nco/mpncwa.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 "ncap.h"
#include "libnco.h"

Include dependency graph for mpncwa.c:

Go to the source code of this file.

Defines
#define	MAIN_PROGRAM_FILE
Functions
int	main (int argc, char **argv)
Variables
size_t	ncap_ncl_dpt_crr = 0UL
size_t *	ncap_ln_nbr_crr
char **	ncap_fl_spt_glb

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Define Documentation

#define MAIN_PROGRAM_FILE

Definition at line 70 of file mpncwa.c.

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Function Documentation

int main (  int  argc, char **  argv )

Definition at line 80 of file mpncwa.c. References prs_sct::att_lst, ptr_unn::bp, copyright_prn(), ptr_unn::cp, prs_sct::dmn_in, prs_sct::dmn_out, double_CEWI, ptr_unn::dp, EXIT_FAILURE, EXIT_SUCCESS, False, FILE, prs_sct::fl_in, prs_sct::fl_out, ptr_unn::fp, getopt_long, var_sct_tag::has_mss_val, var_sct_tag::id, dmn_sct_tag::id, idx_all_wrk_ass, prs_sct::in_id, int_CEWI, var_sct_tag::is_crd_var, ptr_unn::lp, lst_prs_2D(), msg_bfr_lng, msg_tag_tkn_wrt_rqs, msg_tag_tkn_wrt_rsp, msg_tag_wrk_rqs, msg_tag_wrk_rsp, var_sct_tag::mss_val, option::name, prs_sct::nbr_att, var_sct_tag::nbr_dim, prs_sct::nbr_dmn_in, prs_sct::nbr_dmn_out, NC_BYTE, NC_CHAR, NC_DOUBLE, NC_FLOAT, NC_FORMAT_64BIT, NC_FORMAT_CLASSIC, NC_FORMAT_NETCDF4, NC_GLOBAL, NC_INT, NC_MAX_DIMS, NC_NOERR, NC_NOFILL, NC_NOWRITE, NC_SHARE, NC_SHORT, NC_WRITE, ncap_ln_nbr_crr, ncap_ncl_dpt_crr, ncap_ncwa_scn(), nco_att_cpy(), nco_bool, nco_close(), nco_cmd_ln_sng(), nco_cnt_run(), nco_cnv_ccm_ccsm_cf_inq(), nco_create_mode_prs(), nco_dfl_case_nc_type_err(), nco_dmn_dfn(), nco_dmn_dpl(), nco_dmn_fll(), nco_dmn_lmt_mrg(), nco_dmn_lst_ass_var(), nco_dmn_lst_free(), nco_dmn_lst_mk(), nco_dmn_xrf(), nco_enddef(), nco_exit(), nco_exit_gracefully(), nco_fl_cmp_err_chk(), nco_fl_lst_mk(), nco_fl_mk_lcl(), nco_fl_mv(), 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_varid(), nco_lbr_vrs_prn(), nco_lmt_evl(), nco_lmt_lst_free(), nco_lmt_prs(), nco_lst_comma2hash(), nco_lst_srt_nm_id(), nco_malloc(), nco_malloc_flg(), nco_mpi_att_cat(), nco_mss_val_cp(), nco_mss_val_mk(), nco_nm_id_lst_free(), nco_op_avg, nco_op_avgsqr, nco_op_max, nco_op_min, nco_op_ne, nco_op_nil, nco_op_prs_rlt(), nco_op_rms, nco_op_rmssdn, nco_op_sqravg, nco_op_sqrt, nco_op_ttl, prs_sct::nco_op_typ, nco_op_typ_get(), nco_open(), nco_openmp_ini(), nco_pck_map_nil, nco_pck_plc_nil, nco_put_att(), nco_put_var1(), nco_put_vara(), nco_realloc(), NCO_REC_DMN_UNDEFINED, nco_set_fill(), nco_sng_lst_free(), nco_spn_lck_brk, nco_spn_lck_us, nco_thr_att_cat(), nco_typ_cnv_rth(), nco_typ_lng(), nco_usg_prn(), nco_var_avg(), nco_var_cnf_dmn(), nco_var_cnf_typ(), nco_var_dfn(), nco_var_dpl(), nco_var_dvd(), nco_var_fll(), nco_var_free(), 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_msk(), 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(), var_sct_tag::nm, no_argument, prs_sct::ntl_scn, NULL_CEWI, omp_get_thread_num(), optarg, optind, prs_sct::out_id, prg_nm_get(), prg_prs(), required_argument, rnk_mgr, ptr_unn::sp, prs_sct::sym_tbl, prs_sct::sym_tbl_nbr, var_sct_tag::sz, var_sct_tag::tally, tkn_wrt_rqs_dny, tkn_wrt_rqs_ntv, tkn_wrt_rqs_xcp, True, var_sct_tag::type, type, option::val, var_sct_tag::val, prs_sct::var_LHS, ptr_unn::vp, and wrk_id_bfr_lng. { nco_bool DO_CONFORM_MSK=False; /* Did nco_var_cnf_dmn() find truly conforming mask? */ nco_bool DO_CONFORM_WGT=False; /* Did nco_var_cnf_dmn() find truly conforming weight? */ 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_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 MULTIPLY_BY_TALLY=False; /* Not currently implemented */ nco_bool MUST_CONFORM=False; /* [flg] Must nco_var_cnf_dmn() find truly conforming variables? */ nco_bool CNV_CCM_CCSM_CF; nco_bool NORMALIZE_BY_TALLY=True; /* Not currently implemented */ nco_bool NORMALIZE_BY_WEIGHT=True; /* Not currently implemented */ nco_bool NRM_BY_DNM=True; /* Option N Normalize by denominator */ nco_bool REMOVE_REMOTE_FILES_AFTER_PROCESSING=True; /* Option R */ nco_bool WGT_MSK_CRD_VAR=True; /* [flg] Weight and/or mask coordinate variables */ nco_bool opt_a_flg=False; /* Option a */ char **dmn_avg_lst_in=NULL_CEWI; /* Option a */ char **fl_lst_abb=NULL; /* Option n */ char **fl_lst_in=NULL_CEWI; 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 *msk_nm=NULL; char *msk_sng=NULL; /* Mask string to be "parsed" and values given to msk_nm, msk_val, op_typ_rlt */ char *nco_op_typ_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 *time_bfr_srt; char *wgt_nm=NULL; const char * const CVS_Id="$Id: mpncwa.c,v 1.35 2006/02/26 07:41:55 zender Exp $"; const char * const CVS_Revision="$Revision: 1.35 $"; const char * const opt_sht_lst="4Aa:CcD:d:FhIl:M:m:nNOo:p:rRST:t:v:Ww:xy:z:-:"; dmn_sct **dim=NULL_CEWI; dmn_sct **dmn_out=NULL_CEWI; dmn_sct **dmn_avg=NULL_CEWI; double msk_val=1.0; /* Option M */ 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 dmn_avg_nbr=0; int fl_idx=int_CEWI; 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 idx_avg; int in_id; int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */ int nbr_dmn_fl; int nbr_dmn_out=0; 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; /* Operation type */ int op_typ_rlt=0; /* Option o */ int opt; int out_id; int rcd=NC_NOERR; /* [rcd] Return code */ int rec_dmn_id=NCO_REC_DMN_UNDEFINED; /* [id] Record dimension ID in input file */ 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; nm_id_sct *dmn_lst; nm_id_sct *xtr_lst=NULL; /* xtr_lst may be alloc()'d from NULL with -c option */ nm_id_sct *dmn_avg_lst; prs_sct prs_arg; /* I/O [sct] Global information required in ncwa parser */ time_t time_crr_time_t; 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; var_sct *msk=NULL; var_sct *msk_out=NULL; var_sct *wgt=NULL; var_sct *wgt_avg=NULL; var_sct *wgt_out=NULL; #ifdef ENABLE_MPI /* Declare all MPI-specific variables here */ MPI_Status mpi_stt; /* [enm] Status check to decode msg_tag_typ */ 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 */ /* 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'}, {"average",required_argument,0,'a'}, {"avg",required_argument,0,'a'}, {"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'}, {"history",no_argument,0,'h'}, {"hst",no_argument,0,'h'}, {"wgt_msk_crd_var",no_argument,0,'I'}, {"local",required_argument,0,'l'}, {"lcl",required_argument,0,'l'}, {"mask-variable",required_argument,0,'m'}, {"mask_variable",required_argument,0,'m'}, {"mask",required_argument,0,'m'}, {"msk_var",required_argument,0,'m'}, {"msk_nm",required_argument,0,'m'}, {"mask-value",required_argument,0,'M'}, {"mask_value",required_argument,0,'M'}, {"msk_val",required_argument,0,'M'}, {"nintap",required_argument,0,'n'}, {"nmr",no_argument,0,'N'}, {"numerator",no_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'}, {"truth_condition",required_argument,0,'T'}, {"msk_cmp_typ",required_argument,0,'T'}, {"op_rlt",required_argument,0,'T'}, {"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'}, {"normalize-by-tally",no_argument,0,'W',}, {"exclude",no_argument,0,'x'}, {"xcl",no_argument,0,'x'}, {"weight",no_argument,0,'w'}, {"wgt",no_argument,0,'w'}, {"wgt_var",no_argument,0,'w'}, {"operation",required_argument,0,'y'}, {"op_typ",required_argument,0,'y'}, {"mask_string",required_argument,0,'z'}, {"msk_sng",required_argument,0,'z'}, {"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 ENABLE_MPI /* MPI Initialization */ MPI_Init(&argc,&argv); MPI_Comm_size(MPI_COMM_WORLD,&prc_nbr); MPI_Comm_rank(MPI_COMM_WORLD,&prc_rnk); #endif /* !ENABLE_MPI */ /* 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 */ time_bfr_srt=time_bfr_srt; /* CEWI: Avert compiler warning that variable is set but never used */ NORMALIZE_BY_TALLY=NORMALIZE_BY_TALLY; /* CEWI: Avert compiler warning that variable is set but never used */ NORMALIZE_BY_WEIGHT=NORMALIZE_BY_WEIGHT; /* CEWI: Avert compiler warning that variable is set but never used */ /* 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 'a': /* Dimensions over which to average hyperslab */ if(opt_a_flg){ (void)fprintf(fp_stdout,"%s: ERROR Option -a appears more than once\n",prg_nm); (void)fprintf(fp_stdout,"%s: HINT Use -a dim1,dim2,... not -a dim1 -a dim2 ...\n",prg_nm); (void)nco_usg_prn(); nco_exit(EXIT_FAILURE); } /* endif */ dmn_avg_lst_in=lst_prs_2D(optarg,",",&dmn_avg_nbr); opt_a_flg=True; 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 appending to history global attribute */ HISTORY_APPEND=!HISTORY_APPEND; break; case 'I': /* [flg] Weight and/or mask coordinate variables */ WGT_MSK_CRD_VAR=!WGT_MSK_CRD_VAR; break; case 'l': /* Local path prefix for files retrieved from remote file system */ fl_pth_lcl=(char *)strdup(optarg); break; case 'm': /* Name of variable to use as mask in reducing. Default is none */ msk_nm=(char *)strdup(optarg); break; case 'M': /* Good data defined by relation to mask value. Default is 1. */ msk_val=strtod(optarg,(char **)NULL); break; case 'N': NRM_BY_DNM=False; NORMALIZE_BY_TALLY=False; NORMALIZE_BY_WEIGHT=False; break; case 'n': NORMALIZE_BY_WEIGHT=False; (void)fprintf(fp_stdout,"%s: ERROR This option has been disabled while I rethink its implementation\n",prg_nm); nco_exit(EXIT_FAILURE); 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. */ 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; #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",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': /* Relational operator type. Default is 0, eq, equality */ op_typ_rlt=nco_op_prs_rlt(optarg); 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 'W': NORMALIZE_BY_TALLY=False; (void)fprintf(fp_stdout,"%s: ERROR This option has been disabled while I rethink its implementation\n",prg_nm); nco_exit(EXIT_FAILURE); break; case 'w': /* Variable to use as weight in reducing. Default is none */ wgt_nm=(char *)strdup(optarg); break; case 'x': /* Exclude rather than extract variables specified with -v */ EXCLUDE_INPUT_LIST=True; break; case 'y': /* Operation type */ nco_op_typ_sng=(char *)strdup(optarg); nco_op_typ=nco_op_typ_get(nco_op_typ_sng); break; case 'z': /* Mask string to be parsed */ msk_sng=(char *)strdup(optarg); 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 */ /* Parse mask string */ if(msk_sng){ int zero=0; /* Set arguments for scan */ prs_arg.fl_in=NULL; /* [sng] Input data file */ prs_arg.in_id=0; /* [id] Input data file ID */ prs_arg.fl_out=NULL; /* [sng] Output data file */ prs_arg.out_id=0; /* [id] Output data file ID */ prs_arg.att_lst=NULL; /* [sct] Attributes in script */ prs_arg.nbr_att=&zero; /* [nbr] Number of attributes in script */ prs_arg.dmn_in=NULL; /* [dmn_in] List of all dimensions in input */ prs_arg.nbr_dmn_in=0; /* [nbr] Number of dimensions in input */ prs_arg.dmn_out=NULL; /* pointer to list of dims in output */ prs_arg.nbr_dmn_out=&zero; /* number of dims in above list */ prs_arg.sym_tbl=NULL; /* [fnc] Symbol table for functions */ prs_arg.sym_tbl_nbr=0; /* [nbr] Number of functions in table */ prs_arg.ntl_scn=False; /* [flg] Initial scan of script */ prs_arg.var_LHS=NULL; /* [var] LHS cast variable */ prs_arg.nco_op_typ=nco_op_nil; /* [enm] Operation type */ /* Initialize line counter */ ncap_ln_nbr_crr=(size_t *)nco_realloc(ncap_ln_nbr_crr,ncap_ncl_dpt_crr+1UL); ncap_ln_nbr_crr[ncap_ncl_dpt_crr]=1UL; /* [cnt] Line number incremented in ncap.l */ if(ncap_ncwa_scn(&prs_arg,msk_sng,&msk_nm,&msk_val,&op_typ_rlt) == 0) nco_exit(EXIT_FAILURE); } /* endif msk_sng */ /* Ensure we do not attempt to normalize by non-existent weight */ if(wgt_nm == NULL) NORMALIZE_BY_WEIGHT=False; /* 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); /* 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); /* 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); /* Merge hyperslab limit information into dimension structures */ if(lmt_nbr > 0) (void)nco_dmn_lmt_mrg(dim,nbr_dmn_xtr,lmt,lmt_nbr); /* Not specifying any dimensions is interpreted as specifying all dimensions */ if(dmn_avg_nbr == 0){ dmn_avg_nbr=nbr_dmn_xtr; dmn_avg_lst_in=(char **)nco_malloc(dmn_avg_nbr*sizeof(char *)); for(idx=0;idx<dmn_avg_nbr;idx++){ dmn_avg_lst_in[idx]=(char *)strdup(dmn_lst[idx].nm); } /* end loop over idx */ (void)fprintf(stderr,"%s: INFO No dimensions specified with -a, therefore reducing (averaging, taking minimum, etc.) over all dimensions\n",prg_nm); } /* end if dmn_avg_nbr == 0 */ /* Dimension list no longer needed */ dmn_lst=nco_nm_id_lst_free(dmn_lst,nbr_dmn_xtr); if(dmn_avg_nbr > 0){ if(dmn_avg_nbr > nbr_dmn_xtr){ (void)fprintf(fp_stdout,"%s: ERROR More reducing dimensions than extracted dimensions\n",prg_nm); nco_exit(EXIT_FAILURE); } /* end if */ /* Create structured list of reducing dimension names and IDs */ dmn_avg_lst=nco_dmn_lst_mk(in_id,dmn_avg_lst_in,dmn_avg_nbr); /* Dimension average list no longer needed */ if(dmn_avg_nbr > 0) dmn_avg_lst_in=nco_sng_lst_free(dmn_avg_lst_in,dmn_avg_nbr); /* Form list of reducing dimensions from extracted input dimensions */ dmn_avg=(dmn_sct **)nco_malloc(dmn_avg_nbr*sizeof(dmn_sct *)); for(idx_avg=0;idx_avg<dmn_avg_nbr;idx_avg++){ for(idx=0;idx<nbr_dmn_xtr;idx++){ if(!strcmp(dmn_avg_lst[idx_avg].nm,dim[idx]->nm)) break; } /* end loop over idx_avg */ if(idx != nbr_dmn_xtr){ dmn_avg[idx_avg]=dim[idx]; }else{ (void)fprintf(stderr,"%s: WARNING reducing dimension \"%s\" is not contained in any variable in extraction list\n",prg_nm,dmn_avg_lst[idx_avg].nm); /* Collapse dimension average list by omitting irrelevent dimension */ (void)memmove(dmn_avg_lst+idx_avg*sizeof(nm_id_sct),dmn_avg_lst+(idx_avg+1)*sizeof(nm_id_sct),(dmn_avg_nbr-idx_avg-1)*sizeof(nm_id_sct)); --dmn_avg_nbr; dmn_avg_lst=(nm_id_sct *)nco_realloc(dmn_avg_lst,dmn_avg_nbr*sizeof(nm_id_sct)); dmn_avg=(dmn_sct **)nco_realloc(dmn_avg,dmn_avg_nbr*sizeof(dmn_sct *)); } /* end else */ } /* end loop over idx_avg */ /* Make sure no reducing dimension is specified more than once */ for(idx=0;idx<dmn_avg_nbr;idx++){ for(idx_avg=0;idx_avg<dmn_avg_nbr;idx_avg++){ if(idx_avg != idx){ if(dmn_avg[idx]->id == dmn_avg[idx_avg]->id){ (void)fprintf(fp_stdout,"%s: ERROR %s specified more than once in reducing list\n",prg_nm,dmn_avg[idx]->nm); nco_exit(EXIT_FAILURE); } /* end if */ } /* end if */ } /* end loop over idx_avg */ } /* end loop over idx */ /* Dimensions to be averaged will not appear in output file */ dmn_out=(dmn_sct **)nco_malloc((nbr_dmn_xtr-dmn_avg_nbr)*sizeof(dmn_sct *)); nbr_dmn_out=0; for(idx=0;idx<nbr_dmn_xtr;idx++){ for(idx_avg=0;idx_avg<dmn_avg_nbr;idx_avg++){ if(!strcmp(dmn_avg_lst[idx_avg].nm,dim[idx]->nm)) break; } /* end loop over idx_avg */ if(idx_avg == dmn_avg_nbr){ dmn_out[nbr_dmn_out]=nco_dmn_dpl(dim[idx]); (void)nco_dmn_xrf(dim[idx],dmn_out[nbr_dmn_out]); nbr_dmn_out++; } /* end if */ } /* end loop over idx_avg */ /* Dimension average list no longer needed */ dmn_avg_lst=nco_nm_id_lst_free(dmn_avg_lst,dmn_avg_nbr); if(nbr_dmn_out != nbr_dmn_xtr-dmn_avg_nbr){ (void)fprintf(fp_stdout,"%s: ERROR nbr_dmn_out != nbr_dmn_xtr-dmn_avg_nbr\n",prg_nm); nco_exit(EXIT_FAILURE); } /* end if */ } /* dmn_avg_nbr <= 0 */ /* Is this an CCM/CCSM/CF-format history tape? */ CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(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,dmn_avg,dmn_avg_nbr,&var_fix,&var_fix_out,&nbr_var_fix,&var_prc,&var_prc_out,&nbr_var_prc); /* We now have final list of variables to extract. Phew. */ if(dbg_lvl > 0){ for(idx=0;idx<nbr_xtr;idx++) (void)fprintf(stderr,"var[%d]->nm = %s, ->id=[%d]\n",idx,var[idx]->nm,var[idx]->id); for(idx=0;idx<nbr_var_fix;idx++) (void)fprintf(stderr,"var_fix[%d]->nm = %s, ->id=[%d]\n",idx,var_fix[idx]->nm,var_fix[idx]->id); for(idx=0;idx<nbr_var_prc;idx++) (void)fprintf(stderr,"var_prc[%d]->nm = %s, ->id=[%d]\n",idx,var_prc[idx]->nm,var_prc[idx]->id); } /* end if */ #ifdef ENABLE_MPI if(prc_rnk == rnk_mgr){ /* MPI manager code */ #endif /* !ENABLE_MPI */ /* Open output file */ fl_out_tmp=nco_fl_out_open(fl_out,FORCE_APPEND,FORCE_OVERWRITE,fl_out_fmt,&out_id); if(dbg_lvl > 4) (void)fprintf(stderr,"Input, output file IDs = %d, %d\n",in_id,out_id); /* Copy all 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); 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 */ /* Define dimensions in output file */ (void)nco_dmn_dfn(fl_out,out_id,dmn_out,nbr_dmn_out); /* Define variables in output file, copy their attributes */ (void)nco_var_dfn(in_id,fl_out,out_id,var_out,nbr_xtr,dmn_out,nbr_dmn_out,nco_pck_plc_nil,nco_pck_map_nil); #ifdef ENABLE_MPI } /* prc_rnk != rnk_mgr */ #endif /* !ENABLE_MPI */ /* Add new missing values to output file while in define mode */ if(msk_nm != NULL){ for(idx=0;idx<nbr_var_prc;idx++){ /* Define for var_prc_out because mss_val for var_prc will be overwritten in nco_var_mtd_refresh */ if(!var_prc_out[idx]->has_mss_val){ var_prc_out[idx]->has_mss_val=True; var_prc_out[idx]->mss_val=nco_mss_val_mk(var_prc[idx]->type); #ifdef ENABLE_MPI if(prc_rnk == rnk_mgr) #endif /* !ENABLE_MPI */ (void)nco_put_att(out_id,var_prc_out[idx]->id,"missing_value",var_prc_out[idx]->type,1,var_prc_out[idx]->mss_val.vp); } /* end if */ } /* end for */ } /* end if */ #ifdef ENABLE_MPI if(prc_rnk == rnk_mgr){ /* MPI manager code */ #endif /* !ENABLE_MPI */ /* 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 */ (void)nco_enddef(out_id); #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_COMM_WORLD); if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)malloc((fl_nm_lng+1)*sizeof(char)); MPI_Bcast(fl_out_tmp,fl_nm_lng+1,MPI_CHAR,0,MPI_COMM_WORLD); 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 */ /* Zero start vectors for all output variables */ (void)nco_var_srt_zero(var_out,nbr_xtr); /* 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(dbg_lvl > 0) (void)fprintf(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,&FILE_RETRIEVED_FROM_REMOTE_LOCATION); if(dbg_lvl > 0) (void)fprintf(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_open(fl_in,NC_NOWRITE,in_id_arr+thr_idx); in_id=in_id_arr[0]; /* Perform various error-checks on input file */ if(False) (void)nco_fl_cmp_err_chk(); /* Find weighting variable in input file */ if(wgt_nm != NULL){ int wgt_id; rcd=nco_inq_varid(in_id,wgt_nm,&wgt_id); /* fxm: TODO #111 core dump if wgt has dimension not in extraction list */ wgt=nco_var_fll(in_id,wgt_id,wgt_nm,dim,nbr_dmn_xtr); /* Retrieve weighting variable */ /* NB: nco_var_get() with same nc_id contains OpenMP critical region */ (void)nco_var_get(in_id,wgt); /* fxm: Perhaps should allocate default tally array for wgt here That way, when wgt conforms to the first var_prc_out and it therefore does not get a tally array copied by nco_var_dpl() in nco_var_cnf_dmn(), it will at least have space for a tally array. TODO #114. */ } /* end if */ /* Find mask variable in input file */ if(msk_nm != NULL){ int msk_id; rcd=nco_inq_varid(in_id,msk_nm,&msk_id); /* fxm: TODO #111 core dump if msk has dimension not in extraction list */ msk=nco_var_fll(in_id,msk_id,msk_nm,dim,nbr_dmn_xtr); /* Retrieve mask variable */ /* NB: nco_var_get() with same nc_id contains OpenMP critical region */ (void)nco_var_get(in_id,msk); } /* end if */ #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_COMM_WORLD,&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 */ /* Workers close output file before sending next msg_tag_wrk_rqs */ /* fxm csz 20050924: Safe? Can't other process have write token here? */ 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_COMM_WORLD); /* 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_COMM_WORLD); } /* 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_COMM_WORLD); /* Receive msg_tag_wrk_rsp */ MPI_Recv(msg_bfr,msg_bfr_lng,MPI_INT,0,msg_tag_wrk_rsp,MPI_COMM_WORLD,&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 */ #ifdef _OPENMP /* OpenMP notes: firstprivate(): msk_out and wgt_out must be NULL on first call to nco_var_cnf_dmn() shared(): msk and wgt are not altered within loop private(): wgt_avg does not need initialization */ #pragma omp parallel for default(none) firstprivate(DO_CONFORM_MSK,DO_CONFORM_WGT,msk_out,wgt_out) private(idx,in_id,wgt_avg) shared(MULTIPLY_BY_TALLY,MUST_CONFORM,NRM_BY_DNM,WGT_MSK_CRD_VAR,dbg_lvl,dmn_avg,dmn_avg_nbr,fp_stderr,fp_stdout,in_id_arr,msk,msk_nm,msk_val,nbr_var_prc,nco_op_typ,op_typ_rlt,out_id,prg_nm,rcd,var_prc,var_prc_out,wgt,wgt_nm) #endif /* !_OPENMP */ /* UP and SMP codes main loop over variables */ for(idx=0;idx<nbr_var_prc;idx++){ /* Process all variables in current file */ #endif /* !ENABLE_MPI */ 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); /* Allocate and, if necessary, initialize accumulation space for all processed variables */ var_prc_out[idx]->sz=var_prc[idx]->sz; /* if((var_prc_out[idx]->tally=var_prc[idx]->tally=(long *)nco_malloc_flg(var_prc_out[idx]->sz*sizeof(long))) == NULL){*/ /* fxm: verify that var_prc->tally is not needed */ if((var_prc_out[idx]->tally=(long *)nco_malloc_flg(var_prc_out[idx]->sz*sizeof(long))) == NULL){ (void)fprintf(fp_stdout,"%s: ERROR Unable to malloc() %ld*%ld bytes for tally buffer for variable %s in main()\n",prg_nm_get(),var_prc_out[idx]->sz,(long)sizeof(long),var_prc_out[idx]->nm); nco_exit(EXIT_FAILURE); } /* end if err */ (void)nco_zero_long(var_prc_out[idx]->sz,var_prc_out[idx]->tally); 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",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); } /* end if err */ (void)nco_var_zero(var_prc_out[idx]->type,var_prc_out[idx]->sz,var_prc_out[idx]->val); (void)nco_var_mtd_refresh(in_id,var_prc[idx]); /* Retrieve variable from disk into memory */ if(dbg_lvl > 4) (void)fprintf(fp_stdout,"%s: DEBUG: fxm TODO nco354 About to nco_var_get() %s\n",prg_nm,var_prc[idx]->nm); /* NB: nco_var_get() with same nc_id contains OpenMP critical region */ (void)nco_var_get(in_id,var_prc[idx]); if(dbg_lvl > 4) (void)fprintf(fp_stdout,"%s: DEBUG: fxm TODO nco354 Finished nco_var_get() %s\n",prg_nm,var_prc[idx]->nm); /* Convert char, short, long, int types to doubles before arithmetic */ var_prc[idx]=nco_typ_cnv_rth(var_prc[idx],nco_op_typ); var_prc_out[idx]=nco_typ_cnv_rth(var_prc_out[idx],nco_op_typ); if(msk_nm != NULL && (!var_prc[idx]->is_crd_var || WGT_MSK_CRD_VAR)){ msk_out=nco_var_cnf_dmn(var_prc[idx],msk,msk_out,MUST_CONFORM,&DO_CONFORM_MSK); /* If msk and var did not conform then do not mask var! */ if(DO_CONFORM_MSK){ msk_out=nco_var_cnf_typ(var_prc[idx]->type,msk_out); /* mss_val for var_prc has been overwritten in nco_var_mtd_refresh() */ if(!var_prc[idx]->has_mss_val){ var_prc[idx]->has_mss_val=True; var_prc[idx]->mss_val=nco_mss_val_mk(var_prc[idx]->type); } /* end if */ /* Mask by changing variable to missing value where condition is false */ (void)nco_var_msk(var_prc[idx]->type,var_prc[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,msk_val,op_typ_rlt,msk_out->val,var_prc[idx]->val); } /* end if */ } /* end if */ /* Perform non-linear transformations before weighting */ switch(nco_op_typ){ case nco_op_avgsqr: /* Square variable before weighting */ case nco_op_rms: /* Square variable before weighting */ case nco_op_rmssdn: /* Square variable before weighting */ (void)nco_var_mlt(var_prc[idx]->type,var_prc[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,var_prc[idx]->val,var_prc[idx]->val); break; default: /* All other operations are linear, do nothing to them yet */ break; } /* end case */ if(wgt_nm != NULL && (!var_prc[idx]->is_crd_var || WGT_MSK_CRD_VAR)){ /* fxm: nco_var_cnf_dmn() has bug where it does not allocate tally array for weights that do already conform to var_prc. TODO #114. */ wgt_out=nco_var_cnf_dmn(var_prc[idx],wgt,wgt_out,MUST_CONFORM,&DO_CONFORM_WGT); if(DO_CONFORM_WGT){ wgt_out=nco_var_cnf_typ(var_prc[idx]->type,wgt_out); /* Weight after any initial non-linear operation so, e.g., variable is squared but not weights */ /* Weight variable by taking product of weight and variable */ (void)nco_var_mlt(var_prc[idx]->type,var_prc[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,wgt_out->val,var_prc[idx]->val); } /* end if weights conformed */ } /* end if weight was specified and then tested for conformance */ /* Copy (masked) (weighted) values from var_prc to var_prc_out */ (void)memcpy((void *)(var_prc_out[idx]->val.vp),(void *)(var_prc[idx]->val.vp),var_prc_out[idx]->sz*nco_typ_lng(var_prc_out[idx]->type)); /* 20050516: fxm: destruction of var_prc_out in nco_var_avg() leaves dangling pointers in var_out? */ /* Reduce variable over specified dimensions (tally array is set here) NB: var_prc_out[idx] is new, so corresponding var_out[idx] is dangling */ var_prc_out[idx]=nco_var_avg(var_prc_out[idx],dmn_avg,dmn_avg_nbr,nco_op_typ); /* var_prc_out[idx]->val now holds numerator of averaging expression documented in NCO User's Guide Denominator is also tricky due to sundry normalization options These logical switches are VERY tricky---be careful modifying them */ if(NRM_BY_DNM && DO_CONFORM_WGT && (!var_prc[idx]->is_crd_var || WGT_MSK_CRD_VAR)){ /* Duplicate wgt_out as wgt_avg so that wgt_out is not contaminated by any averaging operation and may be reused on next variable. Free wgt_avg after each use but continue to reuse wgt_out */ wgt_avg=nco_var_dpl(wgt_out); if(var_prc[idx]->has_mss_val){ double mss_val_dbl=double_CEWI; /* Set denominator to missing value at all locations where variable is missing value If this is accomplished by setting weight to missing value wherever variable is missing value then weight must not be re-used by next variable (which might conform but have missing values in different locations) This is one good reason to copy wgt_out into disposable wgt_avg for each new variable */ /* First, make sure wgt_avg has same missing value as variable */ (void)nco_mss_val_cp(var_prc[idx],wgt_avg); /* Copy missing value into double precision variable */ switch(wgt_avg->type){ case NC_FLOAT: mss_val_dbl=wgt_avg->mss_val.fp[0]; break; case NC_DOUBLE: mss_val_dbl=wgt_avg->mss_val.dp[0]; break; case NC_INT: mss_val_dbl=wgt_avg->mss_val.lp[0]; break; case NC_SHORT: mss_val_dbl=wgt_avg->mss_val.sp[0]; break; case NC_CHAR: mss_val_dbl=wgt_avg->mss_val.cp[0]; break; case NC_BYTE: mss_val_dbl=wgt_avg->mss_val.bp[0]; break; default: nco_dfl_case_nc_type_err(); break; } /* end switch */ /* Second, mask wgt_avg where variable is missing value */ (void)nco_var_msk(wgt_avg->type,wgt_avg->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,mss_val_dbl,nco_op_ne,var_prc[idx]->val,wgt_avg->val); } /* endif weight must be checked for missing values */ /* Free current input buffer */ var_prc[idx]->val.vp=nco_free(var_prc[idx]->val.vp); if(msk_nm != NULL && DO_CONFORM_MSK){ /* Must mask weight in same fashion as variable was masked If msk and var did not conform then do not mask wgt Ensure wgt_avg has a missing value */ if(!wgt_avg->has_mss_val){ wgt_avg->has_mss_val=True; wgt_avg->mss_val=nco_mss_val_mk(wgt_avg->type); } /* end if */ /* Mask by changing weight to missing value where condition is false */ (void)nco_var_msk(wgt_avg->type,wgt_avg->sz,wgt_avg->has_mss_val,wgt_avg->mss_val,msk_val,op_typ_rlt,msk_out->val,wgt_avg->val); } /* endif weight must be masked */ /* fxm: temporary kludge to make sure weight has tally space wgt_avg may lack valid tally array in ncwa because wgt_avg is created, sometimes, before the tally array for var_prc_out[idx] is created. When this occurs the nco_var_dpl() call in nco_var_cnf_dmn() does not copy tally array into wgt_avg. See related note about this above. TODO #114.*/ if(wgt_avg->sz > 0) if((wgt_avg->tally=(long *)nco_realloc(wgt_avg->tally,wgt_avg->sz*sizeof(long))) == NULL){ (void)fprintf(fp_stdout,"%s: ERROR Unable to realloc() %ld*%ld bytes for tally buffer for weight %s in main()\n",prg_nm_get(),wgt_avg->sz,(long)sizeof(long),wgt_avg->nm); nco_exit(EXIT_FAILURE); } /* end if */ /* Average weight over specified dimensions (tally array is set here) */ wgt_avg=nco_var_avg(wgt_avg,dmn_avg,dmn_avg_nbr,nco_op_avg); if(MULTIPLY_BY_TALLY){ /* NB: Currently this is not implemented */ /* Multiply numerator (weighted sum of variable) by tally We deviously accomplish this by dividing denominator by tally */ (void)nco_var_nrm(wgt_avg->type,wgt_avg->sz,wgt_avg->has_mss_val,wgt_avg->mss_val,wgt_avg->tally,wgt_avg->val); } /* endif */ /* Divide numerator by denominator */ /* Diagnose common PEBCAK before it causes core dump */ if(var_prc_out[idx]->sz == 1L && var_prc_out[idx]->type == NC_INT && var_prc_out[idx]->val.lp[0] == 0){ (void)fprintf(fp_stdout,"%s: ERROR Weight in denominator weight = 0.0, will cause SIGFPE\n%s: HINT Sum of masked, averaged weights must be non-zero\n%s: HINT A possible workaround is to remove variable \"%s\" from output file using \"%s -x -v %s ...\"\n%s: Expecting core dump...now!\n",prg_nm,prg_nm,prg_nm,var_prc_out[idx]->nm,prg_nm,var_prc_out[idx]->nm,prg_nm); } /* end if */ /* Divide numerator by masked, averaged, weights */ switch(nco_op_typ){ case nco_op_avg: /* Normalize sum by weighted tally to create mean */ case nco_op_sqravg: /* Normalize sum by weighted tally to create mean */ case nco_op_avgsqr: /* Normalize sum of squares by weighted tally to create mean square */ case nco_op_rms: /* Normalize sum of squares by weighted tally to create mean square */ case nco_op_sqrt: /* Normalize sum by weighted tally to create mean */ case nco_op_rmssdn: /* Normalize sum of squares by weighted tally-1 to create mean square for sdn */ (void)nco_var_dvd(var_prc_out[idx]->type,var_prc_out[idx]->sz,var_prc_out[idx]->has_mss_val,var_prc_out[idx]->mss_val,wgt_avg->val,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 */ break; default: (void)fprintf(fp_stdout,"%s: ERROR Illegal nco_op_typ in weighted normalization\n",prg_nm); nco_exit(EXIT_FAILURE); break; } /* end switch */ /* Free wgt_avg, but keep wgt_out, after each use */ if(wgt_avg != NULL) wgt_avg=nco_var_free(wgt_avg); /* End of branch for normalization when weights were specified */ }else if(NRM_BY_DNM){ /* Branch for normalization when no weights were specified Normalization is just due to tally */ switch(nco_op_typ){ case nco_op_avg: /* Normalize sum by tally to create mean */ case nco_op_sqravg: /* Normalize sum by tally to create mean */ case nco_op_avgsqr: /* Normalize sum of squares by tally to create mean square */ case nco_op_rms: /* Normalize sum of squares by tally to create mean square */ case nco_op_sqrt: /* Normalize sum by tally to create mean */ (void)nco_var_nrm(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]->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_out[idx]->has_mss_val,var_prc_out[idx]->mss_val,var_prc_out[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 */ break; default: (void)fprintf(fp_stdout,"%s: ERROR Illegal nco_op_typ in non-weighted normalization\n",prg_nm); nco_exit(EXIT_FAILURE); break; } /* end switch */ }else if(!NRM_BY_DNM){ /* Normalization has been turned off by user, we are done */ ; }else{ (void)fprintf(fp_stdout,"%s: ERROR Unforeseen logical branch in main()\n",prg_nm); nco_exit(EXIT_FAILURE); } /* end if */ /* Some non-linear operations require additional processing */ switch(nco_op_typ){ 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; case nco_op_sqrt: /* Take root of mean to create root mean */ 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 */ (void)nco_var_sqrt(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]->tally,var_prc_out[idx]->val,var_prc_out[idx]->val); break; default: break; } /* end switch */ /* Free tally buffer */ var_prc_out[idx]->tally=(long *)nco_free(var_prc_out[idx]->tally); /* Revert any arithmetic promotion but leave unpacked (for now) */ var_prc_out[idx]=nco_var_cnf_typ(var_prc_out[idx]->typ_upk,var_prc_out[idx]); #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_COMM_WORLD); MPI_Recv(msg_bfr,msg_bfr_lng,MPI_INT,rnk_mgr,msg_tag_tkn_wrt_rsp,MPI_COMM_WORLD,&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){ rcd=nco_open(fl_out_tmp,NC_WRITE|NC_SHARE|NC_SHARE,&out_id); /* Turn off default filling behavior to enhance efficiency */ rcd=nco_set_fill(out_id,NC_NOFILL,&fll_md_old); #endif /* !ENABLE_MPI */ #ifdef _OPENMP #pragma omp critical #endif /* _OPENMP */ /* Common code for UP, SMP, and MPI */ { /* begin OpenMP critical */ /* Copy average to output file then free averaging buffer */ 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 scalar */ (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 array */ } /* end OpenMP critical */ /* Free current output buffer */ var_prc_out[idx]->val.vp=nco_free(var_prc_out[idx]->val.vp); #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 */ if(dbg_lvl > 0) (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]); #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); if(prc_rnk == rnk_mgr) /* This if statement conditions nco_fl_rm() below */ #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 */ /* Remove 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 */ /* ncwa-unique memory */ if(dmn_avg_nbr > 0) dmn_avg=(dmn_sct **)nco_free(dmn_avg); if(msk != NULL) msk=nco_var_free(msk); if(msk_nm != NULL) msk_nm=(char *)nco_free(msk_nm); if(msk_out != NULL) msk_out=nco_var_free(msk_out); if(msk_sng != NULL) msk_sng=(char *)nco_free(msk_sng); if(wgt != NULL) wgt=nco_var_free(wgt); if(wgt_avg != NULL) wgt_avg=nco_var_free(wgt_avg); if(wgt_nm != NULL) wgt_nm=(char *)nco_free(wgt_nm); if(wgt_out != NULL) wgt_out=nco_var_free(wgt_out); /* 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_out > 0) dmn_out=nco_dmn_lst_free(dmn_out,nbr_dmn_out); /* Free variable lists */ if(nbr_xtr > 0) var=nco_var_lst_free(var,nbr_xtr); /* ncwa uses nco_var_lst_free() on var_prc_out because var_out has dangling pointers */ if(nbr_var_fix > 0) var_fix_out=nco_var_lst_free(var_fix_out,nbr_var_fix); if(nbr_var_prc > 0) var_prc_out=nco_var_lst_free(var_prc_out,nbr_var_prc); var_prc=(var_sct **)nco_free(var_prc); var_fix=(var_sct **)nco_free(var_fix); var_out=(var_sct **)nco_free(var_out); #ifdef ENABLE_MPI MPI_Finalize(); #endif /* !ENABLE_MPI */ nco_exit_gracefully(); return EXIT_SUCCESS; } /* end main() */

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Variable Documentation

char** ncap_fl_spt_glb

Definition at line 77 of file mpncwa.c.

size_t* ncap_ln_nbr_crr

Definition at line 76 of file mpncwa.c.

size_t ncap_ncl_dpt_crr = 0UL

Definition at line 75 of file mpncwa.c.

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