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1156 lines
33 KiB
C
1156 lines
33 KiB
C
/*
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Copyright 2007, UCAR/Unidata
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See COPYRIGHT file for copying and redistribution conditions.
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This program benchmarks the write and read of some radar files with
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different chunking and compression parameters set.
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This program only works on classic model netCDF files. That is,
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groups, user-defined types, and other new netCDF-4 features are not
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handled by this program. (Input files may be in netCDF-4 format, but
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they must conform to the classic model for this program to work.)
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For the 3.7 and 4.0 netCDF releases, this program is not expected
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for general use. It may be made safer and more general in future
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releases, but for now, users should use this code with caution.
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$Id: bm_file.c,v 1.64 2010/01/11 19:27:11 ed Exp $
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*/
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#include <nc_tests.h> /* The ERR macro is here... */
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#include <err_macros.h>
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#include <stdio.h>
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#include <string.h>
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#include <time.h>
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#include <sys/time.h> /* Extra high precision time info. */
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#include <math.h>
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#include <sys/types.h>
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#include <sys/stat.h>
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#include <unistd.h>
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#ifdef USE_PARALLEL
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#include <mpi.h>
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#endif
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#include <netcdf.h>
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#define MILLION 1000000
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#define BAD -99
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#define NOMEM -98
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#define MAX_VO 50 /* Max number of var options on command line. */
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#define MAX_DIMS 7 /* Max dim for variables in input file. */
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/* This struct holds data about what options we want to apply to
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* variable in the created file. (Chunking, compression, etc.) */
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typedef struct {
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int varid;
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int ndims;
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int deflate_num;
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int shuffle;
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size_t chunksize[MAX_DIMS];
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int endian;
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size_t start[MAX_DIMS], count[MAX_DIMS], inc[MAX_DIMS];
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} VAR_OPTS_T;
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/* This macro prints an error message with line number and name of
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* test program. */
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#define ERR1(n) do { \
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fflush(stdout); /* Make sure our stdout is synced with stderr. */ \
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fprintf(stderr, "Sorry! Unexpected result, %s, line: %d - %s\n", \
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__FILE__, __LINE__, nc_strerror(n)); \
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return n; \
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} while (0)
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#ifdef USE_PARALLEL
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/* Error handling code for MPI calls. */
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#define MPIERR(e) do { \
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MPI_Error_string(e, err_buffer, &resultlen); \
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printf("MPI error, line %d, file %s: %s\n", __LINE__, __FILE__, err_buffer); \
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MPI_Finalize(); \
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return 2; \
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} while (0)
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#endif
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/* This function will fill the start and count arrays for the reads
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* and writes. */
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static int
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get_starts_counts(int ndims, size_t *dimlen, int p, int my_rank,
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int slow_count, int use_scs, VAR_OPTS_T *vo,
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int *num_steps, int *start_inc, int *slice_len,
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size_t *last_count, size_t *start, size_t *count)
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{
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int extra_step = 0;
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int total[NC_MAX_VAR_DIMS];
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int total_len;
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int s, d;
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/* User has specified start/count/inc for this var. Parallel runs
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* not allowed yet. */
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if (use_scs)
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{
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/* Set the starts and counts for each dim, the len of the slice,
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* the total len of the data, and the total extent of the
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* dataset in each dimension. */
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for (d = 0, *slice_len = 1, total_len = 1; d < vo->ndims; d++)
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{
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start[d] = vo->start[d];
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count[d] = vo->count[d];
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(*slice_len) *= count[d];
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total_len *= dimlen[d];
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}
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/* The start increment is provided by the user. */
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*start_inc = vo->inc[0];
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/* How many steps to write/read these data? */
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*num_steps = total_len / (*slice_len);
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/* Init this for the total extent in each dim. */
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for (d = 0; d < vo->ndims; d++)
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total[d] = 0;
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/* Check our numbers if we apply increments to start, and read
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* count, for this many steps. */
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for (s = 0; s < *num_steps; s++)
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{
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for (d = 0; d < vo->ndims; d++)
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{
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total[d] += count[d];
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if (total[d] >= dimlen[d])
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break;
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}
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if (d != vo->ndims)
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break;
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}
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/* If the numbers didn't come out clean, then figure out the
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* last set of counts needed to completely read the data. */
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if (s == (*num_steps) - 1)
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*last_count = count[0];
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else
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{
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(*num_steps)++;
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*last_count = dimlen[0] - total[0];
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}
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}
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else
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{
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*start_inc = dimlen[0]/slow_count;
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while (*start_inc * slow_count < dimlen[0])
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(*start_inc)++;
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*slice_len = *start_inc;
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start[0] = *start_inc * my_rank;
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if (start[0] > dimlen[0])
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{
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fprintf(stderr, "slow_count too large for this many processors, "
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"start_inc=%d, slow_count=%d, p=%d, my_rank=%d start[0]=%ld\n",
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*start_inc, slow_count, p, my_rank, start[0]);
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return 2;
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}
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count[0] = *start_inc;
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for (d = 1; d < ndims; d++)
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{
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start[d] = 0;
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count[d] = dimlen[d];
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*slice_len *= dimlen[d];
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}
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*num_steps = (float)dimlen[0] / (*start_inc * p);
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if ((float)dimlen[0] / (*start_inc * p) != dimlen[0] / (*start_inc * p))
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{
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extra_step++;
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(*num_steps)++;
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}
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if (p > 1)
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{
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if (!extra_step)
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*last_count = 0;
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else
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{
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int left;
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left = dimlen[0] - (*num_steps - 1) * *start_inc * p;
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if (left > (my_rank + 1) * *start_inc)
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*last_count = *start_inc;
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else
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{
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if (left - my_rank * *start_inc < 0)
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*last_count = 0;
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else
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*last_count = left - my_rank * *start_inc;
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}
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}
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}
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else
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*last_count = dimlen[0] - (*num_steps - 1) * *start_inc;
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}
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return 0;
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}
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/* This function finds the size of a file. */
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static size_t
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file_size(char* name)
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{
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struct stat stbuf;
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stat(name, &stbuf);
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return stbuf.st_size;
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}
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/* Check attribute number a of variable varid in copied file ncid2 to ensure
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* it is the same as the corresponding attribute in original file ncid1. */
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static int
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check_att(int ncid1, int ncid2, int varid, int a)
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{
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int typeid, typeid2;
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size_t len, len2, typelen;
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char name[NC_MAX_NAME + 1];
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void *d = NULL, *d2 = NULL;
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int ret = 0;
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/* Check the metadata about the metadata - name, type, length. */
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if ((ret = nc_inq_attname(ncid1, varid, a, name)))
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return ret;
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if ((ret = nc_inq_att(ncid1, varid, name, &typeid, &len)))
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return ret;
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if ((ret = nc_inq_att(ncid2, varid, name, &typeid2, &len2)))
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return ret;
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if (len != len2 || typeid != typeid2)
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return BAD;
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if ((ret = nc_inq_type(ncid1, typeid, NULL, &typelen)))
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return ret;
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/* Get the two attributes, if they are non-zero. */
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if (len)
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{
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if(!(d = malloc(typelen * len)))
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return NOMEM;
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if(!(d2 = malloc(typelen * len)))
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{
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ret = NOMEM;
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goto exit;
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}
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if ((ret = nc_get_att(ncid1, varid, name, d)))
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goto exit;
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if ((ret = nc_get_att(ncid2, varid, name, d2)))
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goto exit;
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/* Are they the same? */
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if (memcmp(d, d2, typelen * len))
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ret = BAD;
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}
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exit:
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/* Free up our resources. */
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if (d)
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free(d);
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if (d2)
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free(d2);
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return ret;
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}
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/* Do two files contain the same data and metadata? */
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static int
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cmp_file(char *file1, char *file2, int *meta_read_us, int *data_read_us,
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int use_par, int par_access, int do_cmp, int p, int my_rank,
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int slow_count, int verbose, int num_vo, VAR_OPTS_T *vo, int use_scs)
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{
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int ncid1, ncid2;
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int unlimdimid, unlimdimid2;
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char name[NC_MAX_NAME + 1], name2[NC_MAX_NAME + 1];
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size_t len, len2;
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#ifdef USE_PARALLEL
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double ftime;
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#endif
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struct timeval start_time, end_time, diff_time;
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void *data = NULL, *data2 = NULL;
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int a, v, d;
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nc_type xtype, xtype2;
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int nvars, ndims, dimids[NC_MAX_VAR_DIMS], natts, real_ndims;
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int nvars2, ndims2, dimids2[NC_MAX_VAR_DIMS], natts2;
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size_t *count = NULL, *start = NULL;
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int slice_len = 1;
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size_t *dimlen = NULL, type_size = 0;
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size_t last_count;
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int start_inc;
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int num_steps, step;
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int ret = NC_NOERR;
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/* Note in the code below I only want to time stuff for file2. */
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/* Read the metadata for both files. */
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if (use_par)
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{
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#ifdef USE_PARALLEL
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if ((ret = nc_open_par(file1, 0, MPI_COMM_WORLD, MPI_INFO_NULL, &ncid1)))
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ERR1(ret);
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MPI_Barrier(MPI_COMM_WORLD);
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ftime = MPI_Wtime();
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if ((ret = nc_open_par(file2, 0, MPI_COMM_WORLD, MPI_INFO_NULL, &ncid2)))
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ERR1(ret);
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*meta_read_us += (MPI_Wtime() - ftime) * MILLION;
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#else
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return NC_EPARINIT;
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#endif
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}
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else
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{
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if ((ret = nc_open(file1, 0, &ncid1)))
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ERR1(ret);
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if (gettimeofday(&start_time, NULL)) ERR;
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if ((ret = nc_open(file2, 0, &ncid2)))
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ERR1(ret);
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if (gettimeofday(&end_time, NULL)) ERR;
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if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
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*meta_read_us += (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
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}
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if (verbose)
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printf("%d: reading metadata took %d micro-seconds\n",
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my_rank, *meta_read_us);
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/* Check the counts of dims, vars, and atts. */
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if ((ret = nc_inq(ncid1, &ndims, &nvars, &natts, &unlimdimid)))
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ERR1(ret);
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if ((ret = nc_inq(ncid1, &ndims2, &nvars2, &natts2, &unlimdimid2)))
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ERR1(ret);
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if (ndims != ndims2 || nvars != nvars2 || natts != natts2 ||
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unlimdimid != unlimdimid2)
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ERR1(BAD);
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/* Check dims. */
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for (d = 0; d < ndims; d++)
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{
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if ((ret = nc_inq_dim(ncid1, d, name, &len)))
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ERR1(ret);
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if ((ret = nc_inq_dim(ncid2, d, name2, &len2)))
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ERR1(ret);
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if (len != len2 || strcmp(name, name2))
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ERR1(BAD);
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}
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/* Check global atts. */
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for (a = 0; a < natts; a++)
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if ((ret = check_att(ncid1, ncid2, NC_GLOBAL, a)))
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ERR1(ret);
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/* Check the variables. */
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for (v = 0; v < nvars; v++)
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{
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/* Learn about this var in both files. */
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if ((ret = nc_inq_var(ncid1, v, name, &xtype, &ndims, dimids, &natts)))
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return ret;
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if ((ret = nc_inq_var(ncid2, v, name2, &xtype2, &ndims2, dimids2, &natts2)))
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return ret;
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/* Check var metadata. */
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if (strcmp(name, name2) || xtype != xtype2 || ndims != ndims2 || natts != natts2)
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return BAD;
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for (d = 0; d < ndims; d++)
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if (dimids[d] != dimids2[d])
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return BAD;
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/* Check the attributes. */
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for (a = 0; a < natts; a++)
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if ((ret = check_att(ncid1, ncid2, v, a)))
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ERR1(ret);
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/* Check the data, one slice at a time. (slicing along slowest
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* varying dimension.) */
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/* Allocate memory for our start and count arrays. If ndims = 0
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this is a scalar, which I will treat as a 1-D array with one
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element. */
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real_ndims = ndims ? ndims : 1;
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if (!(start = malloc(real_ndims * sizeof(size_t))))
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ERR1(NC_ENOMEM);
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if (!(count = malloc(real_ndims * sizeof(size_t))))
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ERR1(NC_ENOMEM);
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/* The start array will be all zeros, except the first element,
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which will be the slice number. Count will be the dimension
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size, except for the first element, which will be one, because
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we will copy one slice at a time. For this we need the var
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shape. */
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if (!(dimlen = malloc(real_ndims * sizeof(size_t))))
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ERR1(NC_ENOMEM);
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for (d=0; d<ndims; d++)
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if ((ret = nc_inq_dimlen(ncid1, dimids[d], &dimlen[d])))
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ERR1(ret);
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/* If this is a scalar, then set the dimlen to 1. */
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if (ndims == 0)
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dimlen[0] = 1;
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if ((ret = get_starts_counts(ndims, dimlen, p, my_rank, slow_count, use_scs,
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&vo[v], &num_steps, &start_inc, &slice_len,
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&last_count, start, count)))
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return ret;
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if (verbose)
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printf("%d: num_steps=%d, start_inc=%d, slice_len=%d, last_count=%ld\n",
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my_rank, num_steps, start_inc, slice_len, last_count);
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/* If there are no records, we're done. */
|
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if (!dimlen[0])
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goto exit;
|
|
|
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/* Find the size of this type. */
|
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if ((ret = nc_inq_type(ncid1, xtype, NULL, &type_size)))
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return ret;
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|
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/* I will read all this data the same way I eat a large pizze -
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* one slice at a time. */
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if (!(data = malloc(slice_len * type_size)))
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ERR1(NC_ENOMEM);
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if (!(data2 = malloc(slice_len * type_size)))
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ERR1(NC_ENOMEM);
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|
|
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/* Check the var data for each slice. */
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/* for (step = 0; !ret && step < num_steps; step++)*/
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for (step = 0; !ret && step < num_steps; step++)
|
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{
|
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if (step == num_steps - 1 && last_count)
|
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count[0] = last_count;
|
|
|
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/* Read data from file1. */
|
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if (nc_get_vara(ncid1, v, start, count, data)) ERR;
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|
|
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/* Read data from file2. */
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#ifdef USE_PARALLEL
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ftime = MPI_Wtime();
|
|
#else
|
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if (gettimeofday(&start_time, NULL)) ERR;
|
|
#endif
|
|
if (nc_get_vara(ncid2, v, start, count, data2)) ERR;
|
|
#ifdef USE_PARALLEL
|
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*data_read_us += (MPI_Wtime() - ftime) * MILLION;
|
|
#else
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if (gettimeofday(&end_time, NULL)) ERR;
|
|
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
|
|
*data_read_us += (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
|
|
#endif
|
|
if (verbose)
|
|
printf("%d: reading copy step %d, var %d took %d micro-seconds\n",
|
|
my_rank, step, v, *data_read_us);
|
|
|
|
/* Check data. */
|
|
if (do_cmp)
|
|
if (memcmp(data, data2, slice_len * type_size))
|
|
ERR1(BAD);
|
|
|
|
/* Increment the start index for the slowest-varying
|
|
* dimension. */
|
|
start[0] += start_inc;
|
|
}
|
|
|
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exit:
|
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if (data) free(data);
|
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if (data2) free(data2);
|
|
if (dimlen) free(dimlen);
|
|
if (start) free(start);
|
|
if (count) free(count);
|
|
}
|
|
|
|
if ((ret = nc_close(ncid1)))
|
|
ERR1(ret);
|
|
if ((ret = nc_close(ncid2)))
|
|
ERR1(ret);
|
|
|
|
return 0;
|
|
}
|
|
|
|
/* Copy a netCDF file, changing cmode if desired, applying chuncking,
|
|
* deflate, shuffle, and endianness parameters if desired. */
|
|
static
|
|
int copy_file(char *file_name_in, char *file_name_out, int cmode_out,
|
|
int num_vo, VAR_OPTS_T *vo, int *meta_read_us, int *meta_write_us,
|
|
int *data_read_us, int *data_write_us, int *in_format, int use_par,
|
|
int par_access, long long *num_bytes, int p, int my_rank,
|
|
int slow_count, int verbose, int use_scs, int endianness,
|
|
int convert_unlim)
|
|
{
|
|
int ncid_in, ncid_out;
|
|
int natts, nvars, ndims, unlimdimid;
|
|
char name[NC_MAX_NAME + 1];
|
|
size_t len;
|
|
size_t last_count;
|
|
int a, v, d;
|
|
int ret;
|
|
struct timeval start_time, end_time, diff_time;
|
|
#ifdef USE_PARALLEL
|
|
double ftime;
|
|
#endif
|
|
|
|
if (use_par)
|
|
{
|
|
#ifdef USE_PARALLEL
|
|
ftime = MPI_Wtime();
|
|
if ((ret = nc_open_par(file_name_in, 0, MPI_COMM_WORLD, MPI_INFO_NULL, &ncid_in)))
|
|
ERR1(ret);
|
|
*meta_read_us += (MPI_Wtime() - ftime) * MILLION;
|
|
#else
|
|
return NC_EPARINIT;
|
|
#endif
|
|
}
|
|
else
|
|
{
|
|
if (gettimeofday(&start_time, NULL)) ERR;
|
|
if ((ret = nc_open(file_name_in, 0, &ncid_in)))
|
|
ERR1(ret);
|
|
if (gettimeofday(&end_time, NULL)) ERR;
|
|
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
|
|
*meta_read_us += (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
|
|
}
|
|
if (verbose)
|
|
printf("%d: reading metadata took %d micro-seconds.\n", my_rank, *meta_read_us);
|
|
|
|
/* Only classic model files may be used as input. */
|
|
if ((ret = nc_inq_format(ncid_in, in_format)))
|
|
ERR1(ret);
|
|
if (*in_format == NC_FORMAT_NETCDF4)
|
|
ERR1(NC_ENOTNC3);
|
|
|
|
if (strlen(file_name_out))
|
|
{
|
|
if (use_par)
|
|
{
|
|
#ifdef USE_PARALLEL
|
|
if ((ret = nc_create_par(file_name_out, cmode_out, MPI_COMM_WORLD,
|
|
MPI_INFO_NULL, &ncid_out)))
|
|
ERR1(ret);
|
|
#else
|
|
return NC_EPARINIT;
|
|
#endif
|
|
}
|
|
else
|
|
{
|
|
#define SIXTEEN_MEG 16777216
|
|
#define PREEMPTION .75
|
|
#define NELEMS 7919
|
|
if ((ret = nc_set_chunk_cache(SIXTEEN_MEG, NELEMS, PREEMPTION)))
|
|
ERR1(ret);
|
|
if ((ret = nc_create(file_name_out, cmode_out, &ncid_out)))
|
|
ERR1(ret);
|
|
}
|
|
}
|
|
|
|
if ((ret = nc_inq(ncid_in, &ndims, &nvars, &natts, &unlimdimid)))
|
|
ERR1(ret);
|
|
|
|
if (strlen(file_name_out))
|
|
{
|
|
/* Copy dims. */
|
|
for (d = 0; d < ndims; d++)
|
|
{
|
|
if ((ret = nc_inq_dim(ncid_in, d, name, &len)))
|
|
ERR1(ret);
|
|
if (convert_unlim)
|
|
{
|
|
if ((ret = nc_def_dim(ncid_out, name, len, NULL)))
|
|
ERR1(ret);
|
|
}
|
|
else
|
|
{
|
|
if ((ret = nc_def_dim(ncid_out, name,
|
|
(d == unlimdimid) ? NC_UNLIMITED : len,
|
|
NULL)))
|
|
ERR1(ret);
|
|
}
|
|
}
|
|
|
|
/* Copy global atts. */
|
|
for (a = 0; a < natts; a++)
|
|
{
|
|
if (nc_inq_attname(ncid_in, NC_GLOBAL, a, name)) ERR;
|
|
if (nc_copy_att(ncid_in, NC_GLOBAL, name, ncid_out, NC_GLOBAL)) ERR;
|
|
}
|
|
|
|
/* Copy the variable metadata. */
|
|
for (v = 0; v < nvars; v++)
|
|
{
|
|
char name[NC_MAX_NAME + 1];
|
|
char att_name[NC_MAX_NAME + 1];
|
|
nc_type xtype;
|
|
int ndims, dimids[NC_MAX_VAR_DIMS], natts;
|
|
int varid_out;
|
|
int a, o1;
|
|
int ret = NC_NOERR;
|
|
|
|
/* Learn about this var. */
|
|
if ((ret = nc_inq_var(ncid_in, v, name, &xtype, &ndims, dimids, &natts)))
|
|
return ret;
|
|
|
|
/* Create the output var. */
|
|
if (nc_def_var(ncid_out, name, xtype, ndims, dimids, &varid_out)) ERR;
|
|
|
|
/* Set the output endianness. For simplicity in this program,
|
|
* all vars get the same endianness. But there's no reason why
|
|
* this couldn't be varied from var to var, though it is hard to
|
|
* see why one would do so. */
|
|
if (endianness)
|
|
if (nc_def_var_endian(ncid_out, varid_out, endianness)) ERR;
|
|
|
|
/* Sent chunking and compression if specified in the var options. */
|
|
for (o1 = 0; o1 < num_vo; o1++)
|
|
if (vo[o1].varid == v)
|
|
{
|
|
if (vo[o1].chunksize[0])
|
|
{
|
|
if (nc_def_var_chunking(ncid_out, v, 0, vo[o1].chunksize)) ERR;
|
|
}
|
|
else
|
|
{
|
|
if (nc_def_var_chunking(ncid_out, v, 1, NULL)) ERR;
|
|
}
|
|
if (vo[o1].deflate_num != -1)
|
|
if (nc_def_var_deflate(ncid_out, v, vo[o1].shuffle, 1, vo[o1].deflate_num)) ERR;
|
|
break;
|
|
}
|
|
|
|
/* Copy the attributes. */
|
|
for (a=0; a<natts; a++)
|
|
{
|
|
if (nc_inq_attname(ncid_in, v, a, att_name)) ERR;
|
|
if (nc_copy_att(ncid_in, v, att_name, ncid_out, varid_out)) ERR;
|
|
}
|
|
}
|
|
|
|
#ifdef USE_PARALLEL
|
|
ftime = MPI_Wtime();
|
|
#else
|
|
if (gettimeofday(&start_time, NULL)) ERR;
|
|
#endif
|
|
if ((ret = nc_enddef(ncid_out)))
|
|
ERR1(ret);
|
|
#ifdef USE_PARALLEL
|
|
*meta_write_us += (MPI_Wtime() - ftime) * MILLION;
|
|
#else
|
|
if (gettimeofday(&end_time, NULL)) ERR;
|
|
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
|
|
*meta_write_us += (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
|
|
#endif
|
|
|
|
if (verbose)
|
|
printf("%d: copying %d vars, %d global atts, and %d dims took %d micro-seconds\n",
|
|
my_rank, nvars, natts, ndims, *meta_write_us);
|
|
}
|
|
|
|
/* Copy the variable data. */
|
|
for (v = 0; v < nvars; v++)
|
|
{
|
|
char name[NC_MAX_NAME + 1];
|
|
nc_type xtype;
|
|
int ndims, dimids[NC_MAX_VAR_DIMS], natts, real_ndims;
|
|
int d;
|
|
void *data = NULL;
|
|
size_t *count = NULL, *start = NULL;
|
|
int slice_len = 1;
|
|
size_t *dimlen = NULL;
|
|
int ret = NC_NOERR;
|
|
size_t type_size;
|
|
char type_name[NC_MAX_NAME+1];
|
|
int start_inc;
|
|
int step, num_steps;
|
|
int var_num_bytes;
|
|
|
|
/* Learn about this var. */
|
|
if ((ret = nc_inq_var(ncid_in, v, name, &xtype, &ndims, dimids, &natts)))
|
|
return ret;
|
|
|
|
/* Later on, we will need to know the size of this type. */
|
|
if ((ret = nc_inq_type(ncid_in, xtype, type_name, &type_size)))
|
|
return ret;
|
|
|
|
/* Allocate memory for our start and count arrays. If ndims = 0
|
|
this is a scalar, which I will treat as a 1-D array with one
|
|
element. */
|
|
real_ndims = ndims ? ndims : 1;
|
|
|
|
/* Get the variable shape information. */
|
|
if (!(dimlen = malloc(real_ndims * sizeof(size_t))))
|
|
ERR1(NC_ENOMEM);
|
|
for (d = 0; d < ndims; d++)
|
|
if ((ret = nc_inq_dimlen(ncid_in, dimids[d], &dimlen[d])))
|
|
ERR1(ret);
|
|
|
|
if (!(start = malloc(real_ndims * sizeof(size_t))))
|
|
ERR1(NC_ENOMEM);
|
|
if (!(count = malloc(real_ndims * sizeof(size_t))))
|
|
ERR1(NC_ENOMEM);
|
|
|
|
/* If this is really a scalar, then set the dimlen to 1. */
|
|
if (ndims == 0)
|
|
dimlen[0] = 1;
|
|
|
|
/* Get the start and count arrays, and also the increment of the
|
|
* start array zeroth element, the number of read steps, the
|
|
* length of a slice in number of elements, and the count needed
|
|
* for the final read, in the cases where the length of the
|
|
* zeroth dimension is not evenly divisible by slow_count. The
|
|
* variable slow_count is the number of elements in the slowest
|
|
* varying (i.e. the zeroth) dimension to read at one time. For
|
|
* vars with an unlimited dimension, this is the number of
|
|
* records to read at once. */
|
|
if ((ret = get_starts_counts(ndims, dimlen, p, my_rank, slow_count, use_scs,
|
|
&vo[v], &num_steps, &start_inc, &slice_len,
|
|
&last_count, start, count)))
|
|
return ret;
|
|
if (verbose)
|
|
printf("%d: num_steps=%d, start_inc=%d, slice_len=%d, last_count=%ld\n",
|
|
my_rank, num_steps, start_inc, slice_len, last_count);
|
|
|
|
/* If there are no records, we're done. */
|
|
if (!dimlen[0])
|
|
goto exit;
|
|
|
|
/* Allocate memory for one slice. */
|
|
if (!(data = malloc(slice_len * type_size)))
|
|
return NC_ENOMEM;
|
|
|
|
/* Copy the var data one slice at a time. */
|
|
for (step = 0; !ret && step < num_steps; step++)
|
|
{
|
|
/* Make sure count is not too big. */
|
|
if (step == num_steps - 1 && last_count)
|
|
count[0] = last_count;
|
|
|
|
/* for (d=0; d<ndims; d++) */
|
|
/* printf("start[%d]=%d count[%d]=%d dimlen[%d]=%d, step=%d\n", */
|
|
/* d, start[d], d, count[d], d, dimlen[d], step); */
|
|
|
|
/* Read input data. */
|
|
#ifdef USE_PARALLEL
|
|
ftime = MPI_Wtime();
|
|
#else
|
|
if (gettimeofday(&start_time, NULL)) ERR;
|
|
#endif
|
|
if ((ret = nc_get_vara(ncid_in, v, start, count, data)))
|
|
ERR1(ret);
|
|
|
|
#ifdef USE_PARALLEL
|
|
*data_read_us += (MPI_Wtime() - ftime) * MILLION;
|
|
#else
|
|
if (gettimeofday(&end_time, NULL)) ERR;
|
|
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
|
|
*data_read_us += (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
|
|
#endif
|
|
if (verbose)
|
|
printf("%d: reading step %d, var %d took %d micro-seconds\n",
|
|
my_rank, step, v, *data_read_us);
|
|
|
|
/* Write the data to the output file. */
|
|
if (strlen(file_name_out))
|
|
{
|
|
#ifdef USE_PARALLEL
|
|
ftime = MPI_Wtime();
|
|
#else
|
|
if (gettimeofday(&start_time, NULL)) ERR;
|
|
#endif
|
|
if ((ret = nc_put_vara(ncid_out, v, start, count, data)))
|
|
ERR1(ret);
|
|
#ifdef USE_PARALLEL
|
|
*data_write_us += (MPI_Wtime() - ftime) * MILLION;
|
|
#else
|
|
if (gettimeofday(&end_time, NULL)) ERR;
|
|
if (nc4_timeval_subtract(&diff_time, &end_time, &start_time)) ERR;
|
|
*data_write_us += (int)diff_time.tv_sec * MILLION + (int)diff_time.tv_usec;
|
|
#endif
|
|
if (verbose)
|
|
printf("%d: writing step %d, var %d took %d micro-seconds\n",
|
|
my_rank, step, v, *data_write_us);
|
|
}
|
|
|
|
/* Increment start index. */
|
|
start[0] += start_inc;
|
|
} /* next step */
|
|
|
|
/* Calculate the data read and write rates in MB/sec. */
|
|
for (d = 0, var_num_bytes = type_size; d < ndims; d++)
|
|
var_num_bytes *= dimlen[d];
|
|
(*num_bytes) += var_num_bytes;
|
|
|
|
exit:
|
|
if (data) free(data);
|
|
if (dimlen) free(dimlen);
|
|
if (start) free(start);
|
|
if (count) free(count);
|
|
} /* next var */
|
|
|
|
if (nc_close(ncid_in)) ERR;
|
|
if (strlen(file_name_out))
|
|
if (nc_close(ncid_out)) ERR;
|
|
|
|
return NC_NOERR;
|
|
}
|
|
|
|
#define NDIMS 3
|
|
#define MAX_DEFLATE 9
|
|
#define INPUT_FILE "/upc/share/testdata/nssl/mosaic3d_nc/tile1/20070803-2300.netcdf"
|
|
#define COLON ":"
|
|
#define COMMA ","
|
|
|
|
#define USAGE "\
|
|
[-v] Verbose\n\
|
|
[-o file] Output file name\n\
|
|
[-f N] Output format (1 - classic, 2 - 64-bit offset, 3 - netCDF-4, 4 - netCDF4/CLASSIC)\n\
|
|
[-h] Print output header\n\
|
|
[-c V:Z:S:C:C:C[,V:Z:S:C:C:C, etc.]] Deflate, shuffle, and chunking parameters for vars\n\
|
|
[-t V:S:S:S[,V:S:S:S, etc.]] Starts for reads/writes\n\
|
|
[-u V:C:C:C[,V:C:C:C, etc.]] Counts for reads/writes\n\
|
|
[-r V:I:I:I[,V:I:I:I, etc.]] Incs for reads/writes\n\
|
|
[-d] Doublecheck output by rereading each value\n\
|
|
[-m] Do compare of each data value during doublecheck (slow for large files!)\n\
|
|
[-p] Use parallel I/O\n\
|
|
[-s N] Denom of fraction of slowest varying dimension read.\n\
|
|
[-i] Use MPIIO (only relevant for parallel builds).\n\
|
|
[-l] Convert unlimited dimensions to fixed dimensions.\n\
|
|
[-e 1|2] Set the endianness of output (1=little 2=big).\n\
|
|
file Name of netCDF file\n"
|
|
|
|
static void
|
|
usage(void)
|
|
{
|
|
fprintf(stderr, "bm_file -v [-s N]|[-t V:S:S:S -u V:C:C:C -r V:I:I:I] -o file_out -f N -h"
|
|
" -c V:C:C,V:C:C:C -d -m -p -i -e 1|2 -l file\n%s", USAGE);
|
|
}
|
|
|
|
int
|
|
main(int argc, char **argv)
|
|
{
|
|
int num_vo = 0;
|
|
extern int optind;
|
|
extern int opterr;
|
|
extern char *optarg;
|
|
char file_in[NC_MAX_NAME + 1], file_out[NC_MAX_NAME + 1] = {""};
|
|
int c;
|
|
int out_format, in_format, header = 0, doublecheck = 0;
|
|
int convert_unlim = 0;
|
|
char *str1, *str2, *token, *subtoken;
|
|
char *saveptr1, *saveptr2;
|
|
int i, ndims, o1;
|
|
int cmode = 0;
|
|
int mpiio = 0;
|
|
int meta_read_us = 0, meta_write_us = 0, data_read_us = 0, data_write_us = 0;
|
|
int meta_read2_us = 0, data_read2_us = 0;
|
|
int tmeta_read_us = 0, tmeta_write_us = 0, tdata_read_us = 0, tdata_write_us = 0;
|
|
int tmeta_read2_us = 0, tdata_read2_us = 0;
|
|
VAR_OPTS_T vo[MAX_VO];
|
|
int use_par = 0, par_access = 0;
|
|
int do_cmp = 0, verbose = 0;
|
|
int ret;
|
|
float read_rate, write_rate, reread_rate;
|
|
int slow_count = 10, use_scs = 0;
|
|
int endianness = 0;
|
|
long long num_bytes = 0;
|
|
int p = 1, my_rank = 0;
|
|
int v, d;
|
|
|
|
#ifdef USE_PARALLEL
|
|
MPI_Init(&argc, &argv);
|
|
MPI_Errhandler_set(MPI_COMM_WORLD, MPI_ERRORS_RETURN);
|
|
|
|
MPI_Comm_rank(MPI_COMM_WORLD, &my_rank);
|
|
MPI_Comm_size(MPI_COMM_WORLD, &p);
|
|
#endif
|
|
|
|
for (o1 = 0; o1 < MAX_VO; o1++)
|
|
for (i = 0; i < MAX_DIMS; i++)
|
|
vo[o1].chunksize[i] = 0;
|
|
|
|
while ((c = getopt(argc, argv, "vo:f:hc:dpms:it:u:r:e:l")) != EOF)
|
|
switch(c)
|
|
{
|
|
case 'v':
|
|
verbose++;
|
|
break;
|
|
case 'o':
|
|
strcpy(file_out, optarg);
|
|
break;
|
|
case 'f':
|
|
sscanf(optarg, "%d", &out_format);
|
|
switch (out_format)
|
|
{
|
|
case NC_FORMAT_CLASSIC:
|
|
break;
|
|
case NC_FORMAT_64BIT_OFFSET:
|
|
cmode = NC_64BIT_OFFSET;
|
|
break;
|
|
case NC_FORMAT_CDF5:
|
|
cmode = NC_CDF5;
|
|
break;
|
|
case NC_FORMAT_NETCDF4:
|
|
cmode = NC_NETCDF4;
|
|
break;
|
|
case NC_FORMAT_NETCDF4_CLASSIC:
|
|
cmode = NC_NETCDF4|NC_CLASSIC_MODEL;
|
|
break;
|
|
default:
|
|
usage();
|
|
return 1;
|
|
}
|
|
break;
|
|
case 'h':
|
|
header++;
|
|
break;
|
|
case 'c':
|
|
for (num_vo = 0, str1 = optarg; ; num_vo++, str1 = NULL)
|
|
{
|
|
int got_z = 0, got_s = 0;
|
|
if (num_vo > MAX_VO)
|
|
return 1;
|
|
if (!(token = strtok_r(str1, COMMA, &saveptr1)))
|
|
break;
|
|
for (ndims = 0, str2 = token; ; str2 = NULL)
|
|
{
|
|
int tmp_int;
|
|
if (!(subtoken = strtok_r(str2, COLON, &saveptr2)))
|
|
break;
|
|
if (str2)
|
|
sscanf(subtoken, "%d", &(vo[num_vo].varid));
|
|
else if (!got_z++)
|
|
sscanf(subtoken, "%d", &(vo[num_vo].deflate_num));
|
|
else if (!got_s++)
|
|
sscanf(subtoken, "%d", &(vo[num_vo].shuffle));
|
|
else
|
|
{
|
|
sscanf(subtoken, "%d", &tmp_int);
|
|
vo[num_vo].chunksize[ndims++] = tmp_int;
|
|
}
|
|
}
|
|
vo[num_vo].ndims = ndims;
|
|
}
|
|
break;
|
|
case 't':
|
|
for (num_vo = 0, str1 = optarg; ; num_vo++, str1 = NULL)
|
|
{
|
|
if (num_vo > MAX_VO)
|
|
return 1;
|
|
if (!(token = strtok_r(str1, COMMA, &saveptr1)))
|
|
break;
|
|
for (ndims = 0, str2 = token; ; str2 = NULL)
|
|
{
|
|
if (!(subtoken = strtok_r(str2, COLON, &saveptr2)))
|
|
break;
|
|
if (str2)
|
|
sscanf(subtoken, "%d", &(vo[num_vo].varid));
|
|
else
|
|
sscanf(subtoken, "%ld", &(vo[num_vo].start[ndims++]));
|
|
}
|
|
vo[num_vo].ndims = ndims;
|
|
}
|
|
use_scs++;
|
|
break;
|
|
case 'u':
|
|
for (num_vo = 0, str1 = optarg; ; num_vo++, str1 = NULL)
|
|
{
|
|
if (num_vo > MAX_VO)
|
|
return 1;
|
|
if (!(token = strtok_r(str1, COMMA, &saveptr1)))
|
|
break;
|
|
for (ndims = 0, str2 = token; ; str2 = NULL)
|
|
{
|
|
if (!(subtoken = strtok_r(str2, COLON, &saveptr2)))
|
|
break;
|
|
if (str2)
|
|
sscanf(subtoken, "%d", &(vo[num_vo].varid));
|
|
else
|
|
sscanf(subtoken, "%ld", &(vo[num_vo].count[ndims++]));
|
|
}
|
|
vo[num_vo].ndims = ndims;
|
|
}
|
|
break;
|
|
case 'r':
|
|
for (num_vo = 0, str1 = optarg; ; num_vo++, str1 = NULL)
|
|
{
|
|
if (num_vo > MAX_VO)
|
|
return 1;
|
|
if (!(token = strtok_r(str1, COMMA, &saveptr1)))
|
|
break;
|
|
for (ndims = 0, str2 = token; ; str2 = NULL)
|
|
{
|
|
if (!(subtoken = strtok_r(str2, COLON, &saveptr2)))
|
|
break;
|
|
if (str2)
|
|
sscanf(subtoken, "%d", &(vo[num_vo].varid));
|
|
else
|
|
sscanf(subtoken, "%ld", &(vo[num_vo].inc[ndims++]));
|
|
}
|
|
vo[num_vo].ndims = ndims;
|
|
}
|
|
break;
|
|
case 'd':
|
|
doublecheck++;
|
|
break;
|
|
case 'm':
|
|
do_cmp++;
|
|
doublecheck++;
|
|
break;
|
|
case 'p':
|
|
use_par++;
|
|
break;
|
|
case 'i':
|
|
mpiio++;
|
|
break;
|
|
case 's':
|
|
sscanf(optarg, "%d", &slow_count);
|
|
break;
|
|
case 'e':
|
|
sscanf(optarg, "%d", &endianness);
|
|
break;
|
|
case 'l':
|
|
convert_unlim++;
|
|
break;
|
|
case '?':
|
|
usage();
|
|
return 1;
|
|
}
|
|
|
|
if (mpiio)
|
|
cmode |= NC_MPIIO;
|
|
|
|
if (use_scs)
|
|
{
|
|
if (use_par)
|
|
{
|
|
printf("Can't use start/count/slice for parallel runs yet!\n");
|
|
return 2;
|
|
}
|
|
}
|
|
else
|
|
{
|
|
if (slow_count < p)
|
|
slow_count = p;
|
|
if (slow_count % p)
|
|
{
|
|
printf("slow_count must be even multiple of p\n");
|
|
return 2;
|
|
}
|
|
}
|
|
|
|
argc -= optind;
|
|
argv += optind;
|
|
|
|
/* If no file arguments left, report and exit */
|
|
if (argc < 1)
|
|
{
|
|
printf("no file specified\n");
|
|
return 0;
|
|
}
|
|
|
|
/* Get the name of the file to copy. */
|
|
strcpy(file_in, argv[0]);
|
|
|
|
/* Verbose mode seems a bit stupid, but it's really useful when you
|
|
* are running in batch mode on a supercomputer, and can't use
|
|
* anything else to figure out what the heck is going on. */
|
|
if (verbose && !my_rank)
|
|
{
|
|
printf("copying %s to %s on %d processors with endianness %d and...\n",
|
|
file_in, file_out, p, endianness);
|
|
if (use_scs)
|
|
for (v = 0; v < num_vo; v++)
|
|
{
|
|
printf("options for var %d:\n", vo[v].varid);
|
|
for (d = 0; d < vo[v].ndims; d++)
|
|
printf("start[%d]=%ld, count[%d]=%ld, inc[%d]=%ld\n",
|
|
d, vo[v].start[d], d, vo[v].count[d], d, vo[v].inc[d]);
|
|
}
|
|
else
|
|
printf("slow_count=%d, doublecheck=%d\n", slow_count, doublecheck);
|
|
}
|
|
|
|
/* Copy the file, keeping track of the read and write times for metadata and data. */
|
|
if ((ret = copy_file(file_in, file_out, cmode, num_vo, vo, &meta_read_us, &meta_write_us,
|
|
&data_read_us, &data_write_us, &in_format, use_par, par_access,
|
|
&num_bytes, p, my_rank, slow_count, verbose, use_scs, endianness,
|
|
convert_unlim)))
|
|
return ret;
|
|
|
|
/* If the user wants a double check, make sure the data in the new
|
|
* file is exactly the same. */
|
|
if (doublecheck)
|
|
{
|
|
#ifdef USE_PARALLEL
|
|
MPI_Barrier(MPI_COMM_WORLD);
|
|
#endif
|
|
if ((ret = cmp_file(file_in, file_out, &meta_read2_us, &data_read2_us,
|
|
use_par, par_access, do_cmp, p, my_rank, slow_count,
|
|
verbose, num_vo, vo, use_scs)))
|
|
return ret;
|
|
}
|
|
|
|
if (use_par)
|
|
{
|
|
#ifdef USE_PARALLEL
|
|
MPI_Reduce(&meta_read_us, &tmeta_read_us, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD);
|
|
MPI_Reduce(&meta_write_us, &tmeta_write_us, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD);
|
|
MPI_Reduce(&data_read_us, &tdata_read_us, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD);
|
|
MPI_Reduce(&data_write_us, &tdata_write_us, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD);
|
|
MPI_Reduce(&data_read2_us, &tdata_read2_us, 1, MPI_INT, MPI_MAX, 0, MPI_COMM_WORLD);
|
|
#else
|
|
return NC_EPARINIT;
|
|
#endif
|
|
}
|
|
else
|
|
{
|
|
tmeta_read_us = meta_read_us;
|
|
tmeta_write_us = meta_write_us;
|
|
tdata_read_us = data_read_us;
|
|
tdata_write_us = data_write_us;
|
|
tmeta_read2_us = meta_read2_us;
|
|
tdata_read2_us = data_read2_us;
|
|
}
|
|
|
|
if (verbose)
|
|
printf("num_bytes=%lld tdata_read_us=%d\n", num_bytes, tdata_read_us);
|
|
|
|
read_rate = (float)num_bytes/((float)tdata_read_us/p);
|
|
write_rate = (float)num_bytes/((float)tdata_write_us/p);
|
|
reread_rate = (float)num_bytes/((float)tdata_read2_us/p);
|
|
if (verbose)
|
|
printf("%d: read rate %g, write rate %g, reread_rate %g\n", my_rank, read_rate,
|
|
write_rate, reread_rate);
|
|
|
|
/* Print some output. */
|
|
if (!my_rank)
|
|
{
|
|
/* Does the user want a text header for the data? */
|
|
if (header)
|
|
{
|
|
printf("input format, output_format, input size, output size, meta read time, "
|
|
"meta write time, data read time, data write time, enddianness, ");
|
|
if (doublecheck)
|
|
printf("metadata reread time, data reread time, read rate, "
|
|
"write rate, reread rate, ");
|
|
else
|
|
printf("read rate, write rate, ");
|
|
if (use_par)
|
|
printf("num_proc, ");
|
|
printf("deflate, shuffle, chunksize[0], chunksize[1], chunksize[2], "
|
|
"chunksize[3]\n");
|
|
}
|
|
|
|
printf("%d, %d, %ld, %ld, %d, %d, %d, %d, %d, ", in_format, out_format, file_size(file_in),
|
|
file_size(file_out), tmeta_read_us, tmeta_write_us, tdata_read_us, tdata_write_us,
|
|
endianness);
|
|
if (doublecheck)
|
|
printf("%d, %d, %g, %g, %g, ", tmeta_read2_us, tdata_read2_us, read_rate, write_rate,
|
|
reread_rate);
|
|
else
|
|
printf("%g, %g, ", read_rate, write_rate);
|
|
if (use_par)
|
|
printf("%d, ", p);
|
|
for (o1 = 0; o1 < num_vo; o1++)
|
|
{
|
|
printf("%d, %d, %d, %d, %d, %d ", vo[o1].deflate_num, vo[o1].shuffle,
|
|
(int)vo[o1].chunksize[0], (int)vo[o1].chunksize[1], (int)vo[o1].chunksize[2], (int)vo[o1].chunksize[3]);
|
|
if (o1 != num_vo - 1)
|
|
printf(", ");
|
|
}
|
|
printf("\n");
|
|
}
|
|
|
|
#ifdef USE_PARALLEL
|
|
MPI_Finalize();
|
|
#endif
|
|
|
|
return 0;
|
|
}
|