pack_policy",required_argument,0,'P'},
{"pck_plc",required_argument,0,'P'},
{"path",required_argument,0,'p'},
{"retain",no_argument,0,'R'},
{"rtn",no_argument,0,'R'},
{"revision",no_argument,0,'r'},
{"thr_nbr",required_argument,0,'t'},
{"threads",required_argument,0,'t'},
{"omp_num_threads",required_argument,0,'t'},
{"unpack",no_argument,0,'U'},
{"variable",required_argument,0,'v'},
{"auxiliary",required_argument,0,'X'},
{"exclude",no_argument,0,'x'},
{"xcl",no_argument,0,'x'},
{"help",no_argument,0,'?'},
{"hlp",no_argument,0,'?'},
{0,0,0,0}
}; /* end opt_lng */
int opt_idx=0; /* Index of current long option into opt_lng array */
/* Initialize traversal table */
trv_tbl_init(&trv_tbl);
/* Start timer and save command line */
ddra_info.tmr_flg=nco_tmr_srt;
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_mtd;
cmd_ln=nco_cmd_ln_sng(argc,argv);
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
#ifdef ENABLE_MPI
/* MPI Initialization */
if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
MPI_Init(&argc,&argv);
MPI_Comm_size(mpi_cmm,&prc_nbr);
MPI_Comm_rank(mpi_cmm,&prc_rnk);
#endif /* !ENABLE_MPI */
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
opt=getopt_long(argc,argv,opt_sht_lst,opt_lng,&opt_idx);
/* NB: access to opt_crr is only valid when long_opt is detected */
if(opt == EOF) break; /* Parse positional arguments once getopt_long() returns EOF */
opt_crr=(char *)strdup(opt_lng[opt_idx].name);
/* Process long options without short option counterparts */
if(opt == 0){
if(!strcmp(opt_crr,"bfr_sz_hnt") || !strcmp(opt_crr,"buffer_size_hint")){
bfr_sz_hnt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_byt") || !strcmp(opt_crr,"chunk_byte")){
cnk_sz_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_byt */
if(!strcmp(opt_crr,"cnk_min") || !strcmp(opt_crr,"chunk_min")){
cnk_min_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_min */
if(!strcmp(opt_crr,"cnk_dmn") || !strcmp(opt_crr,"chunk_dimension")){
/* Copy limit argument for later processing */
cnk_arg[cnk_nbr]=(char *)strdup(optarg);
cnk_nbr++;
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_scl") || !strcmp(opt_crr,"chunk_scalar")){
cnk_sz_scl=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_map") || !strcmp(opt_crr,"chunk_map")){
/* Chunking map */
cnk_map_sng=(char *)strdup(optarg);
cnk_map=nco_cnk_map_get(cnk_map_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_plc") || !strcmp(opt_crr,"chunk_policy")){
/* Chunking policy */
cnk_plc_sng=(char *)strdup(optarg);
cnk_plc=nco_cnk_plc_get(cnk_plc_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cln") || !strcmp(opt_crr,"mmr_cln") || !strcmp(opt_crr,"clean")) flg_cln=True; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"drt") || !strcmp(opt_crr,"mmr_drt") || !strcmp(opt_crr,"dirty")) flg_cln=False; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"fl_fmt") || !strcmp(opt_crr,"file_format")) rcd=nco_create_mode_prs(optarg,&fl_out_fmt);
if(!strcmp(opt_crr,"gaa") || !strcmp(opt_crr,"glb_att_add")){
gaa_arg=(char **)nco_realloc(gaa_arg,(gaa_nbr+1)*sizeof(char *));
gaa_arg[gaa_nbr++]=(char *)strdup(optarg);
} /* endif gaa */
if(!strcmp(opt_crr,"hdf4")) nco_fmt_xtn=nco_fmt_xtn_hdf4; /* [enm] Treat file as HDF4 */
if(!strcmp(opt_crr,"hdf_upk") || !strcmp(opt_crr,"hdf_unpack")) nco_upk_cnv=nco_upk_HDF_MOD10; /* [flg] HDF unpack convention: unpacked=scale_factor*(packed-add_offset) */
if(!strcmp(opt_crr,"hdr_pad") || !strcmp(opt_crr,"header_pad")){
hdr_pad=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif "hdr_pad" */
if(!strcmp(opt_crr,"ppc") || !strcmp(opt_crr,"precision_preserving_compression") || !strcmp(opt_crr,"quantize")){
ppc_arg[ppc_nbr]=(char *)strdup(optarg);
ppc_nbr++;
} /* endif "ppc" */
if(!strcmp(opt_crr,"mrd") || !strcmp(opt_crr,"multiple_record_dimension")) nco_mrd_cnv=nco_mrd_allow; /* [enm] Multiple Record Dimension convention */
if(!strcmp(opt_crr,"msa_usr_rdr") || !strcmp(opt_crr,"msa_user_order")) MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"create_ram") || !strcmp(opt_crr,"diskless_all")) RAM_CREATE=True; /* [flg] Open (netCDF3) file(s) in RAM */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"open_ram") || !strcmp(opt_crr,"diskless_all")) RAM_OPEN=True; /* [flg] Create file in RAM */
if(!strcmp(opt_crr,"unn") || !strcmp(opt_crr,"union")) GRP_VAR_UNN=True;
if(!strcmp(opt_crr,"nsx") || !strcmp(opt_crr,"intersection")) GRP_VAR_UNN=False;
if(!strcmp(opt_crr,"upk")){ /* [enm] Unpacking convention to utilize */
nco_upk_cnv=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
} /* endif "hdr_pad" */
if(!strcmp(opt_crr,"vrs") || !strcmp(opt_crr,"version")){
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
nco_exit(EXIT_SUCCESS);
} /* endif "vrs" */
if(!strcmp(opt_crr,"wrt_tmp_fl") || !strcmp(opt_crr,"write_tmp_fl")) WRT_TMP_FL=True;
if(!strcmp(opt_crr,"no_tmp_fl")) WRT_TMP_FL=False;
} /* opt != 0 */
/* Process short options */
switch(opt){
case 0: /* Long options have already been processed, return */
break;
case '3': /* Request netCDF3 output storage format */
fl_out_fmt=NC_FORMAT_CLASSIC;
break;
case '4': /* Catch-all to prescribe output storage format */
if(!strcmp(opt_crr,"64bit")) fl_out_fmt=NC_FORMAT_64BIT; else fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case '6': /* Request netCDF3 64-bit offset output storage format */
fl_out_fmt=NC_FORMAT_64BIT;
break;
case '7': /* Request netCDF4-classic output storage format */
fl_out_fmt=NC_FORMAT_NETCDF4_CLASSIC;
break;
case 'A': /* Toggle FORCE_APPEND */
FORCE_APPEND=!FORCE_APPEND;
break;
case 'a': /* Re-order dimensions */
flg_dmn_prc_usr_spc=True;
dmn_rdr_lst_in=nco_lst_prs_2D(optarg,",",&dmn_rdr_nbr_in);
dmn_rdr_nbr=dmn_rdr_nbr_in;
break;
case 'C': /* Extract all coordinates associated with extracted variables? */
EXTRACT_ASSOCIATED_COORDINATES=False;
break;
case 'c':
EXTRACT_ALL_COORDINATES=True;
break;
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
lmt_nbr++;
break;
case 'F': /* Toggle index convention. Default is 0-based arrays (C-style). */
FORTRAN_IDX_CNV=!FORTRAN_IDX_CNV;
break;
case 'G': /* Apply Group Path Editing (GPE) to output group */
/* NB: GNU getopt() optional argument syntax is ugly (requires "=" sign) so avoid it
http://stackoverflow.com/questions/1052746/getopt-does-not-parse-optional-arguments-to-parameters */
gpe=nco_gpe_prs_arg(optarg);
fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case 'g': /* Copy group argument for later processing */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
grp_lst_in=nco_lst_prs_2D(optarg_lcl,",",&grp_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
break;
case 'h': /* Toggle appending to history global attribute */
HISTORY_APPEND=!HISTORY_APPEND;
break;
case 'L': /* [enm] Deflate level. Default is 0. */
dfl_lvl=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'l': /* Local path prefix for files retrieved from remote file system */
fl_pth_lcl=(char *)strdup(optarg);
break;
case 'M': /* Packing map */
nco_pck_map_sng=(char *)strdup(optarg);
nco_pck_map=nco_pck_map_get(nco_pck_map_sng);
break;
case 'O': /* Toggle FORCE_OVERWRITE */
FORCE_OVERWRITE=!FORCE_OVERWRITE;
break;
case 'o': /* Name of output file */
fl_out=(char *)strdup(optarg);
break;
case 'P': /* Packing policy */
nco_pck_plc_sng=(char *)strdup(optarg);
break;
case 'p': /* Common file path */
fl_pth=(char *)strdup(optarg);
break;
case 'R': /* Toggle removal of remotely-retrieved-files. Default is True. */
RM_RMT_FL_PST_PRC=!RM_RMT_FL_PST_PRC;
break;
case 'r': /* Print CVS program information and copyright notice */
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
(void)nco_lbr_vrs_prn();
(void)nco_cpy_prn();
(void)nco_cnf_prn();
nco_exit(EXIT_SUCCESS);
break;
case 't': /* Thread number */
thr_nbr=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'U': /* Unpacking switch */
nco_pck_plc_sng=(char *)strdup("upk");
break;
case 'v': /* Variables to extract/exclude */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
var_lst_in=nco_lst_prs_2D(optarg_lcl,",",&var_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
xtr_nbr=var_lst_in_nbr;
break;
case 'X': /* Copy auxiliary coordinate argument for later processing */
aux_arg[aux_nbr]=(char *)strdup(optarg);
aux_nbr++;
MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
break;
case 'x': /* Exclude rather than extract variables specified with -v */
EXCLUDE_INPUT_LIST=True;
break;
case '?': /* Print proper usage */
(void)nco_usg_prn();
nco_exit(EXIT_SUCCESS);
break;
case '-': /* Long options are not allowed */
(void)fprintf(stderr,"%s: ERROR Long options are not available in this build. Use single letter options instead.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
break;
default: /* Print proper usage */
(void)fprintf(stdout,"%s ERROR in command-line syntax/options. Please reformulate command accordingly.\n",nco_prg_nm_get());
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
break;
} /* end switch */
if(opt_crr) opt_crr=(char *)nco_free(opt_crr);
} /* end while loop */
/* Set re-order flag */
if(dmn_rdr_nbr > 0) IS_REORDER=True;
/* No re-order dimensions specified implies packing request */
if(dmn_rdr_nbr == 0){
if(nco_pck_plc == nco_pck_plc_nil) nco_pck_plc=nco_pck_plc_get(nco_pck_plc_sng);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: DEBUG Packing map is %s and packing policy is %s\n",nco_prg_nm_get(),nco_pck_map_sng_get(nco_pck_map),nco_pck_plc_sng_get(nco_pck_plc));
} /* dmn_rdr_nbr != 0 */
/* From this point forward, assume ncpdq operator packs or re-orders, not both */
if(dmn_rdr_nbr > 0 && nco_pck_plc != nco_pck_plc_nil){
(void)fprintf(fp_stdout,"%s: ERROR %s does not support simultaneous dimension re-ordering (-a switch) and packing (-P switch).\nHINT: Invoke %s twice, once to re-order (with -a), and once to pack (with -P).\n",nco_prg_nm,nco_prg_nm,nco_prg_nm);
nco_exit(EXIT_FAILURE);
} /* endif */
/* Process positional arguments and fill in filenames */
fl_lst_in=nco_fl_lst_mk(argv,argc,optind,&fl_nbr,&fl_out,&FL_LST_IN_FROM_STDIN);
/* Initialize thread information */
thr_nbr=nco_openmp_ini(thr_nbr);
in_id_arr=(int *)nco_malloc(thr_nbr*sizeof(int));
/* Parse filename */
fl_in=nco_fl_nm_prs(fl_in,0,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
/* Make sure file is on local system and is readable or die trying */
fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
/* Open file using appropriate buffer size hints and verbosity */
if(RAM_OPEN) md_open=NC_NOWRITE|NC_DISKLESS; else md_open=NC_NOWRITE;
rcd+=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,&in_id);
/* Get file format */
(void)nco_inq_format(in_id,&fl_in_fmt);
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
/* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Create reversed dimension list */
if(dmn_rdr_nbr_in > 0){
dmn_rvr_rdr=(nco_bool *)nco_malloc(dmn_rdr_nbr_in*sizeof(nco_bool));
/* Is dimension to be reversed? i.e., does string begin with minus-sign '-'? */
for(idx_rdr=0;idx_rdr<dmn_rdr_nbr_in;idx_rdr++){
if(dmn_rdr_lst_in[idx_rdr][0] == '-'){
dmn_rvr_rdr[idx_rdr]=True;
/* Strip-out '-': Copy string to new memory one past negative sign to avoid losing byte */
optarg_lcl=dmn_rdr_lst_in[idx_rdr];
dmn_rdr_lst_in[idx_rdr]=(char *)strdup(optarg_lcl+1L);
optarg_lcl=(char *)nco_free(optarg_lcl);
}else{
dmn_rvr_rdr[idx_rdr]=False;
} /* !'-' */
} /* !idx_rdr */
} /* !dmn_rdr_nbr_in */
/* Get number of variables, dimensions, and global attributes in file, file format */
(void)trv_tbl_inq((int *)NULL,(int *)NULL,(int *)NULL,&nbr_dmn_fl,(int *)NULL,(int *)NULL,(int *)NULL,(int *)NULL,&nbr_var_fl,trv_tbl);
/* Create list of dimensions to average(ncwa)/re-order(ncpdq) */
if(IS_REORDER) (void)nco_dmn_avg_mk(in_id,dmn_rdr_lst_in,dmn_rdr_nbr_in,flg_dmn_prc_usr_spc,False,trv_tbl,&dmn_rdr_trv,&dmn_rdr_nbr_trv);
/* Fill-in variable structure list for all extracted variables */
var=nco_fll_var_trv(in_id,&xtr_nbr,trv_tbl);
/* Duplicate to output array */
var_out=(var_sct **)nco_malloc(xtr_nbr*sizeof(var_sct *));
for(idx=0;idx<xtr_nbr;idx++){
var_out[idx]=nco_var_dpl(var[idx]);
(void)nco_xrf_var(var[idx],var_out[idx]);
(void)nco_xrf_dmn(var_out[idx]);
} /* end loop over variables */
/* Refresh var_out with dim_out data */
(void)nco_var_dmn_refresh(var_out,xtr_nbr);
/* Is this a CCM/CCSM/CF-format history tape? */
CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(in_id);
/* Divide variable lists into lists of fixed variables and variables to be processed */
(void)nco_var_lst_dvd(var,var_out,xtr_nbr,CNV_CCM_CCSM_CF,True,nco_pck_map,nco_pck_plc,dmn_rdr_trv,dmn_rdr_nbr_trv,&var_fix,&var_fix_out,&nbr_var_fix,&var_prc,&var_prc_out,&nbr_var_prc,trv_tbl);
/* Store processed and fixed variables info into GTT */
(void)nco_var_prc_fix_trv(nbr_var_prc,var_prc,nbr_var_fix,var_fix,trv_tbl);
/* We now have final list of variables to extract. Phew. */
/* Make output and input files consanguinous */
if(fl_out_fmt == NCO_FORMAT_UNDEFINED) fl_out_fmt=fl_in_fmt;
/* Initialize, decode, and set PPC information */
if(ppc_nbr > 0) nco_ppc_ini(in_id,&dfl_lvl,fl_out_fmt,ppc_arg,ppc_nbr,trv_tbl);
/* Verify output file format supports requested actions */
(void)nco_fl_fmt_vet(fl_out_fmt,cnk_nbr,dfl_lvl);
/* Open output file */
fl_out_tmp=nco_fl_out_open(fl_out,&FORCE_APPEND,FORCE_OVERWRITE,fl_out_fmt,&bfr_sz_hnt,RAM_CREATE,RAM_OPEN,WRT_TMP_FL,&out_id);
/* Initialize chunking from user-specified inputs */
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC) rcd+=nco_cnk_ini(in_id,fl_out,cnk_arg,cnk_nbr,cnk_map,cnk_plc,cnk_min_byt,cnk_sz_byt,cnk_sz_scl,&cnk);
if(IS_REORDER){
dmn_sct **dmn_rdr=NULL; /* [sct] Dimension structures to be re-ordered */
/* "dmn_rdr" is only used for input to function nco_var_dmn_rdr_mtd(), that compares dimensions by short name;
this is because the input list of -a are dimension short names; group support is obtained combining with -g option;
on input it contains a list of dimension short names (in "dmn_rdr"), that together with input array "dmn_rvr_rdr"
of flags that determine if dimension at index dmn_rvr_rdr[index] is to be reversed; use cases:
in_grp_8.nc contains the dimensions /g1/lat, /g1/lon, /g2/lat, /g2/lon
ncpdq -O -v lat,lon -a -lat,-lon -g g1,g2 ~/nco/data/in_grp_8.nc out1.nc
"dmn_rdr" contains names ["lat"], ["lon"], striped of '-' (minus) sign and dmn_rvr_rdr contains [True],[True ]
output is reversed /g1/lat, /g1/lon, /g2/lat, /g2/lon
ncpdq -O -v lat,lon -a lat,-lon -g g1,g2 ~/nco/data/in_grp_8.nc out1.nc
"dmn_rdr" contains names ["lat"], ["lon"], and dmn_rvr_rdr contains [False],[True ]
output is reversed /g1/lon, /g2/lon */
/* Form list of re-ordering dimensions from extracted input dimensions */
dmn_rdr=(dmn_sct **)nco_malloc(dmn_rdr_nbr*sizeof(dmn_sct *));
/* Initialize re-ordering dimensions; initialize only short name */
for(idx_rdr=0;idx_rdr<dmn_rdr_nbr_in;idx_rdr++){
dmn_rdr[idx_rdr]=(dmn_sct *)nco_malloc(sizeof(dmn_sct));
dmn_rdr[idx_rdr]->nm=(char *)strdup(dmn_rdr_lst_in[idx_rdr]);
dmn_rdr[idx_rdr]->nm_fll=NULL;
dmn_rdr[idx_rdr]->id=-1;
}
/* Determine and set new dimensionality in metadata of each re-ordered variable */
(void)nco_var_dmn_rdr_mtd_trv(trv_tbl,nbr_var_prc,var_prc,var_prc_out,nbr_var_fix,var_fix,dmn_rdr,dmn_rdr_nbr,dmn_rvr_rdr);
for(idx_rdr=0; idx_rdr<dmn_rdr_nbr_in; idx_rdr++){
dmn_rdr[idx_rdr]->nm=(char *)nco_free(dmn_rdr[idx_rdr]->nm);
dmn_rdr[idx_rdr]=(dmn_sct *)nco_free(dmn_rdr[idx_rdr]);
}
dmn_rdr=(dmn_sct **)nco_free(dmn_rdr);
} /* IS_REORDER */
/* Alter metadata for variables that will be packed */
if(nco_pck_plc != nco_pck_plc_nil){
if(nco_pck_plc != nco_pck_plc_upk){
/* Allocate attribute list container for maximum number of entries */
aed_lst_add_fst=(aed_sct *)nco_malloc(nbr_var_prc*sizeof(aed_sct));
aed_lst_scl_fct=(aed_sct *)nco_malloc(nbr_var_prc*sizeof(aed_sct));
} /* endif packing */
for(idx=0;idx<nbr_var_prc;idx++){
nco_pck_mtd(var_prc[idx],var_prc_out[idx],nco_pck_map,nco_pck_plc);
if(nco_pck_plc != nco_pck_plc_upk){
/* Use same copy of attribute name for all edits */
aed_lst_add_fst[idx].att_nm=add_fst_sng;
aed_lst_scl_fct[idx].att_nm=scl_fct_sng;
} /* endif packing */
} /* end loop over var_prc */
/* Transfer variable type to table. NB: Use processed variables set with new type. MUST be done before definition */
(void)nco_var_typ_trv(nbr_var_prc,var_prc_out,trv_tbl);
} /* nco_pck_plc == nco_pck_plc_nil */
/* Define dimensions, extracted groups, variables, and attributes in output file. NB: record name is NULL */
(void)nco_xtr_dfn(in_id,out_id,&cnk,dfl_lvl,gpe,md5,!FORCE_APPEND,True,False,nco_pck_plc,(char *)NULL,trv_tbl);
/* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(HISTORY_APPEND && FORCE_APPEND) (void)nco_prv_att_cat(fl_in,in_id,out_id);
if(gaa_nbr > 0) (void)nco_glb_att_add(out_id,gaa_arg,gaa_nbr);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
if(thr_nbr > 0 && HISTORY_APPEND) (void)nco_thr_att_cat(out_id,thr_nbr);
/* Turn-off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
/* Take output file out of define mode */
if(hdr_pad == 0UL){
(void)nco_enddef(out_id);
}else{
(void)nco__enddef(out_id,hdr_pad);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: INFO Padding header with %lu extra bytes\n",nco_prg_nm_get(),(unsigned long)hdr_pad);
} /* hdr_pad */
/* Assign zero to start and unity to stride vectors in output variables */
(void)nco_var_srd_srt_set(var_out,xtr_nbr);
/* Copy variable data for non-processed variables */
(void)nco_cpy_fix_var_trv(in_id,out_id,gpe,trv_tbl);
/* Close first input netCDF file */
nco_close(in_id);
/* Loop over input files (not currently used, fl_nbr == 1) */
for(fl_idx=0;fl_idx<fl_nbr;fl_idx++){
/* Parse filename */
if(fl_idx != 0) fl_in=nco_fl_nm_prs(fl_in,fl_idx,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"%s: INFO Input file %d is %s",nco_prg_nm_get(),fl_idx,fl_in);
/* Make sure file is on local system and is readable or die trying */
if(fl_idx != 0) fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
if(nco_dbg_lvl >= nco_dbg_fl && FL_RTR_RMT_LCN) (void)fprintf(stderr,", local file is %s",fl_in);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"\n");
/* Open file once per thread to improve caching */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) rcd+=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,in_id_arr+thr_idx);
/* Timestamp end of metadata setup and disk layout */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_rgl;
#ifdef _OPENMP
#pragma omp parallel for default(none) private(idx,in_id) shared(aed_lst_add_fst,aed_lst_scl_fct,nco_dbg_lvl,dmn_rdr_nbr,gpe,in_id_arr,nbr_var_prc,nco_pck_map,nco_pck_plc,out_id,nco_prg_nm,rcd,var_prc,var_prc_out,nbr_dmn_fl,trv_tbl,IS_REORDER,fl_out_fmt)
#endif /* !_OPENMP */
/* Process all variables in current file */
for(idx=0;idx<nbr_var_prc;idx++){
char *grp_out_fll=NULL; /* [sng] Group name */
int grp_out_id; /* [ID] Group ID (output) */
int var_out_id; /* [ID] Variable ID (output) */
trv_sct *var_trv; /* [sct] Variable GTT object */
in_id=in_id_arr[omp_get_thread_num()];
var_prc[idx]->nc_id=in_id;
if(nco_dbg_lvl >= nco_dbg_var) rcd+=nco_var_prc_crr_prn(idx,var_prc[idx]->nm);
if(nco_dbg_lvl >= nco_dbg_var) (void)fflush(fp_stderr);
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
/* Retrieve variable from disk into memory */
(void)nco_msa_var_get_trv(in_id,var_prc[idx],trv_tbl);
/* If re-ordering */
if(IS_REORDER){
if((var_prc_out[idx]->val.vp=(void *)nco_malloc_flg(var_prc_out[idx]->sz*nco_typ_lng(var_prc_out[idx]->type))) == NULL){
(void)fprintf(fp_stdout,"%s: ERROR Unable to malloc() %ld*%lu bytes for value buffer for variable %s in main()\n",nco_prg_nm_get(),var_prc_out[idx]->sz,(unsigned long)nco_typ_lng(var_prc_out[idx]->type),var_prc_out[idx]->nm);
nco_exit(EXIT_FAILURE);
} /* endif err */
/* Change dimensionionality of values */
(void)nco_var_dmn_rdr_val_trv(var_prc[idx],var_prc_out[idx],trv_tbl);
/* Re-ordering required two value buffers, time to free() input buffer */
var_prc[idx]->val.vp=nco_free(var_prc[idx]->val.vp);
} /* IS_REORDER */
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
/* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
if(grp_out_fll) grp_out_fll=(char *)nco_free(grp_out_fll);
/* Get variable ID */
(void)nco_inq_varid(grp_out_id,var_trv->nm,&var_out_id);
/* Store the output variable ID */
var_prc_out[idx]->id=var_out_id;
if(nco_pck_plc != nco_pck_plc_nil){
/* Copy input variable buffer to processed variable buffer */
/* fxm: this is dangerous and leads to double free()'ing variable buffer */
var_prc_out[idx]->val=var_prc[idx]->val;
/* (Un-)Pack variable according to packing specification */
nco_pck_val(var_prc[idx],var_prc_out[idx],nco_pck_map,nco_pck_plc,aed_lst_add_fst+idx,aed_lst_scl_fct+idx);
} /* endif nco_pck_plc != nco_pck_plc_nil */
if(var_trv->ppc != NC_MAX_INT){
if(var_trv->flg_nsd) (void)nco_ppc_bitmask(var_trv->ppc, var_prc_out[idx]->type, var_prc_out[idx]->sz, var_prc_out[idx]->has_mss_val, var_prc_out[idx]->mss_val, var_prc_out[idx]->val); else (void)nco_ppc_around(var_trv->ppc, var_prc_out[idx]->type, var_prc_out[idx]->sz, var_prc_out[idx]->has_mss_val, var_prc_out[idx]->mss_val, var_prc_out[idx]->val);
} /* endif ppc */
if(nco_is_xcp(var_trv->nm)) nco_xcp_prc(var_trv->nm,var_prc_out[idx]->type,var_prc_out[idx]->sz,(char *)var_prc_out[idx]->val.vp);
#ifdef _OPENMP
#pragma omp critical
#endif /* _OPENMP */
{ /* begin OpenMP critical */
/* Copy variable to output file then free value buffer */
if(var_prc_out[idx]->nbr_dim == 0){
(void)nco_put_var1(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc_out[idx]->val.vp,var_prc_out[idx]->type);
}else{ /* end if variable is scalar */
(void)nco_put_vara(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc_out[idx]->cnt,var_prc_out[idx]->val.vp,var_prc_out[idx]->type);
} /* end if variable is array */
} /* end OpenMP critical */
/* Free current output buffer */
var_prc_out[idx]->val.vp=nco_free(var_prc_out[idx]->val.vp);
} /* end (OpenMP parallel for) loop over idx */
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(fp_stderr,"\n");
/* Write/overwrite packing attributes for newly packed and re-packed variables
Logic here should nearly mimic logic in nco_var_dfn() */
if(nco_pck_plc != nco_pck_plc_nil && nco_pck_plc != nco_pck_plc_upk){
/* ...put file in define mode to allow metadata writing... */
(void)nco_redef(out_id);
/* ...loop through all variables that may have been packed... */
for(idx=0;idx<nbr_var_prc;idx++){
char *grp_out_fll=NULL; /* [sng] Group name */
int grp_out_id; /* [ID] Group ID (output) */
int var_out_id; /* [ID] Variable ID (output) */
trv_sct *var_trv; /* [sct] Variable GTT object */
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
/* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
if(grp_out_fll) grp_out_fll=(char *)nco_free(grp_out_fll);
/* Get variable ID */
(void)nco_inq_varid(grp_out_id,var_trv->nm,&var_out_id);
/* nco_var_dfn() pre-defined dummy packing attributes in output file only for "packable" input variables */
if(nco_pck_plc_typ_get(nco_pck_map,var_prc[idx]->typ_upk,(nc_type *)NULL)){
/* Verify input variable was newly packed by this operator
Writing pre-existing (non-re-packed) attributes here would fail because
nco_pck_dsk_inq() never fills in var->scl_fct.vp and var->add_fst.vp
Logic is same as in nco_var_dfn() (except var_prc[] instead of var[])
If operator newly packed this particular variable... */
if(
/* ...either because operator newly packs all variables... */
(nco_pck_plc == nco_pck_plc_all_new_att) ||
/* ...or because operator newly packs un-packed variables like this one... */
(nco_pck_plc == nco_pck_plc_all_xst_att && !var_prc[idx]->pck_ram) ||
/* ...or because operator re-packs packed variables like this one... */
(nco_pck_plc == nco_pck_plc_xst_new_att && var_prc[idx]->pck_ram)
){
/* Replace dummy packing attributes with final values, or delete them */
if(nco_dbg_lvl >= nco_dbg_io) (void)fprintf(stderr,"%s: main() replacing dummy packing attribute values for variable %s\n",nco_prg_nm,var_prc[idx]->nm);
(void)nco_aed_prc(grp_out_id,aed_lst_add_fst[idx].id,aed_lst_add_fst[idx]);
(void)nco_aed_prc(grp_out_id,aed_lst_scl_fct[idx].id,aed_lst_scl_fct[idx]);
} /* endif variable is newly packed by this operator */
} /* !nco_pck_plc_alw */
} /* end loop over var_prc */
/* Take output file out of define mode */
if(hdr_pad == 0UL) (void)nco_enddef(out_id); else (void)nco__enddef(out_id,hdr_pad);
} /* nco_pck_plc == nco_pck_plc_nil || nco_pck_plc == nco_pck_plc_upk */
/* Close input netCDF file */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) nco_close(in_id_arr[thr_idx]);
/* Remove local copy of file */
if(FL_RTR_RMT_LCN && RM_RMT_FL_PST_PRC) (void)nco_fl_rm(fl_in);
} /* end loop over fl_idx */
/* Close output file and move it from temporary to permanent location */
(void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id);
/* Clean memory unless dirty memory allowed */
if(flg_cln){
/* ncpdq-specific memory cleanup */
if(dmn_rdr_nbr > 0){
if(dmn_rdr_nbr_in > 0) dmn_rdr_lst_in=nco_sng_lst_free(dmn_rdr_lst_in,dmn_rdr_nbr_in);
dmn_rvr_rdr=(nco_bool *)nco_free(dmn_rvr_rdr);
/* Free dimension list pointers */
for(idx_rdr=0; idx_rdr<dmn_rdr_nbr_trv; idx_rdr++){
dmn_rdr_trv[idx_rdr]->nm=(char *)nco_free(dmn_rdr_trv[idx_rdr]->nm);
dmn_rdr_trv[idx_rdr]->nm_fll=(char *)nco_free(dmn_rdr_trv[idx_rdr]->nm_fll);
dmn_rdr_trv[idx_rdr]=(dmn_sct *)nco_free(dmn_rdr_trv[idx_rdr]);
}
dmn_rdr_trv=(dmn_sct **)nco_free(dmn_rdr_trv);
/* Dimension structures in dmn_rdr are owned by dmn and dmn_out, free'd later */
} /* endif dmn_rdr_nbr > 0 */
if(nco_pck_plc != nco_pck_plc_nil){
if(nco_pck_plc_sng) nco_pck_plc_sng=(char *)nco_free(nco_pck_plc_sng);
if(nco_pck_map_sng) nco_pck_map_sng=(char *)nco_free(nco_pck_map_sng);
if(nco_pck_plc != nco_pck_plc_upk){
/* No need for loop over var_prc variables to free attribute values
Variable structures and attribute edit lists share same attribute values
Free them only once, and do it in nco_var_free() */
aed_lst_add_fst=(aed_sct *)nco_free(aed_lst_add_fst);
aed_lst_scl_fct=(aed_sct *)nco_free(aed_lst_scl_fct);
} /* nco_pck_plc == nco_pck_plc_upk */
} /* nco_pck_plc == nco_pck_plc_nil */
/* NCO-generic clean-up */
/* Free individual strings/arrays */
if(cmd_ln) cmd_ln=(char *)nco_free(cmd_ln);
if(cnk_map_sng) cnk_map_sng=(char *)nco_free(cnk_map_sng);
if(cnk_plc_sng) cnk_plc_sng=(char *)nco_free(cnk_plc_sng);
if(fl_in) fl_in=(char *)nco_free(fl_in);
if(fl_out) fl_out=(char *)nco_free(fl_out);
if(fl_out_tmp) fl_out_tmp=(char *)nco_free(fl_out_tmp);
if(fl_pth) fl_pth=(char *)nco_free(fl_pth);
if(fl_pth_lcl) fl_pth_lcl=(char *)nco_free(fl_pth_lcl);
if(in_id_arr) in_id_arr=(int *)nco_free(in_id_arr);
/* Free lists of strings */
if(fl_lst_in && fl_lst_abb == NULL) fl_lst_in=nco_sng_lst_free(fl_lst_in,fl_nbr);
if(fl_lst_in && fl_lst_abb) fl_lst_in=nco_sng_lst_free(fl_lst_in,1);
if(fl_lst_abb) fl_lst_abb=nco_sng_lst_free(fl_lst_abb,abb_arg_nbr);
if(gaa_nbr > 0) gaa_arg=nco_sng_lst_free(gaa_arg,gaa_nbr);
if(var_lst_in_nbr > 0) var_lst_in=nco_sng_lst_free(var_lst_in,var_lst_in_nbr);
/* Free limits */
for(idx=0;idx<aux_nbr;idx++) aux_arg[idx]=(char *)nco_free(aux_arg[idx]);
for(idx=0;idx<lmt_nbr;idx++) lmt_arg[idx]=(char *)nco_free(lmt_arg[idx]);
for(idx=0;idx<ppc_nbr;idx++) ppc_arg[idx]=(char *)nco_free(ppc_arg[idx]);
/* Free chunking information */
for(idx=0;idx<cnk_nbr;idx++) cnk_arg[idx]=(char *)nco_free(cnk_arg[idx]);
if(cnk_nbr > 0) cnk.cnk_dmn=(cnk_dmn_sct **)nco_cnk_lst_free(cnk.cnk_dmn,cnk_nbr);
if(xtr_nbr > 0) var=nco_var_lst_free(var,xtr_nbr);
if(xtr_nbr > 0) var_out=nco_var_lst_free(var_out,xtr_nbr);
var_prc=(var_sct **)nco_free(var_prc);
var_prc_out=(var_sct **)nco_free(var_prc_out);
var_fix=(var_sct **)nco_free(var_fix);
var_fix_out=(var_sct **)nco_free(var_fix_out);
trv_tbl_free(trv_tbl);
for(idx=0;idx<lmt_nbr;idx++) flg_dne[idx].dim_nm=(char *)nco_free(flg_dne[idx].dim_nm);
if(flg_dne) flg_dne=(nco_dmn_dne_t *)nco_free(flg_dne);
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
} /* !flg_cln */
#ifdef ENABLE_MPI
MPI_Finalize();
#endif /* !ENABLE_MPI */
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
var_sct * /* O [sct] Pointer to conforming variable structure */
nco_var_cnf_dmn /* [fnc] Stretch second variable to match dimensions of first variable */
(const var_sct * const var, /* I [ptr] Pointer to variable structure to serve as template */
var_sct * const wgt, /* I [ptr] Pointer to variable structure to make conform to var */
var_sct *wgt_crr, /* I/O [ptr] Pointer to existing conforming variable structure, if any (destroyed when does not conform to var) */
const nco_bool MUST_CONFORM, /* I [flg] Must wgt and var conform? */
nco_bool *DO_CONFORM) /* O [flg] Do wgt and var conform? */
{
/* Threads: Routine is thread safe and calls no unsafe routines */
/* fxm: TODO 226. Is xrf in nco_var_cnf_dmn() really necessary? If not, remove it and make wgt arg const var_sct * const */
/* Purpose: Stretch second variable to match dimensions of first variable
Dimensions in var which are not in wgt will be present in wgt_out, with values
replicated from existing dimensions in wgt.
By default, wgt's dimensions must be subset of var's dimensions (MUST_CONFORM=true)
Calling routine should set MUST_CONFORM=false if wgt and var need not conform
When wgt and var do not conform then then nco_var_cnf_dmn sets *DO_CONFORM=False and returns copy of var with all values set to 1.0
Calling procedure then decides what to do with unity output
MUST_CONFORM is True for ncbo: Variables of like name to be, e.g., differenced, must conform
MUST_CONFORM is False false for ncap, ncflint, ncwa: Some variables to be averaged may not conform to specified weight, e.g., lon will not conform to gw. This is fine and returned wgt_out may be discarded. */
/* There are many inelegant ways to accomplish this (without using C++): */
/* Perhaps most efficient method in general case is to expand weight array until
it is same size as variable array, and then multiply these arrays together
element-by-element in highly vectorized loop (possibly in Fortran or BLAS).
To enhance speed, (enlarged) weight-values array could be static, only re-made
when dimensions of incoming variables change. */
/* Another general method, though more expensive, is to use C to figure out the
multidimensional indices into the one dimensional hyperslab, a la ncks.
Knowing these indices, routine could loop over the one-dimensional array
element by element, choosing the appropriate index into the weight array from
those same multidimensional indices.
This method can also create a static weight-value array that is only destroyed
when an incoming variable changes dimensions from the previous variable. */
/* Another method, which is not completely general, but which may be good enough for
governement work, is to create Fortran subroutines which expect variables of
a given number of dimensions as input.
Creating these functions for up to five dimensions would satisfy most situations
C code would determine which branch to call based on number of dimensions
C++ or Fortran9x overloading could construct this interface more elegantly */
/* An (untested) simplification to some of these methods is to copy the 1-D array
value pointer of variable and cast it to an N-D array pointer
Then C could handle indexing
This method easily produce working, but non-general code
Implementation would require ugly branches or hard-to-understand recursive function calls */
/* Routine assumes weight will never have more dimensions than variable
(otherwise which hyperslab of weight to use would be ill-defined).
However, weight may (and often will) have fewer dimensions than variable */
nco_bool CONFORMABLE=False; /* [flg] wgt can be made to conform to var */
nco_bool USE_DUMMY_WGT=False; /* [flg] Fool NCO into thinking wgt conforms to var */
int idx; /* [idx] Counting index */
int idx_dmn; /* [idx] Dimension index */
int wgt_var_dmn_shr_nbr=0; /* [nbr] Number of dimensions wgt and var share */
var_sct *wgt_out=NULL;
/* Initialize flag to false. Overwrite by true after successful conformance */
*DO_CONFORM=False;
/* Does current weight (wgt_crr) conform to variable's dimensions? */
if(wgt_crr){
/* Test rank first because wgt_crr because of 19960218 bug (invalid dmn_id in old wgt_crr leads to match) */
if(var->nbr_dim == wgt_crr->nbr_dim){
/* Test whether all wgt and var dimensions match in sequence */
for(idx=0;idx<var->nbr_dim;idx++){
/* 20131002: nco_var_cnf_dmn() borken for groups as shown by dimension short-name strcmp() comparison here */
if(strcmp(wgt_crr->dim[idx]->nm,var->dim[idx]->nm)) break;
} /* end loop over dimensions */
if(idx == var->nbr_dim) *DO_CONFORM=True;
} /* end if ranks are equal */
/* 20060425: Weight re-use will not occur if wgt_crr is free()'d here
Some DDRA benchmarks need to know cost of broadcasting weights
To turn off weight re-use and cause broadcasting, execute "else" block below
by (temporarily) using
if(*DO_CONFORM && False){ ....instead of.... if(*DO_CONFORM){
in following condition */
if(*DO_CONFORM){
wgt_out=wgt_crr;
}else{
wgt_crr=nco_var_free(wgt_crr);
wgt_out=NULL;
} /* !*DO_CONFORM */
} /* wgt_crr == NULL */
/* Does original weight (wgt) conform to variable's dimensions? */
if(wgt_out == NULL){
if(var->nbr_dim > 0){
/* Test that all dimensions in wgt appear in var */
for(idx=0;idx<wgt->nbr_dim;idx++){
for(idx_dmn=0;idx_dmn<var->nbr_dim;idx_dmn++){
/* Compare names, not dimension IDs */
/* 20131002: nco_var_cnf_dmn() borken for groups as shown by dimension short-name strcmp() comparison here */
if(!strcmp(wgt->dim[idx]->nm,var->dim[idx_dmn]->nm)){
wgt_var_dmn_shr_nbr++; /* wgt and var share this dimension */
break;
} /* endif */
} /* end loop over var dimensions */
} /* end loop over wgt dimensions */
/* Decide whether wgt and var dimensions conform, are mutually exclusive, or are partially exclusive (an error) */
if(wgt_var_dmn_shr_nbr == wgt->nbr_dim){
/* wgt and var conform */
CONFORMABLE=True;
}else if(wgt_var_dmn_shr_nbr == 0){
/* Dimensions in wgt and var are mutually exclusive */
CONFORMABLE=False;
if(MUST_CONFORM){
(void)fprintf(stdout,"%s: ERROR %s and template %s share no dimensions\n",nco_prg_nm_get(),wgt->nm,var->nm);
nco_exit(EXIT_FAILURE);
}else{
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"\n%s: DEBUG %s and template %s share no dimensions: Not broadcasting %s to %s\n",nco_prg_nm_get(),wgt->nm,var->nm,wgt->nm,var->nm);
USE_DUMMY_WGT=True;
} /* endif */
}else if(wgt->nbr_dim > var->nbr_dim){
/* wgt is larger rank than var---no possibility of conforming */
CONFORMABLE=False;
if(MUST_CONFORM){
(void)fprintf(stdout,"%s: ERROR %s is rank %d but template %s is rank %d: Impossible to broadcast\n",nco_prg_nm_get(),wgt->nm,wgt->nbr_dim,var->nm,var->nbr_dim);
nco_exit(EXIT_FAILURE);
}else{
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"\n%s: DEBUG %s is rank %d but template %s is rank %d: Not broadcasting %s to %s\n",nco_prg_nm_get(),wgt->nm,wgt->nbr_dim,var->nm,var->nbr_dim,wgt->nm,var->nm);
USE_DUMMY_WGT=True;
} /* endif */
}else if(wgt_var_dmn_shr_nbr > 0 && wgt_var_dmn_shr_nbr < wgt->nbr_dim){
/* Some, but not all, of wgt dimensions are in var */
CONFORMABLE=False;
if(MUST_CONFORM){
(void)fprintf(stdout,"%s: ERROR %d dimensions of %s belong to template %s but %d dimensions do not\n",nco_prg_nm_get(),wgt_var_dmn_shr_nbr,wgt->nm,var->nm,wgt->nbr_dim-wgt_var_dmn_shr_nbr);
nco_exit(EXIT_FAILURE);
}else{
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"\n%s: DEBUG %d dimensions of %s belong to template %s but %d dimensions do not: Not broadcasting %s to %s\n",nco_prg_nm_get(),wgt_var_dmn_shr_nbr,wgt->nm,var->nm,wgt->nbr_dim-wgt_var_dmn_shr_nbr,wgt->nm,var->nm);
USE_DUMMY_WGT=True;
} /* endif */
} /* end if */
if(USE_DUMMY_WGT){
/* Variables do not truly conform, but this might be OK, depending on the application, so set DO_CONFORM flag to false and ... */
*DO_CONFORM=False;
/* ... return a dummy weight of 1.0, which allows program logic to pretend variable is weighted, but does not change answers */
wgt_out=nco_var_dpl(var);
(void)vec_set(wgt_out->type,wgt_out->sz,wgt_out->val,1.0);
} /* endif */
if(CONFORMABLE){
if(var->nbr_dim == wgt->nbr_dim){
/* var and wgt conform and are same rank */
/* Test whether all wgt and var dimensions match in sequence */
for(idx=0;idx<var->nbr_dim;idx++){
/* 20131002: nco_var_cnf_dmn() borken for groups as shown by dimension short-name strcmp() comparison here */
if(strcmp(wgt->dim[idx]->nm,var->dim[idx]->nm)) break;
/* if(wgt->dmn_id[idx] != var->dmn_id[idx]) break;*/
} /* end loop over dimensions */
/* If so, take shortcut and copy wgt to wgt_out */
if(idx == var->nbr_dim) *DO_CONFORM=True;
}else{
/* var and wgt conform but are not same rank, set flag to proceed to generic conform routine */
*DO_CONFORM=False;
} /* end else */
} /* endif CONFORMABLE */
}else{
/* var is scalar, if wgt is also then set flag to copy wgt to wgt_out else proceed to generic conform routine */
if(wgt->nbr_dim == 0) *DO_CONFORM=True; else *DO_CONFORM=False;
} /* end else */
if(CONFORMABLE && *DO_CONFORM){
wgt_out=nco_var_dpl(wgt);
(void)nco_xrf_var(wgt,wgt_out);
} /* end if */
} /* end if */
/* Set diagnostic DDRA information DDRA */
/* ddra_info->wgt_brd_flg=(wgt_out == NULL) ? True : False; *//* [flg] Broadcast weight for this variable */
if(wgt_out == NULL){
/* Expand original weight (wgt) to match size of current variable */
char * restrict wgt_cp;
char * restrict wgt_out_cp;
int idx_wgt_var[NC_MAX_DIMS];
int wgt_nbr_dim;
int var_nbr_dmn_m1;
long * restrict var_cnt;
long dmn_ss[NC_MAX_DIMS];
long dmn_var_map[NC_MAX_DIMS];
long dmn_wgt_map[NC_MAX_DIMS];
long var_lmn;
long wgt_lmn;
long var_sz;
size_t wgt_typ_sz;
/* Copy main attributes of variable into output weight */
wgt_out=nco_var_dpl(var);
(void)nco_xrf_var(wgt,wgt_out);
/* wgt_out variable was copied from template var
Modify key fields so its name and type are based on wgt, not var
wgt_out will then be hybrid between wgt and var
Remainder of routine fills wgt_out's var-dimensionality with wgt-values */
wgt_out->nm=(char *)nco_free(wgt_out->nm);
wgt_out->nm=(char *)strdup(wgt->nm);
wgt_out->id=wgt->id;
wgt_out->type=wgt->type;
wgt_out->val.vp=(void *)nco_free(wgt_out->val.vp);
wgt_out->val.vp=(void *)nco_malloc(wgt_out->sz*nco_typ_lng(wgt_out->type));
wgt_cp=(char *)wgt->val.vp;
wgt_out_cp=(char *)wgt_out->val.vp;
wgt_typ_sz=nco_typ_lng(wgt_out->type);
if(wgt_out->nbr_dim == 0){
/* Variable (and weight) are scalars, not arrays */
(void)memcpy(wgt_out_cp,wgt_cp,wgt_typ_sz);
}else if(wgt->nbr_dim == 0){
/* Lesser-ranked input variable is scalar
Expansion in this degenerate case needs no index juggling (reverse-mapping)
Code as special case to speed-up important applications of ncap
for synthetic file creation */
var_sz=var->sz;
for(var_lmn=0;var_lmn<var_sz;var_lmn++){
(void)memcpy(wgt_out_cp+var_lmn*wgt_typ_sz,wgt_cp,wgt_typ_sz);
} /* end loop over var_lmn */
}else{
/* Variable (and therefore wgt_out) are arrays, not scalars */
/* Create forward and reverse mappings from variable's dimensions to weight's dimensions:
dmn_var_map[i] is number of elements between one value of i_th
dimension of variable and next value of i_th dimension, i.e.,
number of elements in memory between indicial increments in i_th dimension.
This is computed as product of one (1) times size of all dimensions (if any) after i_th
dimension in variable.
dmn_wgt_map[i] contains analogous information, except for original weight variable
idx_wgt_var[i] contains index into variable's dimensions of i_th dimension of original weight
idx_var_wgt[i] contains index into original weight's dimensions of i_th dimension of variable
Since weight is a subset of variable, some elements of idx_var_wgt may be "empty", or unused
Since mapping arrays (dmn_var_map and dmn_wgt_map) are ultimately used for a
memcpy() operation, they could (read: should) be computed as byte offsets, not type offsets.
This is why netCDF generic hyperslab routines (ncvarputg(), ncvargetg())
request imap vector to specify offset (imap) vector in bytes. */
for(idx=0;idx<wgt->nbr_dim;idx++){
for(idx_dmn=0;idx_dmn<var->nbr_dim;idx_dmn++){
/* Compare names, not dimension IDs */
/* 20131002: nco_var_cnf_dmn() borken for groups as shown by dimension short-name strcmp() comparison here */
if(!strcmp(var->dim[idx_dmn]->nm,wgt->dim[idx]->nm)){
idx_wgt_var[idx]=idx_dmn;
break;
} /* end if */
/* Sanity check */
if(idx_dmn == var->nbr_dim-1){
(void)fprintf(stdout,"%s: ERROR wgt %s has dimension %s but var %s does not deep in nco_var_cnf_dmn()\n",nco_prg_nm_get(),wgt->nm,wgt->dim[idx]->nm,var->nm);
nco_exit(EXIT_FAILURE);
} /* end if err */
} /* end loop over variable dimensions */
} /* end loop over weight dimensions */
/* Figure out map for each dimension of variable */
for(idx=0;idx<var->nbr_dim;idx++) dmn_var_map[idx]=1L;
for(idx=0;idx<var->nbr_dim-1;idx++)
for(idx_dmn=idx+1;idx_dmn<var->nbr_dim;idx_dmn++)
dmn_var_map[idx]*=var->cnt[idx_dmn];
/* Figure out map for each dimension of weight */
for(idx=0;idx<wgt->nbr_dim;idx++) dmn_wgt_map[idx]=1L;
for(idx=0;idx<wgt->nbr_dim-1;idx++)
for(idx_dmn=idx+1;idx_dmn<wgt->nbr_dim;idx_dmn++)
dmn_wgt_map[idx]*=wgt->cnt[idx_dmn];
/* Define convenience variables to avoid repetitive indirect addressing */
wgt_nbr_dim=wgt->nbr_dim;
var_sz=var->sz;
var_cnt=var->cnt;
var_nbr_dmn_m1=var->nbr_dim-1;
/* var_lmn is offset into 1-D array corresponding to N-D indices dmn_ss */
for(var_lmn=0;var_lmn<var_sz;var_lmn++){
/* dmn_ss are corresponding indices (subscripts) into N-D array */
/* Operations: 1 modulo, 1 pointer offset, 1 user memory fetch
Repetitions: \lmnnbr
Total Counts: \rthnbr=2\lmnnbr, \mmrusrnbr=\lmnnbr
NB: LHS assumed compact and cached, counted RHS offsets and fetches only */
dmn_ss[var_nbr_dmn_m1]=var_lmn%var_cnt[var_nbr_dmn_m1];
for(idx=0;idx<var_nbr_dmn_m1;idx++){
/* Operations: 1 divide, 1 modulo, 2 pointer offset, 2 user memory fetch
Repetitions: \lmnnbr(\dmnnbr-1)
Counts: \rthnbr=4\lmnnbr(\dmnnbr-1), \mmrusrnbr=2\lmnnbr(\dmnnbr-1)
NB: LHS assumed compact and cached, counted RHS offsets and fetches only
NB: Neglected loop arithmetic/compare */
dmn_ss[idx]=(long int)(var_lmn/dmn_var_map[idx]);
dmn_ss[idx]%=var_cnt[idx];
} /* end loop over dimensions */
/* Map (shared) N-D array indices into 1-D index into original weight data */
wgt_lmn=0L;
/* Operations: 1 add, 1 multiply, 3 pointer offset, 3 user memory fetch
Repetitions: \lmnnbr\rnkwgt
Counts: \rthnbr=5\lmnnbr\rnkwgt, \mmrusrnbr=3\lmnnbr\rnkwgt */
for(idx=0;idx<wgt_nbr_dim;idx++) wgt_lmn+=dmn_ss[idx_wgt_var[idx]]*dmn_wgt_map[idx];
/* Operations: 2 add, 2 multiply, 0 pointer offset, 1 system memory copy
Repetitions: \lmnnbr
Counts: \rthnbr=4\lmnnbr, \mmrusrnbr=0, \mmrsysnbr=1 */
(void)memcpy(wgt_out_cp+var_lmn*wgt_typ_sz,wgt_cp+wgt_lmn*wgt_typ_sz,wgt_typ_sz);
} /* end loop over var_lmn */
} /* end if variable (and weight) are arrays, not scalars */
*DO_CONFORM=True;
} /* end if we had to stretch weight to fit variable */
void
nco_dmn_sct_cmp /* [fnc] Check that dims in list 2 are a subset of list 1 and that they are the same size */
(dmn_sct ** const dim_1, /* I [sct] Dimension list 1 */
const int nbr_dmn_1, /* I [nbr] Number of dimension structures in structure list */
dmn_sct **const dim_2, /* I [sct] Dimension list 1 */
const int nbr_dmn_2, /* I [nbr] Number of dimension structures in structure list */
const char *const fl_sng_1, /* I [sng] Name of first file */
const char *fl_sng_2) /* I [sng] Name of second file */
{
int idx;
int jdx;
for(idx=0;idx<nbr_dmn_2;idx++){
for(jdx=0;jdx<nbr_dmn_1;jdx++)
if(!strcmp(dim_2[idx]->nm,dim_1[jdx]->nm)) break;
if(jdx == nbr_dmn_1){
(void)fprintf(stderr,"%s: ERROR dimension \"%s\" in second file %s is not present in first file %s\n",nco_prg_nm_get(),dim_2[idx]->nm,fl_sng_2,fl_sng_1);
nco_exit(EXIT_FAILURE);
} /* end if missing dimension */
if(dim_2[idx]->cnt != dim_1[jdx]->cnt){
(void)fprintf(stderr,"%s: ERROR %sdimension size mismatch: dimension %s in file %s is size %li while dimension %s in file %s is size %li\n",nco_prg_nm_get(),(dim_1[jdx]->is_rec_dmn) ? "record " : "",dim_1[jdx]->nm,fl_sng_1,dim_1[jdx]->cnt,dim_2[idx]->nm,fl_sng_2,dim_2[idx]->cnt);
if(dim_1[idx]->cnt == 1 || dim_2[jdx]->cnt == 1) (void)fprintf(stderr,"%s: HINT Mismatch is due to degenerate (of size 1) dimension. Re-try command after first removing degenerate dimension from one file with, e.g.,\nncwa -a %s %s %s\n",nco_prg_nm_get(),(dim_1[idx]->cnt == 1) ? dim_1[idx]->nm : dim_2[idx]->nm,(dim_1[idx]->cnt == 1) ? fl_sng_1 : fl_sng_2,(dim_1[idx]->cnt == 1) ? fl_sng_1 : fl_sng_2);
nco_exit(EXIT_FAILURE);
} /* endif size mismatch */
} /* end loop over dimensions */
} /* end nco_dmn_sct_cmp() */
double /* O [frc] Double precision representation of var->val.?p[0] */
ptr_unn_2_scl_dbl /* [fnc] Convert first element of NCO variable to a scalar double */
(const ptr_unn val, /* I [sct] Pointer union to convert to scalar double */
const nc_type type) /* I [enm] Type of values pointed to by pointer union */
{
/* Purpose: Return first element of NCO variable converted to a scalar double */
double scl_dbl; /* [sct] Double precision value of scale_factor */
ptr_unn ptr_unn_scl_dbl; /* [unn] Pointer union to double precision value of first element */
/* Variable must be in memory already */
if(val.vp == NULL) {
(void)fprintf(stdout,"%s: ERROR ptr_unn_2_scl_dbl() called with empty val.vp\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
} /* endif */
/* Valid memory address exists */
ptr_unn_scl_dbl.vp=(void *)nco_malloc(nco_typ_lng(NC_DOUBLE)); /* [unn] Pointer union to double precision value of first element */
(void)nco_val_cnf_typ(type,val,NC_DOUBLE,ptr_unn_scl_dbl);
scl_dbl=ptr_unn_scl_dbl.dp[0];
ptr_unn_scl_dbl.vp=nco_free(ptr_unn_scl_dbl.vp);
return scl_dbl;
} /* end ptr_unn_2_scl_dbl() */
int
main(int argc,char **argv)
{
char **fl_lst_abb=NULL; /* Option a */
char **fl_lst_in;
char **gaa_arg=NULL; /* [sng] Global attribute arguments */
char **var_lst_in=NULL_CEWI;
char *aux_arg[NC_MAX_DIMS];
char *cmd_ln;
char *cnk_arg[NC_MAX_DIMS];
char *cnk_map_sng=NULL_CEWI; /* [sng] Chunking map */
char *cnk_plc_sng=NULL_CEWI; /* [sng] Chunking policy */
char *fl_in=NULL;
char *fl_out=NULL; /* Option o */
char *fl_out_tmp=NULL; /* MPI CEWI */
char *fl_pth=NULL; /* Option p */
char *fl_pth_lcl=NULL; /* Option l */
char *lmt_arg[NC_MAX_DIMS];
char *opt_crr=NULL; /* [sng] String representation of current long-option name */
char *optarg_lcl=NULL; /* [sng] Local copy of system optarg */
char *rec_dmn_nm=NULL; /* [sng] New record dimension name */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
const char * const CVS_Id="$Id$";
const char * const CVS_Revision="$Revision$";
const char * const opt_sht_lst="3467ACcD:d:FHhL:l:n:Oo:p:rRSt:u:v:X:x-:";
cnk_dmn_sct **cnk_dmn=NULL_CEWI;
dmn_sct *rec_dmn;
dmn_sct **dim;
dmn_sct **dmn_out;
extern char *optarg;
extern int optind;
/* Using naked stdin/stdout/stderr in parallel region generates warning
Copy appropriate filehandle to variable scoped shared in parallel clause */
FILE * const fp_stderr=stderr; /* [fl] stderr filehandle CEWI */
FILE * const fp_stdout=stdout; /* [fl] stdout filehandle CEWI */
int *in_id_arr;
int abb_arg_nbr=0;
int aux_nbr=0; /* [nbr] Number of auxiliary coordinate hyperslabs specified */
int cnk_map=nco_cnk_map_nil; /* [enm] Chunking map */
int cnk_nbr=0; /* [nbr] Number of chunk sizes */
int cnk_plc=nco_cnk_plc_nil; /* [enm] Chunking policy */
int dfl_lvl=NCO_DFL_LVL_UNDEFINED; /* [enm] Deflate level */
int fl_idx;
int fl_nbr=0;
int fl_in_fmt; /* [enm] Input file format */
int fl_out_fmt=NCO_FORMAT_UNDEFINED; /* [enm] Output file format */
int fll_md_old; /* [enm] Old fill mode */
int gaa_nbr=0; /* [nbr] Number of global attributes to add */
int idx;
int jdx;
int in_id;
int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */
int md_open; /* [enm] Mode flag for nc_open() call */
int nbr_dmn_fl;
int nbr_dmn_xtr;
int nbr_var_fix; /* nbr_var_fix gets incremented */
int nbr_var_fl;
int nbr_var_prc; /* nbr_var_prc gets incremented */
int xtr_nbr=0; /* xtr_nbr won't otherwise be set for -c with no -v */
int opt;
int out_id;
int rcd=NC_NOERR; /* [rcd] Return code */
int rec_dmn_id=NCO_REC_DMN_UNDEFINED;
int thr_idx; /* [idx] Index of current thread */
int thr_nbr=int_CEWI; /* [nbr] Thread number Option t */
int var_lst_in_nbr=0;
lmt_sct **aux=NULL_CEWI; /* Auxiliary coordinate limits */
lmt_sct **lmt;
lmt_all_sct **lmt_all_lst; /* List of *lmt_all structures */
long idx_rec_out=0L; /* idx_rec_out gets incremented */
nco_bool CNV_CCM_CCSM_CF;
nco_bool EXCLUDE_INPUT_LIST=False; /* Option c */
nco_bool EXTRACT_ALL_COORDINATES=False; /* Option c */
nco_bool EXTRACT_ASSOCIATED_COORDINATES=True; /* Option C */
nco_bool FL_RTR_RMT_LCN;
nco_bool FL_LST_IN_APPEND=True; /* Option H */
nco_bool FL_LST_IN_FROM_STDIN=False; /* [flg] fl_lst_in comes from stdin */
nco_bool FORCE_APPEND=False; /* Option A */
nco_bool FORCE_OVERWRITE=False; /* Option O */
nco_bool FORTRAN_IDX_CNV=False; /* Option F */
nco_bool HISTORY_APPEND=True; /* Option h */
nco_bool MSA_USR_RDR=False; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
nco_bool RAM_CREATE=False; /* [flg] Create file in RAM */
nco_bool RAM_OPEN=False; /* [flg] Open (netCDF3-only) file(s) in RAM */
nco_bool RM_RMT_FL_PST_PRC=True; /* Option R */
nco_bool WRT_TMP_FL=True; /* [flg] Write output to temporary file */
nco_bool flg_cln=False; /* [flg] Clean memory prior to exit */
nm_id_sct *dmn_lst;
nm_id_sct *xtr_lst=NULL; /* xtr_lst may be alloc()'d from NULL with -c option */
size_t bfr_sz_hnt=NC_SIZEHINT_DEFAULT; /* [B] Buffer size hint */
size_t cnk_min_byt=NCO_CNK_SZ_MIN_BYT_DFL; /* [B] Minimize size of variable to chunk */
size_t cnk_sz_byt=0UL; /* [B] Chunk size in bytes */
size_t cnk_sz_scl=0UL; /* [nbr] Chunk size scalar */
size_t hdr_pad=0UL; /* [B] Pad at end of header section */
var_sct **var;
var_sct **var_fix;
var_sct **var_fix_out;
var_sct **var_out;
var_sct **var_prc;
var_sct **var_prc_out;
#ifdef ENABLE_MPI
/* Declare all MPI-specific variables here */
MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
MPI_Info mpi_nfo=MPI_INFO_NULL; /* [sct] File geometry hints */
MPI_Status mpi_stt; /* [enm] Status check to decode msg_tag_typ */
nco_bool TKN_WRT_FREE=True; /* [flg] Write-access to output file is available */
int fl_nm_lng; /* [nbr] Output file name length */
int msg_bfr[msg_bfr_lng]; /* [bfr] Buffer containing var, idx, tkn_wrt_rsp */
int msg_tag_typ; /* [enm] MPI message tag type */
int prc_rnk; /* [idx] Process rank */
int prc_nbr=0; /* [nbr] Number of MPI processes */
int tkn_wrt_rsp; /* [enm] Response to request for write token */
int var_wrt_nbr=0; /* [nbr] Variables written to output file until now */
int rnk_wrk; /* [idx] Worker rank */
int wrk_id_bfr[wrk_id_bfr_lng]; /* [bfr] Buffer for rnk_wrk */
#endif /* !ENABLE_MPI */
static struct option opt_lng[]={ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
{"cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"clean",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"mmr_cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"dirty",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"mmr_drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"msa_usr_rdr",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"msa_user_order",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"ram_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"create_ram",no_argument,0,0}, /* [flg] Create file in RAM */
{"open_ram",no_argument,0,0}, /* [flg] Open (netCDF3) file(s) in RAM */
{"diskless_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"wrt_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"write_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"no_tmp_fl",no_argument,0,0}, /* [flg] Do not write output to temporary file */
{"version",no_argument,0,0},
{"vrs",no_argument,0,0},
/* Long options with argument, no short option counterpart */
{"bfr_sz_hnt",required_argument,0,0}, /* [B] Buffer size hint */
{"buffer_size_hint",required_argument,0,0}, /* [B] Buffer size hint */
{"cnk_byt",required_argument,0,0}, /* [B] Chunk size in bytes */
{"chunk_byte",required_argument,0,0}, /* [B] Chunk size in bytes */
{"cnk_dmn",required_argument,0,0}, /* [nbr] Chunk size */
{"chunk_dimension",required_argument,0,0}, /* [nbr] Chunk size */
{"cnk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"chunk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"cnk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"chunk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"cnk_plc",required_argument,0,0}, /* [nbr] Chunking policy */
{"chunk_policy",required_argument,0,0}, /* [nbr] Chunking policy */
{"cnk_scl",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"chunk_scalar",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"fl_fmt",required_argument,0,0},
{"file_format",required_argument,0,0},
{"gaa",required_argument,0,0}, /* [sng] Global attribute add */
{"glb_att_add",required_argument,0,0}, /* [sng] Global attribute add */
{"hdr_pad",required_argument,0,0},
{"header_pad",required_argument,0,0},
/* Long options with short counterparts */
{"3",no_argument,0,'3'},
{"4",no_argument,0,'4'},
{"64bit",no_argument,0,'4'},
{"netcdf4",no_argument,0,'4'},
{"7",no_argument,0,'7'},
{"append",no_argument,0,'A'},
{"coords",no_argument,0,'c'},
{"crd",no_argument,0,'c'},
{"no-coords",no_argument,0,'C'},
{"no-crd",no_argument,0,'C'},
{"debug",required_argument,0,'D'},
{"nco_dbg_lvl",required_argument,0,'D'},
{"dimension",required_argument,0,'d'},
{"dmn",required_argument,0,'d'},
{"fortran",no_argument,0,'F'},
{"ftn",no_argument,0,'F'},
{"fl_lst_in",no_argument,0,'H'},
{"file_list",no_argument,0,'H'},
{"history",no_argument,0,'h'},
{"hst",no_argument,0,'h'},
{"dfl_lvl",required_argument,0,'L'}, /* [enm] Deflate level */
{"deflate",required_argument,0,'L'}, /* [enm] Deflate level */
{"local",required_argument,0,'l'},
{"lcl",required_argument,0,'l'},
{"nintap",required_argument,0,'n'},
{"overwrite",no_argument,0,'O'},
{"ovr",no_argument,0,'O'},
{"output",required_argument,0,'o'},
{"fl_out",required_argument,0,'o'},
{"path",required_argument,0,'p'},
{"retain",no_argument,0,'R'},
{"rtn",no_argument,0,'R'},
{"revision",no_argument,0,'r'},
{"suspend", no_argument,0,'S'},
{"thr_nbr",required_argument,0,'t'},
{"threads",required_argument,0,'t'},
{"omp_num_threads",required_argument,0,'t'},
{"ulm_nm",required_argument,0,'u'},
{"rcd_nm",required_argument,0,'u'},
{"variable",required_argument,0,'v'},
{"auxiliary",required_argument,0,'X'},
{"exclude",no_argument,0,'x'},
{"xcl",no_argument,0,'x'},
{"help",no_argument,0,'?'},
{"hlp",no_argument,0,'?'},
{0,0,0,0}
}; /* end opt_lng */
int opt_idx=0; /* Index of current long option into opt_lng array */
#ifdef ENABLE_MPI
/* MPI Initialization */
MPI_Init(&argc,&argv);
MPI_Comm_size(mpi_cmm,&prc_nbr);
MPI_Comm_rank(mpi_cmm,&prc_rnk);
#endif /* !ENABLE_MPI */
/* Start clock and save command line */
cmd_ln=nco_cmd_ln_sng(argc,argv);
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
opt=getopt_long(argc,argv,opt_sht_lst,opt_lng,&opt_idx);
/* NB: access to opt_crr is only valid when long_opt is detected */
if(opt == EOF) break; /* Parse positional arguments once getopt_long() returns EOF */
opt_crr=(char *)strdup(opt_lng[opt_idx].name);
/* Process long options without short option counterparts */
if(opt == 0){
if(!strcmp(opt_crr,"bfr_sz_hnt") || !strcmp(opt_crr,"buffer_size_hint")){
bfr_sz_hnt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_byt") || !strcmp(opt_crr,"chunk_byte")){
cnk_sz_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_byt */
if(!strcmp(opt_crr,"cnk_min") || !strcmp(opt_crr,"chunk_min")){
cnk_min_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_min */
if(!strcmp(opt_crr,"cnk_dmn") || !strcmp(opt_crr,"chunk_dimension")){
/* Copy limit argument for later processing */
cnk_arg[cnk_nbr]=(char *)strdup(optarg);
cnk_nbr++;
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_scl") || !strcmp(opt_crr,"chunk_scalar")){
cnk_sz_scl=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_map") || !strcmp(opt_crr,"chunk_map")){
/* Chunking map */
cnk_map_sng=(char *)strdup(optarg);
cnk_map=nco_cnk_map_get(cnk_map_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_plc") || !strcmp(opt_crr,"chunk_policy")){
/* Chunking policy */
cnk_plc_sng=(char *)strdup(optarg);
cnk_plc=nco_cnk_plc_get(cnk_plc_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cln") || !strcmp(opt_crr,"mmr_cln") || !strcmp(opt_crr,"clean")) flg_cln=True; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"drt") || !strcmp(opt_crr,"mmr_drt") || !strcmp(opt_crr,"dirty")) flg_cln=False; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"fl_fmt") || !strcmp(opt_crr,"file_format")) rcd=nco_create_mode_prs(optarg,&fl_out_fmt);
if(!strcmp(opt_crr,"gaa") || !strcmp(opt_crr,"glb_att_add")){
gaa_arg=(char **)nco_realloc(gaa_arg,(gaa_nbr+1)*sizeof(char *));
gaa_arg[gaa_nbr++]=(char *)strdup(optarg);
} /* endif gaa */
if(!strcmp(opt_crr,"hdr_pad") || !strcmp(opt_crr,"header_pad")){
hdr_pad=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif "hdr_pad" */
if(!strcmp(opt_crr,"msa_usr_rdr") || !strcmp(opt_crr,"msa_user_order")) MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"create_ram") || !strcmp(opt_crr,"diskless_all")) RAM_CREATE=True; /* [flg] Open (netCDF3) file(s) in RAM */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"open_ram") || !strcmp(opt_crr,"diskless_all")) RAM_OPEN=True; /* [flg] Create file in RAM */
if(!strcmp(opt_crr,"vrs") || !strcmp(opt_crr,"version")){
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
nco_exit(EXIT_SUCCESS);
} /* endif "vrs" */
if(!strcmp(opt_crr,"wrt_tmp_fl") || !strcmp(opt_crr,"write_tmp_fl")) WRT_TMP_FL=True;
if(!strcmp(opt_crr,"no_tmp_fl")) WRT_TMP_FL=False;
} /* opt != 0 */
/* Process short options */
switch(opt){
case 0: /* Long options have already been processed, return */
break;
case '3': /* Request netCDF3 output storage format */
fl_out_fmt=NC_FORMAT_CLASSIC;
break;
case '4': /* Catch-all to prescribe output storage format */
if(!strcmp(opt_crr,"64bit")) fl_out_fmt=NC_FORMAT_64BIT; else fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case '6': /* Request netCDF3 64-bit offset output storage format */
fl_out_fmt=NC_FORMAT_64BIT;
break;
case '7': /* Request netCDF4-classic output storage format */
fl_out_fmt=NC_FORMAT_NETCDF4_CLASSIC;
break;
case 'A': /* Toggle FORCE_APPEND */
FORCE_APPEND=!FORCE_APPEND;
break;
case 'C': /* Extract all coordinates associated with extracted variables? */
EXTRACT_ASSOCIATED_COORDINATES=False;
break;
case 'c':
EXTRACT_ALL_COORDINATES=True;
break;
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
lmt_nbr++;
break;
case 'F': /* Toggle index convention. Default is 0-based arrays (C-style). */
FORTRAN_IDX_CNV=!FORTRAN_IDX_CNV;
break;
case 'H': /* Toggle writing input file list attribute */
FL_LST_IN_APPEND=!FL_LST_IN_APPEND;
break;
case 'h': /* Toggle appending to history global attribute */
HISTORY_APPEND=!HISTORY_APPEND;
break;
case 'L': /* [enm] Deflate level. Default is 0. */
dfl_lvl=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'l': /* Local path prefix for files retrieved from remote file system */
fl_pth_lcl=(char *)strdup(optarg);
break;
case 'n': /* NINTAP-style abbreviation of files to process */
fl_lst_abb=nco_lst_prs_2D(optarg,",",&abb_arg_nbr);
if(abb_arg_nbr < 1 || abb_arg_nbr > 6){
(void)fprintf(stdout,"%s: ERROR Incorrect abbreviation for file list\n",nco_prg_nm);
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
} /* end if */
break;
case 'O': /* Toggle FORCE_OVERWRITE */
FORCE_OVERWRITE=!FORCE_OVERWRITE;
break;
case 'o': /* Name of output file */
fl_out=(char *)strdup(optarg);
break;
case 'p': /* Common file path */
fl_pth=(char *)strdup(optarg);
break;
case 'R': /* Toggle removal of remotely-retrieved-files. Default is True. */
RM_RMT_FL_PST_PRC=!RM_RMT_FL_PST_PRC;
break;
case 'r': /* Print CVS program information and copyright notice */
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
(void)nco_lbr_vrs_prn();
(void)nco_cpy_prn();
(void)nco_cnf_prn();
nco_exit(EXIT_SUCCESS);
break;
#ifdef ENABLE_MPI
case 'S': /* Suspend with signal handler to facilitate debugging */
if(signal(SIGUSR1,nco_cnt_run) == SIG_ERR) (void)fprintf(fp_stdout,"%s: ERROR Could not install suspend handler.\n",nco_prg_nm);
while(!nco_spn_lck_brk) usleep(nco_spn_lck_us); /* Spinlock. fxm: should probably insert a sched_yield */
break;
#endif /* !ENABLE_MPI */
case 't': /* Thread number */
thr_nbr=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'u': /* New record dimension name */
rec_dmn_nm=(char *)strdup(optarg);
break;
case 'v': /* Variables to extract/exclude */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
var_lst_in=nco_lst_prs_2D(optarg_lcl,",",&var_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
xtr_nbr=var_lst_in_nbr;
break;
case 'X': /* Copy auxiliary coordinate argument for later processing */
aux_arg[aux_nbr]=(char *)strdup(optarg);
aux_nbr++;
MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
break;
case 'x': /* Exclude rather than extract variables specified with -v */
EXCLUDE_INPUT_LIST=True;
break;
case '?': /* Print proper usage */
(void)nco_usg_prn();
nco_exit(EXIT_SUCCESS);
break;
case '-': /* Long options are not allowed */
(void)fprintf(stderr,"%s: ERROR Long options are not available in this build. Use single letter options instead.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
break;
default: /* Print proper usage */
(void)fprintf(stdout,"%s ERROR in command-line syntax/options. Please reformulate command accordingly.\n",nco_prg_nm_get());
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
break;
} /* end switch */
if(opt_crr) opt_crr=(char *)nco_free(opt_crr);
} /* end while loop */
/* Process positional arguments and fill in filenames */
fl_lst_in=nco_fl_lst_mk(argv,argc,optind,&fl_nbr,&fl_out,&FL_LST_IN_FROM_STDIN);
/* Make uniform list of user-specified chunksizes */
if(cnk_nbr > 0) cnk_dmn=nco_cnk_prs(cnk_nbr,cnk_arg);
/* Make uniform list of user-specified dimension limits */
lmt=nco_lmt_prs(lmt_nbr,lmt_arg);
/* Initialize thread information */
thr_nbr=nco_openmp_ini(thr_nbr);
in_id_arr=(int *)nco_malloc(thr_nbr*sizeof(int));
/* Parse filename */
fl_in=nco_fl_nm_prs(fl_in,0,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
/* Make sure file is on local system and is readable or die trying */
fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
/* Open file using appropriate buffer size hints and verbosity */
if(RAM_OPEN) md_open=NC_NOWRITE|NC_DISKLESS; else md_open=NC_NOWRITE;
rcd+=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,&in_id);
/* Parse auxiliary coordinates */
if(aux_nbr > 0){
int aux_idx_nbr;
aux=nco_aux_evl(in_id,aux_nbr,aux_arg,&aux_idx_nbr);
if(aux_idx_nbr > 0){
lmt=(lmt_sct **)nco_realloc(lmt,(lmt_nbr+aux_idx_nbr)*sizeof(lmt_sct *));
int lmt_nbr_new=lmt_nbr+aux_idx_nbr;
int aux_idx=0;
for(int lmt_idx=lmt_nbr;lmt_idx<lmt_nbr_new;lmt_idx++) lmt[lmt_idx]=aux[aux_idx++];
lmt_nbr=lmt_nbr_new;
} /* endif aux */
} /* endif aux_nbr */
/* Get number of variables, dimensions, and record dimension ID of input file */
(void)nco_inq(in_id,&nbr_dmn_fl,&nbr_var_fl,(int *)NULL,&rec_dmn_id);
(void)nco_inq_format(in_id,&fl_in_fmt);
/* Form initial extraction list which may include extended regular expressions */
xtr_lst=nco_var_lst_mk(in_id,nbr_var_fl,var_lst_in,EXCLUDE_INPUT_LIST,EXTRACT_ALL_COORDINATES,&xtr_nbr);
/* Change included variables to excluded variables */
if(EXCLUDE_INPUT_LIST) xtr_lst=nco_var_lst_xcl(in_id,nbr_var_fl,xtr_lst,&xtr_nbr);
/* Is this a CCM/CCSM/CF-format history tape? */
CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(in_id);
/* Add all coordinate variables to extraction list */
if(EXTRACT_ALL_COORDINATES) xtr_lst=nco_var_lst_crd_add(in_id,nbr_dmn_fl,nbr_var_fl,xtr_lst,&xtr_nbr,CNV_CCM_CCSM_CF);
/* Extract coordinates associated with extracted variables */
if(EXTRACT_ASSOCIATED_COORDINATES) xtr_lst=nco_var_lst_crd_ass_add(in_id,xtr_lst,&xtr_nbr,CNV_CCM_CCSM_CF);
/* Sort extraction list by variable ID for fastest I/O */
if(xtr_nbr > 1) xtr_lst=nco_lst_srt_nm_id(xtr_lst,xtr_nbr,False);
/* We now have final list of variables to extract. Phew. */
/* Find coordinate/dimension values associated with user-specified limits
NB: nco_lmt_evl() with same nc_id contains OpenMP critical region */
for(idx=0;idx<lmt_nbr;idx++) (void)nco_lmt_evl(in_id,lmt[idx],0L,FORTRAN_IDX_CNV);
/* Place all dimensions in lmt_all_lst */
lmt_all_lst=(lmt_all_sct **)nco_malloc(nbr_dmn_fl*sizeof(lmt_all_sct *));
/* Initialize lmt_all_sct's */
(void)nco_msa_lmt_all_ntl(in_id,MSA_USR_RDR,lmt_all_lst,nbr_dmn_fl,lmt,lmt_nbr);
/* Find dimensions associated with variables to be extracted */
dmn_lst=nco_dmn_lst_ass_var(in_id,xtr_lst,xtr_nbr,&nbr_dmn_xtr);
/* Fill-in dimension structure for all extracted dimensions */
dim=(dmn_sct **)nco_malloc(nbr_dmn_xtr*sizeof(dmn_sct *));
for(idx=0;idx<nbr_dmn_xtr;idx++) dim[idx]=nco_dmn_fll(in_id,dmn_lst[idx].id,dmn_lst[idx].nm);
/* Dimension list no longer needed */
dmn_lst=nco_nm_id_lst_free(dmn_lst,nbr_dmn_xtr);
/* Merge hyperslab limit information into dimension structures */
if(lmt_nbr > 0) (void)nco_dmn_lmt_mrg(dim,nbr_dmn_xtr,lmt,lmt_nbr);
/* Duplicate input dimension structures for output dimension structures */
dmn_out=(dmn_sct **)nco_malloc(nbr_dmn_xtr*sizeof(dmn_sct *));
for(idx=0;idx<nbr_dmn_xtr;idx++){
dmn_out[idx]=nco_dmn_dpl(dim[idx]);
(void)nco_dmn_xrf(dim[idx],dmn_out[idx]);
} /* end loop over idx */
/* Fill-in variable structure list for all extracted variables */
var=(var_sct **)nco_malloc(xtr_nbr*sizeof(var_sct *));
var_out=(var_sct **)nco_malloc(xtr_nbr*sizeof(var_sct *));
for(idx=0;idx<xtr_nbr;idx++){
var[idx]=nco_var_fll(in_id,xtr_lst[idx].id,xtr_lst[idx].nm,dim,nbr_dmn_xtr);
var_out[idx]=nco_var_dpl(var[idx]);
(void)nco_xrf_var(var[idx],var_out[idx]);
(void)nco_xrf_dmn(var_out[idx]);
} /* end loop over idx */
/* Extraction list no longer needed */
xtr_lst=nco_nm_id_lst_free(xtr_lst,xtr_nbr);
/* Divide variable lists into lists of fixed variables and variables to be processed */
(void)nco_var_lst_dvd(var,var_out,xtr_nbr,CNV_CCM_CCSM_CF,True,nco_pck_plc_nil,nco_pck_map_nil,(dmn_sct **)NULL,0,&var_fix,&var_fix_out,&nbr_var_fix,&var_prc,&var_prc_out,&nbr_var_prc);
#ifdef ENABLE_MPI
if(prc_rnk == rnk_mgr){ /* MPI manager code */
#endif /* !ENABLE_MPI */
/* Make output and input files consanguinous */
if(fl_out_fmt == NCO_FORMAT_UNDEFINED) fl_out_fmt=fl_in_fmt;
/* Verify output file format supports requested actions */
(void)nco_fl_fmt_vet(fl_out_fmt,cnk_nbr,dfl_lvl);
/* Open output file */
fl_out_tmp=nco_fl_out_open(fl_out,FORCE_APPEND,FORCE_OVERWRITE,fl_out_fmt,&bfr_sz_hnt,RAM_CREATE,RAM_OPEN,WRT_TMP_FL,&out_id);
/* Copy global attributes */
(void)nco_att_cpy(in_id,out_id,NC_GLOBAL,NC_GLOBAL,(nco_bool)True);
/* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(HISTORY_APPEND && FORCE_APPEND) (void)nco_prv_att_cat(fl_in,in_id,out_id);
if(gaa_nbr > 0) (void)nco_glb_att_add(out_id,gaa_arg,gaa_nbr);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
if(thr_nbr > 0 && HISTORY_APPEND) (void)nco_thr_att_cat(out_id,thr_nbr);
#ifdef ENABLE_MPI
/* Initialize MPI task information */
if(prc_nbr > 0 && HISTORY_APPEND) (void)nco_mpi_att_cat(out_id,prc_nbr);
#endif /* !ENABLE_MPI */
/* Add input file list global attribute */
if(FL_LST_IN_APPEND && HISTORY_APPEND && FL_LST_IN_FROM_STDIN) (void)nco_fl_lst_att_cat(out_id,fl_lst_in,fl_nbr);
#ifdef ENABLE_MPI
} /* prc_rnk != rnk_mgr */
#endif /* !ENABLE_MPI */
/* ncecat-specific operations */
if(True){
/* Always construct new "record" dimension from scratch */
rec_dmn=(dmn_sct *)nco_malloc(sizeof(dmn_sct));
if(rec_dmn_nm == NULL) rec_dmn->nm=rec_dmn_nm=(char *)strdup("record"); else rec_dmn->nm=rec_dmn_nm;
rec_dmn->id=-1;
rec_dmn->nc_id=-1;
rec_dmn->xrf=NULL;
rec_dmn->val.vp=NULL;
rec_dmn->is_crd_dmn=False;
rec_dmn->is_rec_dmn=True;
rec_dmn->sz=0L;
rec_dmn->cnt=0L;
rec_dmn->srd=0L;
rec_dmn->srt=0L;
rec_dmn->end=rec_dmn->sz-1L;
/* Change existing record dimension, if any, to regular dimension */
for(idx=0;idx<nbr_dmn_xtr;idx++){
/* Is any input dimension a record dimension? */
if(dmn_out[idx]->is_rec_dmn){
dmn_out[idx]->is_rec_dmn=False;
break;
} /* end if */
} /* end loop over idx */
/* Add record dimension to end of dimension list */
nbr_dmn_xtr++;
dmn_out=(dmn_sct **)nco_realloc(dmn_out,nbr_dmn_xtr*sizeof(dmn_sct **));
dmn_out[nbr_dmn_xtr-1]=rec_dmn;
} /* end if */
#ifdef ENABLE_MPI
if(prc_rnk == rnk_mgr){ /* MPI manager code */
#endif /* !ENABLE_MPI */
/* Define dimensions in output file */
(void)nco_dmn_dfn(fl_out,out_id,dmn_out,nbr_dmn_xtr);
#ifdef ENABLE_MPI
} /* prc_rnk != rnk_mgr */
#endif /* !ENABLE_MPI */
if(True){
/* Prepend record dimension to beginning of all vectors for processed variables */
for(idx=0;idx<nbr_var_prc;idx++){
var_prc_out[idx]->nbr_dim++;
var_prc_out[idx]->is_rec_var=True;
var_prc_out[idx]->sz_rec=var_prc_out[idx]->sz;
/* Allocate space to hold dimension IDs */
var_prc_out[idx]->dim=(dmn_sct **)nco_realloc(var_prc_out[idx]->dim,var_prc_out[idx]->nbr_dim*sizeof(dmn_sct *));
var_prc_out[idx]->dmn_id=(int *)nco_realloc(var_prc_out[idx]->dmn_id,var_prc_out[idx]->nbr_dim*sizeof(int));
var_prc_out[idx]->cnt=(long *)nco_realloc(var_prc_out[idx]->cnt,var_prc_out[idx]->nbr_dim*sizeof(long int));
var_prc_out[idx]->end=(long *)nco_realloc(var_prc_out[idx]->end,var_prc_out[idx]->nbr_dim*sizeof(long int));
var_prc_out[idx]->srd=(long *)nco_realloc(var_prc_out[idx]->srd,var_prc_out[idx]->nbr_dim*sizeof(long int));
var_prc_out[idx]->srt=(long *)nco_realloc(var_prc_out[idx]->srt,var_prc_out[idx]->nbr_dim*sizeof(long int));
/* Move current array by one to make room for new record dimension info */
(void)memmove((void *)(var_prc_out[idx]->dim+1),(void *)(var_prc_out[idx]->dim),(var_prc_out[idx]->nbr_dim-1)*sizeof(dmn_sct *));
(void)memmove((void *)(var_prc_out[idx]->dmn_id+1),(void *)(var_prc_out[idx]->dmn_id),(var_prc_out[idx]->nbr_dim-1)*sizeof(int));
(void)memmove((void *)(var_prc_out[idx]->cnt+1),(void *)(var_prc_out[idx]->cnt),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
(void)memmove((void *)(var_prc_out[idx]->end+1),(void *)(var_prc_out[idx]->end),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
(void)memmove((void *)(var_prc_out[idx]->srd+1),(void *)(var_prc_out[idx]->srd),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
(void)memmove((void *)(var_prc_out[idx]->srt+1),(void *)(var_prc_out[idx]->srt),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
/* Insert value for new record dimension */
var_prc_out[idx]->dim[0]=rec_dmn;
var_prc_out[idx]->dmn_id[0]=rec_dmn->id;
var_prc_out[idx]->cnt[0]=1L;
var_prc_out[idx]->end[0]=-1L;
var_prc_out[idx]->srd[0]=-1L;
var_prc_out[idx]->srt[0]=-1L;
} /* end loop over idx */
} /* end if */
#ifdef ENABLE_MPI
if(prc_rnk == rnk_mgr){ /* MPI manager code */
#endif /* !ENABLE_MPI */
/* Define variables in output file, copy their attributes */
(void)nco_var_dfn(in_id,fl_out,out_id,var_out,xtr_nbr,(dmn_sct **)NULL,(int)0,nco_pck_plc_nil,nco_pck_map_nil,dfl_lvl);
#ifdef ENABLE_MPI
} /* prc_rnk != rnk_mgr */
#endif /* !ENABLE_MPI */
/* Assign zero to start and unity to stride vectors in output variables */
(void)nco_var_srd_srt_set(var_out,xtr_nbr);
#ifdef ENABLE_MPI
if(prc_rnk == rnk_mgr){ /* prc_rnk != rnk_mgr */
#endif /* !ENABLE_MPI */
/* Set chunksize parameters */
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC) (void)nco_cnk_sz_set(out_id,lmt_all_lst,nbr_dmn_fl,&cnk_map,&cnk_plc,cnk_sz_scl,cnk_dmn,cnk_nbr);
/* Turn-off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
/* Take output file out of define mode */
if(hdr_pad == 0UL){
(void)nco_enddef(out_id);
}else{
(void)nco__enddef(out_id,hdr_pad);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: INFO Padding header with %lu extra bytes\n",nco_prg_nm_get(),(unsigned long)hdr_pad);
} /* hdr_pad */
#ifdef ENABLE_MPI
} /* prc_rnk != rnk_mgr */
/* Manager obtains output filename and broadcasts to workers */
if(prc_rnk == rnk_mgr) fl_nm_lng=(int)strlen(fl_out_tmp);
MPI_Bcast(&fl_nm_lng,1,MPI_INT,0,mpi_cmm);
if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)nco_malloc((fl_nm_lng+1)*sizeof(char));
MPI_Bcast(fl_out_tmp,fl_nm_lng+1,MPI_CHAR,0,mpi_cmm);
if(prc_rnk == rnk_mgr){ /* MPI manager code */
TKN_WRT_FREE=False;
#endif /* !ENABLE_MPI */
/* Copy variable data for non-processed variables */
(void)nco_var_val_cpy(in_id,out_id,var_fix,nbr_var_fix);
#ifdef ENABLE_MPI
/* Close output file so workers can open it */
nco_close(out_id);
TKN_WRT_FREE=True;
} /* prc_rnk != rnk_mgr */
#endif /* !ENABLE_MPI */
/* Close first input netCDF file */
(void)nco_close(in_id);
/* Loop over input files */
for(fl_idx=0;fl_idx<fl_nbr;fl_idx++){
#ifdef ENABLE_MPI
MPI_Barrier(mpi_cmm);
#endif /* !ENABLE_MPI */
/* Parse filename */
if(fl_idx != 0) fl_in=nco_fl_nm_prs(fl_in,fl_idx,(int *)NULL,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(fp_stderr,"\nInput file %d is %s; ",fl_idx,fl_in);
/* Make sure file is on local system and is readable or die trying */
if(fl_idx != 0) fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(fp_stderr,"local file %s:\n",fl_in);
/* Open file once per thread to improve caching */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) rcd=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,in_id_arr+thr_idx);
#if 0
/* fxm: netCDF4: Change to independent variable reads? */
#ifdef ENABLE_NETCDF4
rcd=nco_open_par(fl_in,NC_MPIIO|NC_NETCDF4,mpi_cmm,mpi_nfo,&in_id);
#endif /* !ENABLE_NETCDF4 */
#endif /* !0 */
/* Perform various error-checks on input file */
if(False) (void)nco_fl_cmp_err_chk();
#ifdef ENABLE_MPI
if(prc_rnk == rnk_mgr){ /* MPI manager code */
/* Compensate for incrementing on each worker's first message */
var_wrt_nbr=-prc_nbr+1;
idx=0;
/* While variables remain to be processed or written... */
while(var_wrt_nbr < nbr_var_prc){
/* Receive message from any worker */
MPI_Recv(wrk_id_bfr,wrk_id_bfr_lng,MPI_INT,MPI_ANY_SOURCE,MPI_ANY_TAG,mpi_cmm,&mpi_stt);
/* Obtain MPI message tag type */
msg_tag_typ=mpi_stt.MPI_TAG;
/* Get sender's prc_rnk */
rnk_wrk=wrk_id_bfr[0];
/* Allocate next variable, if any, to worker */
if(msg_tag_typ == msg_tag_wrk_rqs){
var_wrt_nbr++; /* [nbr] Number of variables written */
/* Worker closed output file before sending msg_tag_wrk_rqs */
TKN_WRT_FREE=True;
if(idx > nbr_var_prc-1){
msg_bfr[0]=idx_all_wrk_ass; /* [enm] All variables already assigned */
msg_bfr[1]=out_id; /* Output file ID */
}else{
/* Tell requesting worker to allocate space for next variable */
msg_bfr[0]=idx; /* [idx] Variable to be processed */
msg_bfr[1]=out_id; /* Output file ID */
msg_bfr[2]=var_prc_out[idx]->id; /* [id] Variable ID in output file */
/* Point to next variable on list */
idx++;
} /* endif idx */
MPI_Send(msg_bfr,msg_bfr_lng,MPI_INT,rnk_wrk,msg_tag_wrk_rsp,mpi_cmm);
/* msg_tag_typ != msg_tag_wrk_rqs */
}else if(msg_tag_typ == msg_tag_tkn_wrt_rqs){
/* Allocate token if free, else ask worker to try later */
if(TKN_WRT_FREE){
TKN_WRT_FREE=False;
msg_bfr[0]=tkn_wrt_rqs_xcp; /* Accept request for write token */
}else{
msg_bfr[0]=tkn_wrt_rqs_dny; /* Deny request for write token */
} /* !TKN_WRT_FREE */
MPI_Send(msg_bfr,msg_bfr_lng,MPI_INT,rnk_wrk,msg_tag_tkn_wrt_rsp,mpi_cmm);
} /* msg_tag_typ != msg_tag_tkn_wrt_rqs */
} /* end while var_wrt_nbr < nbr_var_prc */
}else{ /* prc_rnk != rnk_mgr, end Manager code begin Worker code */
wrk_id_bfr[0]=prc_rnk;
while(1){ /* While work remains... */
/* Send msg_tag_wrk_rqs */
wrk_id_bfr[0]=prc_rnk;
MPI_Send(wrk_id_bfr,wrk_id_bfr_lng,MPI_INT,rnk_mgr,msg_tag_wrk_rqs,mpi_cmm);
/* Receive msg_tag_wrk_rsp */
MPI_Recv(msg_bfr,msg_bfr_lng,MPI_INT,0,msg_tag_wrk_rsp,mpi_cmm,&mpi_stt);
idx=msg_bfr[0];
out_id=msg_bfr[1];
if(idx == idx_all_wrk_ass) break;
else{
var_prc_out[idx]->id=msg_bfr[2];
/* Process this variable same as UP code */
#else /* !ENABLE_MPI */
/* OpenMP with threading over variables, not files */
#ifdef _OPENMP
#pragma omp parallel for default(none) private(idx,in_id) shared(nco_dbg_lvl,fl_nbr,idx_rec_out,in_id_arr,nbr_var_prc,out_id,var_prc,var_prc_out,lmt_all_lst,nbr_dmn_fl,jdx)
#endif /* !_OPENMP */
/* Process all variables in current file */
for(idx=0;idx<nbr_var_prc;idx++){
#endif /* !ENABLE_MPI */
/* Common code for UP and MPI */ /* fxm: requires C99 as is? */
in_id=in_id_arr[omp_get_thread_num()];
if(nco_dbg_lvl >= nco_dbg_var) (void)fprintf(fp_stderr,"%s, ",var_prc[idx]->nm);
if(nco_dbg_lvl >= nco_dbg_var) (void)fflush(fp_stderr);
/* Variables may have different ID, missing_value, type, in each file */
(void)nco_var_mtd_refresh(in_id,var_prc[idx]);
/* Retrieve variable from disk into memory */
/* NB: nco_var_get() with same nc_id contains OpenMP critical region */
(void)nco_var_get(in_id,var_prc[idx]);
/* Size of record dimension is 1 in output file */
var_prc_out[idx]->cnt[0]=1L;
var_prc_out[idx]->srt[0]=idx_rec_out;
#ifdef ENABLE_MPI
/* Obtain token and prepare to write */
while(1){ /* Send msg_tag_tkn_wrt_rqs repeatedly until token obtained */
wrk_id_bfr[0]=prc_rnk;
MPI_Send(wrk_id_bfr,wrk_id_bfr_lng,MPI_INT,rnk_mgr,msg_tag_tkn_wrt_rqs,mpi_cmm);
MPI_Recv(msg_bfr,msg_bfr_lng,MPI_INT,rnk_mgr,msg_tag_tkn_wrt_rsp,mpi_cmm,&mpi_stt);
tkn_wrt_rsp=msg_bfr[0];
/* Wait then re-send request */
if(tkn_wrt_rsp == tkn_wrt_rqs_dny) sleep(tkn_wrt_rqs_ntv); else break;
} /* end while loop waiting for write token */
/* Worker has token---prepare to write */
if(tkn_wrt_rsp == tkn_wrt_rqs_xcp){
if(RAM_OPEN) md_open=NC_WRITE|NC_SHARE|NC_DISKLESS; else md_open=NC_WRITE|NC_SHARE;
rcd=nco_fl_open(fl_out_tmp,md_open,&bfr_sz_hnt,&out_id);
/* Set chunksize parameters */
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC) (void)nco_cnk_sz_set(out_id,lmt_all_lst,nbr_dmn_fl,&cnk_map,&cnk_plc,cnk_sz_scl,cnk_dmn,cnk_nbr);
/* Turn-off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
#else /* !ENABLE_MPI */
#ifdef _OPENMP
#pragma omp critical
#endif /* _OPENMP */
#endif /* !ENABLE_MPI */
{ /* begin OpenMP critical */
/* Write variable into current record in output file */
if(var_prc[idx]->nbr_dim == 0){
(void)nco_put_var1(out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc[idx]->val.vp,var_prc[idx]->type);
}else{ /* end if variable is scalar */
(void)nco_put_vara(out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc_out[idx]->cnt,var_prc[idx]->val.vp,var_prc[idx]->type);
} /* end if variable is array */
/* Free current input buffer */
var_prc[idx]->val.vp=nco_free(var_prc[idx]->val.vp);
} /* end OpenMP critical */
#ifdef ENABLE_MPI
/* Close output file and increment written counter */
nco_close(out_id);
var_wrt_nbr++;
} /* endif tkn_wrt_rqs_xcp */
} /* end else !idx_all_wrk_ass */
} /* end while loop requesting work/token */
} /* endif Worker */
#else /* !ENABLE_MPI */
} /* end (OpenMP parallel for) loop over idx */
#endif /* !ENABLE_MPI */
idx_rec_out++; /* [idx] Index of current record in output file (0 is first, ...) */
if(nco_dbg_lvl > nco_dbg_scl) (void)fprintf(stderr,"\n");
/* Close input netCDF file */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) nco_close(in_id_arr[thr_idx]);
/* Remove local copy of file */
if(FL_RTR_RMT_LCN && RM_RMT_FL_PST_PRC) (void)nco_fl_rm(fl_in);
#ifdef ENABLE_MPI
MPI_Barrier(mpi_cmm);
#endif /* !ENABLE_MPI */
} /* end loop over fl_idx */
#ifdef ENABLE_MPI
/* Manager moves output file (closed by workers) from temporary to permanent location */
if(prc_rnk == rnk_mgr) (void)nco_fl_mv(fl_out_tmp,fl_out);
#else /* !ENABLE_MPI */
/* Close output file and move it from temporary to permanent location */
(void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id);
#endif /* end !ENABLE_MPI */
/* Clean memory unless dirty memory allowed */
if(flg_cln){
/* ncecat-specific memory cleanup */
if(rec_dmn_nm) rec_dmn_nm=(char *)nco_free(rec_dmn_nm);
/* NB: free lmt[] is now referenced within lmt_all_lst[idx] */
for(idx=0;idx<nbr_dmn_fl;idx++)
for(jdx=0;jdx<lmt_all_lst[idx]->lmt_dmn_nbr;jdx++)
lmt_all_lst[idx]->lmt_dmn[jdx]=nco_lmt_free(lmt_all_lst[idx]->lmt_dmn[jdx]);
lmt=(lmt_sct**)nco_free(lmt);
if(nbr_dmn_fl > 0) lmt_all_lst=nco_lmt_all_lst_free(lmt_all_lst,nbr_dmn_fl);
/* NCO-generic clean-up */
/* Free individual strings/arrays */
if(cmd_ln) cmd_ln=(char *)nco_free(cmd_ln);
if(cnk_map_sng) cnk_map_sng=(char *)nco_free(cnk_map_sng);
if(cnk_plc_sng) cnk_plc_sng=(char *)nco_free(cnk_plc_sng);
if(fl_in) fl_in=(char *)nco_free(fl_in);
if(fl_out) fl_out=(char *)nco_free(fl_out);
if(fl_out_tmp) fl_out_tmp=(char *)nco_free(fl_out_tmp);
if(fl_pth) fl_pth=(char *)nco_free(fl_pth);
if(fl_pth_lcl) fl_pth_lcl=(char *)nco_free(fl_pth_lcl);
if(in_id_arr) in_id_arr=(int *)nco_free(in_id_arr);
/* Free lists of strings */
if(fl_lst_in && fl_lst_abb == NULL) fl_lst_in=nco_sng_lst_free(fl_lst_in,fl_nbr);
if(fl_lst_in && fl_lst_abb) fl_lst_in=nco_sng_lst_free(fl_lst_in,1);
if(fl_lst_abb) fl_lst_abb=nco_sng_lst_free(fl_lst_abb,abb_arg_nbr);
if(gaa_nbr > 0) gaa_arg=nco_sng_lst_free(gaa_arg,gaa_nbr);
if(var_lst_in_nbr > 0) var_lst_in=nco_sng_lst_free(var_lst_in,var_lst_in_nbr);
/* Free limits */
for(idx=0;idx<lmt_nbr;idx++) lmt_arg[idx]=(char *)nco_free(lmt_arg[idx]);
for(idx=0;idx<aux_nbr;idx++) aux_arg[idx]=(char *)nco_free(aux_arg[idx]);
if(aux_nbr > 0) aux=(lmt_sct **)nco_free(aux);
/* Free chunking information */
for(idx=0;idx<cnk_nbr;idx++) cnk_arg[idx]=(char *)nco_free(cnk_arg[idx]);
if(cnk_nbr > 0) cnk_dmn=nco_cnk_lst_free(cnk_dmn,cnk_nbr);
/* Free dimension lists */
if(nbr_dmn_xtr > 0) dim=nco_dmn_lst_free(dim,nbr_dmn_xtr-1); /* NB: ncecat has one fewer input than output dimension */
if(nbr_dmn_xtr > 0) dmn_out=nco_dmn_lst_free(dmn_out,nbr_dmn_xtr);
/* Free variable lists */
if(xtr_nbr > 0) var=nco_var_lst_free(var,xtr_nbr);
if(xtr_nbr > 0) var_out=nco_var_lst_free(var_out,xtr_nbr);
var_prc=(var_sct **)nco_free(var_prc);
var_prc_out=(var_sct **)nco_free(var_prc_out);
var_fix=(var_sct **)nco_free(var_fix);
var_fix_out=(var_sct **)nco_free(var_fix_out);
} /* !flg_cln */
#ifdef ENABLE_MPI
MPI_Finalize();
#endif /* !ENABLE_MPI */
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
int /* O [flg] Dimension exists in scope of group (if rcd != NC_NOERR) */
nco_inq_dmn_grp_id /* [fnc] Return location and ID of named dimension in specified group */
(const int nc_id, /* I [id] netCDF group ID */
const char * const dmn_nm, /* I [sng] Dimension name */
int * const dmn_id, /* O [id] Dimension ID in specified group */
int * const grp_id_dmn) /* O [id] Group ID where dimension visible to specified group is defined */
{
/* Purpose: Return location and ID of named dimension in specified group
ncks -O -D 1 -v two_dmn_rec_var ~/nco/data/in_grp.nc ~/foo.nc */
const char fnc_nm[]="nco_inq_dmn_grp_id()"; /* [sng] Function name */
const int flg_prn=1; /* [flg] Retrieve all dimensions in all parent groups */
int dmn_ids[NC_MAX_DIMS]; /* [nbr] Dimensions IDs array */
int dmn_idx; /* [idx] Dimension index */
int dmn_nbr; /* [nbr] Number of dimensions for group */
int rcd; /* [rcd] Return code */
nco_bool grp_dfn_fnd=False; /* [flg] Group of definition has been found */
/* Initialize search to start with specified group */
*grp_id_dmn=nc_id;
rcd=nco_inq_dimid_flg(*grp_id_dmn,dmn_nm,dmn_id);
if(nco_dbg_lvl_get() >= nco_dbg_std){
char *grp_nm_fll; /* [sng] Group name */
char dmn_nm_lcl[NC_MAX_NAME]; /* [sng] Dimension name */
size_t grp_nm_fll_lng; /* [nbr] Length of group name */
(void)nco_inq_grpname_full(*grp_id_dmn,&grp_nm_fll_lng,(char *)NULL);
grp_nm_fll=(char *)nco_malloc((grp_nm_fll_lng+1L)*sizeof(char));
(void)nco_inq_grpname_full(*grp_id_dmn,(size_t *)NULL,grp_nm_fll);
(void)nco_inq_dimids(*grp_id_dmn,&dmn_nbr,dmn_ids,flg_prn);
(void)fprintf(stdout,"%s: %s nco_inq_dimids() reports following dimensions/IDs are visible to group %s:\n",nco_prg_nm_get(),fnc_nm,grp_nm_fll);
for(dmn_idx=0;dmn_idx<dmn_nbr;dmn_idx++){
(void)nco_inq_dimname(*grp_id_dmn,dmn_ids[dmn_idx],dmn_nm_lcl);
(void)fprintf(stdout,"%s/%d,%s",dmn_nm_lcl,dmn_ids[dmn_idx],(dmn_idx == dmn_nbr-1) ? "\n" : ", ");
} /* end loop over dmn */
if(rcd == NC_NOERR) (void)fprintf(stdout,"%s: %s nco_inq_dimid() reports group %s sees dimension %s with ID = %d:\n",nco_prg_nm_get(),fnc_nm,grp_nm_fll,dmn_nm,*dmn_id); else (void)fprintf(stdout,"%s: %s reports group %s does not see dimension %s\n",nco_prg_nm_get(),fnc_nm,grp_nm_fll,dmn_nm);
if(grp_nm_fll) grp_nm_fll=(char *)nco_free(grp_nm_fll);
} /* endif dbg */
/* If dimension is visible to output group, find exactly where it is defined
Search ancestors until group of definition is found ... */
while(!grp_dfn_fnd && (rcd == NC_NOERR)){
/* ... obtain all dimension IDs in current group (_NOT_ in ancestor groups) ... */
(void)nco_inq_dimids(*grp_id_dmn,&dmn_nbr,dmn_ids,0);
/* ... and check each against ID of target dimension */
for(dmn_idx=0;dmn_idx<dmn_nbr;dmn_idx++)
if(dmn_ids[dmn_idx] == *dmn_id) break;
if(nco_dbg_lvl_get() >= nco_dbg_std){
char *grp_nm_fll; /* [sng] Group name */
size_t grp_nm_fll_lng; /* [nbr] Length of group name */
(void)nco_inq_grpname_full(*grp_id_dmn,&grp_nm_fll_lng,(char *)NULL);
grp_nm_fll=(char *)nco_malloc((grp_nm_fll_lng+1L)*sizeof(char));
(void)nco_inq_grpname_full(*grp_id_dmn,(size_t *)NULL,grp_nm_fll);
(void)fprintf(stdout,"%s: %s reports dimension %s was%s defined in group %s\n",nco_prg_nm_get(),fnc_nm,dmn_nm,(dmn_idx < dmn_nbr) ? "" : " not",grp_nm_fll);
if(grp_nm_fll) grp_nm_fll=(char *)nco_free(grp_nm_fll);
} /* endif dbg */
if(dmn_idx < dmn_nbr){
grp_dfn_fnd=True;
}else{
/* Overwrite current group ID with parent group ID */
rcd=nco_inq_grp_parent_flg(*grp_id_dmn,grp_id_dmn);
} /* end else */
} /* end while */
return rcd;
} /* end nco_inq_dmn_grp_id */
nco_bool
nco_find_lat_lon
(int nc_id,
char var_nm_lat[],
char var_nm_lon[],
char **units,
int *lat_id,
int *lon_id,
nc_type *crd_typ)
{
/* Purpose: Find auxiliary coordinate variables that map to latitude/longitude
Find variables with standard_name = "latitude" and "longitude"
Return true if both latitude and longitude standard names are found
Also return needed information about these auxiliary coordinates
Assumes that units and types for latitude and longitude are identical
Caller responsible for memory management for variable names
Memory for unit strings must be freed by caller */
const char fnc_nm[]="nco_find_lat_lon()";
char var_nm[NC_MAX_NAME];
char att_val[NC_MAX_NAME];
int idx;
int nvars=0;
int rcd=NC_NOERR;
int crd_nbr=0;
int var_dimid[NC_MAX_VAR_DIMS]; /* [enm] Dimension ID */
int var_att_nbr; /* [nbr] Number of attributes */
int var_dmn_nbr; /* [nbr] Number of dimensions */
long att_lng;
nc_type var_typ; /* [enm] variable type */
/* Make sure CF tag exists. Currently require CF-1.X value */
if(NCO_GET_ATT_CHAR(nc_id,NC_GLOBAL,"Conventions",att_val) || !strstr(att_val,"CF-1."))
if(nco_dbg_lvl_get() >= nco_dbg_dev) (void)fprintf(stderr,"%s: WARNING %s reports file \"Convention\" attribute is missing or is present but not of the form \"CF-1.X\". Auxiliary coordinate support (i.e., the -X option) cannot be expected to behave well file does not support CF-1.X metadata conventions. Continuing anyway...\n",nco_prg_nm_get(),fnc_nm);
/* Get number of variables */
rcd=nco_inq_nvars(nc_id,&nvars);
/* For each variable, see if standard name is latitude or longitude */
for(idx=0;idx<nvars && crd_nbr<2;idx++){
nco_inq_var(nc_id,idx,var_nm,&var_typ,&var_dmn_nbr,var_dimid,&var_att_nbr);
att_lng=0;
if(!nco_inq_attlen_flg(nc_id,idx,"standard_name",&att_lng)){
NCO_GET_ATT_CHAR(nc_id,idx,"standard_name",att_val);
att_val[att_lng]='\0';
if(!strcmp(att_val,"latitude")){
strcpy(var_nm_lat,var_nm);
*lat_id=idx;
/* Get units; assume same for both lat and lon */
rcd=nco_inq_attlen(nc_id,idx,"units",&att_lng);
if(rcd != NC_NOERR) nco_err_exit(rcd,"nco_find_lat_lon() reports CF convention requires \"latitude\" to have units attribute\n");
*units=(char *)nco_malloc((att_lng+1L)*sizeof(char));
NCO_GET_ATT_CHAR(nc_id,idx,"units",*units);
(*units)[att_lng]='\0';
if(var_dmn_nbr > 1) (void)fprintf(stderr,"%s: WARNING %s reports latitude variable %s has %d dimensions. NCO only supports hyperslabbing of auxiliary coordinate variables with a single dimension. Continuing with unpredictable results...\n",nco_prg_nm_get(),fnc_nm,var_nm,var_dmn_nbr);
/* Assign type; assumed same for both lat and lon */
*crd_typ=var_typ;
crd_nbr++;
} /* endif latitude */
if(!strcmp(att_val,"longitude")){
strcpy(var_nm_lon,var_nm);
*lon_id=idx;
crd_nbr++;
} /* endif longitude */
if(nco_dbg_lvl_get() >= nco_dbg_dev) (void)fprintf(stdout,"%s: DEBUG %s variable <%s>\n",nco_prg_nm_get(),fnc_nm,var_nm);
} /* endif standard_name */
} /* end loop over vars */
if(crd_nbr != 2){
if(nco_dbg_lvl_get() >= nco_dbg_dev) (void)fprintf(stdout,"%s: %s unable to identify lat/lon auxiliary coordinate variables.\n",nco_prg_nm_get(),fnc_nm);
return False;
}else return True;
} /* end nco_find_lat_lon() */
void
nco_ppc_around /* [fnc] Replace op1 values by their values rounded to decimal precision prc */
(const int ppc, /* I [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
const nc_type type, /* I [enm] netCDF type of operand */
const long sz, /* I [nbr] Size (in elements) of operand */
const int has_mss_val, /* I [flg] Flag for missing values */
ptr_unn mss_val, /* I [val] Value of missing value */
ptr_unn op1) /* I/O [val] Values of first operand */
{
/* Threads: Routine is thread safe and calls no unsafe routines */
/* Purpose: Replace op1 values by their values rounded to decimal precision ppc
Similar to numpy.around() function, hence the name around()
Based on implementation by Jeff Whitaker for netcdf4-python described here:
http://netcdf4-python.googlecode.com/svn/trunk/docs/netCDF4-module.html
which invokes the numpy.around() function documented here:
http://docs.scipy.org/doc/numpy/reference/generated/numpy.around.html#numpy.around
A practical discussion of rounding is at
http://stackoverflow.com/questions/20388071/what-are-the-under-the-hood-differences-between-round-and-numpy-round
This mentions the () NumPy source code:
https://github.com/numpy/numpy/blob/7b2f20b406d27364c812f7a81a9c901afbd3600c/numpy/core/src/multiarray/calculation.c#L588
Manually determine scale:
ncap2 -O -v -s 'ppc=2;ppc_abs=abs(ppc);bit_nbr_xct=ppc_abs*ln(10.)/ln(2.);bit_nbr_int=ceil(bit_nbr_xct);scale=pow(2.0,bit_nbr_int);' ~/nco/data/in.nc ~/foo.nc
ncks -H ~/foo.nc
Test full algorithm:
ncks -4 -O -C -v ppc_dbl,ppc_big --ppc ppc_dbl=3 --ppc ppc_big=-2 ~/nco/data/in.nc ~/foo.nc
Compare to Jeff Whitaker's nc3tonc4 results:
nc3tonc4 -o --quantize=ppc_dbl=3,ppc_big=-2 ~/nco/data/in.nc ~/foo.nc
ncks -H -C -v ppc_dbl,ppc_big ~/foo.nc */
/* Rounding is currently defined as op1:=around(op1,ppc) */
/* Use constants defined in math.h */
const double bit_per_dcm_dgt_prc=M_LN10/M_LN2; /* 3.32 [frc] Bits per decimal digit of precision */
double scale; /* [frc] Number by which to scale data to achieve rounding */
float scalef; /* [frc] Number by which to scale data to achieve rounding */
int bit_nbr; /* [nbr] Number of bits required to exceed pow(10,-ppc) */
int ppc_abs; /* [nbr] Absolute value of precision */
long idx;
/* Only numeric types can be quantized */
if(type == NC_CHAR || type == NC_BYTE || type == NC_UBYTE || type == NC_STRING) return;
ppc_abs=abs(ppc);
assert(ppc_abs <= 16);
switch(ppc_abs){
case 0:
bit_nbr=0;
scale=1.0;
break;
case 1:
bit_nbr=4;
scale=16.0;
break;
case 2:
bit_nbr=7;
scale=128.0;
break;
case 3:
bit_nbr=10;
scale=1024.0;
break;
case 4:
bit_nbr=14;
scale=16384.0;
break;
case 5:
bit_nbr=17;
scale=131072.0;
break;
case 6:
bit_nbr=20;
scale=1048576.0;
break;
default:
bit_nbr=(int)ceil(ppc_abs*bit_per_dcm_dgt_prc);
scale=pow(2.0,bit_nbr);
break;
} /* end switch */
if(ppc < 0) scale=1.0/scale;
if(nco_dbg_lvl_get() == nco_dbg_sbr) (void)fprintf(stdout,"%s: INFO nco_ppc_around() reports ppc = %d, bit_nbr= %d, scale = %g\n",nco_prg_nm_get(),ppc,bit_nbr,scale);
/* Typecast pointer to values before access */
(void)cast_void_nctype(type,&op1);
if(has_mss_val) (void)cast_void_nctype(type,&mss_val);
scalef=(float)scale;
switch(type){
case NC_FLOAT:
/* By default do float arithmetic in double precision before converting back to float
Allow --flt to override
NB: Use rint() not lrint()
If ignoring this advice, be sure to bound calls to lrint(), e.g.,
rint_arg=scale*op1.fp[idx];
if(rint_arg > LONG_MIN && rint_arg < LONG_MAX) op1.fp[idx]=(float)lrint(scale*op1.fp[idx])/scale; */
if(!has_mss_val){
if(nco_rth_cnv_get() == nco_rth_flt_flt)
for(idx=0L;idx<sz;idx++) op1.fp[idx]=rintf(scalef*op1.fp[idx])/scalef;
else
for(idx=0L;idx<sz;idx++) op1.fp[idx]=(float)(rint(scale*op1.fp[idx])/scale); /* Coerce to avoid implicit conversions warning */
}else{
const float mss_val_flt=*mss_val.fp;
if(nco_rth_cnv_get() == nco_rth_flt_flt){
for(idx=0;idx<sz;idx++)
if(op1.fp[idx] != mss_val_flt)
op1.fp[idx]=rintf(scalef*op1.fp[idx])/scalef;
}else{
for(idx=0;idx<sz;idx++)
if(op1.fp[idx] != mss_val_flt)
op1.fp[idx]=(float)(rint(scale*op1.fp[idx])/scale); /* Coerce to avoid implicit conversions warning */
} /* end else */
} /* end else */
break;
case NC_DOUBLE:
if(!has_mss_val){
for(idx=0L;idx<sz;idx++) op1.dp[idx]=rint(scale*op1.dp[idx])/scale;
}else{
const double mss_val_dbl=*mss_val.dp;
for(idx=0;idx<sz;idx++)
if(op1.dp[idx] != mss_val_dbl) op1.dp[idx]=rint(scale*op1.dp[idx])/scale;
} /* end else */
break;
case NC_SHORT:
if(!has_mss_val){
for(idx=0L;idx<sz;idx++) op1.sp[idx]=(short int)lrint(scale*op1.sp[idx])/scale;
}else{
const nco_int mss_val_short=*mss_val.sp;
for(idx=0;idx<sz;idx++)
if(op1.sp[idx] != mss_val_short) op1.sp[idx]=(short int)lrint(scale*op1.sp[idx])/scale;
} /* end else */
break;
case NC_USHORT:
if(!has_mss_val){
for(idx=0L;idx<sz;idx++) op1.usp[idx]=(unsigned short int)lrint(scale*op1.usp[idx])/scale;
}else{
const nco_ushort mss_val_ushort=*mss_val.usp;
for(idx=0;idx<sz;idx++)
if(op1.usp[idx] != mss_val_ushort) op1.usp[idx]=(unsigned short int)lrint(scale*op1.usp[idx])/scale;
} /* end else */
break;
case NC_INT:
if(!has_mss_val){
for(idx=0L;idx<sz;idx++) op1.ip[idx]=lrint(scale*op1.ip[idx])/scale;
}else{
const nco_int mss_val_int=*mss_val.ip;
for(idx=0;idx<sz;idx++)
if(op1.ip[idx] != mss_val_int) op1.ip[idx]=lrint(scale*op1.ip[idx])/scale;
} /* end else */
break;
case NC_UINT:
if(!has_mss_val){
for(idx=0L;idx<sz;idx++) op1.uip[idx]=(unsigned int)lrint(scale*op1.uip[idx])/scale;
}else{
const nco_uint mss_val_uint=*mss_val.uip;
for(idx=0;idx<sz;idx++)
if(op1.uip[idx] != mss_val_uint) op1.uip[idx]=(unsigned int)lrint(scale*op1.uip[idx])/scale;
} /* end else */
break;
case NC_INT64:
if(!has_mss_val){
for(idx=0L;idx<sz;idx++) op1.i64p[idx]=lrint(scale*op1.i64p[idx])/scale;
}else{
const nco_int64 mss_val_int64=*mss_val.i64p;
for(idx=0;idx<sz;idx++)
if(op1.i64p[idx] != mss_val_int64) op1.i64p[idx]=lrint(scale*op1.i64p[idx])/scale;
} /* end else */
break;
case NC_UINT64:
if(!has_mss_val){
for(idx=0L;idx<sz;idx++) op1.ui64p[idx]=(unsigned long)lrint(scale*op1.ui64p[idx])/scale;
}else{
const nco_uint64 mss_val_uint64=*mss_val.ui64p;
for(idx=0;idx<sz;idx++)
if(op1.ui64p[idx] != mss_val_uint64) op1.ui64p[idx]=(unsigned long)lrint(scale*op1.ui64p[idx])/scale;
} /* end else */
break;
case NC_CHAR: /* Do nothing for non-numeric types ...*/
case NC_BYTE:
case NC_UBYTE:
case NC_STRING: break;
default:
nco_dfl_case_nc_type_err();
break;
} /* end switch */
/* NB: it is not neccessary to un-typecast pointers to values after access
because we have only operated on local copies of them. */
} /* end nco_ppc_around() */
int /* O [rcd] Return code */
nco_cnv_cf_cll_mth_add /* [fnc] Add cell_methods attributes */
(const int out_id, /* I [id] netCDF file ID */
var_sct * const * const var, /* I [sct] Variable to reduce (e.g., average) (destroyed) */
const int var_nbr, /* I [nbr] Number of variables to be defined */
dmn_sct * const * const dmn_rdc, /* I [sct] Dimensions over which to reduce variable */
const int dmn_nbr_rdc, /* I [sct] Number of dimensions to reduce variable over */
const int nco_op_typ, /* I [enm] Operation type, default is average */
gpe_sct *gpe, /* I [sng] Group Path Editing (GPE) structure */
const clm_bnd_sct * const cb, /* I [sct] Climatology bounds structure */
const trv_tbl_sct * const trv_tbl) /* I [sct] Traversal table */
{
/* Purpose: Add/modify CF cell_methods attribute
http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/build/cf-conventions.html#cell-methods
cell_methods values and description:
point : Data values are representative of points in space or time (instantaneous)
sum : Data values are representative of a sum or accumulation over the cell
maximum_absolute_value : Maximum absolute value
maximum : Maximum
median : Median
mid_range : Average of maximum and minimum
minimum : Minimum
mean : Mean (average value)
mode : Mode (most common value)
range : Absolute difference between maximum and minimum
standard_deviation : Standard deviation
variance : Variance
NCO operation types:
avg Mean value
avgsqr Mean of sum of squares
mabs Maximum absolute value
max Maximum value
mebs Mean absolute value
mibs Minimum absolute value
min Minimum value
rms Root-mean-square (normalized by N)
rmssdn Root-mean square (normalized by N-1)
sqravg Square of the mean
sqrt Square root of the mean
ttl Sum of values */
const char fnc_nm[]="nco_cnv_cf_cll_mth_add()"; /* [sng] Function name */
aed_sct aed; /* [sct] Attribute-edit information */
char att_op_sng[23]; /* [sng] Operation type (longest is nco_op_mabs which translates to "maximum_absolute_value") */
char *att_val=NULL; /* [sng] Coordinates attribute */
char *att_val_cpy; /* [sng] Copy of attribute */
char *grp_out_fll=NULL; /* [sng] Group name */
char *sbs_ptr; /* [sng] Pointer to substring */
char *cll_mth_clm; /* [sng] Cell methods for climatology */
int *dmn_mch; /* [idx] Indices of dimensions reduced in this variable */
int dmn_idx_rdc;
int dmn_idx_var;
int dmn_nbr_mch; /* [nbr] Number of dimension names to add to cell_methods */
int grp_out_id; /* [ID] Group ID (output) */
int nco_op_typ_lcl; /* [enm] Operation type, default is average */
int rcd=NC_NOERR; /* [rcd] Return code */
int var_idx;
int var_out_id; /* [ID] Variable ID (output) */
long int att_lng; /* [nbr] Length of attribute string */
nc_type att_typ; /* [nbr] Attribute type */
nco_bool FIRST_WARNING=True;
nco_bool flg_dpl; /* [flg] New cell_methods attribute duplicates old */
nco_bool mlt_dmn_rdc; /* [flg] Multiple dimension reduction flag */
size_t dmn_sng_lng; /* [nbr] Length of dimension string */
size_t sbs_sng_lng; /* [nbr] Length of substring */
trv_sct *var_trv=NULL; /* [sct] Variable GTT object */
/* Initialize unchanging structure members */
aed.att_nm=strdup("cell_methods");
aed.type=NC_CHAR;
/* Allocate space for maximum number of matching dimensions */
dmn_mch=(int *)nco_calloc(dmn_nbr_rdc,sizeof(int));
if(cb){
if(cb->bnd2clm || cb->clm2clm) cll_mth_clm=strdup("time: mean within years time: mean over years");
if(cb->clm2bnd) cll_mth_clm=strdup("time: mean");
} /* !cb */
/* Process all variables */
for(var_idx=0;var_idx<var_nbr;var_idx++){
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var[var_idx]->nm_fll,trv_tbl);
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
/* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
if(grp_out_fll) grp_out_fll=(char *)nco_free(grp_out_fll);
/* Get variable ID */
(void)nco_inq_varid(grp_out_id,var_trv->nm,&var_out_id);
/* Initialize attribute-edit structure for this variable */
aed.var_nm=var_trv->nm;
aed.id=var_out_id;
aed.sz=0L;
dmn_nbr_mch=0;
flg_dpl=False;
if(cb){
/* Does variable use time coordinate? */
for(dmn_idx_var=0;dmn_idx_var<var_trv->nbr_dmn;dmn_idx_var++)
if(!strcmp(var_trv->var_dmn[dmn_idx_var].dmn_nm,cb->tm_crd_nm)) break;
if(dmn_idx_var < var_trv->nbr_dmn){
/* Stamp with appropriate cell_methods temporal attribute */
att_val=strdup(cll_mth_clm);
aed.sz=strlen(att_val);
aed.type=NC_CHAR;
aed.val.cp=att_val;
aed.mode=aed_overwrite;
(void)nco_aed_prc(grp_out_id,var_out_id,aed);
if(att_val) att_val=(char *)nco_free(att_val);
continue;
} /* !dmn_idx_var */
} /* !cb */
/* cell_methods format: blank-separated phrases of form "dmn1[, dmn2[...]]: op_typ", e.g., "lat, lon: mean" */
for(dmn_idx_var=0;dmn_idx_var<var_trv->nbr_dmn;dmn_idx_var++){
for(dmn_idx_rdc=0;dmn_idx_rdc<dmn_nbr_rdc;dmn_idx_rdc++){
assert(dmn_rdc[dmn_idx_rdc]->nm_fll);
/* Compare full names */
if(!strcmp(var_trv->var_dmn[dmn_idx_var].dmn_nm_fll,dmn_rdc[dmn_idx_rdc]->nm_fll)){
/* Add length of each matching dimension to accumulating attribute size */
aed.sz+=strlen(dmn_rdc[dmn_idx_rdc]->nm);
dmn_mch[dmn_nbr_mch++]=dmn_idx_rdc;
} /* !match */
} /* dmn_idx_rdc */
} /* dmn_idx_var */
assert(dmn_nbr_mch > 0);
/* Preserve rule to always return averages (never extrema or other statistics) of coordinates */
if(var[var_idx]->is_crd_var) nco_op_typ_lcl=nco_op_avg; else nco_op_typ_lcl=nco_op_typ;
/* NUL-terminate before concatenation */
att_op_sng[0]='\0';
switch(nco_op_typ_lcl){
/* Next five operations are defined in CF Conventions */
case nco_op_avg: strcpy(att_op_sng,"mean"); break;
case nco_op_min: strcpy(att_op_sng,"minimum"); break;
case nco_op_max: strcpy(att_op_sng,"maximum"); break;
case nco_op_ttl: strcpy(att_op_sng,"sum"); break;
case nco_op_avgsqr: strcpy(att_op_sng,"variance"); break; /* Mean of sum of squares */
/* Remaining operations are supported by NCO yet are not in CF Conventions */
case nco_op_mabs: strcpy(att_op_sng,"maximum_absolute_value"); break; /* Maximum absolute value */
case nco_op_mebs: strcpy(att_op_sng,"mean_absolute_value"); break; /* Mean absolute value */
case nco_op_mibs: strcpy(att_op_sng,"minimum_absolute_value"); break; /* Minimum absolute value */
case nco_op_sqravg: strcpy(att_op_sng,"square_of_mean"); break; /* Square of mean */
case nco_op_sqrt: strcpy(att_op_sng,"square_root_of_mean"); break; /* Square root of mean */
case nco_op_rms: strcpy(att_op_sng,"root_mean_square"); break; /* Root-mean-square (normalized by N) */
case nco_op_rmssdn: strcpy(att_op_sng,"root_mean_square_nm1"); break; /* Root-mean square normalized by N-1 */
case nco_op_nil: /* nco_op_nil, Undefined operation type */
if(nco_dbg_lvl_get() >= nco_dbg_var) (void)fprintf(stdout,"%s: DEBUG %s reports variable %s cell_method not implemented for operation %d\n",nco_prg_nm_get(),fnc_nm,var_trv->nm_fll,nco_op_typ);
continue;
} /* End switch */
/* Initialize to size of ": " plus length of operation string */
aed.sz+=2L+strlen(att_op_sng);
/* Add room for commas and spaces, i.e., "dmn1, dmn2, dmn3" */
if(dmn_nbr_mch > 1) aed.sz+=2*(dmn_nbr_mch-1);
/* Add room for NUL-terminator */
aed.val.cp=(char *)nco_malloc((aed.sz+1L)*sizeof(char));
aed.val.cp[0]='\0';
/* Build single string by concatenating known matches */
for(int dmn_idx_mch=0;dmn_idx_mch<dmn_nbr_mch;dmn_idx_mch++){
(void)strcat(aed.val.cp,dmn_rdc[dmn_mch[dmn_idx_mch]]->nm);
if(dmn_idx_mch<dmn_nbr_mch-1) (void)strcat(aed.val.cp,", ");
} /* dmn_idx_mch>=dmn_nbr_mch */
(void)strcat(aed.val.cp,": ");
(void)strcat(aed.val.cp,att_op_sng);
/* 20150625: Older versions of CAM, e.g., CAM3, used "cell_method" instead of "cell_methods"
If old attribute is not deleted then the output file will contain both attributes
Does variable already have "cell_method" attribute? */
strcpy(aed.att_nm,"cell_method");
rcd=nco_inq_att_flg(grp_out_id,var_out_id,aed.att_nm,&att_typ,&att_lng);
if(rcd == NC_NOERR){
if(FIRST_WARNING) (void)fprintf(stderr,"%s: WARNING: Variable \"%s\" uses the non-standard attribute name \"cell_method\" instead of \"cell_methods\", the correct attribute name. The CAM3 model (and others?) have this problem. Expect \"double attributes\" in output. This message is printed only once per invocation, although the problem likely occurs in more variables.\n",nco_prg_nm_get(),aed.var_nm);
FIRST_WARNING=False;
} /* endif attribute exists */
/* Does variable already have "cell_methods" attribute? */
strcpy(aed.att_nm,"cell_methods");
rcd=nco_inq_att_flg(grp_out_id,var_out_id,aed.att_nm,&att_typ,&att_lng);
if(rcd == NC_NOERR){
if(att_typ == NC_STRING) (void)fprintf(stderr,"%s: WARNING %s reports existing cell_methods attribute for variable %s is type NC_STRING. Unpredictable results...\n",nco_prg_nm_get(),fnc_nm,aed.var_nm);
if(att_typ != NC_STRING && att_typ != NC_CHAR) (void)fprintf(stderr,"%s: WARNING %s reports existing cell_methods attribute for variable %s is type %s. Unpredictable results...\n",nco_prg_nm_get(),fnc_nm,aed.var_nm,nco_typ_sng(att_typ));
/* Often climatologies are multiply-averaged over time
NCO's treatment of this has changed with time
pre-20140131:
NCO has no special treatment of cell_methods
20140131:
First NCO implementation (ncra, ncea, ncwa) of cell_methods with
20150625:
For example, climate model output is often archived as monthly means in each gridcell
cell_methods attributes of these monthly data begin as "time: mean" (i.e., monthly mean).
We then create a climatology by a sequence of one or two more temporal-averaging steps
The one-step method puts all the months in the hopper and averages those
Variables in the resultiing file may have cell_methods = "time: mean time: mean"
The two-step method first averages the months into four climatological seasons
Then it averages those four seasons into the climatological annual mean
Variables in the resultiing file may have cell_methods = "time: mean time: mean time: mean"
To avoid this redundancy, we check that the new cell_method does not duplicate the old
If it would, then skip adding the new
20160418:
Treatment of multiply-time-averaged quantities requires climatology bounds attribute
One-step methods (e.g., monthly mean) should have time-bounds attribute
cell_methods = "time: mean"
Two-step methods (e.g., climatological March) should have climatology-bounds attribute
cell_methods = "time: mean within years time: mean over years"
Three-step methods (e.g., climatological MAM) should have climatology-bounds attribute
cell_methods = "time: mean within years time: mean over years"
Four-step methods (e.g., climatological ANN) should have time-bounds attribute
cell_methods = "time: mean" */
ptr_unn val_old; /* [sng] Old cell_methods attribute */
val_old.vp=(void *)nco_malloc((att_lng+1L)*sizeof(char));
(void)nco_get_att(grp_out_id,var_out_id,aed.att_nm,val_old.vp,NC_CHAR);
val_old.cp[att_lng]='\0';
if(strstr(val_old.cp,aed.val.cp)) flg_dpl=True;
if(val_old.vp) val_old.vp=(void *)nco_free(val_old.vp);
aed.mode=aed_append;
/* Insert space between existing attribute and appended attribute */
att_val_cpy=(char *)strdup(aed.val.cp);
/* Add one for space character */
aed.sz++;
/* Add one for NUL-terminator */
aed.val.cp=(char *)nco_realloc(aed.val.cp,(aed.sz+1L)*sizeof(char));
aed.val.cp[0]=' ';
aed.val.cp[1]='\0';
(void)strncat(aed.val.cp,att_val_cpy,aed.sz-1L);
if(att_val_cpy) att_val_cpy=(char *)nco_free(att_val_cpy);
}else{ /* !cell_methods attribute already exists */
aed.mode=aed_create;
} /* !cell_methods attribute already exists */
/* Edit attribute */
if(!flg_dpl) (void)nco_aed_prc(grp_out_id,var_out_id,aed);
/* 20150308 */
/* Does variable already have "coordinates" attribute?
NB: This reuses att_nm which has only enough space to hold "cell_methods" */
strcpy(aed.att_nm,"coordinates");
rcd=nco_inq_att_flg(grp_out_id,var_out_id,aed.att_nm,&att_typ,&att_lng);
if(rcd == NC_NOERR && att_typ == NC_CHAR){
/* Remove reduced dimensions from coordinates string
coordinates format: blank-separated names of form "dmn1 [dmn2 [...]] dmnN", e.g., "time lat lon" */
/* Add room for NUL-terminator */
att_val=(char *)nco_malloc((att_lng+1L)*sizeof(char));
rcd=nco_get_att(grp_out_id,var_out_id,aed.att_nm,att_val,att_typ);
/* Reset value from previous use */
aed.val.cp[0]='\0';
att_val[att_lng]='\0';
mlt_dmn_rdc=False;
assert(rcd == NC_NOERR);
for(dmn_idx_var=0;dmn_idx_var<var_trv->nbr_dmn;dmn_idx_var++){
for(dmn_idx_rdc=0;dmn_idx_rdc<dmn_nbr_rdc;dmn_idx_rdc++){
/* Is reduced dimension in variable? */
if(!strcmp(var_trv->var_dmn[dmn_idx_var].dmn_nm_fll,dmn_rdc[dmn_idx_rdc]->nm_fll)){
if(mlt_dmn_rdc){
/* At least one other dimension has already been reduced/excised
Hence multiple dimensions of this variable may be reduced
Start next excision from ending point of last excision, not from disk-values */
strcpy(att_val,aed.val.cp);
att_lng=strlen(aed.val.cp);
} /* endif */
/* Is dimension in current (possibly locally-modified) "coordinates" attribute? NB: Assume short name not full name */
if((sbs_ptr=strstr(att_val,dmn_rdc[dmn_idx_rdc]->nm))){
/* Is this the only dimension in "coordinates" attribute? */
if(!strcmp(dmn_rdc[dmn_idx_rdc]->nm,att_val)){
/* Variable will become scalar so delete "coordinates" attribute */
aed.mode=aed_delete;
}else{ /* endif scalar */
/* Excise dimension from "coordinates" attribute */
dmn_sng_lng=strlen(dmn_rdc[dmn_idx_rdc]->nm);
sbs_sng_lng=(size_t)(sbs_ptr-att_val);
aed.mode=aed_overwrite;
/* Remove whitespace immediately following excised dimension, i.e., count it as part of dimension string
True for all dimensions except final dimension (trailed by a NUL, not a space) */
if(sbs_ptr[dmn_sng_lng] == ' ') dmn_sng_lng++;
aed.sz=att_lng-dmn_sng_lng;
/* Add one for NUL-terminator */
aed.val.cp=(char *)nco_realloc(aed.val.cp,(aed.sz+1L)*sizeof(char));
strncpy(aed.val.cp,att_val,sbs_sng_lng);
aed.val.cp[sbs_sng_lng]='\0';
strcat(aed.val.cp,sbs_ptr+dmn_sng_lng);
} /* endelse scalar */
/* Edit attribute */
(void)nco_aed_prc(grp_out_id,var_out_id,aed);
mlt_dmn_rdc=True;
} /* !match attribute */
} /* !match variable */
} /* dmn_idx_rdc */
} /* dmn_idx_var */
} /* endif attribute exists */
if(att_val) att_val=(char *)nco_free(att_val);
if(aed.val.cp) aed.val.cp=(char *)nco_free(aed.val.cp);
} /* var_idx >= var_nbr */
if(aed.att_nm) aed.att_nm=(char *)nco_free(aed.att_nm);
if(dmn_mch) dmn_mch=(int *)nco_free(dmn_mch);
return NC_NOERR;
} /* end nco_cnv_cf_cll_mth_add() */
int
main(int argc,char **argv)
{
nco_bool CNV_CCM_CCSM_CF;
nco_bool CMD_LN_NTP_VAR=False; /* Option i */
nco_bool CMD_LN_NTP_WGT=True; /* Option w */
nco_bool DO_CONFORM=False; /* Did nco_var_cnf_dmn() find truly conforming variables? */
nco_bool EXCLUDE_INPUT_LIST=False; /* Option c */
nco_bool EXTRACT_ALL_COORDINATES=False; /* Option c */
nco_bool EXTRACT_ASSOCIATED_COORDINATES=True; /* Option C */
nco_bool FILE_1_RETRIEVED_FROM_REMOTE_LOCATION;
nco_bool FILE_2_RETRIEVED_FROM_REMOTE_LOCATION;
nco_bool FIX_REC_CRD=False; /* [flg] Do not interpolate/multiply record coordinate variables */
nco_bool FL_LST_IN_FROM_STDIN=False; /* [flg] fl_lst_in comes from stdin */
nco_bool FORCE_APPEND=False; /* Option A */
nco_bool FORCE_OVERWRITE=False; /* Option O */
nco_bool FORTRAN_IDX_CNV=False; /* Option F */
nco_bool GRP_VAR_UNN=False; /* [flg] Select union of specified groups and variables */
nco_bool HISTORY_APPEND=True; /* Option h */
nco_bool MSA_USR_RDR=False; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order*/
nco_bool MUST_CONFORM=False; /* Must nco_var_cnf_dmn() find truly conforming variables? */
nco_bool RAM_CREATE=False; /* [flg] Create file in RAM */
nco_bool RAM_OPEN=False; /* [flg] Open (netCDF3-only) file(s) in RAM */
nco_bool RM_RMT_FL_PST_PRC=True; /* Option R */
nco_bool WRT_TMP_FL=True; /* [flg] Write output to temporary file */
nco_bool flg_cln=True; /* [flg] Clean memory prior to exit */
char **fl_lst_abb=NULL; /* Option a */
char **fl_lst_in;
char **ntp_lst_in;
char **grp_lst_in=NULL_CEWI;
char **var_lst_in=NULL_CEWI;
char *aux_arg[NC_MAX_DIMS];
char *cmd_ln;
char *cnk_arg[NC_MAX_DIMS];
char *cnk_map_sng=NULL_CEWI; /* [sng] Chunking map */
char *cnk_plc_sng=NULL_CEWI; /* [sng] Chunking policy */
char *fl_in_1=NULL; /* fl_in_1 is nco_realloc'd when not NULL */
char *fl_in_2=NULL; /* fl_in_2 is nco_realloc'd when not NULL */
char *fl_out=NULL; /* Option o */
char *fl_out_tmp;
char *fl_pth=NULL; /* Option p */
char *fl_pth_lcl=NULL; /* Option l */
char *lmt_arg[NC_MAX_DIMS];
char *ntp_nm=NULL; /* Option i */
char *opt_crr=NULL; /* [sng] String representation of current long-option name */
char *optarg_lcl=NULL; /* [sng] Local copy of system optarg */
char *ppc_arg[NC_MAX_VARS]; /* [sng] PPC arguments */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
const char * const CVS_Id="$Id$";
const char * const CVS_Revision="$Revision$";
const char * const opt_sht_lst="3467ACcD:d:Fg:G:hi:L:l:Oo:p:rRt:v:X:xw:-:";
cnk_sct cnk; /* [sct] Chunking structure */
#if defined(__cplusplus) || defined(PGI_CC)
ddra_info_sct ddra_info;
ddra_info.flg_ddra=False;
#else /* !__cplusplus */
ddra_info_sct ddra_info={.flg_ddra=False};
#endif /* !__cplusplus */
double ntp_val_out=double_CEWI; /* Option i */
double wgt_val_1=0.5; /* Option w */
double wgt_val_2=0.5; /* Option w */
extern char *optarg;
extern int optind;
/* Using naked stdin/stdout/stderr in parallel region generates warning
Copy appropriate filehandle to variable scoped shared in parallel clause */
FILE * const fp_stderr=stderr; /* [fl] stderr filehandle CEWI */
FILE * const fp_stdout=stdout; /* [fl] stdout filehandle CEWI */
gpe_sct *gpe=NULL; /* [sng] Group Path Editing (GPE) structure */
int *in_id_1_arr;
int *in_id_2_arr;
int abb_arg_nbr=0;
int aux_nbr=0; /* [nbr] Number of auxiliary coordinate hyperslabs specified */
int cnk_map=nco_cnk_map_nil; /* [enm] Chunking map */
int cnk_nbr=0; /* [nbr] Number of chunk sizes */
int cnk_plc=nco_cnk_plc_nil; /* [enm] Chunking policy */
int dfl_lvl=NCO_DFL_LVL_UNDEFINED; /* [enm] Deflate level */
int fl_idx;
int fl_nbr=0;
int fl_in_fmt_1; /* [enm] Input file format */
int fl_in_fmt_2; /* [enm] Input file format */
int fl_out_fmt=NCO_FORMAT_UNDEFINED; /* [enm] Output file format */
int fll_md_old; /* [enm] Old fill mode */
int has_mss_val=False;
int idx;
int in_id_1;
int in_id_2;
int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */
int md_open; /* [enm] Mode flag for nc_open() call */
int nbr_dmn_fl;
int nbr_ntp;
int nbr_var_fix; /* nbr_var_fix gets incremented */
int nbr_var_fl;
int nbr_var_prc; /* nbr_var_prc gets incremented */
int xtr_nbr=0; /* xtr_nbr won't otherwise be set for -c with no -v */
int opt;
int out_id;
int ppc_nbr=0; /* [nbr] Number of PPC arguments */
int rcd=NC_NOERR; /* [rcd] Return code */
int thr_idx; /* [idx] Index of current thread */
int thr_nbr=int_CEWI; /* [nbr] Thread number Option t */
int var_lst_in_nbr=0;
int grp_lst_in_nbr=0; /* [nbr] Number of groups explicitly specified by user */
md5_sct *md5=NULL; /* [sct] MD5 configuration */
size_t bfr_sz_hnt=NC_SIZEHINT_DEFAULT; /* [B] Buffer size hint */
size_t cnk_min_byt=NCO_CNK_SZ_MIN_BYT_DFL; /* [B] Minimize size of variable to chunk */
size_t cnk_sz_byt=0UL; /* [B] Chunk size in bytes */
size_t cnk_sz_scl=0UL; /* [nbr] Chunk size scalar */
size_t hdr_pad=0UL; /* [B] Pad at end of header section */
val_unn val_gnr_unn; /* Generic container for arrival point or weight */
var_sct *wgt_1=NULL_CEWI;
var_sct *wgt_2=NULL_CEWI;
var_sct *wgt_out_1=NULL;
var_sct *wgt_out_2=NULL;
var_sct **var;
var_sct **var_fix;
var_sct **var_fix_out;
var_sct **var_out;
var_sct **var_prc_1;
var_sct **var_prc_2;
var_sct **var_prc_out;
trv_tbl_sct *trv_tbl=NULL; /* [lst] Traversal table */
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
#ifdef ENABLE_MPI
/* Declare all MPI-specific variables here */
MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
int prc_rnk; /* [idx] Process rank */
int prc_nbr=0; /* [nbr] Number of MPI processes */
#endif /* !ENABLE_MPI */
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
{"cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"clean",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"mmr_cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"dirty",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"mmr_drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"hdf4",no_argument,0,0}, /* [flg] Treat file as HDF4 */
{"hdf_upk",no_argument,0,0}, /* [flg] HDF unpack convention: unpacked=scale_factor*(packed-add_offset) */
{"hdf_unpack",no_argument,0,0}, /* [flg] HDF unpack convention: unpacked=scale_factor*(packed-add_offset) */
{"msa_usr_rdr",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"msa_user_order",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"fix_rec_crd",no_argument,0,0}, /* [flg] Do not interpolate/multiply record coordinate variables */
{"ram_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"create_ram",no_argument,0,0}, /* [flg] Create file in RAM */
{"open_ram",no_argument,0,0}, /* [flg] Open (netCDF3) file(s) in RAM */
{"diskless_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"wrt_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"write_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"no_tmp_fl",no_argument,0,0}, /* [flg] Do not write output to temporary file */
{"intersection",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"nsx",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"union",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"unn",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"version",no_argument,0,0},
{"vrs",no_argument,0,0},
/* Long options with argument, no short option counterpart */
{"bfr_sz_hnt",required_argument,0,0}, /* [B] Buffer size hint */
{"buffer_size_hint",required_argument,0,0}, /* [B] Buffer size hint */
{"cnk_byt",required_argument,0,0}, /* [B] Chunk size in bytes */
{"chunk_byte",required_argument,0,0}, /* [B] Chunk size in bytes */
{"cnk_dmn",required_argument,0,0}, /* [nbr] Chunk size */
{"chunk_dimension",required_argument,0,0}, /* [nbr] Chunk size */
{"cnk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"chunk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"cnk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"chunk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"cnk_plc",required_argument,0,0}, /* [nbr] Chunking policy */
{"chunk_policy",required_argument,0,0}, /* [nbr] Chunking policy */
{"cnk_scl",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"chunk_scalar",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"fl_fmt",required_argument,0,0},
{"file_format",required_argument,0,0},
{"hdr_pad",required_argument,0,0},
{"header_pad",required_argument,0,0},
{"ppc",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"precision_preserving_compression",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"quantize",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
/* Long options with short counterparts */
{"3",no_argument,0,'3'},
{"4",no_argument,0,'4'},
{"64bit",no_argument,0,'4'},
{"netcdf4",no_argument,0,'4'},
{"append",no_argument,0,'A'},
{"coords",no_argument,0,'c'},
{"crd",no_argument,0,'c'},
{"no-coords",no_argument,0,'C'},
{"no-crd",no_argument,0,'C'},
{"debug",required_argument,0,'D'},
{"nco_dbg_lvl",required_argument,0,'D'},
{"dimension",required_argument,0,'d'},
{"dmn",required_argument,0,'d'},
{"fortran",no_argument,0,'F'},
{"ftn",no_argument,0,'F'},
{"gpe",required_argument,0,'G'}, /* [sng] Group Path Edit (GPE) */
{"grp",required_argument,0,'g'},
{"group",required_argument,0,'g'},
{"history",no_argument,0,'h'},
{"hst",no_argument,0,'h'},
{"interpolate",required_argument,0,'i'},
{"ntp",required_argument,0,'i'},
{"dfl_lvl",required_argument,0,'L'}, /* [enm] Deflate level */
{"deflate",required_argument,0,'L'}, /* [enm] Deflate level */
{"local",required_argument,0,'l'},
{"lcl",required_argument,0,'l'},
{"overwrite",no_argument,0,'O'},
{"ovr",no_argument,0,'O'},
{"output",required_argument,0,'o'},
{"fl_out",required_argument,0,'o'},
{"path",required_argument,0,'p'},
{"retain",no_argument,0,'R'},
{"rtn",no_argument,0,'R'},
{"revision",no_argument,0,'r'},
{"thr_nbr",required_argument,0,'t'},
{"threads",required_argument,0,'t'},
{"omp_num_threads",required_argument,0,'t'},
{"variable",required_argument,0,'v'},
{"weight",required_argument,0,'w'},
{"wgt_var",no_argument,0,'w'},
{"auxiliary",required_argument,0,'X'},
{"exclude",no_argument,0,'x'},
{"xcl",no_argument,0,'x'},
{"help",no_argument,0,'?'},
{"hlp",no_argument,0,'?'},
{0,0,0,0}
}; /* end opt_lng */
int opt_idx=0; /* Index of current long option into opt_lng array */
/* Start timer and save command line */
ddra_info.tmr_flg=nco_tmr_srt;
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_mtd;
cmd_ln=nco_cmd_ln_sng(argc,argv);
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
#ifdef ENABLE_MPI
/* MPI Initialization */
if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
MPI_Init(&argc,&argv);
MPI_Comm_size(mpi_cmm,&prc_nbr);
MPI_Comm_rank(mpi_cmm,&prc_rnk);
#endif /* !ENABLE_MPI */
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
opt=getopt_long(argc,argv,opt_sht_lst,opt_lng,&opt_idx);
/* NB: access to opt_crr is only valid when long_opt is detected */
if(opt == EOF) break; /* Parse positional arguments once getopt_long() returns EOF */
opt_crr=(char *)strdup(opt_lng[opt_idx].name);
/* Process long options without short option counterparts */
if(opt == 0){
if(!strcmp(opt_crr,"bfr_sz_hnt") || !strcmp(opt_crr,"buffer_size_hint")){
bfr_sz_hnt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_byt") || !strcmp(opt_crr,"chunk_byte")){
cnk_sz_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_byt */
if(!strcmp(opt_crr,"cnk_min") || !strcmp(opt_crr,"chunk_min")){
cnk_min_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_min */
if(!strcmp(opt_crr,"cnk_dmn") || !strcmp(opt_crr,"chunk_dimension")){
/* Copy limit argument for later processing */
cnk_arg[cnk_nbr]=(char *)strdup(optarg);
cnk_nbr++;
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_scl") || !strcmp(opt_crr,"chunk_scalar")){
cnk_sz_scl=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_map") || !strcmp(opt_crr,"chunk_map")){
/* Chunking map */
cnk_map_sng=(char *)strdup(optarg);
cnk_map=nco_cnk_map_get(cnk_map_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_plc") || !strcmp(opt_crr,"chunk_policy")){
/* Chunking policy */
cnk_plc_sng=(char *)strdup(optarg);
cnk_plc=nco_cnk_plc_get(cnk_plc_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cln") || !strcmp(opt_crr,"mmr_cln") || !strcmp(opt_crr,"clean")) flg_cln=True; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"drt") || !strcmp(opt_crr,"mmr_drt") || !strcmp(opt_crr,"dirty")) flg_cln=False; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"fix_rec_crd")) FIX_REC_CRD=True; /* [flg] Do not interpolate/multiply record coordinate variables */
if(!strcmp(opt_crr,"fl_fmt") || !strcmp(opt_crr,"file_format")) rcd=nco_create_mode_prs(optarg,&fl_out_fmt);
if(!strcmp(opt_crr,"hdf4")) nco_fmt_xtn=nco_fmt_xtn_hdf4; /* [enm] Treat file as HDF4 */
if(!strcmp(opt_crr,"hdf_upk") || !strcmp(opt_crr,"hdf_unpack")) nco_upk_cnv=nco_upk_HDF; /* [flg] HDF unpack convention: unpacked=scale_factor*(packed-add_offset) */
if(!strcmp(opt_crr,"hdr_pad") || !strcmp(opt_crr,"header_pad")){
hdr_pad=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif "hdr_pad" */
if(!strcmp(opt_crr,"msa_usr_rdr") || !strcmp(opt_crr,"msa_user_order")) MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
if(!strcmp(opt_crr,"ppc") || !strcmp(opt_crr,"precision_preserving_compression") || !strcmp(opt_crr,"quantize")){
ppc_arg[ppc_nbr]=(char *)strdup(optarg);
ppc_nbr++;
} /* endif "ppc" */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"create_ram") || !strcmp(opt_crr,"diskless_all")) RAM_CREATE=True; /* [flg] Open (netCDF3) file(s) in RAM */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"open_ram") || !strcmp(opt_crr,"diskless_all")) RAM_OPEN=True; /* [flg] Create file in RAM */
if(!strcmp(opt_crr,"unn") || !strcmp(opt_crr,"union")) GRP_VAR_UNN=True;
if(!strcmp(opt_crr,"nsx") || !strcmp(opt_crr,"intersection")) GRP_VAR_UNN=False;
if(!strcmp(opt_crr,"vrs") || !strcmp(opt_crr,"version")){
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
nco_exit(EXIT_SUCCESS);
} /* endif "vrs" */
if(!strcmp(opt_crr,"wrt_tmp_fl") || !strcmp(opt_crr,"write_tmp_fl")) WRT_TMP_FL=True;
if(!strcmp(opt_crr,"no_tmp_fl")) WRT_TMP_FL=False;
} /* opt != 0 */
/* Process short options */
switch(opt){
case 0: /* Long options have already been processed, return */
break;
case '3': /* Request netCDF3 output storage format */
fl_out_fmt=NC_FORMAT_CLASSIC;
break;
case '4': /* Catch-all to prescribe output storage format */
if(!strcmp(opt_crr,"64bit")) fl_out_fmt=NC_FORMAT_64BIT; else fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case '6': /* Request netCDF3 64-bit offset output storage format */
fl_out_fmt=NC_FORMAT_64BIT;
break;
case '7': /* Request netCDF4-classic output storage format */
fl_out_fmt=NC_FORMAT_NETCDF4_CLASSIC;
break;
case 'A': /* Toggle FORCE_APPEND */
FORCE_APPEND=!FORCE_APPEND;
break;
case 'C': /* Extract all coordinates associated with extracted variables? */
EXTRACT_ASSOCIATED_COORDINATES=False;
break;
case 'c':
EXTRACT_ALL_COORDINATES=True;
break;
case 'D': /* The debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
lmt_nbr++;
break;
case 'F': /* Toggle index convention. Default is 0-based arrays (C-style). */
FORTRAN_IDX_CNV=!FORTRAN_IDX_CNV;
break;
case 'G': /* Apply Group Path Editing (GPE) to output group */
/* NB: GNU getopt() optional argument syntax is ugly (requires "=" sign) so avoid it
http://stackoverflow.com/questions/1052746/getopt-does-not-parse-optional-arguments-to-parameters */
gpe=nco_gpe_prs_arg(optarg);
fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case 'g': /* Copy group argument for later processing */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
grp_lst_in=nco_lst_prs_2D(optarg_lcl,",",&grp_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
break;
case 'h': /* Toggle appending to history global attribute */
HISTORY_APPEND=!HISTORY_APPEND;
break;
case 'i':
/* Name of variable to guide interpolation. Default is none */
ntp_lst_in=nco_lst_prs_2D(optarg,",",&nbr_ntp);
if(nbr_ntp > 2){
(void)fprintf(stdout,"%s: ERROR too many arguments to -i\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
} /* end if */
ntp_nm=ntp_lst_in[0];
ntp_val_out=strtod(ntp_lst_in[1],&sng_cnv_rcd);
if(*sng_cnv_rcd) nco_sng_cnv_err(ntp_lst_in[1],"strtod",sng_cnv_rcd);
CMD_LN_NTP_VAR=True;
CMD_LN_NTP_WGT=False;
break;
case 'L': /* [enm] Deflate level. Default is 0. */
dfl_lvl=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'l': /* Local path prefix for files retrieved from remote file system */
fl_pth_lcl=(char *)strdup(optarg);
break;
case 'O': /* Toggle FORCE_OVERWRITE */
FORCE_OVERWRITE=!FORCE_OVERWRITE;
break;
case 'o': /* Name of output file */
fl_out=(char *)strdup(optarg);
break;
case 'p': /* Common file path */
fl_pth=(char *)strdup(optarg);
break;
case 'R': /* Toggle removal of remotely-retrieved-files. Default is True. */
RM_RMT_FL_PST_PRC=!RM_RMT_FL_PST_PRC;
break;
case 'r': /* Print CVS program information and copyright notice */
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
(void)nco_lbr_vrs_prn();
(void)nco_cpy_prn();
(void)nco_cnf_prn();
nco_exit(EXIT_SUCCESS);
break;
case 't': /* Thread number */
thr_nbr=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'v': /* Variables to extract/exclude */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
var_lst_in=nco_lst_prs_2D(optarg_lcl,",",&var_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
xtr_nbr=var_lst_in_nbr;
break;
case 'w':
/* Weight(s) for interpolation. Default is wgt_val_1=wgt_val_2=0.5 */
ntp_lst_in=nco_lst_prs_2D(optarg,",",&nbr_ntp);
if(nbr_ntp > 2){
(void)fprintf(stdout,"%s: ERROR too many arguments to -w\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
}else if(nbr_ntp == 2){
wgt_val_1=strtod(ntp_lst_in[0],&sng_cnv_rcd);
if(*sng_cnv_rcd) nco_sng_cnv_err(ntp_lst_in[0],"strtod",sng_cnv_rcd);
wgt_val_2=strtod(ntp_lst_in[1],&sng_cnv_rcd);
if(*sng_cnv_rcd) nco_sng_cnv_err(ntp_lst_in[1],"strtod",sng_cnv_rcd);
}else if(nbr_ntp == 1){
wgt_val_1=strtod(ntp_lst_in[0],&sng_cnv_rcd);
if(*sng_cnv_rcd) nco_sng_cnv_err(ntp_lst_in[0],"strtod",sng_cnv_rcd);
wgt_val_2=1.0-wgt_val_1;
} /* end else */
CMD_LN_NTP_WGT=True;
break;
case 'X': /* Copy auxiliary coordinate argument for later processing */
aux_arg[aux_nbr]=(char *)strdup(optarg);
aux_nbr++;
MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
break;
case 'x': /* Exclude rather than extract variables specified with -v */
EXCLUDE_INPUT_LIST=True;
break;
case '?': /* Print proper usage */
(void)nco_usg_prn();
nco_exit(EXIT_SUCCESS);
break;
case '-': /* Long options are not allowed */
(void)fprintf(stderr,"%s: ERROR Long options are not available in this build. Use single letter options instead.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
break;
default: /* Print proper usage */
(void)fprintf(stdout,"%s ERROR in command-line syntax/options. Please reformulate command accordingly.\n",nco_prg_nm_get());
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
break;
} /* end switch */
if(opt_crr) opt_crr=(char *)nco_free(opt_crr);
} /* end while loop */
if(CMD_LN_NTP_VAR && CMD_LN_NTP_WGT){
(void)fprintf(stdout,"%s: ERROR interpolating variable (-i) and fixed weight(s) (-w) both set\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
}else if(!CMD_LN_NTP_VAR && !CMD_LN_NTP_WGT){
(void)fprintf(stdout,"%s: ERROR interpolating variable (-i) or fixed weight(s) (-w) must be set\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
} /* end else */
/* Process positional arguments and fill in filenames */
fl_lst_in=nco_fl_lst_mk(argv,argc,optind,&fl_nbr,&fl_out,&FL_LST_IN_FROM_STDIN);
/* Initialize thread information */
thr_nbr=nco_openmp_ini(thr_nbr);
in_id_1_arr=(int *)nco_malloc(thr_nbr*sizeof(int));
in_id_2_arr=(int *)nco_malloc(thr_nbr*sizeof(int));
/* Parse filenames */
fl_idx=0; /* Input file _1 */
fl_in_1=nco_fl_nm_prs(fl_in_1,fl_idx,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"%s: INFO Input file %d is %s",nco_prg_nm_get(),fl_idx,fl_in_1);
/* Make sure file is on local system and is readable or die trying */
fl_in_1=nco_fl_mk_lcl(fl_in_1,fl_pth_lcl,&FILE_1_RETRIEVED_FROM_REMOTE_LOCATION);
if(nco_dbg_lvl >= nco_dbg_fl && FILE_1_RETRIEVED_FROM_REMOTE_LOCATION) (void)fprintf(stderr,", local file is %s",fl_in_1);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"\n");
/* Open file once per thread to improve caching */
if(RAM_OPEN) md_open=NC_NOWRITE|NC_DISKLESS; else md_open=NC_NOWRITE;
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) rcd+=nco_fl_open(fl_in_1,md_open,&bfr_sz_hnt,in_id_1_arr+thr_idx);
in_id_1=in_id_1_arr[0];
fl_idx=1; /* Input file _2 */
fl_in_2=nco_fl_nm_prs(fl_in_2,fl_idx,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"%s: INFO Input file %d is %s",nco_prg_nm_get(),fl_idx,fl_in_2);
/* Make sure file is on local system and is readable or die trying */
fl_in_2=nco_fl_mk_lcl(fl_in_2,fl_pth_lcl,&FILE_2_RETRIEVED_FROM_REMOTE_LOCATION);
if(nco_dbg_lvl >= nco_dbg_fl && FILE_2_RETRIEVED_FROM_REMOTE_LOCATION) (void)fprintf(stderr,", local file is %s",fl_in_2);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"\n");
/* Open file once per thread to improve caching */
if(RAM_OPEN) md_open=NC_NOWRITE|NC_DISKLESS; else md_open=NC_NOWRITE;
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) rcd+=nco_fl_open(fl_in_2,md_open,&bfr_sz_hnt,in_id_2_arr+thr_idx);
in_id_2=in_id_2_arr[0];
(void)nco_inq_format(in_id_1,&fl_in_fmt_1);
(void)nco_inq_format(in_id_2,&fl_in_fmt_2);
trv_tbl_init(&trv_tbl);
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id_1,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
/* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Get number of variables, dimensions, and global attributes in file, file format */
(void)trv_tbl_inq((int *)NULL,(int *)NULL,(int *)NULL,&nbr_dmn_fl,(int *)NULL,(int *)NULL,(int *)NULL,(int *)NULL,&nbr_var_fl,trv_tbl);
/* Fill-in variable structure list for all extracted variables */
var=nco_fll_var_trv(in_id_1,&xtr_nbr,trv_tbl);
var_out=(var_sct **)nco_malloc(xtr_nbr*sizeof(var_sct *));
for(int var_idx=0;var_idx<xtr_nbr;var_idx++)
var_out[var_idx]=nco_var_dpl(var[var_idx]);
/* Is this a CCM/CCSM/CF-format history tape? */
CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(in_id_1);
/* Divide variable lists into lists of fixed variables and variables to be processed */
(void)nco_var_lst_dvd(var,var_out,xtr_nbr,CNV_CCM_CCSM_CF,FIX_REC_CRD,nco_pck_plc_nil,nco_pck_map_nil,(dmn_sct **)NULL,0,&var_fix,&var_fix_out,&nbr_var_fix,&var_prc_1,&var_prc_out,&nbr_var_prc,trv_tbl);
/* Store processed and fixed variables info into GTT */
(void)nco_var_prc_fix_trv(nbr_var_prc,var_prc_1,nbr_var_fix,var_fix,trv_tbl);
/* Make output and input files consanguinous */
if(fl_out_fmt == NCO_FORMAT_UNDEFINED) fl_out_fmt=fl_in_fmt_1;
/* Initialize, decode, and set PPC information */
if(ppc_nbr > 0) nco_ppc_ini(in_id_1,&dfl_lvl,fl_out_fmt,ppc_arg,ppc_nbr,trv_tbl);
/* Verify output file format supports requested actions */
(void)nco_fl_fmt_vet(fl_out_fmt,cnk_nbr,dfl_lvl);
/* Open output file */
fl_out_tmp=nco_fl_out_open(fl_out,FORCE_APPEND,FORCE_OVERWRITE,fl_out_fmt,&bfr_sz_hnt,RAM_CREATE,RAM_OPEN,WRT_TMP_FL,&out_id);
/* Initialize chunking from user-specified inputs */
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC) rcd+=nco_cnk_ini(in_id_1,fl_out,cnk_arg,cnk_nbr,cnk_map,cnk_plc,cnk_min_byt,cnk_sz_byt,cnk_sz_scl,&cnk);
/* Transfer variable type to table. NOTE: Using var/xtr_nbr containing all variables (processed, fixed) */
(void)nco_var_typ_trv(xtr_nbr,var,trv_tbl);
/* Define dimensions, extracted groups, variables, and attributes in output file */
(void)nco_xtr_dfn(in_id_1,out_id,&cnk,dfl_lvl,gpe,md5,!FORCE_APPEND,True,False,nco_pck_plc_nil,(char *)NULL,trv_tbl);
/* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(HISTORY_APPEND && FORCE_APPEND) (void)nco_prv_att_cat(fl_in_1,in_id_1,out_id);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
if(thr_nbr > 0 && HISTORY_APPEND) (void)nco_thr_att_cat(out_id,thr_nbr);
/* Turn off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
/* Take output file out of define mode */
if(hdr_pad == 0UL){
(void)nco_enddef(out_id);
}else{
(void)nco__enddef(out_id,hdr_pad);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: INFO Padding header with %lu extra bytes\n",nco_prg_nm_get(),(unsigned long)hdr_pad);
} /* hdr_pad */
/* Assign zero to start and unity to stride vectors in output variables */
(void)nco_var_srd_srt_set(var_out,xtr_nbr);
/* Copy variable data for non-processed variables */
(void)nco_cpy_fix_var_trv(in_id_1,out_id,gpe,trv_tbl);
/* Perform various error-checks on input file */
if(False) (void)nco_fl_cmp_err_chk();
/* ncflint-specific stuff: */
/* Find the weighting variable in input file */
if(CMD_LN_NTP_VAR){
var_sct *ntp_1=NULL;
var_sct *ntp_2=NULL;
var_sct *ntp_var_out;
/* Turn arrival point into pseudo-variable */
val_gnr_unn.d=ntp_val_out; /* Generic container for arrival point or weight */
ntp_var_out=scl_mk_var(val_gnr_unn,NC_DOUBLE);
int xtr_nbr_ntp_1;
int xtr_nbr_ntp_2;
var_sct ** var_ntp_1;
var_sct ** var_ntp_2;
/* Fill-in variable structure list for all variables named "ntp_nm" NOTE: using table from file 1 */
var_ntp_1=nco_var_trv(in_id_1,ntp_nm,&xtr_nbr_ntp_1,trv_tbl);
var_ntp_2=nco_var_trv(in_id_2,ntp_nm,&xtr_nbr_ntp_2,trv_tbl);
if (xtr_nbr_ntp_1) ntp_1=var_ntp_1[0];
if (xtr_nbr_ntp_2) ntp_2=var_ntp_2[0];
if(!xtr_nbr_ntp_1 || !xtr_nbr_ntp_2){
(void)fprintf(fp_stdout,"%s: ERROR Variable %s is not present in input file. ncflint assumes same file structure for both input files\n",nco_prg_nm_get(),ntp_nm);
nco_exit(EXIT_FAILURE);
} /* endif */
/* Read */
(void)nco_msa_var_get_trv(in_id_1,ntp_1,trv_tbl);
(void)nco_msa_var_get_trv(in_id_2,ntp_2,trv_tbl);
/* Currently, only support scalar variables */
if(ntp_1->sz > 1 || ntp_2->sz > 1){
(void)fprintf(stdout,"%s: ERROR interpolation variable %s must be scalar\n",nco_prg_nm_get(),ntp_nm);
nco_exit(EXIT_FAILURE);
} /* end if */
/* Weights must be NC_DOUBLE */
ntp_1=nco_var_cnf_typ((nc_type)NC_DOUBLE,ntp_1);
ntp_2=nco_var_cnf_typ((nc_type)NC_DOUBLE,ntp_2);
/* Check for degenerate case */
if(ntp_1->val.dp[0] == ntp_2->val.dp[0]){
(void)fprintf(stdout,"%s: ERROR Interpolation variable %s is identical (%g) in input files, therefore unable to interpolate.\n",nco_prg_nm_get(),ntp_nm,ntp_1->val.dp[0]);
nco_exit(EXIT_FAILURE);
} /* end if */
/* Turn weights into pseudo-variables */
wgt_1=nco_var_dpl(ntp_2);
wgt_2=nco_var_dpl(ntp_var_out);
/* Subtract to find interpolation distances */
(void)nco_var_sbt(ntp_1->type,ntp_1->sz,ntp_1->has_mss_val,ntp_1->mss_val,ntp_var_out->val,wgt_1->val);
(void)nco_var_sbt(ntp_1->type,ntp_1->sz,ntp_1->has_mss_val,ntp_1->mss_val,ntp_1->val,wgt_2->val);
(void)nco_var_sbt(ntp_1->type,ntp_1->sz,ntp_1->has_mss_val,ntp_1->mss_val,ntp_1->val,ntp_2->val);
/* Normalize to obtain final interpolation weights */
(void)nco_var_dvd(wgt_1->type,wgt_1->sz,wgt_1->has_mss_val,wgt_1->mss_val,ntp_2->val,wgt_1->val);
(void)nco_var_dvd(wgt_2->type,wgt_2->sz,wgt_2->has_mss_val,wgt_2->mss_val,ntp_2->val,wgt_2->val);
for(idx=0;idx<xtr_nbr_ntp_1;idx++) var_ntp_1[idx]=nco_var_free(var_ntp_1[idx]);
for(idx=0;idx<xtr_nbr_ntp_2;idx++) var_ntp_2[idx]=nco_var_free(var_ntp_2[idx]);
var_ntp_1=(var_sct **)nco_free(var_ntp_1);
var_ntp_2=(var_sct **)nco_free(var_ntp_2);
if(ntp_var_out) ntp_var_out=nco_var_free(ntp_var_out);
} /* end if CMD_LN_NTP_VAR */
if(CMD_LN_NTP_WGT){
val_gnr_unn.d=wgt_val_1; /* Generic container for arrival point or weight */
wgt_1=scl_mk_var(val_gnr_unn,NC_DOUBLE);
val_gnr_unn.d=wgt_val_2; /* Generic container for arrival point or weight */
wgt_2=scl_mk_var(val_gnr_unn,NC_DOUBLE);
} /* end if CMD_LN_NTP_WGT */
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"wgt_1 = %g, wgt_2 = %g\n",wgt_1->val.dp[0],wgt_2->val.dp[0]);
/* Create structure list for second file */
var_prc_2=(var_sct **)nco_malloc(nbr_var_prc*sizeof(var_sct *));
/* Timestamp end of metadata setup and disk layout */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_rgl;
/* Loop over each interpolated variable */
#ifdef _OPENMP
/* OpenMP notes:
shared(): msk and wgt are not altered within loop
private(): wgt_avg does not need initialization */
# pragma omp parallel for default(none) firstprivate(wgt_1,wgt_2,wgt_out_1,wgt_out_2) private(DO_CONFORM,idx,in_id_1,in_id_2,has_mss_val) shared(MUST_CONFORM,nco_dbg_lvl,fl_in_1,fl_in_2,fl_out,gpe,in_id_1_arr,in_id_2_arr,nbr_var_prc,out_id,nco_prg_nm,var_prc_1,var_prc_2,var_prc_out,nbr_dmn_fl,trv_tbl)
#endif /* !_OPENMP */
for(idx=0;idx<nbr_var_prc;idx++){
/* Note: Using object 2 from table 1, only one table built, assumes same structure for processed objects in both files */
char *grp_out_fll=NULL; /* [sng] Group name */
int grp_id_1; /* [ID] Group ID */
int grp_id_2; /* [ID] Group ID */
int grp_out_id; /* [ID] Group ID (output) */
int var_out_id; /* [ID] Variable ID (output) */
trv_sct *var_trv_1;/* [sct] Variable GTT object */
trv_sct *var_trv_2;/* [sct] Variable GTT object */
if(nco_dbg_lvl >= nco_dbg_var) (void)fprintf(fp_stderr,"%s, ",var_prc_1[idx]->nm);
if(nco_dbg_lvl >= nco_dbg_var) (void)fflush(fp_stderr);
in_id_1=in_id_1_arr[omp_get_thread_num()];
in_id_2=in_id_2_arr[omp_get_thread_num()];
var_prc_2[idx]=nco_var_dpl(var_prc_1[idx]);
/* Obtain variable GTT object using full variable name */
var_trv_1=trv_tbl_var_nm_fll(var_prc_1[idx]->nm_fll,trv_tbl);
var_trv_2=trv_tbl_var_nm_fll(var_prc_2[idx]->nm_fll,trv_tbl);
if(!var_trv_2){
(void)fprintf(fp_stdout,"%s: ERROR Variable %s is not present in second input file. ncflint assumes same structure for processed objects in both files\n",nco_prg_nm_get(),var_trv_1->nm_fll);
nco_exit(EXIT_FAILURE);
} /* endif */
/* Obtain group ID */
(void)nco_inq_grp_full_ncid(in_id_1,var_trv_1->grp_nm_fll,&grp_id_1);
(void)nco_inq_grp_full_ncid(in_id_2,var_trv_2->grp_nm_fll,&grp_id_2);
(void)nco_var_mtd_refresh(grp_id_2,var_prc_2[idx]);
/* Read */
(void)nco_msa_var_get_trv(in_id_1,var_prc_1[idx],trv_tbl);
(void)nco_msa_var_get_trv(in_id_2,var_prc_2[idx],trv_tbl);
/* Set var_prc_1 and var_prc_2 to correct size */
var_prc_1[idx]->sz=var_prc_out[idx]->sz;
var_prc_2[idx]->sz=var_prc_out[idx]->sz;
/* Stretch second variable to match dimensions of first variable */
wgt_out_1=nco_var_cnf_dmn(var_prc_out[idx],wgt_1,wgt_out_1,MUST_CONFORM,&DO_CONFORM);
wgt_out_2=nco_var_cnf_dmn(var_prc_out[idx],wgt_2,wgt_out_2,MUST_CONFORM,&DO_CONFORM);
var_prc_1[idx]=nco_var_cnf_typ((nc_type)NC_DOUBLE,var_prc_1[idx]);
var_prc_2[idx]=nco_var_cnf_typ((nc_type)NC_DOUBLE,var_prc_2[idx]);
/* Allocate and, if necesssary, initialize space for processed variable */
var_prc_out[idx]->sz=var_prc_1[idx]->sz;
/* NB: must not try to free() same tally buffer twice */
/* var_prc_out[idx]->tally=var_prc_1[idx]->tally=(long *)nco_malloc(var_prc_out[idx]->sz*sizeof(long int));*/
var_prc_out[idx]->tally=(long *)nco_malloc(var_prc_out[idx]->sz*sizeof(long int));
(void)nco_zero_long(var_prc_out[idx]->sz,var_prc_out[idx]->tally);
/* Weight variable by taking product of weight with variable */
(void)nco_var_mlt(var_prc_1[idx]->type,var_prc_1[idx]->sz,var_prc_1[idx]->has_mss_val,var_prc_1[idx]->mss_val,wgt_out_1->val,var_prc_1[idx]->val);
(void)nco_var_mlt(var_prc_2[idx]->type,var_prc_2[idx]->sz,var_prc_2[idx]->has_mss_val,var_prc_2[idx]->mss_val,wgt_out_2->val,var_prc_2[idx]->val);
/* Change missing_value of var_prc_2, if any, to missing_value of var_prc_1, if any */
has_mss_val=nco_mss_val_cnf(var_prc_1[idx],var_prc_2[idx]);
/* NB: fxm: use tally to determine when to "unweight" answer? TODO */
(void)nco_var_add_tll_ncflint(var_prc_1[idx]->type,var_prc_1[idx]->sz,has_mss_val,var_prc_1[idx]->mss_val,var_prc_out[idx]->tally,var_prc_1[idx]->val,var_prc_2[idx]->val);
/* Re-cast output variable to original type */
var_prc_2[idx]=nco_var_cnf_typ(var_prc_out[idx]->type,var_prc_2[idx]);
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv_1->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv_1->grp_nm_fll);
/* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
if(grp_out_fll) grp_out_fll=(char *)nco_free(grp_out_fll);
/* Get variable ID */
(void)nco_inq_varid(grp_out_id,var_trv_1->nm,&var_out_id);
/* Store the output variable ID */
var_prc_out[idx]->id=var_out_id;
if(var_trv_1->ppc != NC_MAX_INT){
if(var_trv_1->flg_nsd) (void)nco_ppc_bitmask(var_trv_1->ppc,var_prc_2[idx]->type,var_prc_out[idx]->sz,var_prc_out[idx]->has_mss_val,var_prc_out[idx]->mss_val,var_prc_2[idx]->val); else (void)nco_ppc_around(var_trv_1->ppc,var_prc_2[idx]->type,var_prc_out[idx]->sz,var_prc_out[idx]->has_mss_val,var_prc_out[idx]->mss_val,var_prc_2[idx]->val);
} /* endif ppc */
if(nco_is_xcp(var_trv_1->nm)) nco_xcp_prc(var_trv_1->nm,var_prc_2[idx]->type,var_prc_out[idx]->sz,(char *)var_prc_2[idx]->val.vp);
#ifdef _OPENMP
# pragma omp critical
#endif /* _OPENMP */
{ /* begin OpenMP critical */
/* Copy interpolations to output file */
if(!var_prc_out[idx]->nbr_dim) (void)nco_put_var1(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc_2[idx]->val.vp,var_prc_2[idx]->type); else (void)nco_put_vara(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc_out[idx]->cnt,var_prc_2[idx]->val.vp,var_prc_2[idx]->type);
} /* end OpenMP critical */
/* Free dynamically allocated buffers */
if(var_prc_1[idx]) var_prc_1[idx]=nco_var_free(var_prc_1[idx]);
if(var_prc_2[idx]) var_prc_2[idx]=nco_var_free(var_prc_2[idx]);
if(var_prc_out[idx]) var_prc_out[idx]=nco_var_free(var_prc_out[idx]);
} /* end (OpenMP parallel for) loop over idx */
if(nco_dbg_lvl >= nco_dbg_var) (void)fprintf(stderr,"\n");
/* Close input netCDF files */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) nco_close(in_id_1_arr[thr_idx]);
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) nco_close(in_id_2_arr[thr_idx]);
/* Close output file and move it from temporary to permanent location */
(void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id);
/* Remove local copy of file */
if(FILE_1_RETRIEVED_FROM_REMOTE_LOCATION && RM_RMT_FL_PST_PRC) (void)nco_fl_rm(fl_in_1);
if(FILE_2_RETRIEVED_FROM_REMOTE_LOCATION && RM_RMT_FL_PST_PRC) (void)nco_fl_rm(fl_in_2);
/* Clean memory unless dirty memory allowed */
if(flg_cln){
/* ncflint-specific memory */
if(fl_in_1) fl_in_1=(char *)nco_free(fl_in_1);
if(fl_in_2) fl_in_2=(char *)nco_free(fl_in_2);
var_prc_1=(var_sct **)nco_free(var_prc_1);
var_prc_2=(var_sct **)nco_free(var_prc_2);
if(wgt_1) wgt_1=(var_sct *)nco_var_free(wgt_1);
if(wgt_2) wgt_2=(var_sct *)nco_var_free(wgt_2);
if(wgt_out_1) wgt_out_1=(var_sct *)nco_var_free(wgt_out_1);
if(wgt_out_2) wgt_out_2=(var_sct *)nco_var_free(wgt_out_2);
/* NCO-generic clean-up */
/* Free individual strings/arrays */
if(cmd_ln) cmd_ln=(char *)nco_free(cmd_ln);
if(cnk_map_sng) cnk_map_sng=(char *)nco_free(cnk_map_sng);
if(cnk_plc_sng) cnk_plc_sng=(char *)nco_free(cnk_plc_sng);
if(fl_out) fl_out=(char *)nco_free(fl_out);
if(fl_out_tmp) fl_out_tmp=(char *)nco_free(fl_out_tmp);
if(fl_pth) fl_pth=(char *)nco_free(fl_pth);
if(fl_pth_lcl) fl_pth_lcl=(char *)nco_free(fl_pth_lcl);
if(in_id_1_arr) in_id_1_arr=(int *)nco_free(in_id_1_arr);
if(in_id_2_arr) in_id_2_arr=(int *)nco_free(in_id_2_arr);
/* Free lists of strings */
if(fl_lst_in && fl_lst_abb == NULL) fl_lst_in=nco_sng_lst_free(fl_lst_in,fl_nbr);
if(fl_lst_in && fl_lst_abb) fl_lst_in=nco_sng_lst_free(fl_lst_in,1);
if(fl_lst_abb) fl_lst_abb=nco_sng_lst_free(fl_lst_abb,abb_arg_nbr);
if(var_lst_in_nbr > 0) var_lst_in=nco_sng_lst_free(var_lst_in,var_lst_in_nbr);
/* Free limits */
for(idx=0;idx<aux_nbr;idx++) aux_arg[idx]=(char *)nco_free(aux_arg[idx]);
for(idx=0;idx<lmt_nbr;idx++) lmt_arg[idx]=(char *)nco_free(lmt_arg[idx]);
for(idx=0;idx<ppc_nbr;idx++) ppc_arg[idx]=(char *)nco_free(ppc_arg[idx]);
/* Free chunking information */
for(idx=0;idx<cnk_nbr;idx++) cnk_arg[idx]=(char *)nco_free(cnk_arg[idx]);
if(cnk_nbr > 0) cnk.cnk_dmn=(cnk_dmn_sct **)nco_cnk_lst_free(cnk.cnk_dmn,cnk_nbr);
var=(var_sct **)nco_free(var);
var_out=(var_sct **)nco_free(var_out);
var_prc_out=(var_sct **)nco_free(var_prc_out);
if(nbr_var_fix > 0) var_fix=nco_var_lst_free(var_fix,nbr_var_fix);
if(nbr_var_fix > 0) var_fix_out=nco_var_lst_free(var_fix_out,nbr_var_fix);
trv_tbl_free(trv_tbl);
for(idx=0;idx<lmt_nbr;idx++) flg_dne[idx].dim_nm=(char *)nco_free(flg_dne[idx].dim_nm);
if(flg_dne) flg_dne=(nco_dmn_dne_t *)nco_free(flg_dne);
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
} /* !flg_cln */
#ifdef ENABLE_MPI
MPI_Finalize();
#endif /* !ENABLE_MPI */
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
int /* O [nbr] Thread number */
nco_openmp_ini /* [fnc] Initialize OpenMP threading environment */
(const int thr_nbr) /* I [nbr] User-requested thread number */
{
/* Purpose: Initialize OpenMP multi-threading environment
Honor user-requested thread number, balance against known code efficiency,
print diagnostics
Returns thr_nbr=1 in three situations:
1. UP codes (not threaded)
2. SMP codes compiled with compilers which lack OpenMP support
3. SMP codes where single thread requested/advised
Otherwise returns system-dependent thr_nbr */
/* Using naked stdin/stdout/stderr in parallel region generates warning
Copy appropriate filehandle to variable scoped shared in parallel clause */
char *nvr_OMP_NUM_THREADS; /* [sng] Environment variable OMP_NUM_THREADS */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
FILE * const fp_stderr=stderr; /* [fl] stderr filehandle CEWI */
nco_bool USR_SPC_THR_RQS=False;
int dyn_thr=1; /* [flg] Allow system to dynamically set number of threads */
int ntg_OMP_NUM_THREADS=int_CEWI; // [nbr] OMP_NUM_THREADS environment variable
int prc_nbr_max; /* [nbr] Maximum number of processors available */
int thr_nbr_act; /* O [nbr] Number of threads NCO uses */
int thr_nbr_max_fsh=4; /* [nbr] Maximum number of threads program can use efficiently */
int thr_nbr_max=int_CEWI; /* [nbr] Maximum number of threads system allows */
int thr_nbr_rqs=int_CEWI; /* [nbr] Number of threads to request */
#ifndef _OPENMP
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(fp_stderr,"%s: INFO Build compiler lacked (or user turned off) OpenMP support. Code will execute with single thread in Uni-Processor (UP) mode.\n",nco_prg_nm_get());
return (int)1;
#endif /* !_OPENMP */
/* Strategy:
0. Determine maximum number of threads system will allocate (thr_nbr_max)
1. Command-line thread request, if any, overrides automatic algorithm
2. If no command-line request then system allocates OMP_NUM_THREADS if possible
3. Reduce maximum number of threads available to system to thr_nbr_max_fsh
Many operators cannot use more than thr_nbr_max_fsh ~ 2--4 threads efficiently
Play nice: Set dynamic threading so that system can make efficiency decisions
When dynamic threads are set, system never allocates more than thr_nbr_max_fsh */
if(thr_nbr < 0){
(void)fprintf(fp_stderr,"%s: ERROR User-requested thread number = %d is less than zero\n",nco_prg_nm_get(),thr_nbr);
nco_exit(EXIT_FAILURE);
} /* endif err */
if(thr_nbr == 0)
if(nco_dbg_lvl_get() >= nco_dbg_scl && nco_dbg_lvl_get() != nco_dbg_dev )
(void)fprintf(fp_stderr,"%s: INFO User did not specify thread request > 0 on command line. NCO will automatically assign threads based on OMP_NUM_THREADS environment and machine capabilities.\nHINT: Not specifiying any --thr_nbr (or specifying --thr_nbr=0) causes NCO to try to pick the optimal thread number. Specifying --thr_nbr=1 tells NCO to execute in Uni-Processor (UP) (i.e., single-threaded) mode.\n",nco_prg_nm_get());
if(thr_nbr > 0) USR_SPC_THR_RQS=True;
prc_nbr_max=omp_get_num_procs(); /* [nbr] Maximum number of processors available */
if(omp_in_parallel()){
(void)fprintf(fp_stderr,"%s: ERROR Attempted to get maximum thread number from within parallel region\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
}else{
thr_nbr_max=omp_get_max_threads(); /* [nbr] Maximum number of threads system allows */
} /* end error */
if(nco_dbg_lvl_get() >= nco_dbg_scl && nco_dbg_lvl_get() != nco_dbg_dev){
if((nvr_OMP_NUM_THREADS=getenv("OMP_NUM_THREADS"))) ntg_OMP_NUM_THREADS=(int)strtol(nvr_OMP_NUM_THREADS,&sng_cnv_rcd,NCO_SNG_CNV_BASE10); /* [sng] Environment variable OMP_NUM_THREADS */
if(nvr_OMP_NUM_THREADS && *sng_cnv_rcd) nco_sng_cnv_err(nvr_OMP_NUM_THREADS,"strtol",sng_cnv_rcd);
(void)fprintf(fp_stderr,"%s: INFO Environment variable OMP_NUM_THREADS ",nco_prg_nm_get());
if(ntg_OMP_NUM_THREADS > 0) (void)fprintf(fp_stderr,"= %d\n",ntg_OMP_NUM_THREADS); else (void)fprintf(fp_stderr,"does not exist\n");
(void)fprintf(fp_stderr,"%s: INFO omp_get_num_procs() reports number of processors available is %d\n",nco_prg_nm_get(),prc_nbr_max);
(void)fprintf(fp_stderr,"%s: INFO omp_get_max_threads() reports maximum number of threads system allows is %d\n",nco_prg_nm_get(),thr_nbr_max);
} /* endif dbg */
if(USR_SPC_THR_RQS){
/* Try to honor user-specified thread request... */
thr_nbr_rqs=thr_nbr; /* [nbr] Number of threads to request */
/* ...if possible... */
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(fp_stderr,"%s: INFO Command-line requests %d thread%s\n",nco_prg_nm_get(),thr_nbr,(thr_nbr > 1) ? "s" : "");
if(thr_nbr > thr_nbr_max){
(void)fprintf(fp_stderr,"%s: WARNING Reducing user-requested thread number = %d to maximum thread number allowed = %d\n",nco_prg_nm_get(),thr_nbr,thr_nbr_max);
thr_nbr_rqs=thr_nbr_max; /* [nbr] Number of threads to request */
} /* endif */
}else{ /* !USR_SPC_THR_RQS */
/* Otherwise use automatic thread allocation algorithm */
/* Request maximum number of threads permitted */
thr_nbr_rqs=thr_nbr_max; /* [nbr] Number of threads to request */
/* Restrict threading on per-program basis to play nicely with others */
switch(nco_prg_id_get()){
/* Operators with pre-set thread limit
NB: All operators currently have default restrictions
2007: Only ncwa and ncap2 have a chance to scale on non-parallel filesystems
ncap2 may, one day, see a big performance boost from threading
However, as of 20090327, ncap2 threading may be buggy due to ANTLR
Moreover, we want to prevent hogging processes on 32-way nodes
until/unless clear benefits of threading are demonstrated.
2015: Threads improve ncks regridding performance by 2-3x on ACME ~1-20 GB netCDF3 files */
case ncap:
/* 20090327: Restrict ncap2 to one thread until ANTLR threading resolved */
thr_nbr_max_fsh=1;
break;
case ncecat:
case ncrcat:
/* ncecat and ncrcat are extremely I/O intensive
Maximum efficiency when one thread reads from input file while other writes to output file */
// 20140219: Turn-off OpenMP until thoroughly tested
// thr_nbr_max_fsh=2;
thr_nbr_max_fsh=1;
break;
case ncks:
// 20150529: Turn-on OpenMP for regridder
thr_nbr_max_fsh=16;
break;
case ncwa:
// 20150530: Turn-on OpenMP for debugging
// 20150610: Eight threads with ncwa seemed to work for a little while, then it got flaky. Turned-off for 4.5.0 release
// 20150622: Allowing eight threads again for debugging with -D 3
// 20150701: Firmly established that netCDF4 involvement hoses threading because HDF5 is not threadsafe by default
// 20150710: Turned-off for 4.5.1 release
// Symptoms of bugs, if any, show up with
// cd ~/nco/bm;nco_bm.pl --regress ncwa;cd -
thr_nbr_max_fsh=1;
if(nco_dbg_lvl_get() >= nco_dbg_scl) thr_nbr_max_fsh=1;
break;
/* Operators with higher maximum pre-set thread limit (NB: not all of these are threaded!) */
case ncra:
thr_nbr_max_fsh=1;
if(nco_dbg_lvl_get() >= nco_dbg_scl) thr_nbr_max_fsh=1;
break;
case ncbo:
case ncatted:
case ncfe:
case ncflint:
case ncpdq:
case ncrename:
case ncge:
// 20140219: Turn-off OpenMP until thoroughly tested
// thr_nbr_max_fsh=4;
thr_nbr_max_fsh=1;
break;
default: nco_dfl_case_prg_id_err(); break;
} /* end case */
/* Automatic algorithm tries to play nice with others */
(void)omp_set_dynamic(dyn_thr); /* [flg] Allow system to dynamically set number of threads */
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(fp_stderr,"%s: INFO omp_set_dynamic() used to %s OS to dynamically set threads\n",nco_prg_nm_get(),(dyn_thr ? "ALLOW" : "DISALLOW"));
dyn_thr=omp_get_dynamic(); /* [flg] Allow system to dynamically set number of threads */
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(fp_stderr,"%s: INFO omp_get_dynamic() reports system will%s utilize dynamic threading\n",nco_prg_nm_get(),(dyn_thr ? "" : " NOT"));
/* Apply program/system limitations */
if(thr_nbr_max > thr_nbr_max_fsh){
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(fp_stderr,"%s: INFO Reducing default thread number from %d to %d, an operator-dependent \"play-nice\" number set in nco_openmp_ini()\n",nco_prg_nm_get(),thr_nbr_max,thr_nbr_max_fsh);
thr_nbr_rqs=thr_nbr_max_fsh; /* [nbr] Number of threads to request */
} /* endif */
} /* !USR_SPC_THR_RQS */
#ifdef ENABLE_NETCDF4
if(nco_prg_id_get() != ncks && nco_prg_id_get() != ncwa && nco_prg_id_get() != ncra && thr_nbr_rqs > 1){
if(USR_SPC_THR_RQS && nco_dbg_lvl_get() >= nco_dbg_fl) (void)fprintf(stdout,"%s: WARNING This is TODO nco939. Requested threading with netCDF4 (HDF5) support. The NCO thread request algorithm considers user-input, environment variables, and software and hardware limitations in determining the number of threads to request, thr_nbr_rqs. At this point NCO would request result %d threads from a netCDF3-based library. However, this NCO was built with netCDF4, which relies on HDF5. netCDF4 is not thread-safe unless HDF5 is configured with the (non-default) --enable-threadsafe option. NCO currently has no way to know whether HDF5 was built thread-safe. Hence, all netCDF4-based operators are currently restricted to a single thread. The program will now automatically set thr_nbr_rqs = 1.\nThis unfortunate limitation is necessary to keep the NCO developers sane. If you want/need threading in netCDF4-based NCO, please politely yet firmly request of the Unidata netCDF developers that better thread support be built into netCDF4, and request of the HDF5 developers that they make the --enable-threadsafe option compatible with all HDF5 libraries and APIs, including Fortran (which, as of HDF5 1.8.0 in 2008, is incompatible with --enable-threadsafe).\n",nco_prg_nm_get(),thr_nbr_rqs);
thr_nbr_rqs=1;
} /* endif */
#endif /* !ENABLE_NETCDF4 */
/* Set thread number */
if(omp_in_parallel()){
(void)fprintf(fp_stderr,"%s: ERROR Attempted to set thread number from within parallel region\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
}else{
(void)omp_set_num_threads(thr_nbr_rqs);
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(fp_stderr,"%s: INFO omp_set_num_threads() used to set execution environment to spawn teams of %d thread(s)\n",nco_prg_nm_get(),thr_nbr_rqs);
} /* end error */
thr_nbr_act=omp_get_max_threads();
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(fp_stderr,"%s: INFO After using omp_set_num_threads() to adjust for any user requests/NCO optimizations, omp_get_max_threads() reports that a parallel construct here/now would spawn %d thread(s)\n",nco_prg_nm_get(),thr_nbr_act);
#ifdef _OPENMP
if(nco_dbg_lvl_get() >= nco_dbg_scl){
# pragma omp parallel default(none) shared(thr_nbr_act)
{ /* begin OpenMP parallel */
# pragma omp single nowait
{ /* begin OpenMP single */
thr_nbr_act=omp_get_num_threads(); /* [nbr] Number of threads NCO uses */
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(fp_stderr,"%s: INFO Small parallel test region spawned team of %d thread(s)\n",nco_prg_nm_get(),thr_nbr_act);
} /* end OpenMP single */
} /* end OpenMP parallel */
} /* end dbg */
#endif /* !_OPENMP */
/* Issue any warnings about OpenMP credibility during debugging phase */
if(True)
if((nco_prg_id_get() == ncwa || nco_prg_id_get() == ncra) && thr_nbr_act > 1)
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(fp_stderr,"%s: WARNING OpenMP threading active with %d threads but not guaranteed to work on this operator. If strange behavior (e.g., NaN results) ensues, manually turn-off multi-threading by specifying \"-t 1\" option.\n",nco_prg_nm_get(),thr_nbr_act);
return thr_nbr_act; /* O [nbr] Number of threads NCO uses */
} /* end nco_openmp_ini() */
void
nco_ppc_set_dflt /* Set PPC value for all non-coordinate variables for --ppc default */
(const int nc_id, /* I [id] netCDF input file ID */
const char * const ppc_arg, /* I [sng] User input for precision-preserving compression */
trv_tbl_sct * const trv_tbl) /* I/O [sct] Traversal table */
{
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
int ppc_val;
nco_bool flg_nsd=True; /* [flg] PPC is NSD */
if(ppc_arg[0] == '.'){
flg_nsd=False; /* DSD */
ppc_val=(int)strtol(ppc_arg+1L,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(ppc_arg+1L,"strtol",sng_cnv_rcd);
}else{ /* NSD */
ppc_val=(int)strtol(ppc_arg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(ppc_arg,"strtol",sng_cnv_rcd);
if(ppc_val <= 0){
(void)fprintf(stdout,"%s ERROR Number of Significant Digits (NSD) must be positive. Default is specified as %d. HINT: Decimal Significant Digit (DSD) rounding does accept negative arguments (number of digits in front of the decimal point). However, the DSD argument must be prefixed by a period or \"dot\", e.g., \"--ppc foo=.-2\", to distinguish it from NSD quantization.\n",nco_prg_nm_get(),ppc_val);
nco_exit(EXIT_FAILURE);
} /* endif */
} /* end if */
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
if(trv_tbl->lst[idx_tbl].nco_typ == nco_obj_typ_var && !trv_tbl->lst[idx_tbl].is_crd_var){
/* Allow "default" to affect only floating point types */
if(trv_tbl->lst[idx_tbl].var_typ == NC_FLOAT || trv_tbl->lst[idx_tbl].var_typ == NC_DOUBLE){
/* Prevent "default" from applying to coordinate and bounds variables */
int grp_id;
int var_id;
nco_inq_grp_full_ncid(nc_id,trv_tbl->lst[idx_tbl].grp_nm_fll,&grp_id);
nco_inq_varid(grp_id,trv_tbl->lst[idx_tbl].nm,&var_id);
if(!nco_is_spc_in_cf_att(grp_id,"bounds",var_id) && !nco_is_spc_in_cf_att(grp_id,"climatology",var_id) && !nco_is_spc_in_cf_att(grp_id,"coordinates",var_id)){
trv_tbl->lst[idx_tbl].ppc=ppc_val;
trv_tbl->lst[idx_tbl].flg_nsd=flg_nsd;
} /* endif */
} /* endif */
} /* endif */
} /* endfor */
} /* end nco_ppc_set_dflt() */
void
nco_ppc_ini /* Set PPC based on user specifications */
(const int nc_id, /* I [id] netCDF input file ID */
int *dfl_lvl, /* O [enm] Deflate level */
const int fl_out_fmt, /* I [enm] Output file format */
char * const ppc_arg[], /* I [sng] List of user-specified PPCs */
const int ppc_arg_nbr, /* I [nbr] Number of PPC specified */
trv_tbl_sct * const trv_tbl) /* I/O [sct] Traversal table */
{
int ppc_arg_idx; /* [idx] Index over ppc_arg (i.e., separate invocations of "--ppc var1[,var2]=val") */
int ppc_var_idx; /* [idx] Index over ppc_lst (i.e., all names explicitly specified in all "--ppc var1[,var2]=val" options) */
int ppc_var_nbr=0;
kvm_sct *ppc_lst; /* [sct] List of all PPC specifications */
kvm_sct kvm;
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC){
/* If user did not explicitly set deflate level for this file ... */
if(*dfl_lvl == NCO_DFL_LVL_UNDEFINED){
*dfl_lvl=1;
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(stderr,"%s: INFO Precision-Preserving Compression (PPC) automatically activating file-wide deflation level = %d\n",nco_prg_nm_get(),*dfl_lvl);
} /* endif */
}else{
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(stderr,"%s: INFO Requested Precision-Preserving Compression (PPC) on netCDF3 output dataset. Unlike netCDF4, netCDF3 does not support internal compression. To take full advantage of PPC consider writing file as netCDF4 enhanced (e.g., %s -4 ...) or classic (e.g., %s -7 ...). Or consider compressing the netCDF3 file afterwards with, e.g., gzip or bzip2. File must then be uncompressed with, e.g., gunzip or bunzip2 before netCDF readers will recognize it. See http://nco.sf.net/nco.html#ppc for more information on PPC strategies.\n",nco_prg_nm_get(),nco_prg_nm_get(),nco_prg_nm_get());
} /* endelse */
ppc_lst=(kvm_sct *)nco_malloc(NC_MAX_VARS*sizeof(kvm_sct));
/* Parse PPCs */
for(ppc_arg_idx=0;ppc_arg_idx<ppc_arg_nbr;ppc_arg_idx++){
if(!strstr(ppc_arg[ppc_arg_idx],"=")){
(void)fprintf(stdout,"%s: Invalid --ppc specification: %s. Must contain \"=\" sign.\n",nco_prg_nm_get(),ppc_arg[ppc_arg_idx]);
if(ppc_lst) ppc_lst=(kvm_sct *)nco_free(ppc_lst);
nco_exit(EXIT_FAILURE);
} /* endif */
kvm=nco_sng2kvm(ppc_arg[ppc_arg_idx]);
/* nco_sng2kvm() converts argument "--ppc one,two=3" into kvm.key="one,two" and kvm.val=3
Then nco_lst_prs_2D() converts kvm.key into two items, "one" and "two", with the same value, 3 */
if(kvm.key){
int var_idx; /* [idx] Index over variables in current PPC argument */
int var_nbr; /* [nbr] Number of variables in current PPC argument */
char **var_lst;
var_lst=nco_lst_prs_2D(kvm.key,",",&var_nbr);
for(var_idx=0;var_idx<var_nbr;var_idx++){ /* Expand multi-variable specification */
ppc_lst[ppc_var_nbr].key=strdup(var_lst[var_idx]);
ppc_lst[ppc_var_nbr].val=strdup(kvm.val);
ppc_var_nbr++;
} /* end for */
var_lst=nco_sng_lst_free(var_lst,var_nbr);
} /* end if */
} /* end for */
/* PPC "default" specified, set all non-coordinate variables to default first */
for(ppc_var_idx=0;ppc_var_idx<ppc_var_nbr;ppc_var_idx++){
if(!strcasecmp(ppc_lst[ppc_var_idx].key,"default")){
nco_ppc_set_dflt(nc_id,ppc_lst[ppc_var_idx].val,trv_tbl);
break; /* Only one default is needed */
} /* endif */
} /* end for */
/* Set explicit, non-default PPCs that can overwrite default */
for(ppc_var_idx=0;ppc_var_idx<ppc_var_nbr;ppc_var_idx++){
if(!strcasecmp(ppc_lst[ppc_var_idx].key,"default")) continue;
nco_ppc_set_var(ppc_lst[ppc_var_idx].key,ppc_lst[ppc_var_idx].val,trv_tbl);
} /* end for */
/* Unset PPC and flag for all variables with excessive PPC
Operational definition of maximum PPC is maximum decimal precision of float/double = FLT_DIG/DBL_DIG = 7/15 */
const int nco_max_ppc_dbl=15;
const int nco_max_ppc_flt=7;
/* Maximum digits for integers taken based on LONG_MAX ... from limits.h */
const int nco_max_ppc_short=5;
const int nco_max_ppc_ushort=5;
const int nco_max_ppc_int=10;
const int nco_max_ppc_uint=10;
const int nco_max_ppc_int64=19;
const int nco_max_ppc_uint64=20;
int nco_max_ppc=int_CEWI;
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
if(trv_tbl->lst[idx_tbl].ppc != NC_MAX_INT){
switch(trv_tbl->lst[idx_tbl].var_typ){
case NC_FLOAT: nco_max_ppc=nco_max_ppc_flt; break;
case NC_DOUBLE: nco_max_ppc=nco_max_ppc_dbl; break;
case NC_SHORT: nco_max_ppc=nco_max_ppc_short; break;
case NC_USHORT: nco_max_ppc=nco_max_ppc_ushort; break;
case NC_INT: nco_max_ppc=nco_max_ppc_int; break;
case NC_UINT: nco_max_ppc=nco_max_ppc_uint; break;
case NC_INT64: nco_max_ppc=nco_max_ppc_int64; break;
case NC_UINT64: nco_max_ppc=nco_max_ppc_uint64; break;
/* Do nothing for non-numeric types ...*/
case NC_CHAR:
case NC_BYTE:
case NC_UBYTE:
case NC_STRING: break;
default:
nco_dfl_case_nc_type_err();
break;
} /* end switch */
switch(trv_tbl->lst[idx_tbl].var_typ){
/* Floating point types */
case NC_FLOAT:
case NC_DOUBLE:
if(trv_tbl->lst[idx_tbl].ppc > nco_max_ppc){
if(trv_tbl->lst[idx_tbl].flg_nsd) (void)fprintf(stdout,"%s: INFO Number of Significant Digits (NSD) requested = %d too high for variable %s which is of type %s. No quantization or rounding will be performed for this variable. HINT: Maximum precisions for NC_FLOAT and NC_DOUBLE are %d and %d, respectively.\n",nco_prg_nm_get(),trv_tbl->lst[idx_tbl].ppc,trv_tbl->lst[idx_tbl].nm,nco_typ_sng(trv_tbl->lst[idx_tbl].var_typ),nco_max_ppc_flt,nco_max_ppc_dbl);
trv_tbl->lst[idx_tbl].ppc=NC_MAX_INT;
} /* endif */
break;
/* Integer types */
case NC_SHORT:
case NC_USHORT:
case NC_INT:
case NC_UINT:
case NC_INT64:
case NC_UINT64:
if(
/* ...rounding requested with NSD or ... */
(trv_tbl->lst[idx_tbl].flg_nsd) ||
/* ...more rounding requested with DSD than available or ... */
(!trv_tbl->lst[idx_tbl].flg_nsd && (trv_tbl->lst[idx_tbl].ppc < -1*nco_max_ppc)) ||
/* ...more precision requested than integers have or ... */
(!trv_tbl->lst[idx_tbl].flg_nsd && (trv_tbl->lst[idx_tbl].ppc >= 0)) ||
False)
trv_tbl->lst[idx_tbl].ppc=NC_MAX_INT;
break;
case NC_CHAR: /* Do nothing for non-numeric types ...*/
case NC_BYTE:
case NC_UBYTE:
case NC_STRING:
trv_tbl->lst[idx_tbl].ppc=NC_MAX_INT;
break;
default:
nco_dfl_case_nc_type_err();
break;
} /* end switch */
/* For consistency reset flg_nsd as well */
if(trv_tbl->lst[idx_tbl].ppc == NC_MAX_INT) trv_tbl->lst[idx_tbl].flg_nsd=True;
} /* endif */
} /* endfor */
if(ppc_lst) ppc_lst=nco_kvm_lst_free(ppc_lst,ppc_var_nbr);
} /* end nco_ppc_ini() */
int
main(int argc,char **argv)
{
aed_sct *aed_lst=NULL_CEWI;
char **fl_lst_abb=NULL; /* Option n */
char **fl_lst_in;
char **gaa_arg=NULL; /* [sng] Global attribute arguments */
char *aed_arg[NC_MAX_ATTRS];
char *cmd_ln;
char *fl_in=NULL;
char *fl_out=NULL; /* Option o */
char *fl_pth=NULL; /* Option p */
char *fl_pth_lcl=NULL; /* Option l */
char *opt_crr=NULL; /* [sng] String representation of current long-option name */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
const char * const CVS_Id="$Id$";
const char * const CVS_Revision="$Revision$";
const char * const opt_sht_lst="Aa:D:hl:Oo:p:Rr-:";
#if defined(__cplusplus) || defined(PGI_CC)
ddra_info_sct ddra_info;
ddra_info.flg_ddra=False;
#else /* !__cplusplus */
ddra_info_sct ddra_info={.flg_ddra=False};
#endif /* !__cplusplus */
extern char *optarg;
extern int optind;
int abb_arg_nbr=0;
int fl_nbr=0;
int gaa_nbr=0; /* [nbr] Number of global attributes to add */
int nbr_aed=0; /* Option a. NB: nbr_var_aed gets incremented */
int nbr_var_fl;
int nc_id;
int md_open; /* [enm] Mode flag for nc_open() call */
int opt;
int rcd=NC_NOERR; /* [rcd] Return code */
nco_bool FL_RTR_RMT_LCN;
nco_bool FL_LST_IN_FROM_STDIN=False; /* [flg] fl_lst_in comes from stdin */
nco_bool FORCE_APPEND=False; /* Option A */
nco_bool FORCE_OVERWRITE=False; /* Option O */
nco_bool HISTORY_APPEND=True; /* Option h */
nco_bool FL_OUT_NEW=False;
nco_bool RAM_OPEN=False; /* [flg] Open (netCDF3-only) file(s) in RAM */
nco_bool RM_RMT_FL_PST_PRC=True; /* Option R */
nco_bool flg_cln=False; /* [flg] Clean memory prior to exit */
size_t bfr_sz_hnt=NC_SIZEHINT_DEFAULT; /* [B] Buffer size hint */
size_t hdr_pad=0UL; /* [B] Pad at end of header section */
trv_tbl_sct *trv_tbl=NULL; /* [lst] Traversal table */
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
#ifdef ENABLE_MPI
/* Declare all MPI-specific variables here */
MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
int prc_rnk; /* [idx] Process rank */
int prc_nbr=0; /* [nbr] Number of MPI processes */
#endif /* !ENABLE_MPI */
static struct option opt_lng[]={ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
{"cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"clean",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"mmr_cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"dirty",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"mmr_drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"hdf4",no_argument,0,0}, /* [flg] Treat file as HDF4 */
{"ram_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"create_ram",no_argument,0,0}, /* [flg] Create file in RAM */
{"open_ram",no_argument,0,0}, /* [flg] Open (netCDF3) file(s) in RAM */
{"diskless_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"version",no_argument,0,0},
{"vrs",no_argument,0,0},
/* Long options with argument, no short option counterpart */
{"bfr_sz_hnt",required_argument,0,0}, /* [B] Buffer size hint */
{"buffer_size_hint",required_argument,0,0}, /* [B] Buffer size hint */
{"gaa",required_argument,0,0}, /* [sng] Global attribute add */
{"glb_att_add",required_argument,0,0}, /* [sng] Global attribute add */
{"hdr_pad",required_argument,0,0},
{"header_pad",required_argument,0,0},
/* Long options with short counterparts */
{"append",no_argument,0,'A'},
{"attribute",required_argument,0,'a'},
{"debug",required_argument,0,'D'},
{"nco_dbg_lvl",required_argument,0,'D'},
{"history",no_argument,0,'h'},
{"hst",no_argument,0,'h'},
{"local",required_argument,0,'l'},
{"lcl",required_argument,0,'l'},
{"overwrite",no_argument,0,'O'},
{"ovr",no_argument,0,'O'},
{"output",required_argument,0,'o'},
{"fl_out",required_argument,0,'o'},
{"path",required_argument,0,'p'},
{"retain",no_argument,0,'R'},
{"rtn",no_argument,0,'R'},
{"help",no_argument,0,'?'},
{"hlp",no_argument,0,'?'},
{0,0,0,0}
}; /* end opt_lng */
int opt_idx=0; /* Index of current long option into opt_lng array */
/* Start timer and save command line */
ddra_info.tmr_flg=nco_tmr_srt;
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_mtd;
cmd_ln=nco_cmd_ln_sng(argc,argv);
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
#ifdef ENABLE_MPI
/* MPI Initialization */
if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
MPI_Init(&argc,&argv);
MPI_Comm_size(mpi_cmm,&prc_nbr);
MPI_Comm_rank(mpi_cmm,&prc_rnk);
#endif /* !ENABLE_MPI */
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
opt=getopt_long(argc,argv,opt_sht_lst,opt_lng,&opt_idx);
/* NB: access to opt_crr is only valid when long_opt is detected */
if(opt == EOF) break; /* Parse positional arguments once getopt_long() returns EOF */
opt_crr=(char *)strdup(opt_lng[opt_idx].name);
/* Process long options without short option counterparts */
if(opt == 0){
if(!strcmp(opt_crr,"bfr_sz_hnt") || !strcmp(opt_crr,"buffer_size_hint")){
bfr_sz_hnt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cln") || !strcmp(opt_crr,"mmr_cln") || !strcmp(opt_crr,"clean")) flg_cln=True; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"drt") || !strcmp(opt_crr,"mmr_drt") || !strcmp(opt_crr,"dirty")) flg_cln=False; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"gaa") || !strcmp(opt_crr,"glb_att_add")){
gaa_arg=(char **)nco_realloc(gaa_arg,(gaa_nbr+1)*sizeof(char *));
gaa_arg[gaa_nbr++]=(char *)strdup(optarg);
} /* endif gaa */
if(!strcmp(opt_crr,"hdf4")) nco_fmt_xtn=nco_fmt_xtn_hdf4; /* [enm] Treat file as HDF4 */
if(!strcmp(opt_crr,"hdr_pad") || !strcmp(opt_crr,"header_pad")){
hdr_pad=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif "hdr_pad" */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"open_ram") || !strcmp(opt_crr,"diskless_all")) RAM_OPEN=True; /* [flg] Create file in RAM */
if(!strcmp(opt_crr,"vrs") || !strcmp(opt_crr,"version")){
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
nco_exit(EXIT_SUCCESS);
} /* endif "vrs" */
} /* opt != 0 */
/* Process short options */
switch(opt){
case 0: /* Long options have already been processed, return */
break;
case 'A': /* Toggle FORCE_APPEND */
FORCE_APPEND=!FORCE_APPEND;
break;
case 'a': /* Copy argument for later processing */
aed_arg[nbr_aed]=(char *)strdup(optarg);
nbr_aed++;
break;
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
nc_set_log_level(nco_dbg_lvl);
break;
case 'h': /* Toggle appending to history global attribute */
HISTORY_APPEND=!HISTORY_APPEND;
break;
case 'l': /* Local path prefix for files retrieved from remote file system */
fl_pth_lcl=(char *)strdup(optarg);
break;
case 'O': /* Toggle FORCE_OVERWRITE */
FORCE_OVERWRITE=!FORCE_OVERWRITE;
break;
case 'o': /* Name of output file */
fl_out=(char *)strdup(optarg);
break;
case 'p': /* Common file path */
fl_pth=(char *)strdup(optarg);
break;
case 'R': /* Toggle removal of remotely-retrieved-files. Default is True. */
RM_RMT_FL_PST_PRC=!RM_RMT_FL_PST_PRC;
break;
case 'r': /* Print CVS program information and copyright notice */
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
(void)nco_lbr_vrs_prn();
(void)nco_cpy_prn();
(void)nco_cnf_prn();
nco_exit(EXIT_SUCCESS);
break;
case '?': /* Print proper usage */
(void)nco_usg_prn();
nco_exit(EXIT_SUCCESS);
break;
case '-': /* Long options are not allowed */
(void)fprintf(stderr,"%s: ERROR Long options are not available in this build. Use single letter options instead.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
break;
default: /* Print proper usage */
(void)fprintf(stdout,"%s ERROR in command-line syntax/options. Please reformulate command accordingly.\n",nco_prg_nm_get());
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
} /* end switch */
if(opt_crr) opt_crr=(char *)nco_free(opt_crr);
} /* end while loop */
/* Process positional arguments and fill in filenames */
fl_lst_in=nco_fl_lst_mk(argv,argc,optind,&fl_nbr,&fl_out,&FL_LST_IN_FROM_STDIN);
if(fl_out) FL_OUT_NEW=True; else fl_out=(char *)strdup(fl_lst_in[0]);
if(nbr_aed == 0){
(void)fprintf(stdout,"%s: ERROR must specify an attribute to edit\n",nco_prg_nm);
nco_usg_prn();
nco_exit(EXIT_FAILURE);
} /* end if */
if(nco_dbg_lvl_get() >= nco_dbg_var) (void)fprintf(stdout,"%s: DEBUG attribute assumed to hold missing data is named \"%s\"\n",nco_prg_nm_get(),nco_mss_val_sng_get());
/* Make uniform list of user-specified attribute edit structures */
if(nbr_aed > 0) aed_lst=nco_prs_aed_lst(nbr_aed,aed_arg);
/* We now have final list of attributes to edit */
/* Parse filename */
fl_in=nco_fl_nm_prs(fl_in,0,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
/* Make sure file is on local system and is readable or die trying */
fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
if(FL_OUT_NEW){
/* Obtain user consent, if needed, to overwrite output file (or die trying) */
if(!FORCE_OVERWRITE) nco_fl_overwrite_prm(fl_out);
/* Copy input file to output file and then search through output,
changing names on the fly. This avoids possible XDR translation
performance penalty of copying each variable with netCDF. */
(void)nco_fl_cp(fl_in,fl_out);
/* Ensure output file is user/owner-writable */
(void)nco_fl_chmod(fl_out);
} /* end if FL_OUT_NEW */
/* Open file. Writing must be enabled and file should be in define mode for renaming */
/* if(nco_dbg_lvl == 8) md_open|=NC_SHARE;*/
if(RAM_OPEN) md_open=NC_WRITE|NC_DISKLESS; else md_open=NC_WRITE;
rcd+=nco_fl_open(fl_out,md_open,&bfr_sz_hnt,&nc_id);
(void)nco_redef(nc_id);
/* Get number of variables in file */
(void)nco_inq(nc_id,(int *)NULL,&nbr_var_fl,(int *)NULL,(int *)NULL);
/* Initialize traversal table */
trv_tbl_init(&trv_tbl);
/* Construct GTT (Group Traversal Table) */
(void)nco_bld_trv_tbl(nc_id,trv_pth,(int)0,NULL,(int)0,NULL,False,False,NULL,(int)0,NULL,(int) 0,False,False,False,False,True,nco_pck_plc_nil,&flg_dne,trv_tbl);
/* Timestamp end of metadata setup and disk layout */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_rgl;
for(int idx_aed=0;idx_aed<nbr_aed;idx_aed++){
if(!aed_lst[idx_aed].var_nm){
/* Variable name is blank so edit same attribute for all variables */
(void)nco_aed_prc_var_all(nc_id,aed_lst[idx_aed],trv_tbl);
}else if(strpbrk(aed_lst[idx_aed].var_nm,".*^$\\[]()<>+?|{}")){
/* Variable name contains a "regular expression" (rx) */
trv_tbl_sct *trv_tbl_rx;
char **var_lst_in; /* I [sng] User-specified list of variables */
int var_lst_in_nbr; /* I [nbr] Number of variables in list */
var_lst_in=nco_lst_prs_2D(aed_lst[idx_aed].var_nm,",",&var_lst_in_nbr);
trv_tbl_init(&trv_tbl_rx);
/* Use regular expressions in aed structure to construct traversal table
Variables marked for extraction will then have the attributes edited */
(void)nco_bld_trv_tbl(nc_id,trv_pth,(int)0,NULL,(int)0,NULL,False,False,NULL,(int)0,var_lst_in,var_lst_in_nbr,False,False,False,False,False,nco_pck_plc_nil,&flg_dne,trv_tbl_rx);
/* Edit same attribute for all variables marked for extraction */
(void)nco_aed_prc_var_xtr(nc_id,aed_lst[idx_aed],trv_tbl_rx);
trv_tbl_free(trv_tbl_rx);
var_lst_in=nco_sng_lst_free(var_lst_in,var_lst_in_nbr);
}else if(!strcasecmp(aed_lst[idx_aed].var_nm,"group")){
/* Variable name of "group" means edit group attributes */
(void)nco_aed_prc_grp(nc_id,aed_lst[idx_aed],trv_tbl);
}else if(!strcasecmp(aed_lst[idx_aed].var_nm,"global")){
/* Variable name of "global" means edit global attributes */
(void)nco_aed_prc_glb(nc_id,aed_lst[idx_aed],trv_tbl);
}else{
/* Regular ole' variable name means edits attributes that match absoluted and relative names */
(void)nco_aed_prc_var_nm(nc_id,aed_lst[idx_aed],trv_tbl);
} /* end var_nm */
} /* end loop over aed structures */
/* Catenate the time-stamped command line to the "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(nc_id,cmd_ln);
/* Take output file out of define mode */
if(hdr_pad == 0UL){
(void)nco_enddef(nc_id);
}else{
(void)nco__enddef(nc_id,hdr_pad);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: INFO Padding header with %lu extra bytes\n",nco_prg_nm_get(),(unsigned long)hdr_pad);
} /* hdr_pad */
/* Close the open netCDF file */
nco_close(nc_id);
/* Remove local copy of file */
if(FL_RTR_RMT_LCN && RM_RMT_FL_PST_PRC) (void)nco_fl_rm(fl_in);
/* Clean memory unless dirty memory allowed */
if(flg_cln){
/* ncatted-specific memory */
for(int idx=0;idx<nbr_aed;idx++) aed_arg[idx]=(char *)nco_free(aed_arg[idx]);
for(int idx=0;idx<nbr_aed;idx++){
if(aed_lst[idx].att_nm) aed_lst[idx].att_nm=(char *)nco_free(aed_lst[idx].att_nm);
if(aed_lst[idx].var_nm) aed_lst[idx].var_nm=(char *)nco_free(aed_lst[idx].var_nm);
aed_lst[idx].val.vp=(void *)nco_free(aed_lst[idx].val.vp);
} /* end for */
if(nbr_aed > 0) aed_lst=(aed_sct *)nco_free(aed_lst);
/* NCO-generic clean-up */
/* Free individual strings/arrays */
if(cmd_ln) cmd_ln=(char *)nco_free(cmd_ln);
if(fl_in) fl_in=(char *)nco_free(fl_in);
if(fl_out) fl_out=(char *)nco_free(fl_out);
if(fl_pth) fl_pth=(char *)nco_free(fl_pth);
if(fl_pth_lcl) fl_pth_lcl=(char *)nco_free(fl_pth_lcl);
/* Free lists of strings */
if(fl_lst_in && fl_lst_abb == NULL) fl_lst_in=nco_sng_lst_free(fl_lst_in,fl_nbr);
if(fl_lst_in && fl_lst_abb) fl_lst_in=nco_sng_lst_free(fl_lst_in,1);
if(fl_lst_abb) fl_lst_abb=nco_sng_lst_free(fl_lst_abb,abb_arg_nbr);
if(gaa_nbr > 0) gaa_arg=nco_sng_lst_free(gaa_arg,gaa_nbr);
trv_tbl_free(trv_tbl);
} /* !flg_cln */
#ifdef ENABLE_MPI
MPI_Finalize();
#endif /* !ENABLE_MPI */
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
nco_bool
nco_find_lat_lon_trv
(const int nc_id, /* I [ID] netCDF file ID */
const trv_sct * const var_trv, /* I [sct] Variable to search for "standard_name" attribute */
const char * const att_val_trg, /* I [sng] Attribute value to find ("latitude" or "longitude") */
char **var_nm_fll, /* I/O [sng] Full name of variable that has "latitude" or "longitude" attributes */
int *dmn_id, /* I/O [id] Dimension ID of "latitude" and "longitude" */
nc_type *crd_typ, /* I/O [enm] netCDF type of both "latitude" and "longitude" */
char units[]) /* I/O [sng] Units of both "latitude" and "longitude" */
{
/* Purpose: Find auxiliary coordinate variables that map to latitude/longitude
Find variables with standard_name = "latitude" and "longitude"
Return true if both latitude and longitude standard names are found
Also return needed information about these auxiliary coordinates
Assumes that units and types for latitude and longitude are identical
Caller responsible for memory management for variable names
Memory for unit strings must be freed by caller */
const char fnc_nm[]="nco_find_lat_lon_trv()";
char att_nm[NC_MAX_NAME]; /* [sng] Attribute name */
char var_nm[NC_MAX_NAME];
int grp_id; /* [id] Group ID */
int var_id; /* [id] Variable ID */
int var_dimid[NC_MAX_VAR_DIMS]; /* [enm] Dimension ID */
int var_att_nbr; /* [nbr] Number of attributes */
int var_dmn_nbr; /* [nbr] Number of dimensions */
nc_type var_typ; /* [enm] variable type */
assert(var_trv->nco_typ == nco_obj_typ_var);
/* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv->grp_nm_fll,&grp_id);
/* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_trv->nm,&var_id);
/* Find number of attributes */
(void)nco_inq_var(grp_id,var_id,var_nm,&var_typ,&var_dmn_nbr,var_dimid,&var_att_nbr);
assert(var_att_nbr == var_trv->nbr_att);
for(int idx_att=0;idx_att<var_att_nbr;idx_att++){
/* Skip attribute if not "standard_name" */
(void)nco_inq_attname(grp_id,var_id,idx_att,att_nm);
if(strcmp(att_nm,"standard_name")) continue;
char att_val[NC_MAX_NAME+1];
long att_lng;
(void)nco_inq_attlen(grp_id,var_id,"standard_name",&att_lng);
(void)NCO_GET_ATT_CHAR(grp_id,var_id,"standard_name",att_val);
att_val[att_lng]='\0';
/* Match parameter name to find ("latitude" or "longitude") */
if(!strcmp(att_val,att_val_trg)){
/* Assume same units (degrees or radians) for both lat and lon */
int rcd=nco_inq_attlen_flg(grp_id,var_id,"units",&att_lng);
if(rcd != NC_NOERR){
if(nco_dbg_lvl_get() >= nco_dbg_var) (void)fprintf(stdout,"%s: %s reports CF convention requires \"latitude\" to have units attribute\n",nco_prg_nm_get(),fnc_nm);
return False;
} /* endif */
NCO_GET_ATT_CHAR(grp_id,var_id,"units",units);
units[att_lng]='\0';
if(var_dmn_nbr > 1) (void)fprintf(stderr,"%s: WARNING %s reports latitude variable %s has %d dimensions. NCO only supports hyperslabbing of auxiliary coordinate variables with a single dimension. Continuing with unpredictable results...\n",nco_prg_nm_get(),fnc_nm,var_nm,var_dmn_nbr);
/* Copy values to export */
*var_nm_fll=(char *)strdup(var_trv->nm_fll);
*crd_typ=var_typ;
*dmn_id=var_dimid[0];
return True;
} /* strcmp() */
} /* end loop over attributes */
return False;
} /* end nco_find_lat_lon_trv() */
int
main(int argc,char **argv)
{
nco_bool CNV_CCM_CCSM_CF;
nco_bool CPY_GLB_METADATA=True; /* Option M */
nco_bool EXCLUDE_INPUT_LIST=False; /* Option c */
nco_bool EXTRACT_ALL_COORDINATES=False; /* Option c */
nco_bool EXTRACT_ASSOCIATED_COORDINATES=True; /* Option C */
nco_bool FL_RTR_RMT_LCN;
nco_bool FL_LST_IN_APPEND=True; /* Option H */
nco_bool FL_LST_IN_FROM_STDIN=False; /* [flg] fl_lst_in comes from stdin */
nco_bool FORCE_APPEND=False; /* Option A */
nco_bool FORCE_OVERWRITE=False; /* Option O */
nco_bool FORTRAN_IDX_CNV=False; /* Option F */
nco_bool GROUP_AGGREGATE=False; /* Option G */
nco_bool GRP_VAR_UNN=False; /* [flg] Select union of specified groups and variables */
nco_bool HISTORY_APPEND=True; /* Option h */
nco_bool HAVE_LIMITS=False; /* [flg] Are there user limits? (-d) */
nco_bool MSA_USR_RDR=False; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
nco_bool RAM_CREATE=False; /* [flg] Create file in RAM */
nco_bool RAM_OPEN=False; /* [flg] Open (netCDF3-only) file(s) in RAM */
nco_bool RM_RMT_FL_PST_PRC=True; /* Option R */
nco_bool USE_MM3_WORKAROUND=False; /* [flg] Faster copy on Multi-record Multi-variable netCDF3 files */
nco_bool WRT_TMP_FL=True; /* [flg] Write output to temporary file */
nco_bool RECORD_AGGREGATE=True; /* Option G */
nco_bool flg_cln=True; /* [flg] Clean memory prior to exit */
char **fl_lst_abb=NULL; /* Option a */
char **fl_lst_in;
char **gaa_arg=NULL; /* [sng] Global attribute arguments */
char **grp_lst_in=NULL;
char **var_lst_in=NULL_CEWI;
char *aux_arg[NC_MAX_DIMS];
char *cmd_ln;
char *cnk_arg[NC_MAX_DIMS];
char *cnk_map_sng=NULL_CEWI; /* [sng] Chunking map */
char *cnk_plc_sng=NULL_CEWI; /* [sng] Chunking policy */
char *fl_in=NULL;
char *fl_out=NULL; /* Option o */
char *fl_out_tmp;
char *fl_pth=NULL; /* Option p */
char *fl_pth_lcl=NULL; /* Option l */
char *gpe_arg=NULL; /* [sng] GPE argument */
char *grp_out=NULL; /* [sng] Group name */
char *lmt_arg[NC_MAX_DIMS];
char *opt_crr=NULL; /* [sng] String representation of current long-option name */
char *optarg_lcl=NULL; /* [sng] Local copy of system optarg */
char *ppc_arg[NC_MAX_VARS]; /* [sng] PPC arguments */
char *rec_dmn_nm=NULL; /* [sng] New record dimension name */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
/* NCO_GRP_OUT_SFX_LNG is number of consecutive numeric digits automatically generated as group name suffixes */
#define NCO_GRP_OUT_SFX_LNG 2
char grp_out_sfx[NCO_GRP_OUT_SFX_LNG+1L];
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
const char * const CVS_Id="$Id$";
const char * const CVS_Revision="$Revision$";
const char * const opt_sht_lst="3467ACcD:d:Fg:G:HhL:l:Mn:Oo:p:rRt:u:v:X:x-:";
cnk_sct cnk; /* [sct] Chunking structure */
#if defined(__cplusplus) || defined(PGI_CC)
ddra_info_sct ddra_info;
ddra_info.flg_ddra=False;
#else /* !__cplusplus */
ddra_info_sct ddra_info={.flg_ddra=False};
#endif /* !__cplusplus */
extern char *optarg;
extern int optind;
/* Using naked stdin/stdout/stderr in parallel region generates warning
Copy appropriate filehandle to variable scoped shared in parallel clause */
FILE * const fp_stderr=stderr; /* [fl] stderr filehandle CEWI */
FILE *fp_bnr=NULL; /* [fl] Unformatted binary output file handle */
gpe_sct *gpe=NULL; /* [sng] Group Path Editing (GPE) structure */
int *in_id_arr=NULL;
int abb_arg_nbr=0;
int aux_nbr=0; /* [nbr] Number of auxiliary coordinate hyperslabs specified */
int cnk_map=nco_cnk_map_nil; /* [enm] Chunking map */
int cnk_nbr=0; /* [nbr] Number of chunk sizes */
int cnk_plc=nco_cnk_plc_nil; /* [enm] Chunking policy */
int dfl_lvl=NCO_DFL_LVL_UNDEFINED; /* [enm] Deflate level */
int fl_idx;
int fl_nbr=0;
int fl_in_fmt; /* [enm] Input file format */
int fl_out_fmt=NCO_FORMAT_UNDEFINED; /* [enm] Output file format */
int fll_md_old; /* [enm] Old fill mode */
int gaa_nbr=0; /* [nbr] Number of global attributes to add */
int gpe_id; /* [id] Group ID of GPE path (diagnostic only) */
int grp_lst_in_nbr=0; /* [nbr] Number of groups explicitly specified by user */
int idx;
int in_id;
int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */
int lmt_nbr_rgn=0; /* Option d. Original limit number for GTT initialization */
int md_open; /* [enm] Mode flag for nc_open() call */
int nbr_dmn_fl;
int nbr_var_fix; /* nbr_var_fix gets incremented */
int nbr_var_fl;
int nbr_var_prc; /* nbr_var_prc gets incremented */
int xtr_nbr=0; /* xtr_nbr won't otherwise be set for -c with no -v */
int opt;
int out_id;
int ppc_nbr=0; /* [nbr] Number of PPC arguments */
int rcd=NC_NOERR; /* [rcd] Return code */
int thr_idx; /* [idx] Index of current thread */
int thr_nbr=int_CEWI; /* [nbr] Thread number Option t */
int var_idx;
int var_lst_in_nbr=0;
long idx_rec_out=0L; /* idx_rec_out gets incremented */
md5_sct *md5=NULL; /* [sct] MD5 configuration */
size_t bfr_sz_hnt=NC_SIZEHINT_DEFAULT; /* [B] Buffer size hint */
size_t cnk_min_byt=NCO_CNK_SZ_MIN_BYT_DFL; /* [B] Minimize size of variable to chunk */
size_t cnk_sz_byt=0UL; /* [B] Chunk size in bytes */
size_t cnk_sz_scl=0UL; /* [nbr] Chunk size scalar */
size_t grp_out_lng; /* [nbr] Length of original, canonicalized GPE specification filename component */
size_t hdr_pad=0UL; /* [B] Pad at end of header section */
var_sct **var=NULL;
var_sct **var_fix;
var_sct **var_fix_out;
var_sct **var_out=NULL;
var_sct **var_prc;
var_sct **var_prc_out;
trv_tbl_sct *trv_tbl=NULL; /* [lst] Traversal table */
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
#ifdef ENABLE_MPI
/* Declare all MPI-specific variables here */
MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
int prc_rnk; /* [idx] Process rank */
int prc_nbr=0; /* [nbr] Number of MPI processes */
#endif /* !ENABLE_MPI */
static struct option opt_lng[]={ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
{"cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"clean",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"mmr_cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"dirty",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"mmr_drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"gag",no_argument,0,0}, /* [flg] Group aggregation */
{"aggregate_group",no_argument,0,0}, /* [flg] Group aggregation */
{"hdf4",no_argument,0,0}, /* [flg] Treat file as HDF4 */
{"md5_dgs",no_argument,0,0}, /* [flg] Perform MD5 digests */
{"md5_digest",no_argument,0,0}, /* [flg] Perform MD5 digests */
{"mrd",no_argument,0,0}, /* [enm] Multiple Record Dimension convention */
{"multiple_record_dimension",no_argument,0,0}, /* [enm] Multiple Record Dimension convention */
{"msa_usr_rdr",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"msa_user_order",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"ram_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"create_ram",no_argument,0,0}, /* [flg] Create file in RAM */
{"open_ram",no_argument,0,0}, /* [flg] Open (netCDF3) file(s) in RAM */
{"diskless_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"wrt_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"write_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"no_tmp_fl",no_argument,0,0}, /* [flg] Do not write output to temporary file */
{"intersection",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"nsx",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"union",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"unn",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"version",no_argument,0,0},
{"vrs",no_argument,0,0},
/* Long options with argument, no short option counterpart */
{"bfr_sz_hnt",required_argument,0,0}, /* [B] Buffer size hint */
{"buffer_size_hint",required_argument,0,0}, /* [B] Buffer size hint */
{"cnk_byt",required_argument,0,0}, /* [B] Chunk size in bytes */
{"chunk_byte",required_argument,0,0}, /* [B] Chunk size in bytes */
{"cnk_dmn",required_argument,0,0}, /* [nbr] Chunk size */
{"chunk_dimension",required_argument,0,0}, /* [nbr] Chunk size */
{"cnk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"chunk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"cnk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"chunk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"cnk_plc",required_argument,0,0}, /* [nbr] Chunking policy */
{"chunk_policy",required_argument,0,0}, /* [nbr] Chunking policy */
{"cnk_scl",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"chunk_scalar",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"fl_fmt",required_argument,0,0},
{"file_format",required_argument,0,0},
{"gaa",required_argument,0,0}, /* [sng] Global attribute add */
{"glb_att_add",required_argument,0,0}, /* [sng] Global attribute add */
{"hdr_pad",required_argument,0,0},
{"header_pad",required_argument,0,0},
{"ppc",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"precision_preserving_compression",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"quantize",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
/* Long options with short counterparts */
{"3",no_argument,0,'3'},
{"4",no_argument,0,'4'},
{"64bit",no_argument,0,'4'},
{"netcdf4",no_argument,0,'4'},
{"append",no_argument,0,'A'},
{"coords",no_argument,0,'c'},
{"crd",no_argument,0,'c'},
{"no-coords",no_argument,0,'C'},
{"no-crd",no_argument,0,'C'},
{"debug",required_argument,0,'D'},
{"nco_dbg_lvl",required_argument,0,'D'},
{"dimension",required_argument,0,'d'},
{"dmn",required_argument,0,'d'},
{"fortran",no_argument,0,'F'},
{"ftn",no_argument,0,'F'},
{"gpe",required_argument,0,'G'}, /* [sng] Group Path Edit (GPE) */
{"group",required_argument,0,'g'},
{"grp",required_argument,0,'g'},
{"fl_lst_in",no_argument,0,'H'},
{"file_list",no_argument,0,'H'},
{"history",no_argument,0,'h'},
{"hst",no_argument,0,'h'},
{"dfl_lvl",required_argument,0,'L'}, /* [enm] Deflate level */
{"deflate",required_argument,0,'L'}, /* [enm] Deflate level */
{"local",required_argument,0,'l'},
{"lcl",required_argument,0,'l'},
{"no_glb_mtd",no_argument,0,'M'},
{"suppress_global_metadata",no_argument,0,'M'},
{"nintap",required_argument,0,'n'},
{"overwrite",no_argument,0,'O'},
{"ovr",no_argument,0,'O'},
{"output",required_argument,0,'o'},
{"fl_out",required_argument,0,'o'},
{"path",required_argument,0,'p'},
{"retain",no_argument,0,'R'},
{"rtn",no_argument,0,'R'},
{"revision",no_argument,0,'r'},
{"thr_nbr",required_argument,0,'t'},
{"threads",required_argument,0,'t'},
{"omp_num_threads",required_argument,0,'t'},
{"ulm_nm",required_argument,0,'u'},
{"rcd_nm",required_argument,0,'u'},
{"variable",required_argument,0,'v'},
{"auxiliary",required_argument,0,'X'},
{"exclude",no_argument,0,'x'},
{"xcl",no_argument,0,'x'},
{"help",no_argument,0,'?'},
{"hlp",no_argument,0,'?'},
{0,0,0,0}
}; /* end opt_lng */
int opt_idx=0; /* Index of current long option into opt_lng array */
/* Start timer and save command line */
ddra_info.tmr_flg=nco_tmr_srt;
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_mtd;
cmd_ln=nco_cmd_ln_sng(argc,argv);
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
#ifdef ENABLE_MPI
/* MPI Initialization */
if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
MPI_Init(&argc,&argv);
MPI_Comm_size(mpi_cmm,&prc_nbr);
MPI_Comm_rank(mpi_cmm,&prc_rnk);
#endif /* !ENABLE_MPI */
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
opt=getopt_long(argc,argv,opt_sht_lst,opt_lng,&opt_idx);
/* NB: access to opt_crr is only valid when long_opt is detected */
if(opt == EOF) break; /* Parse positional arguments once getopt_long() returns EOF */
opt_crr=(char *)strdup(opt_lng[opt_idx].name);
/* Process long options without short option counterparts */
if(opt == 0){
if(!strcmp(opt_crr,"bfr_sz_hnt") || !strcmp(opt_crr,"buffer_size_hint")){
bfr_sz_hnt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_byt") || !strcmp(opt_crr,"chunk_byte")){
cnk_sz_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_byt */
if(!strcmp(opt_crr,"cnk_min") || !strcmp(opt_crr,"chunk_min")){
cnk_min_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_min */
if(!strcmp(opt_crr,"cnk_dmn") || !strcmp(opt_crr,"chunk_dimension")){
/* Copy limit argument for later processing */
cnk_arg[cnk_nbr]=(char *)strdup(optarg);
cnk_nbr++;
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_scl") || !strcmp(opt_crr,"chunk_scalar")){
cnk_sz_scl=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_map") || !strcmp(opt_crr,"chunk_map")){
/* Chunking map */
cnk_map_sng=(char *)strdup(optarg);
cnk_map=nco_cnk_map_get(cnk_map_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_plc") || !strcmp(opt_crr,"chunk_policy")){
/* Chunking policy */
cnk_plc_sng=(char *)strdup(optarg);
cnk_plc=nco_cnk_plc_get(cnk_plc_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cln") || !strcmp(opt_crr,"mmr_cln") || !strcmp(opt_crr,"clean")) flg_cln=True; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"drt") || !strcmp(opt_crr,"mmr_drt") || !strcmp(opt_crr,"dirty")) flg_cln=False; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"fl_fmt") || !strcmp(opt_crr,"file_format")) rcd=nco_create_mode_prs(optarg,&fl_out_fmt);
if(!strcmp(opt_crr,"gaa") || !strcmp(opt_crr,"glb_att_add")){
gaa_arg=(char **)nco_realloc(gaa_arg,(gaa_nbr+1)*sizeof(char *));
gaa_arg[gaa_nbr++]=(char *)strdup(optarg);
} /* endif gaa */
if(!strcmp(opt_crr,"gag") || !strcmp(opt_crr,"aggregate_group")) GROUP_AGGREGATE=True; /* [flg] Aggregate files into groups not records */
if(!strcmp(opt_crr,"hdf4")) nco_fmt_xtn=nco_fmt_xtn_hdf4; /* [enm] Treat file as HDF4 */
if(!strcmp(opt_crr,"hdr_pad") || !strcmp(opt_crr,"header_pad")){
hdr_pad=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif "hdr_pad" */
if(!strcmp(opt_crr,"md5_dgs") || !strcmp(opt_crr,"md5_digest")){
if(!md5) md5=nco_md5_ini();
md5->dgs=True;
if(nco_dbg_lvl >= nco_dbg_std) (void)fprintf(stderr,"%s: INFO Will perform MD5 digests of input and output hyperslabs\n",nco_prg_nm_get());
} /* endif "md5_dgs" */
if(!strcmp(opt_crr,"mrd") || !strcmp(opt_crr,"multiple_record_dimension")) nco_mrd_cnv=nco_mrd_allow; /* [enm] Multiple Record Dimension convention */
if(!strcmp(opt_crr,"msa_usr_rdr") || !strcmp(opt_crr,"msa_user_order")) MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
if(!strcmp(opt_crr,"ppc") || !strcmp(opt_crr,"precision_preserving_compression") || !strcmp(opt_crr,"quantize")){
ppc_arg[ppc_nbr]=(char *)strdup(optarg);
ppc_nbr++;
} /* endif "ppc" */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"create_ram") || !strcmp(opt_crr,"diskless_all")) RAM_CREATE=True; /* [flg] Open (netCDF3) file(s) in RAM */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"open_ram") || !strcmp(opt_crr,"diskless_all")) RAM_OPEN=True; /* [flg] Create file in RAM */
if(!strcmp(opt_crr,"unn") || !strcmp(opt_crr,"union")) GRP_VAR_UNN=True;
if(!strcmp(opt_crr,"nsx") || !strcmp(opt_crr,"intersection")) GRP_VAR_UNN=False;
if(!strcmp(opt_crr,"vrs") || !strcmp(opt_crr,"version")){
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
nco_exit(EXIT_SUCCESS);
} /* endif "vrs" */
if(!strcmp(opt_crr,"wrt_tmp_fl") || !strcmp(opt_crr,"write_tmp_fl")) WRT_TMP_FL=True;
if(!strcmp(opt_crr,"no_tmp_fl")) WRT_TMP_FL=False;
} /* opt != 0 */
/* Process short options */
switch(opt){
case 0: /* Long options have already been processed, return */
break;
case '3': /* Request netCDF3 output storage format */
fl_out_fmt=NC_FORMAT_CLASSIC;
break;
case '4': /* Catch-all to prescribe output storage format */
if(!strcmp(opt_crr,"64bit")) fl_out_fmt=NC_FORMAT_64BIT; else fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case '6': /* Request netCDF3 64-bit offset output storage format */
fl_out_fmt=NC_FORMAT_64BIT;
break;
case '7': /* Request netCDF4-classic output storage format */
fl_out_fmt=NC_FORMAT_NETCDF4_CLASSIC;
break;
case 'A': /* Toggle FORCE_APPEND */
FORCE_APPEND=!FORCE_APPEND;
break;
case 'C': /* Extract all coordinates associated with extracted variables? */
EXTRACT_ASSOCIATED_COORDINATES=False;
break;
case 'c':
EXTRACT_ALL_COORDINATES=True;
break;
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
lmt_nbr++;
lmt_nbr_rgn=lmt_nbr;
HAVE_LIMITS=True;
break;
case 'F': /* Toggle index convention. Default is 0-based arrays (C-style). */
FORTRAN_IDX_CNV=!FORTRAN_IDX_CNV;
break;
case 'G': /* Apply Group Path Editing (GPE) to output group */
/* NB: GNU getopt() optional argument syntax is ugly (requires "=" sign) so avoid it
http://stackoverflow.com/questions/1052746/getopt-does-not-parse-optional-arguments-to-parameters */
gpe=nco_gpe_prs_arg(optarg);
grp_out=(char *)strdup(gpe->nm_cnn); /* [sng] Group name */
grp_out_lng=gpe->lng_cnn;
GROUP_AGGREGATE=True;
break;
case 'g': /* Copy group argument for later processing */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
grp_lst_in=nco_lst_prs_2D(optarg_lcl,",",&grp_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
break;
case 'H': /* Toggle writing input file list attribute */
FL_LST_IN_APPEND=!FL_LST_IN_APPEND;
break;
case 'h': /* Toggle appending to history global attribute */
HISTORY_APPEND=!HISTORY_APPEND;
break;
case 'L': /* [enm] Deflate level. Default is 0. */
dfl_lvl=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'l': /* Local path prefix for files retrieved from remote file system */
fl_pth_lcl=(char *)strdup(optarg);
break;
case 'M': /* Toggle copying global metadata */
CPY_GLB_METADATA=!CPY_GLB_METADATA;
break;
case 'n': /* NINTAP-style abbreviation of files to process */
fl_lst_abb=nco_lst_prs_2D(optarg,",",&abb_arg_nbr);
if(abb_arg_nbr < 1 || abb_arg_nbr > 6){
(void)fprintf(stdout,"%s: ERROR Incorrect abbreviation for file list\n",nco_prg_nm);
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
} /* end if */
break;
case 'O': /* Toggle FORCE_OVERWRITE */
FORCE_OVERWRITE=!FORCE_OVERWRITE;
break;
case 'o': /* Name of output file */
fl_out=(char *)strdup(optarg);
break;
case 'p': /* Common file path */
fl_pth=(char *)strdup(optarg);
break;
case 'R': /* Toggle removal of remotely-retrieved-files. Default is True. */
RM_RMT_FL_PST_PRC=!RM_RMT_FL_PST_PRC;
break;
case 'r': /* Print CVS program information and copyright notice */
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
(void)nco_lbr_vrs_prn();
(void)nco_cpy_prn();
(void)nco_cnf_prn();
nco_exit(EXIT_SUCCESS);
break;
case 't': /* Thread number */
thr_nbr=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'u': /* New record dimension name */
rec_dmn_nm=(char *)strdup(optarg);
break;
case 'v': /* Variables to extract/exclude */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
var_lst_in=nco_lst_prs_2D(optarg_lcl,",",&var_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
xtr_nbr=var_lst_in_nbr;
break;
case 'X': /* Copy auxiliary coordinate argument for later processing */
aux_arg[aux_nbr]=(char *)strdup(optarg);
aux_nbr++;
MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
break;
case 'x': /* Exclude rather than extract variables specified with -v */
EXCLUDE_INPUT_LIST=True;
break;
case '?': /* Print proper usage */
(void)nco_usg_prn();
nco_exit(EXIT_SUCCESS);
break;
case '-': /* Long options are not allowed */
(void)fprintf(stderr,"%s: ERROR Long options are not available in this build. Use single letter options instead.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
break;
default: /* Print proper usage */
(void)fprintf(stdout,"%s ERROR in command-line syntax/options. Please reformulate command accordingly.\n",nco_prg_nm_get());
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
break;
} /* end switch */
if(opt_crr) opt_crr=(char *)nco_free(opt_crr);
} /* end while loop */
trv_tbl_init(&trv_tbl);
if(GROUP_AGGREGATE){
RECORD_AGGREGATE=!GROUP_AGGREGATE;
fl_out_fmt=NC_FORMAT_NETCDF4;
} /* !GROUP_AGGREGATE */
/* Process positional arguments and fill in filenames */
fl_lst_in=nco_fl_lst_mk(argv,argc,optind,&fl_nbr,&fl_out,&FL_LST_IN_FROM_STDIN);
/* Parse filename */
fl_in=nco_fl_nm_prs(fl_in,0,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
/* Make sure file is on local system and is readable or die trying */
fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
if(RAM_OPEN) md_open=NC_NOWRITE|NC_DISKLESS; else md_open=NC_NOWRITE;
/* Open file using appropriate buffer size hints and verbosity */
rcd+=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,&in_id);
(void)nco_inq_format(in_id,&fl_in_fmt);
if(RECORD_AGGREGATE){
/* Initialize thread information */
thr_nbr=nco_openmp_ini(thr_nbr);
in_id_arr=(int *)nco_malloc(thr_nbr*sizeof(int));
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
/* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Get number of variables, dimensions, and global attributes in file, file format */
(void)trv_tbl_inq((int *)NULL,(int *)NULL,(int *)NULL,&nbr_dmn_fl,(int *)NULL,(int *)NULL,(int *)NULL,(int *)NULL,&nbr_var_fl,trv_tbl);
/* Fill-in variable structure list for all extracted variables */
var=nco_fll_var_trv(in_id,&xtr_nbr,trv_tbl);
var_out=(var_sct **)nco_malloc(xtr_nbr*sizeof(var_sct *));
for(var_idx=0;var_idx<xtr_nbr;var_idx++) var_out[var_idx]=nco_var_dpl(var[var_idx]);
/* Is this a CCM/CCSM/CF-format history tape? */
CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(in_id);
/* Divide variable lists into lists of fixed variables and variables to be processed */
(void)nco_var_lst_dvd(var,var_out,xtr_nbr,CNV_CCM_CCSM_CF,True,nco_pck_plc_nil,nco_pck_map_nil,(dmn_sct **)NULL,0,&var_fix,&var_fix_out,&nbr_var_fix,&var_prc,&var_prc_out,&nbr_var_prc,trv_tbl);
/* Store processed and fixed variables info into GTT */
(void)nco_var_prc_fix_trv(nbr_var_prc,var_prc,nbr_var_fix,var_fix,trv_tbl);
} /* !RECORD_AGGREGATE */
/* Make output and input files consanguinous */
if(fl_out_fmt == NCO_FORMAT_UNDEFINED) fl_out_fmt=fl_in_fmt;
/* Initialize, decode, and set PPC information */
if(ppc_nbr > 0) nco_ppc_ini(in_id,&dfl_lvl,fl_out_fmt,ppc_arg,ppc_nbr,trv_tbl);
/* Verify output file format supports requested actions */
(void)nco_fl_fmt_vet(fl_out_fmt,cnk_nbr,dfl_lvl);
/* Open output file */
fl_out_tmp=nco_fl_out_open(fl_out,FORCE_APPEND,FORCE_OVERWRITE,fl_out_fmt,&bfr_sz_hnt,RAM_CREATE,RAM_OPEN,WRT_TMP_FL,&out_id);
/* Initialize chunking from user-specified inputs */
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC) rcd+=nco_cnk_ini(in_id,fl_out,cnk_arg,cnk_nbr,cnk_map,cnk_plc,cnk_min_byt,cnk_sz_byt,cnk_sz_scl,&cnk);
/* ncecat-specific operations */
if(RECORD_AGGREGATE){
if(!rec_dmn_nm) rec_dmn_nm=(char *)strdup("record");
/* Prepend record dimension to beginning of all vectors for processed variables */
for(idx=0;idx<nbr_var_prc;idx++){
var_prc_out[idx]->nbr_dim++;
var_prc_out[idx]->is_rec_var=True;
var_prc_out[idx]->sz_rec=var_prc_out[idx]->sz;
/* Allocate space to hold dimension IDs */
var_prc_out[idx]->dim=(dmn_sct **)nco_realloc(var_prc_out[idx]->dim,var_prc_out[idx]->nbr_dim*sizeof(dmn_sct *));
var_prc_out[idx]->dmn_id=(int *)nco_realloc(var_prc_out[idx]->dmn_id,var_prc_out[idx]->nbr_dim*sizeof(int));
var_prc_out[idx]->cnt=(long *)nco_realloc(var_prc_out[idx]->cnt,var_prc_out[idx]->nbr_dim*sizeof(long int));
var_prc_out[idx]->end=(long *)nco_realloc(var_prc_out[idx]->end,var_prc_out[idx]->nbr_dim*sizeof(long int));
var_prc_out[idx]->srd=(long *)nco_realloc(var_prc_out[idx]->srd,var_prc_out[idx]->nbr_dim*sizeof(long int));
var_prc_out[idx]->srt=(long *)nco_realloc(var_prc_out[idx]->srt,var_prc_out[idx]->nbr_dim*sizeof(long int));
/* Moves current array by one to make room for new record dimension info */
(void)memmove((void *)(var_prc_out[idx]->dim+1),(void *)(var_prc_out[idx]->dim),(var_prc_out[idx]->nbr_dim-1)*sizeof(dmn_sct *));
(void)memmove((void *)(var_prc_out[idx]->dmn_id+1),(void *)(var_prc_out[idx]->dmn_id),(var_prc_out[idx]->nbr_dim-1)*sizeof(int));
(void)memmove((void *)(var_prc_out[idx]->cnt+1L),(void *)(var_prc_out[idx]->cnt),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
(void)memmove((void *)(var_prc_out[idx]->end+1L),(void *)(var_prc_out[idx]->end),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
(void)memmove((void *)(var_prc_out[idx]->srd+1L),(void *)(var_prc_out[idx]->srd),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
(void)memmove((void *)(var_prc_out[idx]->srt+1L),(void *)(var_prc_out[idx]->srt),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
/* Insert value for new record dimension */
var_prc_out[idx]->cnt[0]=1L;
var_prc_out[idx]->end[0]=-1L;
var_prc_out[idx]->srd[0]=-1L;
var_prc_out[idx]->srt[0]=-1L;
} /* end loop over idx */
/* Define dimensions, extracted groups, variables, and attributes in output file */
(void)nco_xtr_dfn(in_id,out_id,&cnk,dfl_lvl,gpe,md5,!FORCE_APPEND,True,False,nco_pck_plc_nil,rec_dmn_nm,trv_tbl);
/* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(HISTORY_APPEND && FORCE_APPEND) (void)nco_prv_att_cat(fl_in,in_id,out_id);
if(gaa_nbr > 0) (void)nco_glb_att_add(out_id,gaa_arg,gaa_nbr);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
/* Add input file list global attribute */
if(FL_LST_IN_APPEND && HISTORY_APPEND && FL_LST_IN_FROM_STDIN) (void)nco_fl_lst_att_cat(out_id,fl_lst_in,fl_nbr);
if(thr_nbr > 0 && HISTORY_APPEND) (void)nco_thr_att_cat(out_id,thr_nbr);
/* Turn-off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
/* Take output file out of define mode */
if(hdr_pad == 0UL){
(void)nco_enddef(out_id);
}else{
(void)nco__enddef(out_id,hdr_pad);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: INFO Padding header with %lu extra bytes\n",nco_prg_nm_get(),(unsigned long)hdr_pad);
} /* hdr_pad */
/* Assign zero to start and unity to stride vectors in output variables */
(void)nco_var_srd_srt_set(var_out,xtr_nbr);
/* Copy variable data for non-processed variables */
(void)nco_cpy_fix_var_trv(in_id,out_id,gpe,trv_tbl);
/* Close first input netCDF file */
(void)nco_close(in_id);
/* Timestamp end of metadata setup and disk layout */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_rgl;
} /* !RECORD_AGGREGATE */
if(GROUP_AGGREGATE){
#ifndef ENABLE_NETCDF4
(void)fprintf(stderr,"%s: ERROR GAG requires netCDF4 capabilities. HINT: Rebuild NCO with netCDF4 enabled.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
#endif /* ENABLE_NETCDF4 */
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"%s: INFO Group Aggregation (GAG) feature enabled\n",nco_prg_nm_get());
if(fl_out_fmt != NC_FORMAT_NETCDF4){
(void)fprintf(stderr,"%s: ERROR Group Aggregation requires netCDF4 output format but user explicitly requested format = %s\n",nco_prg_nm_get(),nco_fmt_sng(fl_out_fmt));
nco_exit(EXIT_FAILURE);
} /* endif err */
} /* !GROUP_AGGREGATE */
/* Loop over input files */
for(fl_idx=0;fl_idx<fl_nbr;fl_idx++){
/* Parse filename */
if(fl_idx) fl_in=nco_fl_nm_prs(fl_in,fl_idx,(int *)NULL,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"%s: INFO Input file %d is %s",nco_prg_nm_get(),fl_idx,fl_in);
/* Make sure file is on local system and is readable or die trying */
if(fl_idx) fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
if(nco_dbg_lvl >= nco_dbg_fl && FL_RTR_RMT_LCN) (void)fprintf(stderr,", local file is %s",fl_in);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"\n");
if(GROUP_AGGREGATE){
size_t gpe_arg_lng; /* [nbr] Length of group specification */
if(grp_out){
/* Append enumerated counter to end of user-specified root group path */
sprintf(grp_out_sfx,"%02d",fl_idx);
gpe_arg_lng=grp_out_lng+NCO_GRP_OUT_SFX_LNG+gpe->lng_edt;
gpe_arg=(char *)nco_malloc((gpe_arg_lng+1L)*sizeof(char));
(void)strcpy(gpe_arg,grp_out);
(void)strcat(gpe_arg,grp_out_sfx);
if(gpe->edt) (void)strcat(gpe_arg,gpe->edt);
}else{
/* Use filename stub as group name */
char *stb_srt_psn; /* [sng] Starting position of "stub", i.e., last component of filename */
size_t fl_in_lng; /* [nbr] Length of filename */
size_t sfx_fst; /* [nbr] Offset of suffix from start of string */
size_t sfx_lng; /* [nbr] Suffix has this many characters */
/* Is there a .nc, .cdf, .nc3, or .nc4 suffix? or an .hdf, .HDF, .h5, .H5, or .he5 suffix? */
fl_in_lng=strlen(fl_in);
sfx_lng=3L;
sfx_fst=fl_in_lng-sfx_lng;
/* Sample data found in, e.g., ftp://ftp.unidata.ucar.edu/pub/netcdf/sample_data and http://hdfeos.org/zoo
Two versions of HDF-EOS exist: HDF-EOS2 for HDF4, and HDF-EOS5 for HDF5 */
if(strncmp(fl_in+sfx_fst,".nc",sfx_lng) && /* netCDF standard suffix */
strncmp(fl_in+sfx_fst,".H5",sfx_lng) && /* HDF5 suffix used by ICESat GLAS, e.g., GLAH05_633_2103_001_1107_3_01_0001.H5 */
strncmp(fl_in+sfx_fst,".h5",sfx_lng)){ /* HDF5 suffix used by BUV, ICESat GLAS, MABEL, MEaSUREs Ozone, SBUV, e.g., BUV-Nimbus04_L3zm_v01-00-2012m0203t144121.h5, GLAH13_633_2103_001_1317_0_01_0001.h5, mabel_l2_20130927t201800_008_1.h5, MSO3L3zm5_v01-02-2013m0907t142428.h5 */
sfx_lng=4L;
sfx_fst=fl_in_lng-sfx_lng;
if(strncmp(fl_in+sfx_fst,".cdf",sfx_lng) && /* netCDF old-fashioned suffix */
strncmp(fl_in+sfx_fst,".hdf",sfx_lng) && /* HDF-EOS2 (HDF4) suffix used by AIRS, AMSR-E, MODIS, MOPPITT, SeaWiFS, e.g., AIRS.2002.08.01.L3.RetStd_H031.v4.0.21.0.G06104133732.hdf, MSR_E_L2_Rain_V10_200905312326_A.hdf, MOD10CM.A2007001.005.2007108111758.hdf, MOP01-20121231-L1V3.34.10.hdf, S1999001.L3m_DAY_CDOM_cdom_index_9km.hdf */
strncmp(fl_in+sfx_fst,".HDF",sfx_lng) && /* HDF-EOS2 (HDF4) suffix used by TRMM, e.g., 3B43.070901.6A.HDF */
strncmp(fl_in+sfx_fst,".he5",sfx_lng) && /* HDF-EOS5 (HDF5) suffix used by HIRDLS, OMI Aerosols, e.g., HIRDLS-Aura_L3ZAD_v06-00-00-c02_2005d022-2008d077.he5, OMI-Aura_L2-OMAERUV_2013m1004t2338-o49057_v003-2013m1005t053932.he5 */
strncmp(fl_in+sfx_fst,".nc3",sfx_lng) && /* netCDF3 variant suffix */
strncmp(fl_in+sfx_fst,".nc4",sfx_lng)){ /* netCDF4 variant suffix */
(void)fprintf(stderr,"%s: WARNING GAG filename suffix is unusual---using whole filename as group name\n",nco_prg_nm_get());
sfx_lng=0;
} /* endif */
} /* endif */
stb_srt_psn=strrchr(fl_in,'/');
if(!stb_srt_psn) stb_srt_psn=fl_in; else stb_srt_psn++;
gpe_arg_lng=strlen(stb_srt_psn)-sfx_lng;
gpe_arg=(char *)nco_malloc((gpe_arg_lng+1L)*sizeof(char));
gpe_arg=strncpy(gpe_arg,stb_srt_psn,strlen(stb_srt_psn)-sfx_lng);
gpe_arg[gpe_arg_lng]='\0';
/* GPE arguments derived from filenames check for existence of path in output file */
rcd=nco_inq_grp_full_ncid_flg(out_id,gpe_arg,&gpe_id);
/* Existence implies current file may overwrite contents of previous file */
if(rcd == NC_NOERR) (void)fprintf(stderr,"%s: WARNING GAG path \"%s\" automatically derived from stub of filename %s conflicts with existing path in output file. Any input data with same absolute path names as contents of a previous input file will be overwritten. Is the same input file specified multiple times? Is this intentional?\nHINT: To distribute copies of a single input file into different groups, use GPE to generate distinct output group names, e.g., %s -G copy in.nc in.nc out.nc\n",nco_prg_nm_get(),gpe_arg,fl_in,nco_prg_nm_get()); else rcd=NC_NOERR;
} /* !grp_out */
/* Free old structure, if any, before re-use */
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
gpe=nco_gpe_prs_arg(gpe_arg);
gpe_arg=(char *)nco_free(gpe_arg);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: INFO GAG current file has gpe->arg=%s\n",nco_prg_nm_get(),gpe->arg);
/* Open file using appropriate buffer size hints and verbosity */
if(fl_idx) rcd=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,&in_id);
if(fl_idx == 0){
/* fxm: Copy global attributes of first file to root of output file to preserve history attribute */
/* Copy global attributes */
if(CPY_GLB_METADATA) (void)nco_att_cpy(in_id,out_id,NC_GLOBAL,NC_GLOBAL,(nco_bool)True);
/* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(gaa_nbr > 0) (void)nco_glb_att_add(out_id,gaa_arg,gaa_nbr);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
/* Add input file list global attribute */
if(FL_LST_IN_APPEND && HISTORY_APPEND && FL_LST_IN_FROM_STDIN) (void)nco_fl_lst_att_cat(out_id,fl_lst_in,fl_nbr);
} /* endif first file */
trv_tbl_sct *trv_tbl_gpr=NULL; /* [lst] Traversal table for GROUP_AGGREGATE only */
/* Initialize traversal table */
trv_tbl_init(&trv_tbl_gpr);
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr_rgn,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl_gpr);
/* Get number of variables, dimensions, and global attributes in file, file format */
(void)trv_tbl_inq((int *)NULL,(int *)NULL,(int *)NULL,&nbr_dmn_fl,(int *)NULL,(int *)NULL,(int *)NULL,(int *)NULL,&nbr_var_fl,trv_tbl_gpr);
(void)nco_inq_format(in_id,&fl_in_fmt);
/* We now have final list of variables to extract. Phew. */
/* Define extracted groups, variables, and attributes in output file */
(void)nco_xtr_dfn(in_id,out_id,&cnk,dfl_lvl,gpe,md5,CPY_GLB_METADATA,(nco_bool)True,(nco_bool)False,nco_pck_plc_nil,rec_dmn_nm,trv_tbl_gpr);
/* Turn-off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
/* Write extracted data to output file */
(void)nco_xtr_wrt(in_id,out_id,gpe,fp_bnr,md5,HAVE_LIMITS,trv_tbl_gpr);
/* Close input netCDF file */
(void)nco_close(in_id);
/* Free traversal table */
trv_tbl_free(trv_tbl_gpr);
} /* !GROUP_AGGREGATE */
if(RECORD_AGGREGATE){
/* Open file once per thread to improve caching */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) rcd=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,in_id_arr+thr_idx);
/* Perform various error-checks on input file */
if(False) (void)nco_fl_cmp_err_chk();
/* 20120309 Special case to improve copy speed on large blocksize filesystems (MM3s) */
USE_MM3_WORKAROUND=nco_use_mm3_workaround(in_id_arr[0],fl_out_fmt);
if(lmt_nbr > 0) USE_MM3_WORKAROUND=False;
if(!USE_MM3_WORKAROUND){
/* Copy all data variable-by-variable */
;
}else{
/* MM3 workaround algorithm */
/* ncecat-specific MM3 characteristics:
Only coordinates are "fixed" (non-processed) variables
All other variables are "processed"
These variables may be fixed or
record on input yet are all record on output
Makes sense to always use MM3? */
;
} /* endif MM3 workaround */
/* OpenMP with threading over variables, not files */
#ifdef _OPENMP
# pragma omp parallel for default(none) private(in_id) shared(nco_dbg_lvl,fl_nbr,idx_rec_out,in_id_arr,nbr_var_prc,out_id,var_prc,var_prc_out,nbr_dmn_fl,md5,trv_tbl)
#endif /* !_OPENMP */
/* Process all variables in current file */
for(idx=0;idx<nbr_var_prc;idx++){
int grp_id; /* [ID] Group ID (input) */
int grp_out_id; /* [ID] Group ID (output) */
int var_out_id; /* [ID] Variable ID (output) */
trv_sct *var_trv; /* [sct] Variable GTT object */
in_id=in_id_arr[omp_get_thread_num()];
if(nco_dbg_lvl >= nco_dbg_var) (void)fprintf(fp_stderr,"%s, ",var_prc[idx]->nm);
if(nco_dbg_lvl >= nco_dbg_var) (void)fflush(fp_stderr);
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
/* Variables may have different ID, missing_value, type, in each file */
(void)nco_inq_grp_full_ncid(in_id,var_trv->grp_nm_fll,&grp_id);
(void)nco_var_mtd_refresh(grp_id,var_prc[idx]);
/* Read */
(void)nco_msa_var_get_trv(in_id,var_prc[idx],trv_tbl);
/* Size of record dimension is 1 in output file */
var_prc_out[idx]->cnt[0]=1L;
var_prc_out[idx]->srt[0]=idx_rec_out;
/* Write variable into current record in output file */
/* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,var_trv->grp_nm_fll,&grp_out_id);
/* Get variable ID */
(void)nco_inq_varid(grp_out_id,var_trv->nm,&var_out_id);
/* Store the output variable ID */
var_prc_out[idx]->id=var_out_id;
if(var_trv->ppc != NC_MAX_INT){
if(var_trv->flg_nsd) (void)nco_ppc_bitmask(var_trv->ppc,var_prc[idx]->type,var_prc[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,var_prc[idx]->val); else (void)nco_ppc_around(var_trv->ppc,var_prc[idx]->type,var_prc[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,var_prc[idx]->val);
} /* endif ppc */
if(nco_is_xcp(var_trv->nm)) nco_xcp_prc(var_trv->nm,var_prc[idx]->type,var_prc[idx]->sz,(char *)var_prc[idx]->val.vp);
#ifdef _OPENMP
# pragma omp critical
#endif /* _OPENMP */
{ /* begin OpenMP critical */
if(var_prc[idx]->nbr_dim == 0){
(void)nco_put_var1(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc[idx]->val.vp,var_prc[idx]->type);
}else{ /* end if variable is scalar */
(void)nco_put_vara(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc_out[idx]->cnt,var_prc[idx]->val.vp,var_prc[idx]->type);
} /* end if variable is array */
/* Perform MD5 digest of input and output data if requested */
if(md5) (void)nco_md5_chk(md5,var_prc_out[idx]->nm,var_prc_out[idx]->sz*nco_typ_lng(var_prc[idx]->type),out_id,var_prc_out[idx]->srt,var_prc_out[idx]->cnt,var_prc[idx]->val.vp);
/* Free current input buffer */
var_prc[idx]->val.vp=nco_free(var_prc[idx]->val.vp);
} /* end OpenMP critical */
} /* end (OpenMP parallel for) loop over idx */
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"\n");
idx_rec_out++; /* [idx] Index of current record in output file (0 is first, ...) */
/* Close input netCDF file */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) nco_close(in_id_arr[thr_idx]);
} /* !RECORD_AGGREGATE */
/* Remove local copy of file */
if(FL_RTR_RMT_LCN && RM_RMT_FL_PST_PRC) (void)nco_fl_rm(fl_in);
} /* end loop over fl_idx */
/* Close output file and move it from temporary to permanent location */
(void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id);
/* Clean memory unless dirty memory allowed */
if(flg_cln){
/* NCO-generic clean-up */
/* Free individual strings/arrays */
if(cmd_ln) cmd_ln=(char *)nco_free(cmd_ln);
if(cnk_map_sng) cnk_map_sng=(char *)nco_free(cnk_map_sng);
if(cnk_plc_sng) cnk_plc_sng=(char *)nco_free(cnk_plc_sng);
if(grp_out) grp_out=(char *)nco_free(grp_out);
if(fl_in) fl_in=(char *)nco_free(fl_in);
if(fl_out) fl_out=(char *)nco_free(fl_out);
if(fl_out_tmp) fl_out_tmp=(char *)nco_free(fl_out_tmp);
if(fl_pth) fl_pth=(char *)nco_free(fl_pth);
if(fl_pth_lcl) fl_pth_lcl=(char *)nco_free(fl_pth_lcl);
if(in_id_arr) in_id_arr=(int *)nco_free(in_id_arr);
/* Free lists of strings */
if(fl_lst_in && !fl_lst_abb) fl_lst_in=nco_sng_lst_free(fl_lst_in,fl_nbr);
if(fl_lst_in && fl_lst_abb) fl_lst_in=nco_sng_lst_free(fl_lst_in,1);
if(fl_lst_abb) fl_lst_abb=nco_sng_lst_free(fl_lst_abb,abb_arg_nbr);
if(gaa_nbr > 0) gaa_arg=nco_sng_lst_free(gaa_arg,gaa_nbr);
if(var_lst_in_nbr > 0) var_lst_in=nco_sng_lst_free(var_lst_in,var_lst_in_nbr);
/* Free limits */
for(idx=0;idx<aux_nbr;idx++) aux_arg[idx]=(char *)nco_free(aux_arg[idx]);
for(idx=0;idx<lmt_nbr;idx++) lmt_arg[idx]=(char *)nco_free(lmt_arg[idx]);
for(idx=0;idx<ppc_nbr;idx++) ppc_arg[idx]=(char *)nco_free(ppc_arg[idx]);
/* Free chunking information */
for(idx=0;idx<cnk_nbr;idx++) cnk_arg[idx]=(char *)nco_free(cnk_arg[idx]);
if(cnk_nbr > 0) cnk.cnk_dmn=(cnk_dmn_sct **)nco_cnk_lst_free(cnk.cnk_dmn,cnk_nbr);
if(RECORD_AGGREGATE){
/* Free dimension lists */
/* ncecat-specific memory cleanup */
if(rec_dmn_nm) rec_dmn_nm=(char *)nco_free(rec_dmn_nm);
/* Free variable lists */
if(xtr_nbr > 0) var=nco_var_lst_free(var,xtr_nbr);
if(xtr_nbr > 0) var_out=nco_var_lst_free(var_out,xtr_nbr);
var_prc=(var_sct **)nco_free(var_prc);
var_prc_out=(var_sct **)nco_free(var_prc_out);
var_fix=(var_sct **)nco_free(var_fix);
var_fix_out=(var_sct **)nco_free(var_fix_out);
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
if(md5) md5=(md5_sct *)nco_md5_free(md5);
/* Free traversal table */
trv_tbl_free(trv_tbl);
for(idx=0;idx<lmt_nbr;idx++) flg_dne[idx].dim_nm=(char *)nco_free(flg_dne[idx].dim_nm);
if(flg_dne) flg_dne=(nco_dmn_dne_t *)nco_free(flg_dne);
} /* RECORD_AGGREGATE */
} /* !flg_cln */
#ifdef ENABLE_MPI
MPI_Finalize();
#endif /* !ENABLE_MPI */
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
void
nco_ppc_set_var
(const char * const var_nm, /* I [sng] Variable name to find */
const char * const ppc_arg, /* I [sng] User input for precision-preserving compression */
trv_tbl_sct * const trv_tbl) /* I/O [sct] Traversal table */
{
const char sls_chr='/'; /* [chr] Slash character */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
int mch_nbr=0;
int ppc_val;
nco_bool flg_nsd=True; /* [flg] PPC is NSD */
if(ppc_arg[0] == '.'){ /* DSD */
flg_nsd=False;
ppc_val=(int)strtol(ppc_arg+1L,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(ppc_arg+1L,"strtol",sng_cnv_rcd);
}else{ /* NSD */
ppc_val=(int)strtol(ppc_arg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(ppc_arg,"strtol",sng_cnv_rcd);
if(ppc_val <= 0){
(void)fprintf(stdout,"%s ERROR Number of Significant Digits (NSD) must be positive. Specified value for %s is %d. HINT: Decimal Significant Digit (DSD) rounding does accept negative arguments (number of digits in front of the decimal point). However, the DSD argument must be prefixed by a period or \"dot\", e.g., \"--ppc foo=.-2\", to distinguish it from NSD quantization.\n",nco_prg_nm_get(),var_nm,ppc_val);
nco_exit(EXIT_FAILURE);
} /* endif */
} /* end else */
if(strpbrk(var_nm,".*^$\\[]()<>+?|{}")){ /* Regular expression ... */
#ifdef NCO_HAVE_REGEX_FUNCTIONALITY
regmatch_t *result;
regex_t *rx;
size_t rx_prn_sub_xpr_nbr;
rx=(regex_t *)nco_malloc(sizeof(regex_t));
if(strchr(var_nm,sls_chr)){ /* Full name is used */
/* Important difference between full- and short-name matching: Prepend carat to RX so full name matches must start at beginning of variable name */
char *sng2mch;
sng2mch=(char *)nco_malloc(NC_MAX_VARS*sizeof(char *));
sng2mch[0]='\0';
strcat(sng2mch,"^");
strcat(sng2mch,var_nm);
if(regcomp(rx,sng2mch,(REG_EXTENDED | REG_NEWLINE))){ /* Compile regular expression */
(void)fprintf(stdout,"%s: ERROR trv_tbl_set_ppc() error in regular expression \"%s\"\n",nco_prg_nm_get(),var_nm);
nco_exit(EXIT_FAILURE);
} /* endif */
rx_prn_sub_xpr_nbr=rx->re_nsub+1L; /* Number of parenthesized sub-expressions */
result=(regmatch_t *)nco_malloc(sizeof(regmatch_t)*rx_prn_sub_xpr_nbr);
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
if(trv_tbl->lst[idx_tbl].nco_typ == nco_obj_typ_var){
if(!regexec(rx,trv_tbl->lst[idx_tbl].nm_fll,rx_prn_sub_xpr_nbr,result,0)){
trv_tbl->lst[idx_tbl].ppc=ppc_val;
trv_tbl->lst[idx_tbl].flg_nsd=flg_nsd;
mch_nbr++;
} /* endif */
} /* endif */
} /* endfor */
sng2mch=(char *)nco_free(sng2mch);
}else{ /* Relative name is used */
if(regcomp(rx,var_nm,(REG_EXTENDED | REG_NEWLINE))){ /* Compile regular expression */
(void)fprintf(stdout,"%s: ERROR trv_tbl_set_ppc() error in regular expression \"%s\"\n",nco_prg_nm_get(),var_nm);
nco_exit(EXIT_FAILURE);
} /* endif */
rx_prn_sub_xpr_nbr=rx->re_nsub+1L; /* Number of parenthesized sub-expressions */
result=(regmatch_t *)nco_malloc(sizeof(regmatch_t)*rx_prn_sub_xpr_nbr);
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
if(trv_tbl->lst[idx_tbl].nco_typ == nco_obj_typ_var){
if(!regexec(rx,trv_tbl->lst[idx_tbl].nm,rx_prn_sub_xpr_nbr,result,0)){
trv_tbl->lst[idx_tbl].ppc=ppc_val;
trv_tbl->lst[idx_tbl].flg_nsd=flg_nsd;
mch_nbr++;
} /* endif */
} /* endif */
} /* endfor */
} /* end Full name */
regfree(rx); /* Free regular expression data structure */
rx=(regex_t *)nco_free(rx);
result=(regmatch_t *)nco_free(result);
#else /* !NCO_HAVE_REGEX_FUNCTIONALITY */
(void)fprintf(stdout,"%s: ERROR: Sorry, wildcarding (extended regular expression matches to variables) was not built into this NCO executable, so unable to compile regular expression \"%s\".\nHINT: Make sure libregex.a is on path and re-build NCO.\n",nco_prg_nm_get(),var_nm);
nco_exit(EXIT_FAILURE);
#endif /* !NCO_HAVE_REGEX_FUNCTIONALITY */
}else if(strchr(var_nm,sls_chr)){ /* Full name */
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
if(trv_tbl->lst[idx_tbl].nco_typ == nco_obj_typ_var){
if(!strcmp(var_nm,trv_tbl->lst[idx_tbl].nm_fll)){
trv_tbl->lst[idx_tbl].ppc=ppc_val;
trv_tbl->lst[idx_tbl].flg_nsd=flg_nsd;
mch_nbr++;
break; /* Only one match with full name */
} /* endif */
} /* endif */
} /* endfor */
}else{ /* Not full name so set all matching vars */
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
if(trv_tbl->lst[idx_tbl].nco_typ == nco_obj_typ_var){
if(!strcmp(var_nm,trv_tbl->lst[idx_tbl].nm)){
trv_tbl->lst[idx_tbl].ppc=ppc_val;
trv_tbl->lst[idx_tbl].flg_nsd=flg_nsd;
mch_nbr++;
} /* endif */
} /* endif */
} /* endfor */
} /* end Full name */
if(mch_nbr == 0){
(void)fprintf(stdout,"%s: ERROR nco_ppc_set_var() reports user specified variable (or, possibly, regular expression) = \"%s\" does not match any variables in input file\n",nco_prg_nm_get(),var_nm);
nco_exit(EXIT_FAILURE);
} /* endif */
return;
} /* end nco_ppc_set_var() */
nm_id_sct * /* O [sct] Extraction list */
nco_cnv_cf_crd_add /* [fnc] Add coordinates defined by CF convention */
(const int nc_id, /* I netCDF file ID */
nm_id_sct *xtr_lst, /* I/O current extraction list (destroyed) */
int * const xtr_nbr) /* I/O number of variables in current extraction list */
{
/* Purpose: Detect coordinates specified by CF convention and add them to extraction list
http://www.cgd.ucar.edu/cms/eaton/cf-metadata/CF-1.0.html#grid_ex2 */
const char dlm_sng[]=" "; /* [sng] Delimiter string */
const char fnc_nm[]="nco_cnv_cf_crd_add()"; /* [sng] Function name */
char **crd_lst; /* [sng] 1D array of list elements */
char *att_val;
char att_nm[NC_MAX_NAME];
int crd_id;
int idx_att;
int idx_crd;
int idx_var;
int idx_var2;
int nbr_att;
int nbr_crd; /* [nbr] Number of coordinates specified in "coordinates" attribute */
int rcd=NC_NOERR; /* [rcd] Return code */
int var_id;
long att_sz;
nc_type att_typ;
/* ...for each variable in extraction list... */
for(idx_var=0;idx_var<*xtr_nbr;idx_var++){
/* Eschew indirection */
var_id=xtr_lst[idx_var].id;
/* Find number of attributes */
(void)nco_inq_varnatts(nc_id,var_id,&nbr_att);
for(idx_att=0;idx_att<nbr_att;idx_att++){
(void)nco_inq_attname(nc_id,var_id,idx_att,att_nm);
/* Is attribute part of CF convention? */
if(!strcmp(att_nm,"coordinates")){
/* Yes, get list of specified attributes */
(void)nco_inq_att(nc_id,var_id,att_nm,&att_typ,&att_sz);
if(att_typ != NC_CHAR){
(void)fprintf(stderr,"%s: WARNING the \"%s\" attribute for variable %s is type %s, not %s. This violates the CF convention for specifying additional attributes. Therefore %s will skip this attribute.\n",nco_prg_nm_get(),att_nm,xtr_lst[idx_var].nm,nco_typ_sng(att_typ),nco_typ_sng(NC_CHAR),fnc_nm);
return xtr_lst;
} /* end if */
att_val=(char *)nco_malloc((att_sz+1L)*sizeof(char));
if(att_sz > 0) (void)nco_get_att(nc_id,var_id,att_nm,(void *)att_val,NC_CHAR);
/* NUL-terminate attribute */
att_val[att_sz]='\0';
/* Split list into separate coordinate names */
/* using nco_lst_prs_sgl_2D() and not nco_lst_prs_2D */
/* see TODO 944 */
crd_lst=nco_lst_prs_sgl_2D(att_val,dlm_sng,&nbr_crd);
/* ...for each coordinate in "coordinates" attribute... */
for(idx_crd=0;idx_crd<nbr_crd;idx_crd++){
/* Verify "coordinate" exists in input file */
rcd=nco_inq_varid_flg(nc_id,crd_lst[idx_crd],&crd_id);
/* NB: Do not check that dimension by this name exists
CF files often use "coordinates" convention to identify
two-dimensional (or greater) variables which serve as coordinates.
In other words, we want to allow N-D variables to work as coordinates
for the purpose of adding them to the extraction list only. */
if(rcd == NC_NOERR){
/* idx_var2 labels inner loop over variables */
/* Is "coordinate" already on extraction list? */
for(idx_var2=0;idx_var2<*xtr_nbr;idx_var2++){
if(crd_id == xtr_lst[idx_var2].id) break;
} /* end loop over idx_var2 */
if(idx_var2 == *xtr_nbr){
/* Add coordinate to list */
xtr_lst=(nm_id_sct *)nco_realloc((void *)xtr_lst,(*xtr_nbr+1)*sizeof(nm_id_sct));
xtr_lst[*xtr_nbr].nm=(char *)strdup(crd_lst[idx_crd]);
xtr_lst[*xtr_nbr].id=crd_id;
(*xtr_nbr)++; /* NB: Changes size of current loop! */
/* Continue to next coordinate in loop */
continue;
} /* end if coordinate was not already in list */
} /* end if named coordinate exists in input file */
} /* end loop over idx_crd */
/* Free allocated memory */
att_val=(char *)nco_free(att_val);
crd_lst=nco_sng_lst_free(crd_lst,nbr_crd);
} /* !coordinates */
} /* end loop over attributes */
} /* end loop over idx_var */
return xtr_lst;
} /* end nco_cnv_cf_crd_add() */
size_t /* O [nbr] Number of elements successfully written */
nco_bnr_wrt /* [fnc] Write unformatted binary data */
(FILE * const fp_bnr, /* I [fl] Unformatted binary output file handle */
const char * const var_nm, /* I [sng] Variable name */
const long var_sz, /* I [nbr] Variable size */
const nc_type var_typ, /* I [enm] Variable type */
const void * const void_ptr) /* I [ptr] Data to write */
{
/* Purpose: Write unformatted binary data */
/* Testing:
ncks -O -D 3 -B -b foo.bnr ~/nco/data/in.nc ~/foo.nc */
long wrt_nbr; /* [nbr] Number of elements successfully written */
/* Write unformatted data to binary output file */
wrt_nbr=fwrite(void_ptr,(size_t)nco_typ_lng(var_typ),(size_t)var_sz,fp_bnr);
if(wrt_nbr != var_sz){
(void)fprintf(stderr,"%s: ERROR only succeeded in writing %ld of %ld elements of variable %s\n",nco_prg_nm_get(),wrt_nbr,var_sz,var_nm);
nco_exit(EXIT_FAILURE);
} /* end if */
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"%s (%s, %ld x %lu b), ",var_nm,c_typ_nm(var_typ),var_sz,(unsigned long)nco_typ_lng(var_typ));
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fflush(stderr);
return wrt_nbr; /* O [nbr] Number of elements successfully written */
} /* end nco_bnr_wrt() */
void
nco_cnv_ccm_ccsm_cf_date /* [fnc] Fix date variable in averaged CCM/CCSM/CF files */
(const int nc_id, /* I [id] netCDF file ID */
X_CST_PTR_CST_PTR_Y(var_sct,var), /* I/O [sct] Variables in output file */
const int nbr_var) /* I [nbr] Number of variables in list */
{
/* Purpose: Fix date variable in averaged CCM/CCSM/CF files */
char wrn_sng[1000];
int date_idx;
int idx;
int rcd=NC_NOERR; /* [rcd] Return code */
int time_idx;
int nbdate_id;
nco_int day;
nco_int date;
nco_int nbdate;
(void)sprintf(wrn_sng,"Most, but not all, CCM/CCSM/CF files which are in CCM format contain the fields \"nbdate\", \"time\", and \"date\". When the \"date\" field is present but either \"nbdate\" or \"time\" is missing, then %s is unable to construct a meaningful average \"date\" to store in the output file. Therefore the \"date\" variable in your output file may be meaningless.\n",nco_prg_nm_get());
/* Find date variable (NC_INT: current date as 6 digit integer (YYMMDD)) */
for(idx=0;idx<nbr_var;idx++){
if(!strcmp(var[idx]->nm,"date")) break;
} /* end loop over idx */
if(idx == nbr_var) return; else date_idx=idx;
// if(var[date_idx]->type != NC_INT) return; /* 20101026 TODO nco998 problem is that "date" type is NC_DOUBLE here */
/* Find scalar nbdate variable (NC_INT: base date date as 6 digit integer (YYMMDD)) */
rcd=nco_inq_varid_flg(nc_id,"nbdate",&nbdate_id);
if(rcd != NC_NOERR){
(void)fprintf(stderr,"%s: WARNING CCM/CCSM/CF convention file output variable list contains \"date\" but not \"nbdate\"\n",nco_prg_nm_get());
(void)fprintf(stderr,"%s: %s",nco_prg_nm_get(),wrn_sng);
return;
} /* endif */
{ /* begin potential OpenMP critical */
/* Block is critical/thread-safe for identical/distinct in_id's */
(void)nco_get_var1(nc_id,nbdate_id,0L,&nbdate,NC_INT);
} /* end potential OpenMP critical */
/* Find time variable (NC_DOUBLE: current day since nbdate) */
for(idx=0;idx<nbr_var;idx++){
if(!strcmp(var[idx]->nm,"time")) break;
} /* end loop over idx */
if(idx == nbr_var){
(void)fprintf(stderr,"%s: WARNING CCM/CCSM/CF convention file output variable list contains \"date\" and \"nbdate\" yet lacks \"time\"\n",nco_prg_nm_get());
(void)fprintf(stderr,"%s: %s",nco_prg_nm_get(),wrn_sng);
return;
}else{
time_idx=idx;
} /* endif */
/* Assign current day to averaged day number */
day=(nco_int)(var[time_idx]->val.dp[0]);
/* Recompute date variable based on new (averaged) day number */
date=nco_newdate(nbdate,day);
if(var[date_idx]->type == NC_INT){
if(!var[date_idx]->val.ip) return; else var[date_idx]->val.ip[0]=date;
}else if(var[date_idx]->type == NC_DOUBLE){
if(!var[date_idx]->val.dp) return; else var[date_idx]->val.dp[0]=date;
}else{
(void)fprintf(stderr,"%s: WARNING CCM/CCSM/CF convention file output variable \"date\" is not NC_INT or NC_DOUBLE\n",nco_prg_nm_get());
} /* end else */
return; /* 20050109: fxm added return to void function to squelch erroneous gcc-3.4.2 warning */
} /* end nco_cnv_ccm_ccsm_cf_date */
size_t /* O [nbr] Number of elements successfully read */
nco_bnr_rd /* [fnc] Read unformatted binary data */
(FILE * const fp_bnr, /* I [fl] Unformatted binary input file handle */
const char * const var_nm, /* I [sng] Variable name */
const long var_sz, /* I [nbr] Variable size */
const nc_type var_typ, /* I [enm] Variable type */
void * const void_ptr) /* O [ptr] Data to read */
{
/* Purpose: Read unformatted binary data */
/* Testing:
ncks -O -D 73 ~/nco/data/in.nc ~/foo.nc */
long rd_nbr; /* [nbr] Number of elements successfully written */
/* Read unformatted data from binary input file */
rd_nbr=fread(void_ptr,(size_t)nco_typ_lng(var_typ),(size_t)var_sz,fp_bnr);
if(rd_nbr != var_sz){
(void)fprintf(stderr,"%s: ERROR only succeeded in reading %ld of %ld elements into variable %s\n",nco_prg_nm_get(),rd_nbr,var_sz,var_nm);
nco_exit(EXIT_FAILURE);
} /* end if */
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"Binary read of %s (%s, %ld x %lu b)",var_nm,c_typ_nm(var_typ),var_sz,(unsigned long)nco_typ_lng(var_typ));
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fflush(stderr);
return rd_nbr; /* O [nbr] Number of elements successfully written */
} /* end nco_bnr_rd() */