nco/ncks.c File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <time.h>
#include <unistd.h>
#include "nco_getopt.h"
#include <netcdf.h>
#include "libnco.h"

Include dependency graph for ncks.c:

Go to the source code of this file.

Defines
#define	MAIN_PROGRAM_FILE
Functions
int	main (int argc, char **argv)

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Define Documentation

#define MAIN_PROGRAM_FILE

Definition at line 68 of file ncks.c.

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Function Documentation

int main (  int  argc, char **  argv )

Definition at line 72 of file ncks.c. References lmt_all_sct::BASIC_DMN, lmt_sct::cnt, copyright_prn(), lmt_all_sct::dmn_nm, lmt_all_sct::dmn_sz_org, lmt_sct::end, EXIT_FAILURE, EXIT_SUCCESS, False, FILE, getopt_long, lmt_sct::id, lmt_sct::is_rec_dmn, lmt_all_sct::lmt_dmn, lmt_all_sct::lmt_dmn_nbr, lmt_sct::lmt_typ, lst_prs_2D(), lmt_sct::max_sng, lmt_sct::min_sng, option::name, NC_FORMAT_64BIT, NC_FORMAT_CLASSIC, NC_FORMAT_NETCDF4, NC_GLOBAL, NC_MAX_DIMS, NC_MAX_NAME, NC_NOERR, NC_NOFILL, NC_NOWRITE, nco__enddef(), nco_att_cpy(), nco_bnr_close(), nco_bnr_open(), nco_bool, nco_close(), nco_cmd_ln_sng(), nco_cmp_get(), nco_cpy_var_dfn(), nco_cpy_var_dfn_lmt(), nco_cpy_var_val(), nco_cpy_var_val_mlt_lmt(), nco_create_mode_prs(), nco_enddef(), nco_err_exit(), nco_exit(), nco_exit_gracefully(), nco_fl_lst_mk(), nco_fl_mk_lcl(), nco_fl_nm_prs(), nco_fl_out_cls(), nco_fl_out_open(), nco_fl_rm(), nco_free(), nco_hst_att_cat(), nco_inq(), nco_inq_dim(), nco_lbr_vrs_prn(), nco_lmt_all_lst_free(), nco_lmt_evl(), nco_lmt_lst_free(), nco_lmt_prs(), nco_lst_comma2hash(), nco_lst_srt_nm_id(), nco_malloc(), nco_mpi_get(), nco_msa_clc_cnt(), nco_msa_prn_var_val(), nco_msa_wrp_splt(), nco_nm_id_lst_free(), nco_open(), nco_prn_att(), nco_prn_var_dfn(), nco_realloc(), NCO_REC_DMN_UNDEFINED, nco_set_fill(), nco_sng_lst_free(), nco_usg_prn(), nco_var_lst_add_crd(), nco_var_lst_ass_crd_add(), nco_var_lst_mk(), nco_var_lst_xcl(), lmt_sct::nm, no_argument, NULL_CEWI, optarg, optind, prg_nm_get(), prg_prs(), required_argument, lmt_sct::srd, lmt_sct::srd_sng, lmt_sct::srt, True, and lmt_all_sct::WRP. { nco_bool ALPHABETIZE_OUTPUT=True; /* Option a */ nco_bool EXCLUDE_INPUT_LIST=False; /* Option c */ nco_bool FILE_RETRIEVED_FROM_REMOTE_LOCATION; 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 NCO_BNR_WRT=False; /* [flg] Write binary file */ nco_bool PRN_DMN_IDX_CRD_VAL=True; /* [flg] Print leading dimension/coordinate indices/values Option Q */ nco_bool PRN_DMN_UNITS=False; /* [flg] Print dimensional units Option u */ nco_bool PRN_DMN_UNITS_TGL=False; /* [flg] Toggle print dimensional units Option u */ nco_bool PRN_GLB_METADATA=False; /* [flg] Print global metadata */ nco_bool PRN_GLB_METADATA_TGL=False; /* [flg] Toggle print global metadata Option M */ nco_bool PRN_QUIET=False; /* [flg] Turn off all printing to screen */ nco_bool PRN_VAR_DATA=False; /* [flg] Print variable data */ nco_bool PRN_VAR_DATA_TGL=False; /* [flg] Toggle print variable data Option H */ nco_bool PRN_VAR_METADATA=False; /* [flg] Print variable metadata */ nco_bool PRN_VAR_METADATA_TGL=False; /* [flg] Toggle print variable metadata Option m */ nco_bool PRN_VRB=False; /* [flg] Print data and metadata by default */ nco_bool PROCESS_ALL_COORDINATES=False; /* Option c */ nco_bool PROCESS_ASSOCIATED_COORDINATES=True; /* Option C */ nco_bool REMOVE_REMOTE_FILES_AFTER_PROCESSING=True; /* Option R */ char **fl_lst_abb=NULL; /* Option a */ char **fl_lst_in; char **var_lst_in=NULL; char *cmd_ln; char *dlm_sng=NULL; char *fl_bnr=NULL; /* [sng] Unformatted binary output file */ 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 *opt_crr=NULL; /* [sng] String representation of current long-option name */ char *optarg_lcl=NULL; /* [sng] Local copy of system optarg */ char *time_bfr_srt; char dmn_nm[NC_MAX_NAME]; const char * const CVS_Id="$Id: ncks.c,v 1.155 2006/02/26 07:41:55 zender Exp $"; const char * const CVS_Revision="$Revision: 1.155 $"; const char * const opt_sht_lst="4aABb:CcD:d:FHhl:MmOo:Pp:qQrRs:uv:x-:"; extern char *optarg; extern int optind; FILE *fp_bnr=NULL_CEWI; /* [fl] Unformatted binary output file handle */ int abb_arg_nbr=0; int fl_nbr=0; int fl_out_fmt=NC_FORMAT_CLASSIC; /* [enm] Output file format */ int fll_md_old; /* [enm] Old fill mode */ int glb_att_nbr; int idx; int in_id; int jdx; int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */ int nbr_dmn_fl; int nbr_var_fl; int nbr_xtr=0; /* nbr_xtr will not otherwise be set for -c with no -v */ int opt; int rcd=NC_NOERR; /* [rcd] Return code */ int rec_dmn_id=NCO_REC_DMN_UNDEFINED; int var_lst_in_nbr=0; lmt_sct **lmt; lmt_sct **lmt_rgl; /* Regular limits */ lmt_all_sct **lmt_all_lst; /* List of *lmt_all structures */ lmt_all_sct *lmt_all_crr; /* Current lmt_all structure */ long dmn_sz; nm_id_sct *xtr_lst=NULL; /* xtr_lst may be alloc()'d from NULL with -c option */ size_t hdr_pad=0UL; /* [B] Pad at end of header section */ time_t time_crr_time_t; static struct option opt_lng[]= { /* Structure ordered by short option key if possible */ /* Long options with no argument, no short option counterpart */ {"cmp",no_argument,0,0}, {"compiler",no_argument,0,0}, {"mpi_implementation",no_argument,0,0}, /* Long options with argument, no short option counterpart */ {"fl_fmt",required_argument,0,0}, {"file_format",required_argument,0,0}, {"hdr_pad",required_argument,0,0}, {"header_pad",required_argument,0,0}, /* Long options with short counterparts */ {"4",no_argument,0,'4'}, {"64bit",no_argument,0,'4'}, {"netcdf4",no_argument,0,'4'}, {"abc",no_argument,0,'a'}, {"alphabetize",no_argument,0,'a'}, {"append",no_argument,0,'A'}, {"apn",no_argument,0,'A'}, {"bnr",no_argument,0,'B'}, {"binary",no_argument,0,'B'}, {"binary-file",required_argument,0,'b'}, {"fl_bnr",required_argument,0,'b'}, {"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'}, {"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'}, {"history",no_argument,0,'h'}, {"hst",no_argument,0,'h'}, {"hieronymus",no_argument,0,'H'}, /* fxm: need better mnemonic for -H */ {"local",required_argument,0,'l'}, {"lcl",required_argument,0,'l'}, {"lcl",required_argument,0,'l'}, {"metadata",no_argument,0,'m'}, {"mtd",no_argument,0,'m'}, {"Metadata",no_argument,0,'M'}, {"Mtd",no_argument,0,'M'}, {"overwrite",no_argument,0,'O'}, {"ovr",no_argument,0,'O'}, {"output",required_argument,0,'o'}, {"fl_out",required_argument,0,'o'}, {"print",required_argument,0,'P'}, {"prn",required_argument,0,'P'}, {"path",required_argument,0,'p'}, {"quiet",no_argument,0,'q'}, {"retain",no_argument,0,'R'}, {"rtn",no_argument,0,'R'}, {"revision",no_argument,0,'r'}, {"version",no_argument,0,'r'}, {"vrs",no_argument,0,'r'}, {"sng_fmt",required_argument,0,'s'}, {"string",required_argument,0,'s'}, {"units",no_argument,0,'u'}, {"variable",required_argument,0,'v'}, {"exclude",no_argument,0,'x'}, {"xcl",no_argument,0,'x'}, {"help",no_argument,0,'?'}, {0,0,0,0} }; /* end opt_lng */ int opt_idx=0; /* Index of current long option into opt_lng array */ /* Start clock and save command line */ cmd_ln=nco_cmd_ln_sng(argc,argv); time_crr_time_t=time((time_t *)NULL); time_bfr_srt=ctime(&time_crr_time_t); time_bfr_srt=time_bfr_srt; /* Avoid compiler warning until variable is used for something */ fl_bnr=(char *)strdup("ncks.bnr"); /* Get program name and set program enum (e.g., prg=ncra) */ prg_nm=prg_prs(argv[0],&prg); /* 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,"cmp") || !strcmp(opt_crr,"compiler")){ (void)fprintf(stdout,"%s\n",nco_cmp_get()); nco_exit(EXIT_SUCCESS); } /* endif "cmp" */ if(!strcmp(opt_crr,"fl_fmt") || !strcmp(opt_crr,"file_format")) rcd=nco_create_mode_prs(optarg,&fl_out_fmt); if(!strcmp(opt_crr,"hdr_pad") || !strcmp(opt_crr,"header_pad")) hdr_pad=strtoul(optarg,(char **)NULL,10); if(!strcmp(opt_crr,"mpi_implementation")){ (void)fprintf(stdout,"%s\n",nco_mpi_get()); nco_exit(EXIT_SUCCESS); } /* endif "mpi" */ } /* opt != 0 */ /* Process short options */ switch(opt){ case 0: /* Long options have already been processed, return */ break; case '4': /* [flg] 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 'a': /* Toggle ALPHABETIZE_OUTPUT */ ALPHABETIZE_OUTPUT=!ALPHABETIZE_OUTPUT; break; case 'A': /* Toggle FORCE_APPEND */ FORCE_APPEND=!FORCE_APPEND; break; case 'B': /* Set NCO_BNR_WRT */ NCO_BNR_WRT=True; break; case 'b': /* Set file for binary output */ NCO_BNR_WRT=True; fl_bnr=(char *)strdup(optarg); break; case 'C': /* Extract all coordinates associated with extracted variables? */ PROCESS_ASSOCIATED_COORDINATES=!PROCESS_ASSOCIATED_COORDINATES; break; case 'c': /* Add all coordinates to extraction list? */ PROCESS_ALL_COORDINATES=True; break; case 'D': /* Debugging level. Default is 0. */ dbg_lvl=(unsigned short)strtol(optarg,(char **)NULL,10); break; case 'd': /* Copy argument for later processing */ lmt_arg[lmt_nbr]=(char *)strdup(optarg); lmt_nbr++; break; case 'H': /* Toggle printing data to screen */ PRN_VAR_DATA_TGL=True; 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 'm': /* Toggle printing variable metadata to screen */ PRN_VAR_METADATA_TGL=True; break; case 'M': /* Toggle printing global metadata to screen */ PRN_GLB_METADATA_TGL=True; break; case 'O': /* Toggle FORCE_OVERWRITE */ FORCE_OVERWRITE=!FORCE_OVERWRITE; break; case 'o': /* Name of output file */ fl_out=(char *)strdup(optarg); break; case 'F': /* Toggle index convention. Default is 0-based arrays (C-style). */ FORTRAN_IDX_CNV=!FORTRAN_IDX_CNV; break; case 'P': /* Print data to screen, maximal verbosity */ PRN_VRB=True; PROCESS_ASSOCIATED_COORDINATES=!PROCESS_ASSOCIATED_COORDINATES; break; case 'p': /* Common file path */ fl_pth=(char *)strdup(optarg); break; case 'q': /* [flg] Turn off all printing to screen */ PRN_QUIET=True; /* [flg] Turn off all printing to screen */ break; case 'Q': /* Turn off printing of dimension indices and coordinate values */ PRN_DMN_IDX_CRD_VAL=!PRN_DMN_IDX_CRD_VAL; break; case 'R': /* Toggle removal of remotely-retrieved-files. Default is True. */ REMOVE_REMOTE_FILES_AFTER_PROCESSING=!REMOVE_REMOTE_FILES_AFTER_PROCESSING; PRN_QUIET=True; /* [flg] Turn off all printing to screen */ break; case 'r': /* Print CVS program information and copyright notice */ (void)copyright_prn(CVS_Id,CVS_Revision); (void)nco_lbr_vrs_prn(); nco_exit(EXIT_SUCCESS); break; case 's': /* User specified delimiter string for printed output */ dlm_sng=(char *)strdup(optarg); break; case 'u': /* Toggle printing dimensional units */ PRN_DMN_UNITS_TGL=True; break; case 'v': /* Variables to extract/exclude */ /* Replace commas with hashes when within braces (convert back later) */ optarg_lcl=(char *)strdup(optarg); (void)nco_lst_comma2hash(optarg_lcl); var_lst_in=lst_prs_2D(optarg_lcl,",",&var_lst_in_nbr); optarg_lcl=(char *)nco_free(optarg_lcl); nbr_xtr=var_lst_in_nbr; 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_FAILURE); 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",prg_nm_get()); nco_exit(EXIT_FAILURE); break; default: /* Print proper usage */ (void)nco_usg_prn(); nco_exit(EXIT_FAILURE); break; } /* end switch */ if(opt_crr != NULL) 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 dimension limits */ lmt=nco_lmt_prs(lmt_nbr,lmt_arg); /* 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,&FILE_RETRIEVED_FROM_REMOTE_LOCATION); /* Open file for reading */ rcd=nco_open(fl_in,NC_NOWRITE,&in_id); /* Get number of variables, dimensions, and global attributes in file */ (void)nco_inq(in_id,&nbr_dmn_fl,&nbr_var_fl,&glb_att_nbr,&rec_dmn_id); /* Form initial extraction list which may include extended regular expressions */ xtr_lst=nco_var_lst_mk(in_id,nbr_var_fl,var_lst_in,PROCESS_ALL_COORDINATES,&nbr_xtr); /* Change included variables to excluded variables */ if(EXCLUDE_INPUT_LIST) xtr_lst=nco_var_lst_xcl(in_id,nbr_var_fl,xtr_lst,&nbr_xtr); /* Add all coordinate variables to extraction list */ if(PROCESS_ALL_COORDINATES) xtr_lst=nco_var_lst_add_crd(in_id,nbr_dmn_fl,xtr_lst,&nbr_xtr); /* Make sure coordinates associated extracted variables are also on extraction list */ if(PROCESS_ASSOCIATED_COORDINATES) xtr_lst=nco_var_lst_ass_crd_add(in_id,xtr_lst,&nbr_xtr); /* Sort extraction list alphabetically or by variable ID */ if(nbr_xtr > 1) xtr_lst=nco_lst_srt_nm_id(xtr_lst,nbr_xtr,ALPHABETIZE_OUTPUT); /* We now have final list of variables to extract. Phew. */ /* fxm: subroutineize this code block */ /* Place all dimensions in lmt_all_lst */ lmt_all_lst=(lmt_all_sct **)nco_malloc(nbr_dmn_fl*sizeof(lmt_all_sct *)); /* Unlimited dimensions are stored in */ lmt_rgl=(lmt_sct **)nco_malloc(nbr_dmn_fl*sizeof(lmt_sct*)); for(idx=0;idx<nbr_dmn_fl;idx++){ (void)nco_inq_dim(in_id,idx,dmn_nm,&dmn_sz); lmt_all_crr=lmt_all_lst[idx]=(lmt_all_sct *)nco_malloc(sizeof(lmt_all_sct)); lmt_all_crr->lmt_dmn=(lmt_sct **)nco_malloc(sizeof(lmt_sct *)); lmt_all_crr->dmn_nm=strdup(dmn_nm); lmt_all_crr->lmt_dmn_nbr=1; lmt_all_crr->dmn_sz_org=dmn_sz; lmt_all_crr->WRP=False; lmt_all_crr->BASIC_DMN=True; /* Initialize lmt_rgl struct */ lmt_rgl[idx]=(lmt_sct *)nco_malloc(sizeof(lmt_sct)); lmt_rgl[idx]->nm=strdup(lmt_all_crr->dmn_nm); lmt_rgl[idx]->id=idx; lmt_rgl[idx]->is_rec_dmn=(idx == rec_dmn_id ? True : False); lmt_rgl[idx]->srt=0L; lmt_rgl[idx]->end=dmn_sz-1L; lmt_rgl[idx]->cnt=dmn_sz; lmt_rgl[idx]->srd=1L; lmt_rgl[idx]->min_sng=NULL; lmt_rgl[idx]->max_sng=NULL; lmt_rgl[idx]->srd_sng=NULL; /* A hack so we know struct has been initialized */ lmt_rgl[idx]->lmt_typ=-1; lmt_all_crr->lmt_dmn[0]=lmt_rgl[idx]; } /* end loop over dimensions */ /* subroutineize this code block */ /* Add user specified limits lmt_all_lst */ for(idx=0;idx<lmt_nbr;idx++){ /* Find coordinate/dimension values associated with user-specified limits NB: nco_lmt_evl() with same nc_id contains OpenMP critical region */ (void)nco_lmt_evl(in_id,lmt[idx],0L,FORTRAN_IDX_CNV); for(jdx=0;jdx<nbr_dmn_fl;jdx++) { if(!strcmp(lmt[idx]->nm,lmt_all_lst[jdx]->dmn_nm)){ lmt_all_crr=lmt_all_lst[jdx]; lmt_all_crr->BASIC_DMN=False; if(lmt_all_crr->lmt_dmn[0]->lmt_typ == -1) { lmt_all_crr->lmt_dmn[0]=lmt[idx]; }else{ lmt_all_crr->lmt_dmn=(lmt_sct **)nco_realloc(lmt_all_crr->lmt_dmn,((lmt_all_crr->lmt_dmn_nbr)+1)*sizeof(lmt_sct *)); lmt_all_crr->lmt_dmn[(lmt_all_crr->lmt_dmn_nbr)++]=lmt[idx]; } /* endif */ break; } /* end if */ } /* end loop over dimensions */ /* Dimension in limit not found */ if(jdx == nbr_dmn_fl){ (void)fprintf(stderr,"Unable to find limit dimension %s in list\n ",lmt[idx]->nm); nco_exit(EXIT_FAILURE); } /* end if err */ } /* end loop over idx */ /* Split up wrapped limits */ for(idx=0;idx<nbr_dmn_fl;idx++) if(lmt_all_lst[idx]->BASIC_DMN == False) (void)nco_msa_wrp_splt(lmt_all_lst[idx]); /* Find and store final size of each dimension */ for(idx=0;idx<nbr_dmn_fl;idx++){ (void)nco_msa_clc_cnt(lmt_all_lst[idx]); } /* end loop over dimensions */ if(PRN_VRB || (fl_out == NULL && !PRN_VAR_DATA_TGL && !PRN_VAR_METADATA_TGL && !PRN_GLB_METADATA_TGL)){ /* Verbose printing simply means assume user wants the deluxe frills by default */ if(PRN_DMN_UNITS_TGL) PRN_DMN_UNITS=False; else PRN_DMN_UNITS=True; if(PRN_VAR_DATA_TGL) PRN_VAR_DATA=False; else PRN_VAR_DATA=True; if(PRN_VAR_METADATA_TGL) PRN_VAR_METADATA=False; else PRN_VAR_METADATA=True; /* Assume user wants to see global metadata unless variable extraction is invoked */ if(var_lst_in == NULL) PRN_GLB_METADATA=True; if(PRN_GLB_METADATA_TGL) PRN_GLB_METADATA=!PRN_GLB_METADATA; }else{ /* end if PRN_VRB */ /* Default is to print data and metadata to screen if output file is not specified */ if(PRN_DMN_UNITS_TGL) PRN_DMN_UNITS=True; else PRN_DMN_UNITS=False; if(PRN_VAR_DATA_TGL) PRN_VAR_DATA=True; else PRN_VAR_DATA=False; if(PRN_VAR_METADATA_TGL) PRN_VAR_METADATA=True; else PRN_VAR_METADATA=False; if(PRN_GLB_METADATA_TGL) PRN_GLB_METADATA=True; else PRN_GLB_METADATA=False; } /* endelse */ /* PRN_QUIET is catch-all which turns off all printing to screen */ if(PRN_QUIET) PRN_VAR_DATA=PRN_VAR_METADATA=PRN_GLB_METADATA=False; if(NCO_BNR_WRT && fl_out == NULL){ /* Native binary files depend on writing netCDF file to enter generic I/O logic */ (void)fprintf(stdout,"%s: ERROR Native binary files cannot be written unless netCDF output filename also specified. HINT: Repeat command with throw-away netCDF file specified for output file (e.g., -o foo.nc)\n",prg_nm_get()); } /* endif NCO_BNR_WRT */ if(fl_out != NULL){ int out_id; /* Open output file */ fl_out_tmp=nco_fl_out_open(fl_out,FORCE_APPEND,FORCE_OVERWRITE,fl_out_fmt,&out_id); /* Copy global attributes */ (void)nco_att_cpy(in_id,out_id,NC_GLOBAL,NC_GLOBAL,True); /* Catenate timestamped command line to "history" global attribute */ if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln); for(idx=0;idx<nbr_xtr;idx++){ int var_out_id; /* Define variable in output file */ if(lmt_nbr > 0) var_out_id=nco_cpy_var_dfn_lmt(in_id,out_id,rec_dmn_id,xtr_lst[idx].nm,lmt_all_lst,nbr_dmn_fl); else var_out_id=nco_cpy_var_dfn(in_id,out_id,rec_dmn_id,xtr_lst[idx].nm); /* Copy variable's attributes */ (void)nco_att_cpy(in_id,out_id,xtr_lst[idx].id,var_out_id,True); } /* end loop over idx */ /* Turn off default filling behavior to enhance efficiency */ rcd=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(dbg_lvl > 1) (void)fprintf(stderr,"%s: INFO Padding header with %lu extra bytes \n",prg_nm_get(),(unsigned long)hdr_pad); } /* hdr_pad */ /* [fnc] Open unformatted binary data file for writing */ if(NCO_BNR_WRT) fp_bnr=nco_bnr_open(fl_bnr); /* Copy variable data */ for(idx=0;idx<nbr_xtr;idx++){ if(dbg_lvl > 2 && !NCO_BNR_WRT) (void)fprintf(stderr,"%s, ",xtr_lst[idx].nm); if(dbg_lvl > 0) (void)fflush(stderr); /* Old hyperslab routines */ /* NB: nco_cpy_var_val_lmt() contains OpenMP critical region */ /* if(lmt_nbr > 0) (void)nco_cpy_var_val_lmt(in_id,out_id,fp_bnr,NCO_BNR_WRT,xtr_lst[idx].nm,lmt,lmt_nbr); else (void)nco_cpy_var_val(in_id,out_id,fp_bnr,NCO_BNR_WRT,xtr_lst[idx].nm); */ /* Multi-slab routines */ /* NB: nco_cpy_var_val_mlt_lmt() contains OpenMP critical region */ if(lmt_nbr > 0) (void)nco_cpy_var_val_mlt_lmt(in_id,out_id,fp_bnr,NCO_BNR_WRT,xtr_lst[idx].nm,lmt_all_lst,nbr_dmn_fl); else (void)nco_cpy_var_val(in_id,out_id,fp_bnr,NCO_BNR_WRT,xtr_lst[idx].nm); } /* end loop over idx */ /* [fnc] Close unformatted binary data file */ if(NCO_BNR_WRT) (void)nco_bnr_close(fp_bnr,fl_bnr); /* Close output file and move it from temporary to permanent location */ (void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id); } /* end if fl_out != NULL */ if(PRN_GLB_METADATA){ (void)fprintf(stdout,"Opened file %s: dimensions = %i, variables = %i, global atts. = %i, id = %i\n",fl_in,nbr_dmn_fl,nbr_var_fl,glb_att_nbr,in_id); if(rec_dmn_id != NCO_REC_DMN_UNDEFINED){ char rec_dmn_nm[NC_MAX_NAME]; long rec_dmn_sz; (void)nco_inq_dim(in_id,rec_dmn_id,rec_dmn_nm,&rec_dmn_sz); (void)fprintf(stdout,"Record dimension: name = %s, size = %li\n\n",rec_dmn_nm,rec_dmn_sz); } /* end if */ /* Print all global attributes */ (void)nco_prn_att(in_id,NC_GLOBAL); } /* endif PRN_GLB_METADATA */ if(PRN_VAR_METADATA){ for(idx=0;idx<nbr_xtr;idx++){ /* Print variable's definition */ (void)nco_prn_var_dfn(in_id,xtr_lst[idx].nm); /* Print variable's attributes */ (void)nco_prn_att(in_id,xtr_lst[idx].id); } /* end loop over idx */ } /* end if PRN_VAR_METADATA */ /* if(PRN_VAR_DATA){ */ /* NB: nco_prn_var_val_lmt() with same nc_id contains OpenMP critical region */ /* for(idx=0;idx<nbr_xtr;idx++) (void)nco_prn_var_val_lmt(in_id,xtr_lst[idx].nm,lmt,lmt_nbr,dlm_sng,FORTRAN_IDX_CNV,PRN_DMN_UNITS,PRN_DMN_IDX_CRD_VAL); } */ if(PRN_VAR_DATA){ /* NB: nco_msa_prn_var_val() with same nc_id contains OpenMP critical region */ for(idx=0;idx<nbr_xtr;idx++) (void)nco_msa_prn_var_val(in_id,xtr_lst[idx].nm,lmt_all_lst,nbr_dmn_fl,dlm_sng,FORTRAN_IDX_CNV,PRN_DMN_UNITS,PRN_DMN_IDX_CRD_VAL); } /* end if PRN_VAR_DATA */ /* Extraction list no longer needed */ xtr_lst=nco_nm_id_lst_free(xtr_lst,nbr_xtr); /* Close input netCDF file */ nco_close(in_id); /* Remove local copy of file */ if(FILE_RETRIEVED_FROM_REMOTE_LOCATION && REMOVE_REMOTE_FILES_AFTER_PROCESSING) (void)nco_fl_rm(fl_in); /* ncks-unique memory */ if(fl_bnr != NULL) fl_bnr=(char *)nco_free(fl_bnr); if(nbr_dmn_fl > 0) lmt_all_lst=nco_lmt_all_lst_free(lmt_all_lst,nbr_dmn_fl); if(nbr_dmn_fl > 0) lmt_rgl=nco_lmt_lst_free(lmt_rgl,nbr_dmn_fl); /* NCO-generic clean-up */ /* Free individual strings/arrays */ if(cmd_ln != NULL) cmd_ln=(char *)nco_free(cmd_ln); if(fl_in != NULL) fl_in=(char *)nco_free(fl_in); if(fl_out != NULL) fl_out=(char *)nco_free(fl_out); if(fl_out_tmp != NULL) fl_out_tmp=(char *)nco_free(fl_out_tmp); if(fl_pth != NULL) fl_pth=(char *)nco_free(fl_pth); if(fl_pth_lcl != NULL) fl_pth_lcl=(char *)nco_free(fl_pth_lcl); /* Free lists of strings */ if(fl_lst_in != NULL && fl_lst_abb == NULL) fl_lst_in=nco_sng_lst_free(fl_lst_in,fl_nbr); if(fl_lst_in != NULL && fl_lst_abb != NULL) fl_lst_in=nco_sng_lst_free(fl_lst_in,1); if(fl_lst_abb != NULL) 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<lmt_nbr;idx++) lmt_arg[idx]=(char *)nco_free(lmt_arg[idx]); if(lmt_nbr > 0) lmt=nco_lmt_lst_free(lmt,lmt_nbr); if(rcd != NC_NOERR) nco_err_exit(rcd,"main"); nco_exit_gracefully(); return EXIT_SUCCESS; } /* end main() */

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