Ejemplo n.º 1
0
int
main(int argc, char **argv)
{
    int i,stat;
    int ncid, grpid;
    char* filename;
    char* oldname;
    char* newname;

    switch (argc) {
    case 0:
    case 1:
        usage("No arguments");
	break;
    case 2:
        usage("Too few arguments");
	break;
    case 3:
    default:
	filename = argv[1];
	oldname = argv[2];
	newname = argv[3];
	break;
    }

    if(strlen(filename) == 0)
	usage("bad filename argument");
    if(strlen(oldname) == 0)
	usage("bad old name argument");
    if(strlen(newname) == 0)
	usage("bad new name argument");

    stat = nc_open(filename,NC_WRITE,&ncid);
    check(stat);

#ifdef RENAME_DEBUG
    stat = nc_set_log_level(0);
    check(stat);
    nc_log_hdf5();
#endif

    stat = nc_inq_grp_full_ncid(ncid,oldname,&grpid);
    check(stat);

    stat = nc_rename_grp(grpid,newname);
    check(stat);

    stat = nc_close(ncid);
    check(stat);

    exit(0);
}
Ejemplo n.º 2
0
int
main(int argc, char **argv)
{
nc_set_log_level(0);
   printf("\n*** Testing netcdf-4 dimensions even more.\n");
   printf("*** testing netcdf-4 dimension inheritance...");
   {
#define FILE_NAME "tst_dims3.nc"
#define RANK_time 1
#define GRP_NAME  "G"
#define TIME_NAME "time"
#define VAR2_NAME "z"
#define TIME_RANK 1
#define NUM_TIMES 2
      int ncid, grpid;
      int time_dim, time_dim_in;
      int time_var, z_var;
      size_t len;
      int time_data[NUM_TIMES] = {1, 2} ;
      size_t time_startset[TIME_RANK] = {0} ;
      size_t time_countset[TIME_RANK] = {NUM_TIMES} ;

      /* Create file with unlimited dim and associated coordinate
       * variable in root group, another variable that uses unlimited
       * dim in subgroup. */
      if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR;
      if (nc_def_grp(ncid, GRP_NAME, &grpid)) ERR;
      if (nc_def_dim(ncid, TIME_NAME, NC_UNLIMITED, &time_dim)) ERR;
      if (nc_def_var(ncid, TIME_NAME, NC_INT, TIME_RANK, &time_dim, 
		     &time_var)) ERR;
      if (nc_def_var(grpid, VAR2_NAME, NC_INT, TIME_RANK, &time_dim, 
		     &z_var)) ERR;
      if (nc_enddef(ncid)) ERR;

      /* Assign data to time variable, creating two times */
      if (nc_put_vara(ncid, time_dim, time_startset, time_countset, 
		      time_data)) ERR;

      /* Check the dim len from the root group */
      if (nc_inq_dimlen(ncid, time_dim, &len)) ERR;
      if (len != NUM_TIMES) ERR;

      /* Check the dim len from the sub group */
      if (nc_inq_dimlen(grpid, time_dim, &len)) ERR;
      if (len != NUM_TIMES) ERR;
      if (nc_close(ncid)) ERR;

      /* Now check how many times there are from the subgroup */
      if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
      if (nc_inq_ncid(ncid, GRP_NAME, &grpid)) ERR;
      if (nc_inq_dimid(ncid, TIME_NAME, &time_dim)) ERR;

      /* Check the dim len from the root group */
      if (nc_inq_dimlen(ncid, time_dim, &len)) ERR;
      if (len != NUM_TIMES) ERR;

      /* Check the dim len from the sub group */
      if (nc_inq_dimlen(grpid, time_dim, &len)) ERR;
      if (len != NUM_TIMES) ERR;

      /* Find the dimension by name. */
      if (nc_inq_dimid(grpid, TIME_NAME, &time_dim_in)) ERR;
      if (time_dim_in != time_dim) ERR;

      if (nc_close(ncid)) ERR;
   }
   SUMMARIZE_ERR;
   printf("*** testing a scalar coordinate dimension...");
   {
      int ncid, dimid, varid, stat;
      float data = 42.5;
      
      /* Create a scalar coordinate dimension. The only reason that
       * the user can ever possibly have for doing this is just
       * because they like to make life difficult for poor, poor
       * netCDF programmers, trapped in this horrible place, in a
       * Rocky Mountain valley, drenched in sunlight, with a stream
       * quietly gurgling, deer feeding on the grasses, and all those
       * damn birds chirping! */
      if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR_RET;
      if (nc_def_dim(ncid, "scalar", 0, &dimid)) ERR_RET;
      if (nc_def_var(ncid, "scalar", NC_FLOAT, 0, &dimid, &varid)) ERR_RET;
      if (nc_put_var_float(ncid, varid, &data)) ERR_RET;
      if (nc_close(ncid))
	ERR_RET;
   }
   SUMMARIZE_ERR;
   FINAL_RESULTS;
}
Ejemplo n.º 3
0
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() */
Ejemplo n.º 4
0
Archivo: ncecat.c Proyecto: jsta/nco
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() */
Ejemplo n.º 5
0
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() */
Ejemplo n.º 6
0
int
main(int argc, char **argv)
{
   fprintf(stderr,"Test more renaming.\n");
   fprintf(stderr,"*** test renaming affect on varids...");
   {
      int ncid, dimid1, dimid2, varid1, varid2;
      int dimid_in, varid_in;
      char file_name[NC_MAX_NAME + 1];

      /* Create file with two scalar vars. */
      sprintf(file_name, "%s_coord_to_non_coord.nc", TEST_NAME);
      if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR;
      if (nc_def_var(ncid, D1_NAME, NC_INT, 0, NULL, &varid1)) ERR;
      if (nc_def_var(ncid, D2_NAME, NC_INT, 0, NULL, &varid2)) ERR;
      if (nc_close(ncid)) ERR;

      /* Open the file and rename a var. */
      nc_set_log_level(4);
      if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
      if (nc_rename_var(ncid, varid1, TMP_NAME)) ERR;
      if (nc_close(ncid)) ERR;

      /* Reopen file and check, */
      if (nc_open(file_name, NC_WRITE, &ncid)) ERR;
      if (nc_inq_varid(ncid, TMP_NAME, &varid_in)) ERR;
      /* if (varid_in != varid1) ERR; */
      if (nc_inq_varid(ncid, D1_NAME, &varid_in) != NC_ENOTVAR) ERR;
      if (nc_inq_varid(ncid, D2_NAME, &varid_in)) ERR;
      if (nc_close(ncid)) ERR;
   }
   SUMMARIZE_ERR;
   /* fprintf(stderr,"*** test renaming coord var to non-coord var..."); */
   /* { */
   /*    int ncid, dimid1, dimid2, varid1, varid2; */
   /*    int dimid_in, varid_in; */
   /*    char file_name[NC_MAX_NAME + 1]; */

   /*    /\* Create file with two dims and associated coordinate vars. *\/ */
   /*    sprintf(file_name, "%s_coord_to_non_coord.nc", TEST_NAME); */
   /*    if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR; */
   /*    if (nc_def_dim(ncid, D1_NAME, DIM1_LEN, &dimid1)) ERR; */
   /*    if (nc_def_dim(ncid, D2_NAME, DIM1_LEN, &dimid2)) ERR; */
   /*    if (nc_def_var(ncid, D1_NAME, NC_INT, NDIM1, &dimid1, &varid1)) ERR; */
   /*    if (nc_def_var(ncid, D2_NAME, NC_INT, NDIM1, &dimid2, &varid2)) ERR; */
   /*    if (nc_close(ncid)) ERR; */

   /*    /\* Open the file and rename a var. *\/ */
   /*    nc_set_log_level(4); */
   /*    if (nc_open(file_name, NC_WRITE, &ncid)) ERR; */
   /*    if (nc_rename_var(ncid, varid1, TMP_NAME)) ERR; */
   /*    if (nc_close(ncid)) ERR; */

   /*    /\* Reopen file and check, *\/ */
   /*    if (nc_open(file_name, NC_WRITE, &ncid)) ERR; */
   /*    if (nc_inq_dimid(ncid, D1_NAME, &dimid_in)) ERR; */
   /*    printf("dimid_in %d\n", dimid_in); */
   /*    if (dimid_in != dimid1) ERR; */
   /*    if (nc_inq_dimid(ncid, D2_NAME, &dimid_in)) ERR; */
   /*    if (dimid_in != dimid2) ERR; */
   /*    if (nc_inq_dimid(ncid, TMP_NAME, &dimid_in) != NC_EBADDIM) ERR; */
   /*    if (nc_inq_varid(ncid, TMP_NAME, &varid_in)) ERR; */
   /*    /\* if (varid_in != varid1) ERR; *\/ */
   /*    if (nc_inq_varid(ncid, D1_NAME, &varid_in) != NC_ENOTVAR) ERR; */
   /*    if (nc_close(ncid)) ERR; */

   /*    /\* if (nc_open(file_name, NC_WRITE, &ncid)) ERR; *\/ */
   /*    /\* if (nc_rename_var(ncid, varid2, D1_NAME)) ERR; *\/ */
   /*    /\* if (nc_close(ncid)) ERR; *\/ */

   /*    /\* /\\* Reopen file and check, *\\/ *\/ */
   /*    /\* if (nc_open(file_name, NC_WRITE, &ncid)) ERR; *\/ */
   /*    /\* if (nc_inq_dimid(ncid, D1_NAME, &dimid_in)) ERR; *\/ */
   /*    /\* if (dimid_in != dimid1) ERR; *\/ */
   /*    /\* if (nc_inq_dimid(ncid, D2_NAME, &dimid_in)) ERR; *\/ */
   /*    /\* if (dimid_in != dimid2) ERR; *\/ */
   /*    /\* if (nc_inq_dimid(ncid, TMP_NAME, &dimid_in) != NC_EBADDIM) ERR; *\/ */
   /*    /\* if (nc_inq_varid(ncid, TMP_NAME, &varid_in)) ERR; *\/ */
   /*    /\* if (varid_in != varid1) ERR; *\/ */
   /*    /\* if (nc_inq_varid(ncid, D1_NAME, &varid_in)) ERR; *\/ */
   /*    /\* if (varid_in != varid2) ERR; *\/ */
   /*    /\* if (nc_close(ncid)) ERR; *\/ */
   /* } */
   /* SUMMARIZE_ERR; */
   /* fprintf(stderr,"*** test exchanging names of two coord vars, making them non-coord vars with names same as dims..."); */
   /* { */
   /*    int ncid, dimid1, dimid2, varid1, varid2; */
   /*    int dimid_in, varid_in; */
   /*    char file_name[NC_MAX_NAME + 1]; */

   /*    /\* Create file with dim and associated coordinate var. *\/ */
   /*    sprintf(file_name, "%s_non_coord_to_dim.nc", TEST_NAME); */
   /*    if (nc_create(file_name, NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL, &ncid)) ERR; */
   /*    if (nc_def_dim(ncid, D1_NAME, DIM1_LEN, &dimid1)) ERR; */
   /*    if (nc_def_dim(ncid, D2_NAME, DIM1_LEN, &dimid2)) ERR; */
   /*    if (nc_def_var(ncid, D1_NAME, NC_INT, NDIM1, &dimid1, &varid1)) ERR; */
   /*    if (nc_def_var(ncid, D2_NAME, NC_INT, NDIM1, &dimid2, &varid2)) ERR; */
   /*    if (nc_close(ncid)) ERR; */

   /*    /\* Open the file and rename the vars. *\/ */
   /*    nc_set_log_level(4); */
   /*    if (nc_open(file_name, NC_WRITE, &ncid)) ERR; */
   /*    if (nc_rename_var(ncid, varid1, TMP_NAME)) ERR; */
   /*    nc_sync(ncid); */
   /*    /\* if (nc_rename_var(ncid, varid2, D1_NAME)) ERR; *\/ */
   /*    /\* nc_sync(ncid); *\/ */
   /*    /\* if (nc_rename_var(ncid, varid1, D2_NAME)) ERR; *\/ */
   /*    if (nc_close(ncid)) ERR; */

   /*    /\* Reopen file and check, *\/ */
   /*    if (nc_open(file_name, NC_WRITE, &ncid)) ERR; */
   /*    /\* if (nc_inq_dimid(ncid, D1_NAME, &dimid_in)) ERR; *\/ */
   /*    /\* if (dimid_in != dimid1) ERR; *\/ */
   /*    /\* if (nc_inq_dimid(ncid, D2_NAME, &dimid_in)) ERR; *\/ */
   /*    /\* if (dimid_in != dimid2) ERR; *\/ */
   /*    /\* if (nc_inq_dimid(ncid, TMP_NAME, &dimid_in) != NC_EBADDIM) ERR; *\/ */
   /*    /\* if (nc_inq_varid(ncid, TMP_NAME, &varid_in)) ERR; *\/ */
   /*    /\* if (varid_in != varid1) ERR; *\/ */
   /*    /\* if (nc_inq_varid(ncid, D1_NAME, &varid_in)) ERR; *\/ */
   /*    /\* if (varid_in != varid2) ERR; *\/ */
   /*    if (nc_close(ncid)) ERR; */
   /* } */
   /* SUMMARIZE_ERR; */
   FINAL_RESULTS;
}
Ejemplo n.º 7
0
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() */
Ejemplo n.º 8
0
Archivo: mpncecat.c Proyecto: jsta/nco
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() */
Ejemplo n.º 9
0
Archivo: ncbo.c Proyecto: hdfeos/nco
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() */