scale_file_netcdf.c File Reference

#include "scale_file.h"
#include "netcdf.h"

Include dependency graph for scale_file_netcdf.c:

Go to the source code of this file.

Classes
struct	fileinfo_t
struct	tdim_t
struct	varinfo_t

Macros
#define	MPI_INCLUDED
#define	TEPS   1e-6
#define	NTMAX   102400
#define	MIN(a, b)   ((a)<(b) ? (a) : (b))
#define	CHECK_ERROR(func)
#define	CHECK_PNC_ERROR(func)
#define	ncmpi_inq_attid(a, b, c, d)   NC2_ERR
#define	ncmpi_inq_varid(a, b, c)   NC2_ERR
#define	ncmpi_inq_dimid(a, b, c)   NC2_ERR
#define	NCTYPE2TYPE(nctype, type)
#define	TYPE2NCTYPE(type, nctype)
#define	DEFAULT_DEFLATE_LEVEL   2

Functions
int	file_open_c (int *fid, const char *fname, const int mode, const int icomm)
int	file_get_dim_length_c (int *len, const int fid, const char *dimname, const bool suppress)
int	file_set_option_c (const int fid, const char *filetype, const char *key, const char *val)
int	file_get_nvars_c (int *nvars, const int fid)
int	file_get_varname_c (char *name, const int fid, const int vid, const int len)
int	file_get_datainfo_c (datainfo_t *dinfo, const int fid, const char *varname, const int step, const bool suppress)
int	file_get_step_size_c (int *len, const int fid, const char *varname)
int	file_read_data_c (void *var, const datainfo_t *dinfo, const int precision, const int ntypes, const int dtype, const int *start, const int *count)
int	file_get_attribute_text_c (char *value, const int fid, const char *vname, const char *key, const bool suppress, const int len)
int	file_get_attribute_int_c (int *value, const int fid, const char *vname, const char *key, const bool suppress, const int len)
int	file_get_attribute_float_c (float *value, const int fid, const char *vname, const char *key, const bool suppress, const int len)
int	file_get_attribute_double_c (double *value, const int fid, const char *vname, const char *key, const bool suppress, const int len)
int	file_set_attribute_text_c (const int fid, const char *vname, const char *key, const char *val)
int	file_set_attribute_int_c (const int fid, const char *vname, const char *key, const int *value, const int len)
int	file_set_attribute_float_c (const int fid, const char *vname, const char *key, const float *value, const int len)
int	file_set_attribute_double_c (const int fid, const char *vname, const char *key, const double *value, const int len)
int	file_add_associatedvariable_c (const int fid, const char *vname)
int	file_set_tunits_c (const int fid, const char *time_units, const char *calendar)
int	file_put_axis_c (const int fid, const char *name, const char *desc, const char *units, const char *dim_name, const int dtype, const void *val, const int size, const int precision)
int	file_def_axis_c (const int fid, const char *name, const char *desc, const char *units, const char *dim_name, const int dtype, const int dim_size, const int bounds)
int	file_write_axis_c (const int fid, const char *name, const void *val, const int precision, const int *start, const int *count)
int	file_put_associatedcoordinate_c (const int fid, const char *name, const char *desc, const char *units, const char **dim_names, const int ndims, const int dtype, const void *val, const int precision)
int	file_def_associatedcoordinate_c (const int fid, const char *name, const char *desc, const char *units, const char **dim_names, const int ndims, const int dtype)
int	file_write_associatedcoordinate_c (const int fid, const char *name, const void *val, const int ndims, const int precision, const int *start, const int *count)
int	file_add_variable_c (int *vid, const int fid, const char *varname, const char *desc, const char *units, const char *stdname, const char **dims, const int ndims, const int dtype, const double tint, const char *tstats)
int	file_enddef_c (const int fid)
int	file_redef_c (const int fid)
int	file_attach_buffer_c (const int fid, const int64_t buf_amount)
int	file_detach_buffer_c (const int fid)
int	file_flush_c (const int fid)
int	file_write_data_c (const int fid, const int vid, const void *var, const double t_start, const double t_end, const int ndims, const int precision, const int *start, const int *count)
int	file_close_c (const int fid, const bool abort)

Macro Definition Documentation

MPI_INCLUDED

#define MPI_INCLUDED

Definition at line 3 of file scale_file_netcdf.c.

TEPS

#define TEPS   1e-6

Definition at line 7 of file scale_file_netcdf.c.

NTMAX

#define NTMAX   102400

Definition at line 8 of file scale_file_netcdf.c.

MIN

#define MIN	(		a,
			b
	)		((a)<(b) ? (a) : (b))

Definition at line 10 of file scale_file_netcdf.c.

CHECK_ERROR

#define CHECK_ERROR

(

func

)

Value:

  {                                                             \
    int status_ = (func);                                       \
    if (status_ != NC_NOERR) {                                  \
      if ( ! ERROR_SUPPRESS ) {                                 \
        fprintf(stderr, "Error: at line %d in %s\n", __LINE__, __FILE__);   \
        fprintf(stderr, "       %s\n", nc_strerror(status_));   \
      }                                                         \
      return ERROR_CODE;                                        \
    }                                                           \
  }

Definition at line 14 of file scale_file_netcdf.c.

CHECK_PNC_ERROR

#define CHECK_PNC_ERROR

(

func

)

Value:

  {                                                             \
    fprintf(stderr, "pnetCDF is necessary for shared_mode\n");  \
    fprintf(stderr, "Please re-compile with pnetCDF\n");        \
    return ERROR_CODE;                                          \
  }

Definition at line 40 of file scale_file_netcdf.c.

ncmpi_inq_attid

#define ncmpi_inq_attid	(		a,
			b,
			c,
			d
	)		NC2_ERR

Definition at line 46 of file scale_file_netcdf.c.

ncmpi_inq_varid

#define ncmpi_inq_varid	(		a,
			b,
			c
	)		NC2_ERR

Definition at line 47 of file scale_file_netcdf.c.

ncmpi_inq_dimid

#define ncmpi_inq_dimid	(		a,
			b,
			c
	)		NC2_ERR

Definition at line 48 of file scale_file_netcdf.c.

NCTYPE2TYPE

#define NCTYPE2TYPE	(		nctype,
			type
	)

Value:

  {                                                             \
  switch ( nctype ) {                                           \
  case NC_FLOAT:                                                \
    type = File_REAL4;                                          \
    break;                                                      \
  case NC_DOUBLE:                                               \
    type = File_REAL8;                                          \
    break;                                                      \
  case NC_SHORT:                                                \
    type = File_INTEGER2;                                       \
    break;                                                      \
  case NC_INT:                                                  \
    type = File_INTEGER4;                                       \
    break;                                                      \
  case NC_CHAR:                                                 \
    type = File_TEXT;                                           \
    break;                                                      \
  default:                                                 \
    fprintf(stderr, "unsupported data type: %d\n", xtype);      \
    return ERROR_CODE;                                          \
  }                                                             \
  }

Definition at line 51 of file scale_file_netcdf.c.

TYPE2NCTYPE

#define TYPE2NCTYPE	(		type,
			nctype
	)

Value:

  {                                                             \
  switch ( type ) {                                             \
  case File_REAL4:                                              \
    nctype = NC_FLOAT;                                          \
    break;                                                      \
  case File_REAL8:                                              \
    nctype = NC_DOUBLE;                                         \
    break;                                                      \
  default:                                                      \
    fprintf(stderr, "unsupported data type: %d\n", xtype);      \
    return ERROR_CODE;                                          \
  }                                                             \
  }

Definition at line 75 of file scale_file_netcdf.c.

DEFAULT_DEFLATE_LEVEL

#define DEFAULT_DEFLATE_LEVEL   2

Definition at line 91 of file scale_file_netcdf.c.

Function Documentation

file_open_c()

int file_open_c	(	int *	fid,
		const char *	fname,
		const int	mode,
		const int	icomm
	)

Definition at line 170 of file scale_file_netcdf.c.

{
  int ncid;
  int len;
  int shared_mode;
  char _fname[File_HLONG+4];
  int add_suffix;
  MPI_Comm comm;
 
  if ( nfile >= FILE_MAX ) {
    fprintf(stderr, "exceed max number of file limit\n");
    return ERROR_CODE;
  }
 
  len = strlen(fname);
  strcpy(_fname, fname);
 
  if ( mode==File_FREAD || mode==File_FAPPEND ) {
    FILE *fp = fopen(_fname, "r");
    if ( fp==NULL ) {
      add_suffix = 1;
    } else {
      fclose(fp);
      add_suffix = 0;
    }
  } else
    add_suffix = 1;
 
  if ( add_suffix )
    if (fname[len-3] != '.' || fname[len-2] != 'n' || fname[len-1] != 'c' )
      strcat(_fname, ".nc");
 
  comm = MPI_Comm_f2c(icomm);
  if ( comm == MPI_COMM_NULL || comm == MPI_COMM_SELF )
    shared_mode = 0;
  else
    shared_mode = 1;
 
  switch ( mode ) {
  case File_FREAD:
    if ( shared_mode )
      CHECK_PNC_ERROR( ncmpi_open(comm, _fname, NC_NOWRITE, MPI_INFO_NULL, &ncid) )
    else
      CHECK_ERROR( nc_open(_fname, NC_NOWRITE, &ncid) )
    break;
  case File_FWRITE:
    if ( shared_mode )
      CHECK_PNC_ERROR( ncmpi_create(comm, _fname, NC_CLOBBER|NC_64BIT_OFFSET, MPI_INFO_NULL, &ncid) )
    else
#ifdef NETCDF3
      CHECK_ERROR( nc_create(_fname, NC_CLOBBER|NC_64BIT_OFFSET, &ncid) )
#else
      CHECK_ERROR( nc_create(_fname, NC_CLOBBER|NC_NETCDF4, &ncid) )
#endif
    break;
  case File_FAPPEND:
    if ( shared_mode )
      CHECK_PNC_ERROR( ncmpi_open(comm, _fname, NC_WRITE, MPI_INFO_NULL, &ncid) )
    else
      CHECK_ERROR( nc_open(_fname, NC_WRITE, &ncid) )
    break;
  default:
    fprintf(stderr, "invalid mode type\n");
    return ERROR_CODE;
  }
 
  files[nfile] = (fileinfo_t*) malloc(sizeof(fileinfo_t));
  files[nfile]->ncid = ncid;
  files[nfile]->deflate_level = DEFAULT_DEFLATE_LEVEL;
#if defined(NETCDF3) || defined(PNETCDF)
  if ( mode == File_FWRITE )
    files[nfile]->defmode = 1;
  else
    files[nfile]->defmode = 0;
#endif
 
  files[nfile]->shared_mode = shared_mode;  /* shared-file I/O mode */
  strcpy(files[nfile]->fname, fname);
  *fid = nfile;
 
  nfile++;
 
  return SUCCESS_CODE;
}

References File_HLONG.

Referenced by scale_file::file_get_aggregate().

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file_get_dim_length_c()

int file_get_dim_length_c	(	int *	len,
		const int	fid,
		const char *	dimname,
		const bool	suppress
	)

Definition at line 258 of file scale_file_netcdf.c.

{
  int ncid, dimid;
 
  ERROR_SUPPRESS = suppress;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode ) {
    MPI_Offset l;
    CHECK_PNC_ERROR( ncmpi_inq_dimid(ncid, dimname, &dimid) )
    CHECK_PNC_ERROR( ncmpi_inq_dimlen(ncid, dimid, &l) )
    *len = l;
  } else {
    size_t l;
    CHECK_ERROR( nc_inq_dimid(ncid, dimname, &dimid) )
    CHECK_ERROR( nc_inq_dimlen(ncid, dimid, &l) )
    *len = l;
  }
 
  ERROR_SUPPRESS = 0;
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_get_dimlength().

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file_set_option_c()

int file_set_option_c	(	const int	fid,
		const char *	filetype,
		const char *	key,
		const char *	val
	)

Definition at line 287 of file scale_file_netcdf.c.

{
  if ( strcmp(filetype, "netcdf") != 0 ) return SUCCESS_CODE;
 
  if ( strcmp(key, "deflate_level") == 0 ) {
    if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
    files[fid]->deflate_level = atoi(val);
    return SUCCESS_CODE;
  } else {
    return ERROR_CODE;
  }
}

References SUCCESS_CODE.

Referenced by scale_file::file_set_option().

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file_get_nvars_c()

int file_get_nvars_c	(	int *	nvars,
		const int	fid
	)

Definition at line 303 of file scale_file_netcdf.c.

{
  int ncid;
  int ndims, ngatts, unlimdim;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_inq(ncid, &ndims, nvars, &ngatts, &unlimdim) )
  else
    CHECK_ERROR( nc_inq(ncid, &ndims, nvars, &ngatts, &unlimdim) )
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_create().

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file_get_varname_c()

int file_get_varname_c	(	char *	name,
		const int	fid,
		const int	vid,
		const int	len
	)

Definition at line 320 of file scale_file_netcdf.c.

{
  int ncid, varid;
  char buf[MAX_NC_NAME+1];
  int i;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid  = files[fid]->ncid;
  varid = vid-1; // index starts from 1 in fortran space
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_inq_varname(ncid, varid, buf) )
  else
    CHECK_ERROR( nc_inq_varname(ncid, varid, buf) )
 
  for (i=0; i<MIN(len-1,strlen(buf)); i++)
    name[i] = buf[i];
  name[i] = '\0';
 
  return SUCCESS_CODE;
}

References scale_file::i.

Referenced by scale_file::file_create().

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file_get_datainfo_c()

int file_get_datainfo_c	(	datainfo_t *	dinfo,
		const int	fid,
		const char *	varname,
		const int	step,
		const bool	suppress
	)

Definition at line 345 of file scale_file_netcdf.c.

{
  int ncid, varid;
  nc_type xtype;
  int rank;
  int dimids[RANK_MAX], tdim, uldims[NC_MAX_DIMS];
  char name[NC_MAX_NAME+1];
  char *buf;
  size_t size;
  int natts;
  int i, n;
 
  ERROR_SUPPRESS = suppress;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, varname, &varid) )
  else
    CHECK_ERROR( nc_inq_varid(ncid, varname, &varid) )
 
  // fid
  dinfo->fid = fid;
  // varname
  strcpy(dinfo->varname, varname);
 
  if ( files[fid]->shared_mode ) {
    MPI_Offset l;
    // datatype
    CHECK_PNC_ERROR( ncmpi_inq_vartype(ncid, varid, &xtype) )
    NCTYPE2TYPE(xtype, dinfo->datatype);
    // rank
    CHECK_PNC_ERROR( ncmpi_inq_varndims(ncid, varid, &rank) )
    if ( rank > 0 ) {
#ifdef PNETCDF
      // description
      if ( ncmpi_inq_attlen(ncid, varid, "long_name", &l) == NC_NOERR ) {
        buf = (char*) malloc(l+1);
        CHECK_PNC_ERROR( ncmpi_get_att_text(ncid, varid, "long_name", buf) )
        for (i=0; i<MIN(File_HMID-1,l); i++)
          dinfo->description[i] = buf[i];
        dinfo->description[i] = '\0';
        free(buf);
      } else
        dinfo->description[0] = '\0';
      // units
      if ( ncmpi_inq_attlen(ncid, varid, "units", &l) == NC_NOERR ) {
        buf = (char*) malloc(l+1);
        CHECK_PNC_ERROR( ncmpi_get_att_text(ncid, varid, "units", buf) )
        for (i=0; i<MIN(File_HSHORT-1,l); i++)
          dinfo->units[i] = buf[i];
        dinfo->units[i] = '\0';
        free(buf);
      } else
        dinfo->units[0] = '\0';
      // standard_name
      if ( ncmpi_inq_attlen(ncid, varid, "standard_name", &l) == NC_NOERR ) {
        buf = (char*) malloc(l+1);
        CHECK_PNC_ERROR( ncmpi_get_att_text(ncid, varid, "standard_name", buf) )
        for (i=0; i<MIN(File_HMID-1,l); i++)
          dinfo->standard_name[i] = buf[i];
        dinfo->standard_name[i] = '\0';
        free(buf);
      } else
        dinfo->standard_name[0] = '\0';
#endif
      // dimensions
      CHECK_PNC_ERROR( ncmpi_inq_vardimid(ncid, varid, dimids) )
#if 1
      CHECK_PNC_ERROR( ncmpi_inq_unlimdim(ncid, uldims) )
      n = 1;
#else
      CHECK_PNC_ERROR( ncmpi_inq_unlimdims(ncid, &n, uldims) )
#endif
    }
    // attributes
    dinfo->natts = 0;
    CHECK_PNC_ERROR( ncmpi_inq_varnatts(ncid, varid, &natts) )
    for (i=0; i<natts; i++) {
      CHECK_PNC_ERROR( ncmpi_inq_attname(ncid, varid, i, name) )
      if ( strcmp(name, "long_name") &&
           strcmp(name, "description") &&
           strcmp(name, "units") &&
           strcmp(name, "standard_name") ) {
        strcpy(dinfo->att_name+File_HSHORT*dinfo->natts, name);
        CHECK_PNC_ERROR( ncmpi_inq_atttype(ncid, varid, name, &xtype) )
        NCTYPE2TYPE(xtype, dinfo->att_type[dinfo->natts]);
        CHECK_PNC_ERROR( ncmpi_inq_attlen(ncid, varid, name, &l) )
        dinfo->att_len[dinfo->natts] = l;
        dinfo->natts++;
      }
    }
  } else {
    size_t l;
    // datatype
    CHECK_ERROR( nc_inq_vartype(ncid, varid, &xtype) )
    NCTYPE2TYPE(xtype, dinfo->datatype);
    // rank
    CHECK_ERROR( nc_inq_varndims(ncid, varid, &rank) )
    if ( rank > 0 ) {
      // description
      if ( nc_inq_attlen(ncid, varid, "long_name", &l) == NC_NOERR ) {
        buf = (char*) malloc(l+1);
        CHECK_ERROR( nc_get_att_text(ncid, varid, "long_name", buf) )
      } else if ( nc_inq_attlen(ncid, varid, "description", &l) == NC_NOERR ) { // for WRF file
        buf = (char*) malloc(l+1);
        CHECK_ERROR( nc_get_att_text(ncid, varid, "description", buf) )
      } else
        l = 0;
      for (i=0; i<MIN(File_HMID-1,l); i++)
        dinfo->description[i] = buf[i];
      dinfo->description[i] = '\0';
      if ( l>0 ) free(buf);
      // units
      if ( nc_inq_attlen(ncid, varid, "units", &l) == NC_NOERR ) {
        buf = (char*) malloc(l+1);
        CHECK_ERROR( nc_get_att_text(ncid, varid, "units", buf) )
          for (i=0; i<MIN(File_HSHORT-1,l); i++)
            dinfo->units[i] = buf[i];
        dinfo->units[i] = '\0';
        free(buf);
      } else
        dinfo->units[0] = '\0';
      // standard_name
      if ( nc_inq_attlen(ncid, varid, "standard_name", &l) == NC_NOERR ) {
        buf = (char*) malloc(l+1);
        CHECK_ERROR( nc_get_att_text(ncid, varid, "standard_name", buf) )
        for (i=0; i<MIN(File_HMID-1,l); i++)
          dinfo->standard_name[i] = buf[i];
        dinfo->standard_name[i] = '\0';
        free(buf);
      } else
        dinfo->standard_name[0] = '\0';
      // dimension
      CHECK_ERROR( nc_inq_vardimid(ncid, varid, dimids) )
#ifdef NETCDF3
      CHECK_ERROR( nc_inq_unlimdim(ncid, uldims) )
      n = 1;
#else
      CHECK_ERROR( nc_inq_unlimdims(ncid, &n, uldims) )
#endif
    }
    // attributes
    dinfo->natts = 0;
    CHECK_ERROR( nc_inq_varnatts(ncid, varid, &natts) )
    for (i=0; i<natts; i++) {
      CHECK_ERROR( nc_inq_attname(ncid, varid, i, name) )
      if ( strcmp(name, "long_name") &&
           strcmp(name, "description") &&
           strcmp(name, "units") &&
           strcmp(name, "standard_name") ) {
        strcpy(dinfo->att_name+File_HSHORT*dinfo->natts, name);
        CHECK_ERROR( nc_inq_atttype(ncid, varid, name, &xtype) )
        NCTYPE2TYPE(xtype, dinfo->att_type[dinfo->natts]);
        CHECK_ERROR( nc_inq_attlen(ncid, varid, name, &l) )
        dinfo->att_len[dinfo->natts] = l;
        dinfo->natts++;
      }
    }
  }
  
  if ( rank > 0 ) {
    tdim = -1;
    for ( i=0; i<n; i++ ) {
      if ( uldims[i] == dimids[0] ) {
        tdim = uldims[i];
        break;
      }
    }
    if (rank > RANK_MAX) {
      fprintf(stderr, "rank exceeds limit: %d\n", rank);
      return ERROR_CODE;
    }
    dinfo->rank = tdim >= 0 ? rank -1 : rank; // do not count time dimension
    // dim_name and dim_size
    for (i=0; i<dinfo->rank; i++) {
      // note: C and Fortran orders are opposite
      if ( files[fid]->shared_mode ) {
        MPI_Offset size_;
        CHECK_PNC_ERROR( ncmpi_inq_dim(ncid, dimids[rank-i-1], name, &size_) )
        size = (size_t)size_;
      }
      else
        CHECK_ERROR( nc_inq_dim(ncid, dimids[rank-i-1], name, &size) )
        if ( strlen(name) > File_HSHORT-1 ) {
          fprintf(stderr, "Length of the dimension name (%s) is too long (should be < %d).\n", name, File_HSHORT);
          return ERROR_CODE;
        }
      strncpy(dinfo->dim_name+i*File_HSHORT, name, File_HSHORT);
      dinfo->dim_size[i] = size;
    }
 
    dinfo->step = step;
    if ( tdim >= 0 ) {
      if ( files[fid]->shared_mode ) {
        MPI_Offset idx[2];
        MPI_Offset l;
        // time_end
        CHECK_PNC_ERROR( ncmpi_inq_dimname(ncid, tdim, name) )
        CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, name, &varid) )
        idx[0] = step - 1;
        CHECK_PNC_ERROR( ncmpi_get_var1_double_all(ncid, varid, idx, &(dinfo->time_end)) )
        // units
        CHECK_PNC_ERROR( ncmpi_inq_attlen  (ncid, varid, "units", &l) )
        buf = (char*) malloc(l+1);
        CHECK_PNC_ERROR( ncmpi_get_att_text(ncid, varid, "units", buf) )
        for (i=0; i<MIN(File_HMID-1,l); i++)
          dinfo->time_units[i] = buf[i];
        dinfo->time_units[i] = '\0';
        free(buf);
        // calendar
#ifdef PNETCDF
        if ( ncmpi_inq_attlen(ncid, varid, "calendar", &l) == NC_NOERR ) {
          buf = (char*) malloc(l+1);
          CHECK_PNC_ERROR( ncmpi_get_att_text(ncid, varid, "calendar", buf) )
          for (i=0; i<MIN(File_HSHORT-1,l); i++)
            dinfo->calendar[i] = buf[i];
          dinfo->calendar[i] = '\0';
          free(buf);
        } else
          dinfo->calendar[0] = '\0';
#endif
        // time_start
        strcat(name, "_bnds");
        CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, name, &varid) )
        idx[1] = 0;
        CHECK_PNC_ERROR( ncmpi_get_var1_double_all(ncid, varid, idx, &(dinfo->time_start)) )
      } else {
        size_t idx[2];
        size_t l;
        // time_end
        CHECK_ERROR( nc_inq_dimname(ncid, tdim, name) )
        if ( nc_inq_varid(ncid, name, &varid) == NC_NOERR ) {
          idx[0] = step - 1;
          CHECK_ERROR( nc_get_var1_double(ncid, varid, idx, &(dinfo->time_end)) )
          // units
          CHECK_ERROR( nc_inq_attlen  (ncid, varid, "units", &l) )
          buf = (char*) malloc(l+1);
          CHECK_ERROR( nc_get_att_text(ncid, varid, "units", buf) )
          for (i=0; i<MIN(File_HMID-1,l); i++)
            dinfo->time_units[i] = buf[i];
          dinfo->time_units[i] = '\0';
          free(buf);
          // calendar
          if ( nc_inq_attlen(ncid, varid, "calendar", &l) == NC_NOERR ) {
            buf = (char*) malloc(l+1);
            CHECK_ERROR( nc_get_att_text(ncid, varid, "calendar", buf) )
            for (i=0; i<MIN(File_HSHORT-1,l); i++)
              dinfo->calendar[i] = buf[i];
            dinfo->calendar[i] = '\0';
            free(buf);
          } else
            dinfo->calendar[0] = '\0';
          // time_start
          strcat(name, "_bnds");
          CHECK_ERROR( nc_inq_varid(ncid, name, &varid) )
          idx[1] = 0;
          CHECK_ERROR( nc_get_var1_double(ncid, varid, idx, &(dinfo->time_start)) )
        } else {
          dinfo->time_start = 0.0;
          dinfo->time_end = 0.0;
          dinfo->time_units[0] = '\0';
          dinfo->calendar[0] = '\0';
        }
      }
      dinfo->has_tdim = 1;
    } else {
      if ( step > 1 ) { // if variable does not have time dimention, step > 1 should not exist
        fprintf(stderr, "requested step is larger than tdim: step=%d tdim=%d\n", step, tdim);
        return ERROR_CODE;
      }
      dinfo->has_tdim = 0;
      dinfo->time_start = 0.0;
      dinfo->time_end = 0.0;
      dinfo->time_units[0] = '\0';
      dinfo->calendar[0] = '\0';
    }
  } else {
    dinfo->rank = 0;
    dinfo->description[0]   = '\0';
    dinfo->units[0]         = '\0';
    dinfo->standard_name[0] = '\0';
    dinfo->has_tdim = 0;
    dinfo->time_start = 0.0;
    dinfo->time_end = 0.0;
    dinfo->time_units[0] = '\0';
    dinfo->calendar[0] = '\0';
  }
 
  ERROR_SUPPRESS = 0;
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_variable(), and scale_file::file_get_stepsize().

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file_get_step_size_c()

int file_get_step_size_c	(	int *	len,
		const int	fid,
		const char *	varname
	)

Definition at line 643 of file scale_file_netcdf.c.

{
  int ncid, varid;
 
  int dimids[RANK_MAX], uldims[NC_MAX_DIMS], tdim;
  int n, i;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, varname, &varid) )
  else
    CHECK_ERROR( nc_inq_varid(ncid, varname, &varid) )
 
  if ( files[fid]->shared_mode ) {
    CHECK_PNC_ERROR( ncmpi_inq_vardimid(ncid, varid, dimids) )
    CHECK_PNC_ERROR( ncmpi_inq_unlimdim(ncid, uldims) )
    n = uldims[0] < 0 ? 0 : 1;
  } else {
    CHECK_ERROR( nc_inq_vardimid(ncid, varid, dimids) )
#ifdef NETCDF3
    CHECK_ERROR( nc_inq_unlimdim(ncid, uldims) )
    n = uldims[0] < 0 ? 0 : 1;
#else
    CHECK_ERROR( nc_inq_unlimdims(ncid, &n, uldims) )
#endif
  }
  
  tdim = -1;
  for ( i=0; i<n; i++ ) {
    if ( uldims[i] == dimids[0] ) {
      tdim = uldims[i];
      break;
    }
  }
 
  if ( tdim > 0 ) {
    if ( files[fid]->shared_mode ) {
      MPI_Offset l;
      CHECK_PNC_ERROR( ncmpi_inq_dimlen(ncid, tdim, &l) )
      *len = l;
    } else {
      size_t l;
      CHECK_ERROR( nc_inq_dimlen(ncid, tdim, &l) )
      *len = l;
    }
  } else
    *len = 0;
 
  return SUCCESS_CODE;
}

References scale_file::i, and RANK_MAX.

Referenced by scale_file::file_get_stepsize().

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file_read_data_c()

int file_read_data_c	(	void *	var,
		const datainfo_t *	dinfo,
		const int	precision,
		const int	ntypes,
		const int	dtype,
		const int *	start,
		const int *	count
	)

Definition at line 697 of file scale_file_netcdf.c.

{
  int ncid, varid;
  int rank;
  int i;
  int fid;
  size_t *str, *cnt;
  MPI_Datatype dtype_;
  MPI_Offset *strp, *cntp;
  size_t size;
 
  fid = dinfo->fid;
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
  if ( files[fid]->shared_mode ) {
    CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, dinfo->varname, &varid) )
    CHECK_PNC_ERROR( ncmpi_inq_varndims(ncid, varid, &rank) )
    strp = (MPI_Offset*) malloc(sizeof(MPI_Offset)*rank);
    cntp = (MPI_Offset*) malloc(sizeof(MPI_Offset)*rank);
  } else {
    CHECK_ERROR( nc_inq_varid(ncid, dinfo->varname, &varid) )
    CHECK_ERROR( nc_inq_varndims(ncid, varid, &rank) )
  }
  str = (size_t*) malloc(sizeof(size_t)*rank);
  cnt = (size_t*) malloc(sizeof(size_t)*rank);
 
  if ( start==NULL || start[0]<=0 || count==NULL || count[0]<=0 ) {
    for (i=0; i<dinfo->rank; i++) {
      // note: C and Fortran orders are opposite
      str[rank -i-1] = 0;
      cnt[rank -i-1] = dinfo->dim_size[i];
    }
  } else {
    for (i=0; i<dinfo->rank; i++) {
      // note: C and Fortran orders are opposite
      str[rank -i-1] = start[i] - 1;
      cnt[rank -i-1] = count[i];
    }
  }
  if (rank > dinfo->rank) { // have time dimension
    str[0] = dinfo->step - 1;
    cnt[0] = 1;
  }
 
  size = 1;
  for (i=0; i<rank; i++) size *= cnt[i];
 
  if ( files[fid]->shared_mode ) {
#ifdef PNETCDF
    for (i=0; i<rank; i++) {
      strp[i] = (MPI_Offset) str[i];
      cntp[i] = (MPI_Offset) cnt[i];
    }
    free(str);
    free(cnt);
    dtype_ = dtype == 0 ? MPI_DATATYPE_NULL : MPI_Type_f2c(dtype);
    CHECK_PNC_ERROR( ncmpi_iget_vara(ncid, varid, strp, cntp, var, (MPI_Offset) ntypes, dtype_, NULL) )
    free(strp);
    free(cntp);
    if ( dtype_ == MPI_FLOAT ) {
      float factor, offset, misval;
      int l_rescale = 0;
      if ( ncmpi_get_att_float(ncid, varid, "missing_value", &misval) == NC_NOERR )
        if ( misval != RMISS )
          for (i=0; i<size; i++) if ( ((float*)var)[i] == misval ) ((float*)var)[i] = RMISS;
      if ( ncmpi_get_att_float(ncid, varid, "scale_factor", &factor) != NC_NOERR )
        factor = 1.0f;
      else
        l_rescale = 1;
      if ( ncmpi_get_att_float(ncid, varid, "add_offset", &offset) != NC_NOERR )
        offset = 0.0f;
      else
        l_rescale = 1;
      if ( l_rescale ) for (i=0; i<size; i++) ((float*)var)[i] = ((float*)var)[i] * factor + offset;
    } else if ( dtype_ == MPI_DOUBLE ) {
      double factor, offset, misval;
      int l_rescale = 0;
      if ( ncmpi_get_att_double(ncid, varid, "missing_value", &misval) == NC_NOERR )
        if ( (float)misval != (float)RMISS )
          for (i=0; i<size; i++) if ( ((double*)var)[i] == misval ) ((double*)var)[i] = RMISS;
      if ( ncmpi_get_att_double(ncid, varid, "scale_factor", &factor) != NC_NOERR )
        factor = 1.0;
      else
        l_rescale = 1;
      if ( ncmpi_get_att_double(ncid, varid, "add_offset", &offset) != NC_NOERR )
        offset = 0.0;
      else
        l_rescale = 1;
      if ( l_rescale ) for (i=0; i<size; i++) ((double*)var)[i] = ((double*)var)[i] * factor + offset;
    } else {
      float factor, offset, misval;
      if (    ( ncmpi_get_att_float(ncid, varid, "missing_value", &misval) == NC_NOERR ) )
        if ( misval != (float)RMISS ) {
          fprintf(stderr, "missing_value (!=UNDEF) is not supported with a MPI derived type\n");
          return ERROR_CODE;
        }
      if (    ( ncmpi_get_att_float(ncid, varid, "scale_factor", &factor) == NC_NOERR ) 
           || ( ncmpi_get_att_float(ncid, varid, "add_offset",   &offset) == NC_NOERR ) ) {
        fprintf(stderr, "scale_factor and add_offset is not supported with a MPI derived type\n");
        return ERROR_CODE;
      }
    }
#else
    CHECK_PNC_ERROR( dummy )
#endif
  } else {
    switch ( precision ) {
    case 8:
      CHECK_ERROR( nc_get_vara_double(ncid, varid, str, cnt, (double*)var) )
      {
        double factor, offset, misval;
        float a;
        int l_rescale = 0;
        nc_get_att_float(ncid, varid, "missing_value", &a);
        if ( nc_get_att_double(ncid, varid, "missing_value", &misval) == NC_NOERR )
          if ( (float)misval != (float)RMISS )
            for (i=0; i<size; i++) if ( ((double*)var)[i] == misval ) ((double*)var)[i] = RMISS;
        if ( nc_get_att_double(ncid, varid, "scale_factor", &factor) != NC_NOERR )
          factor = 1.0;
        else
          l_rescale = 1;
        if ( nc_get_att_double(ncid, varid, "add_offset", &offset) != NC_NOERR )
          offset = 0.0;
        else
          l_rescale = 1;
        if ( l_rescale ) for (i=0; i<size; i++) ((double*)var)[i] = ((double*)var)[i] * factor + offset;
      }
      break;
    case 4:
      CHECK_ERROR( nc_get_vara_float(ncid, varid, str, cnt, (float*)var) )
      {
        float factor, offset, misval;
        int l_rescale = 0;
        if ( nc_get_att_float(ncid, varid, "missing_value", &misval) == NC_NOERR )
          if ( misval != (float)RMISS )
            for (i=0; i<size; i++) if ( ((float*)var)[i] == misval ) ((float*)var)[i] = RMISS;
        if ( nc_get_att_float(ncid, varid, "scale_factor", &factor) != NC_NOERR )
          factor = 1.0f;
        else
          l_rescale = 1;
        if ( nc_get_att_float(ncid, varid, "add_offset", &offset) != NC_NOERR )
          offset = 0.0f;
        else
          l_rescale = 1;
        if ( l_rescale ) for (i=0; i<size; i++) ((float*)var)[i] = ((float*)var)[i] * factor + offset;
      }
      break;
    default:
      free(str);
      free(cnt);
      fprintf(stderr, "unsupported data precision: %d\n", precision );
      return ERROR_CODE;
    }
    free(str);
    free(cnt);
  }
 
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_get_stepsize().

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file_get_attribute_text_c()

int file_get_attribute_text_c	(	char *	value,
		const int	fid,
		const char *	vname,
		const char *	key,
		const bool	suppress,
		const int	len
	)

Definition at line 864 of file scale_file_netcdf.c.

{
  int ncid;
  int varid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  ERROR_SUPPRESS = suppress;
 
  if ( files[fid]->shared_mode ) {
    MPI_Offset l;
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, vname, &varid) )
 
    CHECK_PNC_ERROR( ncmpi_inq_attlen(ncid, varid, key, &l) )
    if ( len-1 < l ) return ERROR_CODE;
 
    CHECK_PNC_ERROR( ncmpi_get_att_text(ncid, varid, key, value) )
    value[l] = '\0';
  }
  else {
    size_t l;
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_ERROR( nc_inq_varid(ncid, vname, &varid) )
 
    CHECK_ERROR( nc_inq_attlen(ncid, varid, key, &l) )
    if ( len-1 < l ) return ERROR_CODE;
 
    CHECK_ERROR( nc_get_att_text(ncid, varid, key, value) )
    value[l] = '\0';
  }
 
  ERROR_SUPPRESS = 0;
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_variable().

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file_get_attribute_int_c()

int file_get_attribute_int_c	(	int *	value,
		const int	fid,
		const char *	vname,
		const char *	key,
		const bool	suppress,
		const int	len
	)

Definition at line 911 of file scale_file_netcdf.c.

{
  int ncid;
  int varid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  ERROR_SUPPRESS = suppress;
 
  if ( files[fid]->shared_mode ) {
    MPI_Offset l;
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, vname, &varid) )
 
    CHECK_PNC_ERROR( ncmpi_inq_attlen(ncid, varid, key, &l) )
    if ( len != l ) return ERROR_CODE;
    CHECK_PNC_ERROR( ncmpi_get_att_int(ncid, varid, key, value) )
  }
  else {
    size_t l;
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_ERROR( nc_inq_varid(ncid, vname, &varid) )
 
    CHECK_ERROR( nc_inq_attlen(ncid, varid, key, &l) )
    if ( len != l ) return ERROR_CODE;
    CHECK_ERROR( nc_get_att_int(ncid, varid, key, value) )
  }
 
  ERROR_SUPPRESS = 0;
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_variable().

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file_get_attribute_float_c()

int file_get_attribute_float_c	(	float *	value,
		const int	fid,
		const char *	vname,
		const char *	key,
		const bool	suppress,
		const int	len
	)

Definition at line 954 of file scale_file_netcdf.c.

{
  int ncid;
  int varid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  ERROR_SUPPRESS = suppress;
 
  if ( files[fid]->shared_mode ) {
    MPI_Offset l;
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, vname, &varid) )
 
    CHECK_PNC_ERROR( ncmpi_inq_attlen(ncid, varid, key, &l) )
    if ( len != l ) return ERROR_CODE;
    CHECK_PNC_ERROR( ncmpi_get_att_float(ncid, varid, key, value) )
  }
  else {
    size_t l;
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_ERROR( nc_inq_varid(ncid, vname, &varid) )
 
    CHECK_ERROR( nc_inq_attlen(ncid, varid, key, &l) )
    if ( len != l ) return ERROR_CODE;
    CHECK_ERROR( nc_get_att_float(ncid, varid, key, value) )
  }
 
  ERROR_SUPPRESS = 0;
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_variable().

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file_get_attribute_double_c()

int file_get_attribute_double_c	(	double *	value,
		const int	fid,
		const char *	vname,
		const char *	key,
		const bool	suppress,
		const int	len
	)

Definition at line 997 of file scale_file_netcdf.c.

{
  int ncid;
  int varid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  ERROR_SUPPRESS = suppress;
 
  if ( files[fid]->shared_mode ) {
    MPI_Offset l;
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, vname, &varid) )
 
    CHECK_PNC_ERROR( ncmpi_inq_attlen(ncid, varid, key, &l) )
    if ( len != l ) return ERROR_CODE;
    CHECK_PNC_ERROR( ncmpi_get_att_double(ncid, varid, key, value) )
  }
  else {
    size_t l;
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_ERROR( nc_inq_varid(ncid, vname, &varid) )
 
    CHECK_ERROR( nc_inq_attlen(ncid, varid, key, &l) )
    if ( len != l ) return ERROR_CODE;
    CHECK_ERROR( nc_get_att_double(ncid, varid, key, value) )
  }
 
  ERROR_SUPPRESS = 0;
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_variable().

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file_set_attribute_text_c()

int file_set_attribute_text_c	(	const int	fid,
		const char *	vname,
		const char *	key,
		const char *	val
	)

Definition at line 1040 of file scale_file_netcdf.c.

{
  int ncid;
  int varid;
  int attid;
  int ret;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode ) {
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, vname, &varid) )
 
    if ( ncmpi_inq_attid(ncid, varid, key, &attid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  }
  else {
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_ERROR( nc_inq_varid(ncid, vname, &varid) )
 
    if ( nc_inq_attid(ncid, varid, key, &attid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  }
 
  ret = file_redef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, key, strlen(val), val) )
  else
    CHECK_ERROR( nc_put_att_text(ncid, varid, key, strlen(val), val) )
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_variable().

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file_set_attribute_int_c()

int file_set_attribute_int_c	(	const int	fid,
		const char *	vname,
		const char *	key,
		const int *	value,
		const int	len
	)

Definition at line 1081 of file scale_file_netcdf.c.

{
  int ncid;
  int varid;
  int attid;
  int ret;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode ) {
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, vname, &varid) )
 
    if ( ncmpi_inq_attid(ncid, varid, key, &attid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  }
  else {
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_ERROR( nc_inq_varid(ncid, vname, &varid) )
 
    if ( nc_inq_attid(ncid, varid, key, &attid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  }
 
  ret = file_redef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_put_att_int(ncid, varid, key, NC_INT, len, value) )
  else
    CHECK_ERROR( nc_put_att_int(ncid, varid, key, NC_INT, len, value) )
 
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_variable().

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file_set_attribute_float_c()

int file_set_attribute_float_c	(	const int	fid,
		const char *	vname,
		const char *	key,
		const float *	value,
		const int	len
	)

Definition at line 1124 of file scale_file_netcdf.c.

{
  int ncid;
  int varid;
  int attid;
  int ret;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode ) {
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, vname, &varid) )
 
    if ( ncmpi_inq_attid(ncid, varid, key, &attid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  }
  else {
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_ERROR( nc_inq_varid(ncid, vname, &varid) )
 
    if ( nc_inq_attid(ncid, varid, key, &attid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  }
 
  ret = file_redef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_put_att_float(ncid, varid, key, NC_FLOAT, len, value) )
  else
    CHECK_ERROR( nc_put_att_float(ncid, varid, key, NC_FLOAT, len, value) )
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_variable().

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file_set_attribute_double_c()

int file_set_attribute_double_c	(	const int	fid,
		const char *	vname,
		const char *	key,
		const double *	value,
		const int	len
	)

Definition at line 1166 of file scale_file_netcdf.c.

{
  int ncid;
  int varid;
  int attid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode ) {
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, vname, &varid) )
 
    if ( ncmpi_inq_attid(ncid, varid, key, &attid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  }
  else {
    if ( strcmp(vname, "global") == 0 ) {
      varid = NC_GLOBAL;
    } else
      CHECK_ERROR( nc_inq_varid(ncid, vname, &varid) )
 
    if ( nc_inq_attid(ncid, varid, key, &attid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  }
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_put_att_double(ncid, varid, key, NC_DOUBLE, len, value) )
  else
    CHECK_ERROR( nc_put_att_double(ncid, varid, key, NC_DOUBLE, len, value) )
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_variable().

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file_add_associatedvariable_c()

int file_add_associatedvariable_c	(	const int	fid,
		const char *	vname
	)

Definition at line 1204 of file scale_file_netcdf.c.

{
  int ncid, varid;
  int ret;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( nc_inq_varid(ncid, vname, &varid) == NC_NOERR ) // check if existed
    return ALREADY_EXISTED_CODE;
 
  ret = file_redef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_def_var(ncid, vname, NC_INT, 0, 0, &varid) )
  else
    CHECK_ERROR( nc_def_var(ncid, vname, NC_INT, 0, 0, &varid) )
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_add_associatedvariable().

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file_set_tunits_c()

int file_set_tunits_c	(	const int	fid,
		const char *	time_units,
		const char *	calendar
	)

Definition at line 1227 of file scale_file_netcdf.c.

{
  strcpy(files[fid]->time_units, time_units);
  strcpy(files[fid]->calendar, calendar);
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_create().

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file_put_axis_c()

int file_put_axis_c	(	const int	fid,
		const char *	name,
		const char *	desc,
		const char *	units,
		const char *	dim_name,
		const int	dtype,
		const void *	val,
		const int	size,
		const int	precision
	)

Definition at line 1237 of file scale_file_netcdf.c.

{
  int ncid, dimid, varid;
  nc_type xtype = -1;
  int ret;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( nc_inq_varid(ncid, name, &varid) == NC_NOERR ) // check if existed
    return ALREADY_EXISTED_CODE;
 
  ret = file_redef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  if ( nc_inq_dimid(ncid, dim_name, &dimid) != NC_NOERR ) // check if existed
    CHECK_ERROR( nc_def_dim(ncid, dim_name, size, &dimid) )
 
  TYPE2NCTYPE(dtype, xtype);
  CHECK_ERROR( nc_def_var(ncid, name, xtype, 1, &dimid, &varid) )
  if ( strlen(desc)>0  ) CHECK_ERROR( nc_put_att_text(ncid, varid, "long_name", strlen(desc), desc) )
  if ( strlen(units)>0 ) CHECK_ERROR( nc_put_att_text(ncid, varid, "units", strlen(units), units) )
 
  ret = file_enddef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  switch ( precision ) {
  case 8:
    CHECK_ERROR( nc_put_var_double(ncid, varid, (double*)val) )
    break;
  case 4:
    CHECK_ERROR( nc_put_var_float(ncid, varid, (float*)val) )
    break;
  default:
    fprintf(stderr, "unsupported data precision: %d\n", precision);
    return ERROR_CODE;
  }
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_get_dimlength().

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file_def_axis_c()

int file_def_axis_c	(	const int	fid,
		const char *	name,
		const char *	desc,
		const char *	units,
		const char *	dim_name,
		const int	dtype,
		const int	dim_size,
		const int	bounds
	)

Definition at line 1286 of file scale_file_netcdf.c.

{
  int ncid, dimid, varid;
  nc_type xtype = -1;
  int dimids[2];
  char buf[File_HSHORT+6];
  int ret;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode ) {
    if ( ncmpi_inq_varid(ncid, name, &varid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  } else {
    if ( nc_inq_varid(ncid, name, &varid) == NC_NOERR ) return ALREADY_EXISTED_CODE;
  }
 
  ret = file_redef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  TYPE2NCTYPE(dtype, xtype);
  if ( files[fid]->shared_mode ) {
    if ( ncmpi_inq_dimid(ncid, dim_name, &dimid) != NC_NOERR ) // check if existed
      CHECK_PNC_ERROR( ncmpi_def_dim(ncid, dim_name, dim_size, &dimid) )
 
    CHECK_PNC_ERROR( ncmpi_def_var(ncid, name, xtype, 1, &dimid, &varid) )
    if ( strlen(desc)>0  ) CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "long_name", strlen(desc), desc) )
    if ( strlen(units)>0 ) CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "units", strlen(units), units) )
 
    if ( bounds ) {
      dimids[0] = dimid;
      if ( ncmpi_inq_dimid(ncid, "nv", &(dimids[1])) != NC_NOERR ) // first called
        CHECK_PNC_ERROR( ncmpi_def_dim(ncid, "nv", 2, &(dimids[1])) )
      sprintf(buf, "%s_bnds", dim_name);
      CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "bounds", strlen(buf), buf) )
      CHECK_PNC_ERROR( ncmpi_def_var(ncid, buf, NC_DOUBLE, 2, dimids, &varid) )
    }
  } else {
    if ( nc_inq_dimid(ncid, dim_name, &dimid) != NC_NOERR ) // check if existed
      CHECK_ERROR( nc_def_dim(ncid, dim_name, dim_size, &dimid) )
 
    CHECK_ERROR( nc_def_var(ncid, name, xtype, 1, &dimid, &varid) )
    if ( strlen(desc)>0 )  CHECK_ERROR( nc_put_att_text(ncid, varid, "long_name", strlen(desc), desc) )
    if ( strlen(units)>0 ) CHECK_ERROR( nc_put_att_text(ncid, varid, "units", strlen(units), units) )
 
    if ( bounds ) {
      dimids[0] = dimid;
      if ( nc_inq_dimid(ncid, "nv", &(dimids[1])) != NC_NOERR ) // first called
        CHECK_ERROR( nc_def_dim(ncid, "nv", 2, &(dimids[1])) )
      sprintf(buf, "%s_bnds", dim_name);
      CHECK_ERROR( nc_put_att_text(ncid, varid, "bounds", strlen(buf), buf) )
      CHECK_ERROR( nc_def_var(ncid, buf, NC_DOUBLE, 2, dimids, &varid) )
    }
  }
 
  return SUCCESS_CODE;
}

References File_HSHORT.

Referenced by scale_file::file_def_axis().

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file_write_axis_c()

int file_write_axis_c	(	const int	fid,
		const char *	name,
		const void *	val,
		const int	precision,
		const int *	start,
		const int *	count
	)

Definition at line 1351 of file scale_file_netcdf.c.

{
  int ncid, varid;
  int ret;
  MPI_Offset start_[1], count_[1];
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, name, &varid) )
  else
    CHECK_ERROR( nc_inq_varid(ncid, name, &varid) )
 
  ret = file_enddef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  start_[0] = (MPI_Offset) start[0];
  count_[0] = (MPI_Offset) count[0];
 
  switch ( precision ) {
  case 8:
    if ( files[fid]->shared_mode )
      CHECK_PNC_ERROR( ncmpi_iput_vara_double(ncid, varid, start_, count_, val, NULL) )
    else
      CHECK_ERROR( nc_put_var_double(ncid, varid, (double*)val) )
    break;
  case 4:
    if ( files[fid]->shared_mode )
      CHECK_PNC_ERROR( ncmpi_iput_vara_float(ncid, varid, start_, count_, val, NULL) )
    else
      CHECK_ERROR( nc_put_var_float(ncid, varid, (float*)val) )
    break;
  default:
    fprintf(stderr, "unsupported data precision: %d\n", precision);
    return ERROR_CODE;
  }
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_axis().

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file_put_associatedcoordinate_c()

int file_put_associatedcoordinate_c	(	const int	fid,
		const char *	name,
		const char *	desc,
		const char *	units,
		const char **	dim_names,
		const int	ndims,
		const int	dtype,
		const void *	val,
		const int	precision
	)

Definition at line 1397 of file scale_file_netcdf.c.

{
  int ncid, *dimids, varid;
  nc_type xtype = -1;
  int i;
  int ret;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( nc_inq_varid(ncid, name, &varid) == NC_NOERR ) // check if existed
    return ALREADY_EXISTED_CODE;
 
  ret = file_redef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  dimids = malloc(sizeof(int)*ndims);
  for (i=0; i<ndims; i++)
    CHECK_ERROR( nc_inq_dimid(ncid, dim_names[i], dimids+ndims-i-1) )
 
  TYPE2NCTYPE(dtype, xtype);
 
  CHECK_ERROR( nc_def_var(ncid, name, xtype, ndims, dimids, &varid) )
  if ( strlen(desc)>0 )  CHECK_ERROR( nc_put_att_text(ncid, varid, "long_name", strlen(desc), desc) )
  if ( strlen(units)>0 ) CHECK_ERROR( nc_put_att_text(ncid, varid, "units", strlen(units), units) )
  free(dimids);
 
  ret = file_enddef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  switch ( precision ) {
  case 8:
    CHECK_ERROR( nc_put_var_double(ncid, varid, (double*)val) )
    break;
  case 4:
    CHECK_ERROR( nc_put_var_float(ncid, varid, (float*)val) )
    break;
  default:
    fprintf(stderr, "unsupported data precision: %d\n", precision);
    return ERROR_CODE;
  }
 
  return SUCCESS_CODE;
}

References scale_file::i.

Referenced by scale_file::file_def_axis().

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file_def_associatedcoordinate_c()

int file_def_associatedcoordinate_c	(	const int	fid,
		const char *	name,
		const char *	desc,
		const char *	units,
		const char **	dim_names,
		const int	ndims,
		const int	dtype
	)

Definition at line 1450 of file scale_file_netcdf.c.

{
  int ncid, varid;
  nc_type xtype = -1;
  int i;
  int ret;
  int dimids[ndims];
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode ) {
    if ( ncmpi_inq_varid(ncid, name, &varid) == NC_NOERR ) // check if existed
      return ALREADY_EXISTED_CODE;
  } else {
    if ( nc_inq_varid(ncid, name, &varid) == NC_NOERR ) // check if existed
      return ALREADY_EXISTED_CODE;
  }
 
  ret = file_redef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  TYPE2NCTYPE(dtype, xtype);
 
  if ( files[fid]->shared_mode ) {
    for (i=0; i<ndims; i++)
      CHECK_PNC_ERROR( ncmpi_inq_dimid(ncid, dim_names[i], dimids+ndims-i-1) )
 
    CHECK_PNC_ERROR( ncmpi_def_var(ncid, name, xtype, ndims, dimids, &varid) )
    if ( strlen(desc) >0 ) CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "long_name", strlen(desc), desc) )
    if ( strlen(units)>0 ) CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "units", strlen(units), units) )
  }
  else {
    for (i=0; i<ndims; i++)
      CHECK_ERROR( nc_inq_dimid(ncid, dim_names[i], dimids+ndims-i-1) )
 
    CHECK_ERROR( nc_def_var(ncid, name, xtype, ndims, dimids, &varid) )
    if ( strlen(desc) >0 ) CHECK_ERROR( nc_put_att_text(ncid, varid, "long_name", strlen(desc), desc) )
    if ( strlen(units)>0 ) CHECK_ERROR( nc_put_att_text(ncid, varid, "units", strlen(units), units) )
  }
 
  return SUCCESS_CODE;
}

References scale_file::i.

Referenced by scale_file::file_def_associatedcoordinate().

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file_write_associatedcoordinate_c()

int file_write_associatedcoordinate_c	(	const int	fid,
		const char *	name,
		const void *	val,
		const int	ndims,
		const int	precision,
		const int *	start,
		const int *	count
	)

Definition at line 1500 of file scale_file_netcdf.c.

{
  int ncid, varid;
  int ret;
  MPI_Offset start_[ndims], count_[ndims];
  int i;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, name, &varid) )
  else
    CHECK_ERROR( nc_inq_varid(ncid, name, &varid) )
 
  ret = file_enddef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  for (i=0; i<ndims; i++) {
    start_[i] = (MPI_Offset) start[i];
    count_[i] = (MPI_Offset) count[i];
  }
 
  switch ( precision ) {
  case 8:
    if ( files[fid]->shared_mode )
      CHECK_PNC_ERROR( ncmpi_iput_vara_double(ncid, varid, start_, count_, (double*)val, NULL) )
    else
      CHECK_ERROR( nc_put_var_double(ncid, varid, (double*)val) )
    break;
  case 4:
    if ( files[fid]->shared_mode )
      CHECK_PNC_ERROR( ncmpi_iput_vara_float(ncid, varid, start_, count_, (float*)val, NULL) )
    else
      CHECK_ERROR( nc_put_var_float(ncid, varid, (float*)val) )
    break;
  default:
    fprintf(stderr, "unsupported data precision: %d\n", precision);
    return ERROR_CODE;
  }
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_associatedcoordinate().

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file_add_variable_c()

int file_add_variable_c	(	int *	vid,
		const int	fid,
		const char *	varname,
		const char *	desc,
		const char *	units,
		const char *	stdname,
		const char **	dims,
		const int	ndims,
		const int	dtype,
		const double	tint,
		const char *	tstats
	)

Definition at line 1550 of file scale_file_netcdf.c.

{
  int ncid, varid, acid, *acdimids;
  int dimids[NC_MAX_DIMS], dimid;
  char tname[File_HSHORT+1];
  int tdimid, tvarid;
  nc_type xtype = -1;
  char buf[File_HMID+1];
  int i, j, k, m, err;
  int ndims_t, nndims;
  size_t size;
  double rmiss = RMISS;
  char coord[File_HMID+1];
  int has_assoc;
  int new;
  int ret;
 
  if ( nvar >= VAR_MAX ) {
    fprintf(stderr, "exceed max number of variable limit\n");
    return ERROR_CODE;
  }
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  vars[nvar] = (varinfo_t*) malloc(sizeof(varinfo_t));
  vars[nvar]->ncid  = ncid;
  vars[nvar]->t = NULL;
  vars[nvar]->start = NULL;
  vars[nvar]->count = NULL;
  vars[nvar]->ndims = ndims;
 
  ret = file_redef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  // get time variable
  if ( tint > 0.0 ) {
    for ( i=0; i<nt; i++ ) {
      if ( tdims[i]       != NULL &&  // still opened
           tdims[i]->ncid == ncid &&  // same file
           tdims[i]->tint == tint ) { // same time interval
        vars[nvar]->t = tdims[i];
        break;
      }
    }
    if ( vars[nvar]->t == NULL ) {
      tdims[nt] = (tdim_t*) malloc(sizeof(tdim_t));
      tdims[nt]->ncid = ncid;
      tdims[nt]->count = -1;
      tdims[nt]->tint = tint;
      tdims[nt]->tval = (double*) malloc(sizeof(double)*NTMAX);
      // generate name
      m=0;
      for (i=0; i<nt; i++) {
        if ( tdims[i] != NULL && tdims[i]->ncid == ncid ) m++;
      }
      if ( m == 0 ) {
        strcpy(tname, "time");
      } else {
        sprintf(tname, "time%d", m);
      }
      strcpy(tdims[nt]->name, tname);
      // define time dimension and variable
      if ( files[fid]->shared_mode ) {
        CHECK_PNC_ERROR( ncmpi_def_dim(ncid, tname, 0, &tdimid) )
        tdims[nt]->dimid = tdimid;
        CHECK_PNC_ERROR( ncmpi_def_var(ncid, tname, NC_DOUBLE, 1, &tdimid, &tvarid) )
        tdims[nt]->varid = tvarid;
        strcpy(buf, "time");
        CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, tvarid, "long_name", strlen(buf), buf) )
        CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, tvarid, "units", strlen(files[fid]->time_units), files[fid]->time_units) )
        if ( strlen(files[fid]->calendar) > 0 )
          CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, tvarid, "calendar", strlen(files[fid]->calendar), files[fid]->calendar) )
        // define boundary variable
        if ( ncmpi_inq_dimid(ncid, "nv", &(dimids[1])) != NC_NOERR ) // first called
          CHECK_PNC_ERROR( ncmpi_def_dim(ncid, "nv", 2, &(dimids[1])) )
        sprintf(buf, "%s_bnds", tname);
        CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, tvarid, "bounds", strlen(buf), buf) )
        dimids[0] = tdimid;
        CHECK_PNC_ERROR( ncmpi_def_var(ncid, buf, NC_DOUBLE, 2, dimids, &tvarid) )
        tdims[nt]->bndsid = tvarid;
        //CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, tvarid, "units", strlen(files[fid]->time_units), files[fid]->time_units) )
      }
      else {
        CHECK_ERROR( nc_def_dim(ncid, tname, 0, &tdimid) )
        tdims[nt]->dimid = tdimid;
        CHECK_ERROR( nc_def_var(ncid, tname, NC_DOUBLE, 1, &tdimid, &tvarid) )
        tdims[nt]->varid = tvarid;
        strcpy(buf, "time");
        CHECK_ERROR( nc_put_att_text(ncid, tvarid, "long_name", strlen(buf), buf) )
        CHECK_ERROR( nc_put_att_text(ncid, tvarid, "units", strlen(files[fid]->time_units), files[fid]->time_units) )
        if ( strlen(files[fid]->calendar) > 0 )
          CHECK_ERROR( nc_put_att_text(ncid, tvarid, "calendar", strlen(files[fid]->calendar), files[fid]->calendar) )
        // define boundary variable
        if ( nc_inq_dimid(ncid, "nv", &(dimids[1])) != NC_NOERR ) // first called
          CHECK_ERROR( nc_def_dim(ncid, "nv", 2, &(dimids[1])) )
        sprintf(buf, "%s_bnds", tname);
        CHECK_ERROR( nc_put_att_text(ncid, tvarid, "bounds", strlen(buf), buf) )
        dimids[0] = tdimid;
        CHECK_ERROR( nc_def_var(ncid, buf, NC_DOUBLE, 2, dimids, &tvarid) )
        tdims[nt]->bndsid = tvarid;
        //CHECK_ERROR( nc_put_att_text(ncid, tvarid, "units", strlen(files[fid]->time_units), files[fid]->time_units) )
      }
 
      vars[nvar]->t = tdims[nt];
      nt++;
    }
  }
 
  // get dimension IDs
  // note: C and Fortran order are opposite
  ndims_t = ndims;
  if ( tint > 0.0 ) { // add time dimension
    dimids[0] = vars[nvar]->t->dimid;
    ndims_t++;
  }
  for (i=ndims_t-ndims; i<ndims_t; i++) dimids[i] = -1;
 
  has_assoc = 0;
  nndims = 0;
  for (i=0; i<ndims; i++) {
    //printf("%d %s\n", i, dims[i]);
    if ( files[fid]->shared_mode )
       err = ncmpi_inq_dimid(ncid, dims[i], &dimid);
    else
       err = nc_inq_dimid(ncid, dims[i], &dimid);
    if ( err == NC_NOERR ) {
      //printf("not assoc\n");
      new = 1;
      for (k=0; k<nndims; k++) {
        if (dimid == dimids[k]) {
          new = 0;
          break;
        }
      }
      if (new) {
        dimids[ndims_t-(++nndims)] = dimid;
      }
    } else {
      //printf("assoc\n");
      if ( files[fid]->shared_mode ) {
        CHECK_PNC_ERROR( ncmpi_inq_varid(ncid, dims[i], &acid) )
        CHECK_PNC_ERROR( ncmpi_inq_varndims(ncid, acid, &m) )
        acdimids = (int*) malloc((sizeof(int)*m));
        CHECK_PNC_ERROR( ncmpi_inq_vardimid(ncid, acid, acdimids) )
      }
      else {
        CHECK_ERROR( nc_inq_varid(ncid, dims[i], &acid) )
        CHECK_ERROR( nc_inq_varndims(ncid, acid, &m) )
        acdimids = (int*) malloc((sizeof(int)*m));
        CHECK_ERROR( nc_inq_vardimid(ncid, acid, acdimids) )
      }
      for (j=m-1; j>=0; j--) {
        new = 1;
        for (k=0; k<ndims_t; k++) {
          if (acdimids[j] == dimids[k]) {
            new = 0;
            break;
          }
        }
        if (new) {
          if ( nndims >= ndims_t ) {
            fprintf(stderr, "Error: invalid associated coordinates\n");
            return ERROR_CODE;
          }
          dimids[ndims_t-(++nndims)] = acdimids[j];
          //nc_inq_dimname(ncid, acdimids[j], tname);
          //printf("add %s\n", tname);
        }
      }
      free(acdimids);
      has_assoc = 1;
    }
  }
  if (nndims != ndims) {
    fprintf(stderr, "Error: invalid associated coordinates: %d %d %d\n", ndims_t, nndims, ndims);
    return ERROR_CODE;
  }
 
  TYPE2NCTYPE(dtype, xtype);
  if ( files[fid]->shared_mode ) {
    CHECK_PNC_ERROR( ncmpi_def_var(ncid, varname, xtype, ndims_t, dimids, &varid) )
    // put variable attribute
    if ( strlen(desc)   >0 ) CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "long_name", strlen(desc), desc) )
    if ( strlen(units)  >0 ) CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "units", strlen(units), units) )
    if ( strlen(stdname)>0 ) CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "standard_name", strlen(stdname), stdname) )
        
//    CHECK_PNC_ERROR( ncmpi_put_att_double(ncid, varid, _FillValue, xtype, 1, &rmiss) )
    CHECK_PNC_ERROR( ncmpi_put_att_double(ncid, varid, "missing_value", xtype, 1, &rmiss) )
  }
  else {
    CHECK_ERROR( nc_def_var(ncid, varname, xtype, ndims_t, dimids, &varid) )
    // put variable attribute
    if ( strlen(desc)   >0 ) CHECK_ERROR( nc_put_att_text(ncid, varid, "long_name", strlen(desc), desc) )
    if ( strlen(units)  >0 ) CHECK_ERROR( nc_put_att_text(ncid, varid, "units", strlen(units), units) )
    if ( strlen(stdname)>0 ) CHECK_ERROR( nc_put_att_text(ncid, varid, "standard_name", strlen(stdname), stdname) )
    CHECK_ERROR( nc_put_att_double(ncid, varid, _FillValue, xtype, 1, &rmiss) )
    CHECK_ERROR( nc_put_att_double(ncid, varid, "missing_value", xtype, 1, &rmiss) )
  }
  if ( has_assoc ) {
    strcpy(coord, dims[0]);
    for(i=1; i<ndims; i++) {
      if (strlen(coord)+strlen(dims[i])+1 < File_HMID) {
        strcat(coord, " ");
        strcat(coord, dims[i]);
      }
    }
    if ( ndims_t > ndims && strlen(coord)+6 < File_HMID) {
      strcat(coord, " ");
      strcat(coord, vars[nvar]->t->name);
    }
    if ( files[fid]->shared_mode )
      CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "coordinates", strlen(coord), coord) )
    else
      CHECK_ERROR( nc_put_att_text(ncid, varid, "coordinates", strlen(coord), coord) )
  }
 
 
  if ( strcmp(tstats,"none") != 0 ) {
    sprintf(buf, "%s: %s", vars[nvar]->t->name, tstats);
    if ( files[fid]->shared_mode )
      CHECK_PNC_ERROR( ncmpi_put_att_text(ncid, varid, "cell_methods", strlen(buf), buf) )
    else
      CHECK_ERROR( nc_put_att_text(ncid, varid, "cell_methods", strlen(buf), buf) )
  }
 
  // set start and count
  vars[nvar]->ndims_t = ndims_t;
  vars[nvar]->start = (size_t*) malloc(sizeof(size_t)*ndims_t);
  vars[nvar]->count = (size_t*) malloc(sizeof(size_t)*ndims_t);
  for ( i=0; i<ndims_t; i++ ) {
    if ( files[fid]->shared_mode ) {
      MPI_Offset dimlen;
      CHECK_PNC_ERROR( ncmpi_inq_dimlen(ncid, dimids[i], &dimlen) )
      size = (size_t) dimlen;
    }
    else
      CHECK_ERROR( nc_inq_dimlen(ncid, dimids[i], &size) )
    vars[nvar]->count[i] = size;
    vars[nvar]->start[i] = 0;
  }
  if ( tint > 0.0 ) vars[nvar]->count[0] = 1;
 
#ifndef NETCDF3
  // set chunk size and deflate level (NetCDF-4 only)
  if ( ! files[fid]->shared_mode && files[fid]->deflate_level > 0 ) {
    CHECK_ERROR( nc_def_var_chunking(ncid, varid, NC_CHUNKED, vars[nvar]->count) )
    CHECK_ERROR( nc_def_var_deflate(ncid, varid, 0, 1, files[fid]->deflate_level) )
  }
#endif
 
  vars[nvar]->varid = varid;
  *vid = nvar;
  nvar++;
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_def_associatedcoordinate(), and scale_file::file_def_variable().

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file_enddef_c()

int file_enddef_c

(

const int

fid

)

Definition at line 1818 of file scale_file_netcdf.c.

{
  int ncid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
 
  ncid = files[fid]->ncid;
 
  return file_enddef(fid, ncid);
}

Referenced by scale_file::file_enddef().

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file_redef_c()

int file_redef_c

(

const int

fid

)

Definition at line 1829 of file scale_file_netcdf.c.

{
  int ncid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
 
  ncid = files[fid]->ncid;
 
  return file_redef(fid, ncid);
}

Referenced by scale_file::file_redef().

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file_attach_buffer_c()

int file_attach_buffer_c	(	const int	fid,
		const int64_t	buf_amount
	)

Definition at line 1840 of file scale_file_netcdf.c.

{
  int ncid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_buffer_attach(ncid, (MPI_Offset)buf_amount) )
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_attach_buffer().

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file_detach_buffer_c()

int file_detach_buffer_c

(

const int

fid

)

Definition at line 1854 of file scale_file_netcdf.c.

{
  int ncid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_buffer_detach(ncid) )
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_detach_buffer().

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file_flush_c()

int file_flush_c

(

const int

fid

)

Definition at line 1867 of file scale_file_netcdf.c.

{
  int ncid;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  if ( files[fid]->shared_mode )
    CHECK_PNC_ERROR( ncmpi_wait_all(ncid, NC_REQ_ALL, NULL, NULL) )
  else
    CHECK_ERROR( nc_sync(ncid) )
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_flush().

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file_write_data_c()

int file_write_data_c	(	const int	fid,
		const int	vid,
		const void *	var,
		const double	t_start,
		const double	t_end,
		const int	ndims,
		const int	precision,
		const int *	start,
		const int *	count
	)

Definition at line 1882 of file scale_file_netcdf.c.

{
  int ncid, varid;
  MPI_Offset *str, *cnt;
  int ret;
 
  if ( vars[vid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = vars[vid]->ncid;
 
  if ( ndims != vars[vid]->ndims ) {
    fprintf(stderr, "Error: at line %d in %s\n", __LINE__, __FILE__);
    fprintf(stderr, "       dimension size %d is not consistent that was added by file_add_variable %d\n", ndims, (int)vars[vid]->ndims );
    return ERROR_CODE;
  }
 
  ret = file_enddef(fid, ncid);
  if ( ret != SUCCESS_CODE ) return ret;
 
  varid = vars[vid]->varid;
  if ( vars[vid]->t != NULL ) { // have time dimension
    if ( vars[vid]->t->count < 0 ||  // first time
         t_end > vars[vid]->t->t + TEPS ) { // time goes next step
      vars[vid]->t->count += 1;
      vars[vid]->t->t = t_end;
      if ( vars[vid]->t->count > NTMAX-1 ) {
        fprintf(stderr, "time count exceeds the max limit (%d)\n", NTMAX);
        return ERROR_CODE;
      }
      vars[vid]->t->tval[vars[vid]->t->count] = t_end;
      if ( files[fid]->shared_mode ) { // write a new value to variable time
        MPI_Offset index[2];
        index[0] = (MPI_Offset) vars[vid]->t->count;
        CHECK_PNC_ERROR( ncmpi_put_var1_double_all(ncid, vars[vid]->t->varid, index, &t_end) )
        index[1] = 0;
        CHECK_PNC_ERROR( ncmpi_put_var1_double_all(ncid, vars[vid]->t->bndsid, index, &t_start ) )
        index[1] = 1;
        CHECK_PNC_ERROR( ncmpi_put_var1_double_all(ncid, vars[vid]->t->bndsid, index, &t_end ) )
      } else {
        size_t index[2];
        index[0] = vars[vid]->t->count;
        CHECK_ERROR( nc_put_var1_double(ncid, vars[vid]->t->varid, index, &t_end) )
        index[1] = 0;
        CHECK_ERROR( nc_put_var1_double(ncid, vars[vid]->t->bndsid, index, &t_start) )
        index[1] = 1;
        CHECK_ERROR( nc_put_var1_double(ncid, vars[vid]->t->bndsid, index, &t_end) )
      }
      vars[vid]->start[0] = vars[vid]->t->count;
    } else {
      size_t nt = vars[vid]->t->count + 1;
      int flag, n;
      flag = 1;
      for(n=nt-1;n>=0;n--) {
        if ( fabs(vars[vid]->t->tval[n]-t_end) < TEPS ) {
          vars[vid]->start[0] = n;
          flag = 0;
          break;
        }
      }
      if ( flag ) {
        fprintf(stderr, "cannot find time: %f\n", t_end);
        fprintf(stderr, "  time count is : %d, last time is: %f, diff is: %e\n", vars[vid]->t->count < 0, vars[vid]->t->t, vars[vid]->t->t-t_end);
        fprintf(stderr, "  time is: ");
        for (n=0;n<nt;n++) fprintf(stderr, "%f, ", vars[vid]->t->tval[n]);
        fprintf(stderr, "\n");
        return ERROR_CODE;
      }
    }
  }
 
  if ( files[fid]->shared_mode ) {
    int i;
    int ndims_t = vars[vid]->ndims_t;
    str = (MPI_Offset*) malloc(sizeof(MPI_Offset)*(ndims_t));
    cnt = (MPI_Offset*) malloc(sizeof(MPI_Offset)*(ndims_t));
    if ( vars[vid]->t != NULL ) { // have time dimension
      // add time dimension to start[0] and count[0]
      str[0] = vars[vid]->start[0];  // start along the time dimension
      cnt[0] = vars[vid]->count[0];
      for (i=0; i<ndims; i++) {
        str[ndims_t-i-1] = start[i] - 1;
        cnt[ndims_t-i-1] = count[i];
      }
    } else {
      for (i=0; i<ndims; i++) {
        str[ndims-i-1] = start[i] - 1;
        cnt[ndims-i-1] = count[i];
      }
    }
  }
 
  switch (precision) {
  case 8:
    if ( files[fid]->shared_mode )
      CHECK_PNC_ERROR( ncmpi_bput_vara_double(ncid, varid, str, cnt, (double*)var, NULL) )
    else
      CHECK_ERROR( nc_put_vara_double(ncid, varid, vars[vid]->start, vars[vid]->count, (double*)var) )
    break;
  case 4:
    if ( files[fid]->shared_mode )
      CHECK_PNC_ERROR( ncmpi_bput_vara_float(ncid, varid, str, cnt, (float*)var, NULL) )
    else
      CHECK_ERROR( nc_put_vara_float(ncid, varid, vars[vid]->start, vars[vid]->count, (float*)var) )
    break;
  default:
    fprintf(stderr, "unsupported data precision: %d\n", precision);
    return ERROR_CODE;
  }
 
  if ( files[fid]->shared_mode) {
    free(str);
    free(cnt);
  }
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_get_stepsize().

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file_close_c()

int file_close_c	(	const int	fid,
		const bool	abort
	)

Definition at line 2006 of file scale_file_netcdf.c.

{
  int ncid;
  int i;
 
  if ( files[fid] == NULL ) return ALREADY_CLOSED_CODE;
  ncid = files[fid]->ncid;
 
  for (i=0; i<nvar; i++) {
    if ( vars[i] != NULL && vars[i]->ncid == ncid ) {
      free( vars[i]->start );
      free( vars[i]->count );
      free( vars[i] );
      vars[i] = NULL;
    }
  }
 
  for (i=0; i<nt; i++) {
    if ( tdims[i] != NULL && tdims[i]->ncid == ncid ) {
      free( tdims[i]->tval );
      free( tdims[i] );
      tdims[i] = NULL;
    }
  }
 
  if ( files[fid]->shared_mode ) {
    if ( ! abort ) CHECK_PNC_ERROR( ncmpi_close(ncid) )
  } else
    CHECK_ERROR( nc_close(ncid) )
 
  free( files[fid] );
  files[fid] = NULL;
 
  return SUCCESS_CODE;
}

Referenced by scale_file::file_close().

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