nco/ncra.c File Reference

#include <math.h>
#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 ncra.c:

Go to the source code of this file.

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

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Define Documentation

#define gettext (  foo   )     foo

Definition at line 78 of file ncra.c.

#define MAIN_PROGRAM_FILE

Definition at line 86 of file ncra.c.

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Function Documentation

int main (  int  argc, char **  argv )

Definition at line 90 of file ncra.c. References arm_base_time_get(), arm_inq(), var_sct_tag::cnt, copyright_prn(), ptr_unn::dp, var_sct_tag::end, lmt_sct::end, EXIT_FAILURE, EXIT_SUCCESS, False, FILE, getopt_long, gettext, var_sct_tag::has_mss_val, int_CEWI, var_sct_tag::is_crd_var, lmt_sct::is_usr_spc_max, lmt_sct::is_usr_spc_min, lmt_dmn_idx, lmt_sct::lmt_typ, lst_prs_2D(), lmt_sct::max_idx, lmt_sct::min_idx, option::name, var_sct_tag::nbr_dim, NC_FORMAT_64BIT, NC_FORMAT_CLASSIC, NC_FORMAT_NETCDF4, NC_GLOBAL, NC_MAX_DIMS, NC_NOERR, NC_NOFILL, NC_NOWRITE, ncea, nco_arm_time_install(), nco_att_cpy(), nco_bool, nco_close(), nco_cmd_ln_sng(), nco_cnv_ccm_ccsm_cf_date(), nco_cnv_ccm_ccsm_cf_inq(), nco_cnv_mss_val_typ(), nco_create_mode_prs(), nco_dmn_dfn(), nco_dmn_dpl(), nco_dmn_fll(), nco_dmn_lmt_mrg(), nco_dmn_lst_ass_var(), nco_dmn_lst_free(), nco_dmn_xrf(), nco_enddef(), nco_exit(), nco_exit_gracefully(), nco_fl_cmp_err_chk(), nco_fl_lst_att_cat(), 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_int_CEWI, nco_lbr_vrs_prn(), nco_lmt_evl(), nco_lmt_free(), nco_lmt_lst_free(), nco_lmt_prs(), nco_lmt_sct_mk(), nco_lst_comma2hash(), nco_lst_srt_nm_id(), nco_malloc(), nco_nm_id_lst_free(), nco_op_avg, nco_op_avgsqr, nco_op_max, nco_op_min, nco_op_rms, nco_op_rmssdn, nco_op_sqravg, nco_op_sqrt, nco_op_ttl, nco_op_typ_get(), nco_open(), nco_openmp_ini(), nco_opr_drv(), nco_pck_map_nil, nco_pck_plc_all_new_att, nco_pck_plc_get(), nco_pck_plc_nil, nco_put_var1(), nco_put_var_pck(), nco_put_vara(), NCO_REC_DMN_UNDEFINED, nco_set_fill(), nco_sng_lst_free(), nco_thr_att_cat(), nco_typ_cnv_rth(), nco_typ_lng(), nco_usg_prn(), nco_var_cnf_typ(), nco_var_dfn(), nco_var_dpl(), nco_var_fll(), nco_var_get(), nco_var_lst_add_crd(), nco_var_lst_ass_crd_add(), nco_var_lst_dvd(), nco_var_lst_free(), nco_var_lst_mk(), nco_var_lst_xcl(), nco_var_mlt(), nco_var_mtd_refresh(), nco_var_nrm(), nco_var_nrm_sdn(), nco_var_prc_crr_prn(), nco_var_sqrt(), nco_var_srt_zero(), nco_var_val_cpy(), nco_var_zero(), nco_xrf_dmn(), nco_xrf_var(), nco_zero_long(), ncra, ncrcat, no_argument, NULL_CEWI, omp_get_thread_num(), optarg, optind, prg_nm_get(), prg_prs(), rec_crd_chk(), required_argument, lmt_sct::srd, var_sct_tag::srt, lmt_sct::srt, var_sct_tag::sz, var_sct_tag::sz_rec, var_sct_tag::tally, True, var_sct_tag::typ_upk, var_sct_tag::type, type, option::val, var_sct_tag::val, and ptr_unn::vp. { nco_bool CNV_ARM=int_CEWI; nco_bool CNV_CCM_CCSM_CF=int_CEWI; 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_RETRIEVED_FROM_REMOTE_LOCATION; 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 LAST_RECORD=False; nco_bool REMOVE_REMOTE_FILES_AFTER_PROCESSING=True; /* Option R */ char **fl_lst_abb=NULL; /* Option n */ char **fl_lst_in; char **var_lst_in=NULL_CEWI; char *cmd_ln; 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_op_typ_sng=NULL_CEWI; /* [sng] Operation type Option y */ char *nco_pck_plc_sng=NULL_CEWI; /* [sng] Packing policy Option P */ 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; const char * const CVS_Id="$Id: ncra.c,v 1.176 2006/02/26 07:41:55 zender Exp $"; const char * const CVS_Revision="$Revision: 1.176 $"; const char * const opt_sht_lst="4ACcD:d:FHhl:n:Oo:p:P:rRt:v:xY:y:-:"; 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 fl_idx; int fl_nbr=0; int fl_out_fmt=NC_FORMAT_CLASSIC; /* [enm] Output file format */ int fll_md_old; /* [enm] Old fill mode */ int idx=int_CEWI; int in_id; int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */ 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 nbr_xtr=0; /* nbr_xtr won't otherwise be set for -c with no -v */ int nco_op_typ=nco_op_avg; /* [enm] Default operation is averaging */ int nco_pck_plc=nco_pck_plc_nil; /* [enm] Default packing is none */ 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 **lmt=NULL_CEWI; lmt_sct *lmt_rec=NULL_CEWI; long idx_rec; /* [idx] Index of current record in current input file */ long idx_rec_out=0L; /* [idx] Index of current record in output file (0 is first, ...) */ nco_int base_time_srt=nco_int_CEWI; nco_int base_time_crr=nco_int_CEWI; nm_id_sct *dmn_lst; nm_id_sct *xtr_lst=NULL; /* xtr_lst may be alloc()'d from NULL with -c option */ time_t time_crr_time_t; var_sct **var; var_sct **var_fix; var_sct **var_fix_out; var_sct **var_out=NULL_CEWI; var_sct **var_prc; var_sct **var_prc_out; static struct option opt_lng[]= { /* Structure ordered by short option key if possible */ /* Long options with no argument, no short option counterpart */ /* Long options with argument, no short option counterpart */ {"fl_fmt",required_argument,0,0}, {"file_format",required_argument,0,0}, /* Long options with short counterparts */ {"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'}, {"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'}, {"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'}, {"pack",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'}, {"version",no_argument,0,'r'}, {"vrs",no_argument,0,'r'}, {"exclude",no_argument,0,'x'}, {"xcl",no_argument,0,'x'}, {"pseudonym",required_argument,0,'Y'}, {"program",required_argument,0,'Y'}, {"prg_nm",required_argument,0,'Y'}, {"math",required_argument,0,'y'}, {"help",no_argument,0,'?'}, {0,0,0,0} }; /* end opt_lng */ int opt_idx=0; /* Index of current long option into opt_lng array */ #ifdef _LIBINTL_H setlocale(LC_ALL,""); /* LC_ALL sets all localization tokens to same value */ bindtextdomain("nco","/home/zender/share/locale"); /* ${LOCALEDIR} is e.g., /usr/share/locale */ /* MO files should be in ${LOCALEDIR}/es/LC_MESSAGES */ textdomain("nco"); /* PACKAGE is name of program */ #endif /* not _LIBINTL_H */ /* 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 */ #if 0 /* Solaris version of ctime_r() requires three arguments */ ctime_r(&time_crr_time_t,time_bfr_srt); time_bfr_srt[24] = '\0'; /* Remove newline */ #endif /* !0 */ /* 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,"fl_fmt") || !strcmp(opt_crr,"file_format")) rcd=nco_create_mode_prs(optarg,&fl_out_fmt); } /* 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 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. */ 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 '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': /* 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 average */ fl_lst_abb=lst_prs_2D(optarg,",",&abb_arg_nbr); if(abb_arg_nbr < 1 || abb_arg_nbr > 5){ (void)fprintf(stdout,gettext("%s: ERROR Incorrect abbreviation for file list\n"),prg_nm_get()); (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 'P': /* Packing policy */ nco_pck_plc_sng=(char *)strdup(optarg); nco_pck_plc=nco_pck_plc_get(nco_pck_plc_sng); break; case 'R': /* Toggle removal of remotely-retrieved-files. Default is True. */ REMOVE_REMOTE_FILES_AFTER_PROCESSING=!REMOVE_REMOTE_FILES_AFTER_PROCESSING; 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 't': /* Thread number */ thr_nbr=(int)strtol(optarg,(char **)NULL,10); 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 'Y': /* Pseudonym */ /* Call prg_prs to reset pseudonym */ optarg_lcl=(char *)strdup(optarg); if(prg_nm != NULL) prg_nm=(char *)nco_free(prg_nm); prg_nm=prg_prs(optarg_lcl,&prg); optarg_lcl=(char *)nco_free(optarg_lcl); break; case 'y': /* Operation type */ nco_op_typ_sng=(char *)strdup(optarg); if(prg == ncra || prg == ncea ) 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",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 */ if(lmt_nbr > 0) 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,&FILE_RETRIEVED_FROM_REMOTE_LOCATION); /* Open file for reading */ rcd=nco_open(fl_in,NC_NOWRITE,&in_id); /* 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); /* Form initial extraction list which may include extended regular expressions */ xtr_lst=nco_var_lst_mk(in_id,nbr_var_fl,var_lst_in,EXTRACT_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(EXTRACT_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(EXTRACT_ASSOCIATED_COORDINATES) xtr_lst=nco_var_lst_ass_crd_add(in_id,xtr_lst,&nbr_xtr); /* Sort extraction list by variable ID for fastest I/O */ if(nbr_xtr > 1) xtr_lst=nco_lst_srt_nm_id(xtr_lst,nbr_xtr,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); /* Find dimensions associated with variables to be extracted */ dmn_lst=nco_dmn_lst_ass_var(in_id,xtr_lst,nbr_xtr,&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 */ /* Create stand-alone limit structure just for record dimension */ if(prg == ncra || prg == ncrcat){ if(rec_dmn_id == NCO_REC_DMN_UNDEFINED){ (void)fprintf(stdout,gettext("%s: ERROR input file %s lacks a record dimension\n"),prg_nm_get(),fl_in); if(fl_nbr == 1)(void)fprintf(stdout,gettext("%s: HINT Use ncks instead of %s\n"),prg_nm_get(),prg_nm_get()); nco_exit(EXIT_FAILURE); } /* endif */ lmt_rec=nco_lmt_sct_mk(in_id,rec_dmn_id,lmt,lmt_nbr,FORTRAN_IDX_CNV); } /* endif */ /* Is this an CCM/CCSM/CF-format history tape? */ CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(in_id); /* Is this an ARM-format data file? */ CNV_ARM=arm_inq(in_id); /* NB: arm_base_time_get() with same nc_id contains OpenMP critical region */ if(CNV_ARM) base_time_srt=arm_base_time_get(in_id); /* Fill in variable structure list for all extracted variables */ var=(var_sct **)nco_malloc(nbr_xtr*sizeof(var_sct *)); var_out=(var_sct **)nco_malloc(nbr_xtr*sizeof(var_sct *)); for(idx=0;idx<nbr_xtr;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,nbr_xtr); /* Divide variable lists into lists of fixed variables and variables to be processed */ (void)nco_var_lst_dvd(var,var_out,nbr_xtr,CNV_CCM_CCSM_CF,nco_pck_plc_nil,nco_pck_map_nil,NULL,0,&var_fix,&var_fix_out,&nbr_var_fix,&var_prc,&var_prc_out,&nbr_var_prc); /* 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 time-stamped command line to "history" global attribute */ if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln); /* 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); /* Define dimensions in output file */ (void)nco_dmn_dfn(fl_out,out_id,dmn_out,nbr_dmn_xtr); /* Define variables in output file, copy their attributes */ (void)nco_var_dfn(in_id,fl_out,out_id,var_out,nbr_xtr,(dmn_sct **)NULL,(int)0,nco_pck_plc_nil,nco_pck_map_nil); /* Turn off default filling behavior to enhance efficiency */ (void)nco_set_fill(out_id,NC_NOFILL,&fll_md_old); /* Take output file out of define mode */ (void)nco_enddef(out_id); /* Zero start vectors for all output variables */ (void)nco_var_srt_zero(var_out,nbr_xtr); /* Copy variable data for non-processed variables */ (void)nco_var_val_cpy(in_id,out_id,var_fix,nbr_var_fix); /* Close first input netCDF file */ (void)nco_close(in_id); /* Allocate and, if necesssary, initialize accumulation space for processed variables */ for(idx=0;idx<nbr_var_prc;idx++){ if(prg == ncra || prg == ncrcat){ /* Allocate space for only one record */ var_prc_out[idx]->sz=var_prc[idx]->sz=var_prc[idx]->sz_rec; } /* endif */ if(prg == ncra || prg == ncea){ var_prc_out[idx]->tally=var_prc[idx]->tally=(long *)nco_malloc(var_prc_out[idx]->sz*sizeof(long)); (void)nco_zero_long(var_prc_out[idx]->sz,var_prc_out[idx]->tally); var_prc_out[idx]->val.vp=(void *)nco_malloc(var_prc_out[idx]->sz*nco_typ_lng(var_prc_out[idx]->type)); (void)nco_var_zero(var_prc_out[idx]->type,var_prc_out[idx]->sz,var_prc_out[idx]->val); } /* end if */ } /* end loop over idx */ /* Loop over input files */ 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,(int *)NULL,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth); if(dbg_lvl > 0) (void)fprintf(stderr,gettext("\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,&FILE_RETRIEVED_FROM_REMOTE_LOCATION); if(dbg_lvl > 0) (void)fprintf(stderr,gettext("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_open(fl_in,NC_NOWRITE,in_id_arr+thr_idx); in_id=in_id_arr[0]; /* Variables may have different ID, missing_value, type, in each file */ for(idx=0;idx<nbr_var_prc;idx++) (void)nco_var_mtd_refresh(in_id,var_prc[idx]); /* Each file can have a different number of records to process NB: nco_lmt_evl() with same nc_id contains OpenMP critical region */ if(prg == ncra || prg == ncrcat) (void)nco_lmt_evl(in_id,lmt_rec,idx_rec_out,FORTRAN_IDX_CNV); /* NB: arm_base_time_get() with same nc_id contains OpenMP critical region */ if(CNV_ARM) base_time_crr=arm_base_time_get(in_id); /* Perform various error-checks on input file */ if(False) (void)nco_fl_cmp_err_chk(); if(prg == ncra || prg == ncrcat){ /* ncea jumps to else branch */ /* Loop over each record in current file */ if(lmt_rec->srt > lmt_rec->end) (void)fprintf(fp_stdout,gettext("%s: WARNING %s (input file %d) is superfluous\n"),prg_nm_get(),fl_in,fl_idx); for(idx_rec=lmt_rec->srt;idx_rec<=lmt_rec->end;idx_rec+=lmt_rec->srd){ if(fl_idx == fl_nbr-1 && idx_rec >= 1L+lmt_rec->end-lmt_rec->srd) LAST_RECORD=True; /* Process all variables in current record */ if(dbg_lvl > 1) (void)fprintf(fp_stderr,gettext("Record %ld of %s is input record %ld\n"),idx_rec,fl_in,idx_rec_out); #ifdef _OPENMP #pragma omp parallel for default(none) private(idx,in_id) shared(CNV_ARM,base_time_crr,base_time_srt,dbg_lvl,fl_in,fl_out,fp_stderr,idx_rec,idx_rec_out,in_id_arr,LAST_RECORD,nbr_var_prc,nco_op_typ,out_id,prg,rcd,var_prc,var_prc_out) #endif /* !_OPENMP */ for(idx=0;idx<nbr_var_prc;idx++){ in_id=in_id_arr[omp_get_thread_num()]; if(dbg_lvl > 2) rcd+=nco_var_prc_crr_prn(idx,var_prc[idx]->nm); if(dbg_lvl > 0) (void)fflush(fp_stderr); /* Update hyperslab start indices to current record for each variable */ var_prc[idx]->srt[0]=idx_rec; var_prc[idx]->end[0]=idx_rec; var_prc[idx]->cnt[0]=1L; /* 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]); if(prg == ncra){ /* Convert char, short, long, int types to doubles before arithmetic Output variable type is "sticky" so only convert on first record */ if(idx_rec_out == 0) var_prc_out[idx]=nco_typ_cnv_rth(var_prc_out[idx],nco_op_typ); var_prc[idx]=nco_var_cnf_typ(var_prc_out[idx]->type,var_prc[idx]); /* Perform arithmetic operations: avg, min, max, ttl, ... */ nco_opr_drv(idx_rec_out,nco_op_typ,var_prc[idx],var_prc_out[idx]); } /* end if ncra */ /* Append current record to output file */ if(prg == ncrcat){ var_prc_out[idx]->srt[0]=var_prc_out[idx]->end[0]=idx_rec_out; var_prc_out[idx]->cnt[0]=1L; /* Replace this time_offset value with time_offset from initial file base_time */ if(CNV_ARM && !strcmp(var_prc[idx]->nm,"time_offset")) var_prc[idx]->val.dp[0]+=(base_time_crr-base_time_srt); #ifdef _OPENMP #pragma omp critical #endif /* _OPENMP */ if(var_prc_out[idx]->sz_rec > 1) (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_out[idx]->type); else (void)nco_put_var1(out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc[idx]->val.vp,var_prc_out[idx]->type); } /* end if ncrcat */ /* Warn if record coordinate, if any, is not monotonic */ if(prg == ncrcat && var_prc[idx]->is_crd_var) (void)rec_crd_chk(var_prc[idx],fl_in,fl_out,idx_rec,idx_rec_out); /* Convert missing_value, if any, back to unpacked type Otherwise missing_value will be double-promoted when next record read Do not convert after last record otherwise normalization fails due to wrong missing_value type (needs promoted type, not unpacked type) */ if(var_prc[idx]->has_mss_val && var_prc[idx]->type != var_prc[idx]->typ_upk && !LAST_RECORD) var_prc[idx]=nco_cnv_mss_val_typ(var_prc[idx],var_prc[idx]->typ_upk); /* Free current input buffer */ var_prc[idx]->val.vp=nco_free(var_prc[idx]->val.vp); } /* end (OpenMP parallel for) loop over variables */ idx_rec_out++; /* [idx] Index of current record in output file (0 is first, ...) */ if(dbg_lvl > 2) (void)fprintf(fp_stderr,"\n"); } /* end loop over idx_rec */ /* Warn if fewer than number of requested records were read and final file has been processed */ if(lmt_rec->lmt_typ == lmt_dmn_idx && lmt_rec->is_usr_spc_min && lmt_rec->is_usr_spc_max){ long rec_nbr_rqs; /* Number of records user requested */ rec_nbr_rqs=1L+(lmt_rec->max_idx-lmt_rec->min_idx)/lmt_rec->srd; if(fl_idx == fl_nbr-1 && rec_nbr_rqs != idx_rec_out) (void)fprintf(fp_stdout,gettext("%s: WARNING User requested %li records but only %li were found\n"),prg_nm_get(),rec_nbr_rqs,idx_rec_out); } /* end if */ /* Error if no records were read and final file has been processed */ if(idx_rec_out <= 0 && fl_idx == fl_nbr-1){ (void)fprintf(fp_stdout,gettext("%s: ERROR No records lay within specified hyperslab\n"),prg_nm_get()); nco_exit(EXIT_FAILURE); } /* end if */ /* End of ncra, ncrcat section */ }else{ /* ncea */ #ifdef _OPENMP #pragma omp parallel for default(none) private(idx,in_id) shared(dbg_lvl,fl_idx,fp_stderr,in_id_arr,nbr_var_prc,nco_op_typ,rcd,var_prc,var_prc_out) #endif /* !_OPENMP */ for(idx=0;idx<nbr_var_prc;idx++){ /* Process all variables in current file */ in_id=in_id_arr[omp_get_thread_num()]; if(dbg_lvl > 0) rcd+=nco_var_prc_crr_prn(idx,var_prc[idx]->nm); if(dbg_lvl > 0) (void)fflush(fp_stderr); /* Retrieve variable from disk into memory */ (void)nco_var_get(in_id,var_prc[idx]); /* Convert char, short, long, int types to doubles before arithmetic Output variable type is "sticky" so only convert on first record */ if(fl_idx == 0) var_prc_out[idx]=nco_typ_cnv_rth(var_prc_out[idx],nco_op_typ); var_prc[idx]=nco_var_cnf_typ(var_prc_out[idx]->type,var_prc[idx]); /* Perform arithmetic operations: avg, min, max, ttl, ... */ /* Note: fl_idx not idx_rec_out! */ nco_opr_drv(fl_idx,nco_op_typ,var_prc[idx],var_prc_out[idx]); /* Free current input buffer */ var_prc[idx]->val.vp=nco_free(var_prc[idx]->val.vp); } /* end (OpenMP parallel for) loop over idx */ } /* end else ncea */ if(dbg_lvl > 1) (void)fprintf(fp_stderr,"\n"); /* Close input netCDF file */ for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) nco_close(in_id_arr[thr_idx]); /* Dispose local copy of file */ if(FILE_RETRIEVED_FROM_REMOTE_LOCATION && REMOVE_REMOTE_FILES_AFTER_PROCESSING) (void)nco_fl_rm(fl_in); } /* end loop over fl_idx */ /* Normalize, multiply, etc where necessary */ if(prg == ncra || prg == ncea){ #ifdef _OPENMP #pragma omp parallel for default(none) private(idx) shared(nbr_var_prc,nco_op_typ,var_prc,var_prc_out) #endif /* !_OPENMP */ for(idx=0;idx<nbr_var_prc;idx++){ switch(nco_op_typ) { case nco_op_avg: /* Normalize sum by tally to create mean */ case nco_op_sqrt: /* Normalize sum by tally to create mean */ case nco_op_sqravg: /* Normalize sum by tally to create mean */ case nco_op_rms: /* Normalize sum of squares by tally to create mean square */ case nco_op_avgsqr: /* Normalize sum of squares by tally to create mean square */ (void)nco_var_nrm(var_prc_out[idx]->type,var_prc_out[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,var_prc[idx]->tally,var_prc_out[idx]->val); break; case nco_op_rmssdn: /* Normalize sum of squares by tally-1 to create mean square for sdn */ (void)nco_var_nrm_sdn(var_prc_out[idx]->type,var_prc_out[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,var_prc[idx]->tally,var_prc_out[idx]->val); break; case nco_op_min: /* Minimum is already in buffer, do nothing */ case nco_op_max: /* Maximum is already in buffer, do nothing */ case nco_op_ttl: /* Total is already in buffer, do nothing */ default: break; } /* end switch */ /* Some operations require additional processing */ switch(nco_op_typ) { case nco_op_rms: /* Take root of mean of sum of squares to create root mean square */ case nco_op_rmssdn: /* Take root of sdn mean of sum of squares to create root mean square for sdn */ case nco_op_sqrt: /* Take root of mean to create root mean */ (void)nco_var_sqrt(var_prc_out[idx]->type,var_prc_out[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,var_prc[idx]->tally,var_prc_out[idx]->val,var_prc_out[idx]->val); break; case nco_op_sqravg: /* Square mean to create square of the mean (for sdn) */ (void)nco_var_mlt(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,var_prc_out[idx]->val); break; default: break; } /* end switch */ var_prc_out[idx]->tally=var_prc[idx]->tally=(long *)nco_free(var_prc[idx]->tally); } /* end (OpenMP parallel for) loop over variables */ } /* end if */ /* Manually fix YYMMDD date which was mangled by averaging */ if(CNV_CCM_CCSM_CF && prg == ncra) (void)nco_cnv_ccm_ccsm_cf_date(out_id,var_out,nbr_xtr); /* Add time variable to output file NB: arm_time_install() contains OpenMP critical region */ if(CNV_ARM && prg == ncrcat) (void)nco_arm_time_install(out_id,base_time_srt); /* Copy averages to output file and free averaging buffers */ if(prg == ncra || prg == ncea){ for(idx=0;idx<nbr_var_prc;idx++){ /* Revert any arithmetic promotion but leave unpacking (for now) */ var_prc_out[idx]=nco_var_cnf_typ(var_prc_out[idx]->typ_upk,var_prc_out[idx]); /* Packing/Unpacking */ if(nco_pck_plc == nco_pck_plc_all_new_att) var_prc_out[idx]=nco_put_var_pck(out_id,var_prc_out[idx],nco_pck_plc); if(var_prc_out[idx]->nbr_dim == 0){ (void)nco_put_var1(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 a scalar */ /* Size of record dimension is 1 in output file */ if(prg == ncra) var_prc_out[idx]->cnt[0]=1L; (void)nco_put_vara(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 an array */ var_prc_out[idx]->val.vp=nco_free(var_prc_out[idx]->val.vp); } /* end loop over idx */ } /* end if */ /* Close output file and move it from temporary to permanent location */ (void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id); /* ncra-specific memory cleanup */ if(prg == ncra || prg == ncrcat) lmt_rec=nco_lmt_free(lmt_rec); /* 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); if(in_id_arr != NULL) in_id_arr=(int *)nco_free(in_id_arr); /* 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); /* Free dimension lists */ if(nbr_dmn_xtr > 0) dim=nco_dmn_lst_free(dim,nbr_dmn_xtr); if(nbr_dmn_xtr > 0) dmn_out=nco_dmn_lst_free(dmn_out,nbr_dmn_xtr); /* Free variable lists */ if(nbr_xtr > 0) var=nco_var_lst_free(var,nbr_xtr); if(nbr_xtr > 0) var_out=nco_var_lst_free(var_out,nbr_xtr); 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); nco_exit_gracefully(); return EXIT_SUCCESS; } /* end main() */

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