rnm_sct * /* O [sng] Structured list of old, new names */
nco_prs_rnm_lst /* [fnc] Set old_nm, new_nm elements of rename structure */
(const int nbr_rnm, /* I [nbr] Number of elements in rename list */
char * const * const rnm_arg) /* I [sng] Unstructured list of old, new names */
{
/* Purpose: Set old_nm, new_nm elements of rename structure
Routine merely fills rename structure and does not attempt to validate
presence of variables in input netCDF file. */
rnm_sct *rnm_lst;
int idx;
ptrdiff_t lng_arg_1;
ptrdiff_t lng_arg_2;
rnm_lst=(rnm_sct *)nco_malloc((size_t)nbr_rnm*sizeof(rnm_sct));
for(idx=0;idx<nbr_rnm;idx++){
char *comma_1_cp;
/* Find positions of commas and number of characters between (non-inclusive) them */
comma_1_cp=strchr(rnm_arg[idx],',');
/* Before doing any pointer arithmetic, make sure pointers are valid */
if(comma_1_cp == NULL){
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
} /* end if */
lng_arg_1=comma_1_cp-rnm_arg[idx];
lng_arg_2=rnm_arg[idx]+strlen(rnm_arg[idx])-comma_1_cp-1;
/* Exit if length of either argument is zero */
if(lng_arg_1 <= 0 || lng_arg_2 <= 0){
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
} /* end if */
/* Assign pointers to member of rnm_lst */
rnm_lst[idx].old_nm=rnm_arg[idx];
rnm_lst[idx].new_nm=comma_1_cp+1;
/* NUL-terminate arguments */
rnm_lst[idx].old_nm[lng_arg_1]='\0';
rnm_lst[idx].new_nm[lng_arg_2]='\0';
} /* end loop over rnm_lst */
if(dbg_lvl_get() >= nco_dbg_io){
for(idx=0;idx<nbr_rnm;idx++){
(void)fprintf(stderr,"%s\n",rnm_lst[idx].old_nm);
(void)fprintf(stderr,"%s\n",rnm_lst[idx].new_nm);
} /* end loop over idx */
} /* end debug */
return rnm_lst;
} /* end nco_prs_rnm_lst() */
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() */
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() */
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() */
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
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
main(int argc,char **argv)
{
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 FILE_1_RETRIEVED_FROM_REMOTE_LOCATION=False;
nco_bool FILE_2_RETRIEVED_FROM_REMOTE_LOCATION=False;
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 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_ddra=False; /* [flg] DDRA diagnostics */
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_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=NULL;
char *fl_pth=NULL; /* Option p */
char *fl_pth_lcl=NULL; /* Option l */
char *lmt_arg[NC_MAX_DIMS];
char *nco_op_typ_sng=NULL; /* [sng] Operation type */
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 **grp_lst_in=NULL; /* [sng] User-specified list of groups */
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:hL:l:Oo:p:rRt:v:X:xzy:-:";
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={.MRV_flg=False,.flg_ddra=False,.lmn_nbr=0LL,.lmn_nbr_avg=0LL,.lmn_nbr_wgt=0LL,.nco_op_typ=nco_op_nil,.rnk_avg=0,.rnk_var=0,.rnk_wgt=0,.tmr_flg=nco_tmr_srt,.var_idx=0,.wgt_brd_flg=False,.wrd_sz=0};
#endif /* !__cplusplus */
extern char *optarg;
extern int optind;
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 gaa_nbr=0; /* [nbr] Number of global attributes to add */
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_glb_att_1; /* [nbr] Number of global attributes in file */
int nbr_glb_att_2; /* [nbr] Number of global attributes in file */
int nbr_grp_att_1; /* [nbr] Number of group attributes in file */
int nbr_grp_att_2; /* [nbr] Number of group attributes in file */
int nbr_att_var_1; /* [nbr] Number of variable attributes in file */
int nbr_att_var_2; /* [nbr] Number of variable attributes in file */
int nbr_dmn_fl_1; /* [nbr] Number of dimensions in file */
int nbr_dmn_fl_2; /* [nbr] Number of dimensions in file */
int nbr_rec_fl_1; /* [nbr] Number of record dimensions in file */
int nbr_rec_fl_2; /* [nbr] Number of record dimensions in file */
int grp_dpt_fl_1; /* [nbr] Maximum group depth (root = 0) */
int grp_dpt_fl_2; /* [nbr] Maximum group depth (root = 0) */
int grp_lst_in_nbr=0; /* [nbr] Number of groups explicitly specified by user */
int nbr_grp_fl_1; /* [nbr] Number of groups in file */
int nbr_grp_fl_2; /* [nbr] Number of groups in file */
int var_ntm_fl_1; /* [nbr] Number of non-atomic variables in file */
int var_ntm_fl_2; /* [nbr] Number of non-atomic variables in file */
int nbr_var_fl_1; /* [nbr] Number of atomic-type variables in file */
int nbr_var_fl_2; /* [nbr] Number of atomic-type variables in file */
int nbr_gpe_nm; /* [nbr] Number of GPE entries */
int nbr_cmn_nm=0; /* [nbr] Number of common entries */
int nco_op_typ=nco_op_nil; /* [enm] Operation type */
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;
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 */
trv_tbl_sct *trv_tbl_1=NULL; /* [lst] Traversal table input file 1 */
trv_tbl_sct *trv_tbl_2=NULL; /* [lst] Traversal table input file 2 */
gpe_nm_sct *gpe_nm=NULL; /* [sct] GPE name duplicate check array */
nco_cmn_t *cmn_lst=NULL; /* [sct] A list of common names */
nco_dmn_dne_t *flg_dne1=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
nco_dmn_dne_t *flg_dne2=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
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 */
{"ddra",no_argument,0,0}, /* [flg] DDRA diagnostics */
{"mdl_cmp",no_argument,0,0}, /* [flg] DDRA diagnostics */
{"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 */
{"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'},
{"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'},
{"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'},
{"overwrite",no_argument,0,'O'},
{"ovr",no_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'},
{"auxiliary",required_argument,0,'X'},
{"exclude",no_argument,0,'x'},
{"xcl",no_argument,0,'x'},
{"operation",required_argument,0,'y'},
{"op_typ",required_argument,0,'y'},
{"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 */
nbr_gpe_nm=0;
/* 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_dmn */
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,"ddra") || !strcmp(opt_crr,"mdl_cmp")) ddra_info.flg_ddra=flg_ddra=True; /* [flg] DDRA diagnostics */
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; /* [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 */
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 '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);
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 'y': /* User-specified operation type overrides invocation default */
nco_op_typ_sng=(char *)strdup(optarg);
nco_op_typ=nco_op_typ_get(nco_op_typ_sng);
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 */
/* Initialize traversal tables */
(void)trv_tbl_init(&trv_tbl_1);
(void)trv_tbl_init(&trv_tbl_2);
/* Default operation depends on invocation name */
if(nco_op_typ_sng == NULL) nco_op_typ=nco_op_typ_get(nco_op_typ_sng);
/* 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];
/* 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,var_lst_in_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne1,trv_tbl_1);
(void)nco_bld_trv_tbl(in_id_2,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,var_lst_in_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne2,trv_tbl_2);
/* Merge DNE lists before checking */
flg_dne=(nco_dmn_dne_t *)nco_malloc(2*lmt_nbr*sizeof(nco_dmn_dne_t));
/* Merge "dne" lists */
for(int lmt_idx=0;lmt_idx<lmt_nbr;lmt_idx++) flg_dne[lmt_idx]=flg_dne1[lmt_idx];
for(int lmt_idx=0;lmt_idx<lmt_nbr;lmt_idx++) flg_dne[lmt_nbr+lmt_idx]=flg_dne2[lmt_idx];
/* 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(&nbr_glb_att_1,&nbr_grp_att_1,&nbr_att_var_1,&nbr_dmn_fl_1,&nbr_rec_fl_1,&grp_dpt_fl_1,&nbr_grp_fl_1,&var_ntm_fl_1,&nbr_var_fl_1,trv_tbl_1);
(void)trv_tbl_inq(&nbr_glb_att_2,&nbr_grp_att_2,&nbr_att_var_2,&nbr_dmn_fl_2,&nbr_rec_fl_2,&grp_dpt_fl_2,&nbr_grp_fl_2,&var_ntm_fl_2,&nbr_var_fl_2,trv_tbl_2);
(void)nco_inq_format(in_id_1,&fl_in_fmt_1);
(void)nco_inq_format(in_id_2,&fl_in_fmt_2);
/* 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_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_1);
/* 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);
if(gpe){
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"%s: INFO Group Path Edit (GPE) feature enabled\n",nco_prg_nm_get());
if(fl_out_fmt != NC_FORMAT_NETCDF4) (void)fprintf(stderr,"%s: WARNING Group Path Edit (GPE) requires netCDF4 output format in most cases (except flattening) but user explicitly requested output format = %s. This command will fail if the output file requires netCDF4 features like groups or netCDF4 atomic types (e.g., NC_STRING, NC_UBYTE...).\n",nco_prg_nm_get(),nco_fmt_sng(fl_out_fmt));
} /* !gpe */
/* Is this a CCM/CCSM/CF-format history tape? */
CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(in_id_1);
/* Group broadcating (DEFINE mode, True as flg_dfn parameter) */
(void)nco_grp_brd(in_id_1,in_id_2,out_id,&cnk,dfl_lvl,gpe,gpe_nm,nbr_gpe_nm,CNV_CCM_CCSM_CF,nco_op_typ,trv_tbl_1,trv_tbl_2,(nco_bool)True);
/* Copy global attributes from file 1 */
(void)nco_att_cpy(in_id_1,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_1,in_id_1,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);
/* 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 */
/* Group broadcating (WRITE mode, False as flg_dfn parameter) */
(void)nco_grp_brd(in_id_1,in_id_2,out_id,&cnk,dfl_lvl,gpe,gpe_nm,nbr_gpe_nm,CNV_CCM_CCSM_CF,nco_op_typ,trv_tbl_1,trv_tbl_2,(nco_bool)False);
/* 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 */
if(fl_out_tmp) (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){
/* ncbo-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);
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);
trv_tbl_free(trv_tbl_1);
trv_tbl_free(trv_tbl_2);
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
/* Memory management for GPE names */
for(idx=0;idx<nbr_gpe_nm;idx++) gpe_nm[idx].var_nm_fll=(char *)nco_free(gpe_nm[idx].var_nm_fll);
if(nbr_gpe_nm) gpe_nm=(gpe_nm_sct *)nco_free(gpe_nm);
/* Memory management for common names list */
for(idx=0;idx<nbr_cmn_nm;idx++) cmn_lst[idx].nm=(char *)nco_free(cmn_lst[idx].nm);
if(nbr_cmn_nm > 0) cmn_lst=(nco_cmn_t *)nco_free(cmn_lst);
for(idx=0;idx<lmt_nbr;idx++) flg_dne1[idx].dim_nm=(char *)nco_free(flg_dne1[idx].dim_nm);
flg_dne1=(nco_dmn_dne_t *)nco_free(flg_dne1);
for(idx=0;idx<lmt_nbr;idx++) flg_dne2[idx].dim_nm=(char *)nco_free(flg_dne2[idx].dim_nm);
flg_dne2=(nco_dmn_dne_t *)nco_free(flg_dne2);
flg_dne=(nco_dmn_dne_t *)nco_free(flg_dne);
} /* !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() */