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New benchmark programs that write multiple variables
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* benchmarks/C/pnetcdf_put_vara.c
  + This program writes a series of 3D variables with 2D block-block
    partitioning pattern. Each variable is a record variable. The number of
    variables, variable size, number of time records, and the NetCDF file
    format can be customized through command-line options. In addition, option
    '-i', if set, PnetCDF nonblocking APIs will be used to write to the file.
* benchmarks/C/netcdf_put_vara.c
  + This sequential NetCDF-C program writes a series of 3D variables.  Each
    variable is a record variable. The number of variables, variable size,
    number of time records, and the NetCDF file format can be customized
    through command-line options.
  + This program and `C/pnetcdf_put_vara.c` can be used to compare the
    performance of NetCDF and PnetCDF when running sequentially, i.e. one
    process.
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@wkliao
wkliao committed Aug 29, 2024
1 parent 86dc048 commit 20a639d
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5 changes: 3 additions & 2 deletions benchmarks/C/Makefile.am
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Expand Up @@ -13,7 +13,8 @@ LDADD = $(top_builddir)/src/libs/libpnetcdf.la
LDADD += @NETCDF4_LDFLAGS@ @ADIOS_LDFLAGS@ @NETCDF4_LIBS@ @ADIOS_LIBS@

check_PROGRAMS = aggregation \
write_block_read_column
write_block_read_column \
pnetcdf_put_vara

# parallel runs only
# TESTS = $(check_PROGRAMS)
Expand All @@ -35,7 +36,7 @@ NC_FILES = $(check_PROGRAMS:%=$(TESTOUTDIR)/%.nc) \
CLEANFILES = core core.* *.gcda *.gcno *.gcov gmon.out \
$(NC_FILES)

EXTRA_DIST = parallel_run.sh
EXTRA_DIST = parallel_run.sh pnetcdf_put_vara.c

ptest ptests ptest4: $(check_PROGRAMS)
@echo "==========================================================="
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284 changes: 284 additions & 0 deletions benchmarks/C/netcdf_put_vara.c
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@@ -0,0 +1,284 @@
/*********************************************************************
*
* Copyright (C) 2024, Northwestern University and Argonne National Laboratory
* See COPYRIGHT notice in top-level directory.
*
*********************************************************************/

/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* This sequential NetCDF-C program writes a series of 3D variables. Each
* variable is a record variable. The number of variables, variable size,
* number of time records, and the NetCDF file format can be customized through
* command-line options.
*
* To compile:
* % gcc netcdf_put_vara.c -o netcdf_put_vara -I $NETCDF_DIR/include -L $NETCDF_DIR/lib -lnetcdf
*
* Example run command and outputs from running ncdump on the output netCDF
* file produced by this example program:
* % ./netcdf_put_vara -n 4 -t 10 -l 1024 -k 5
* -----------------------------------------------------------
* Output NetCDF file name: testfile.nc
* Output NetCDF file kind: CDF-5
* Total number of variables: 4
* Data type of variables: NC_FLOAT
* Each 2D variable size: 1024 x 1024
* Number of time records: 10
* Total write amount: 167772160 B
* 160.00 MiB
* 0.16 GiB
* variable write time: 0.3411 sec
* Write bandwidth: 469.10 MiB/s
* 0.46 GiB/s
* open-to-close time: 0.9867 sec
* Write bandwidth: 162.15 MiB/s
* 0.16 GiB/s
* -----------------------------------------------------------
*
* % ncdump -h testfile.nc
* netcdf testfile {
* dimensions:
* time = UNLIMITED ; // (10 currently)
* Y = 1024 ;
* X = 1024 ;
* variables:
* float var_0(time, Y, X) ;
* var_0:str_att = "some text attribute 0 type text." ;
* var_0:float_att = 0.f, 1.f, 2.f, 3.f ;
* var_0:short_att = 1234s ;
* float var_1(time, Y, X) ;
* var_1:str_att = "some text attribute 1 type text." ;
* var_1:float_att = 0.f, 1.f, 2.f, 3.f ;
* var_1:short_att = 1234s ;
* float var_2(time, Y, X) ;
* var_2:str_att = "some text attribute 2 type text." ;
* var_2:float_att = 0.f, 1.f, 2.f, 3.f ;
* var_2:short_att = 1234s ;
* float var_3(time, Y, X) ;
* var_3:str_att = "some text attribute 3 type text." ;
* var_3:float_att = 0.f, 1.f, 2.f, 3.f ;
* var_3:short_att = 1234s ;
*
* // global attributes:
* :history = "Thu Aug 29 14:29:35 2024" ;
* }
*
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */

#include <stdio.h>
#include <stdlib.h>
#include <string.h> /* strcpy(), strncpy() */
#include <unistd.h> /* getopt() */
#include <sys/time.h>
#include <netcdf.h>

static int verbose;

#define ERR { \
if (err != NC_NOERR) { \
printf("Error at %s:%d : %s\n", __FILE__,__LINE__, nc_strerror(err)); \
nerrs++; \
} \
}

static double wtime(void)
{
double now_time;
struct timeval etstart;
struct timezone tzp;

if (gettimeofday(&etstart, &tzp) == -1)
perror("Error: calling gettimeofday() not successful.\n");

now_time = ((double)etstart.tv_sec) + /* in seconds */
((double)etstart.tv_usec) / 1000000.0; /* in microseconds */
return now_time;
}

/*----< pnetcdf_io() >-------------------------------------------------------*/
static int
netcdf_io(char *filename,
int kind,
int len,
int nvars,
int ntimes)
{
char name[128], str_att[128], *file_kind;
int i, j, err, nerrs=0;
int cmode, ncid, *varid, dimid[3];
float **buf;
double bw, timing[2];
size_t w_size;
size_t start[3], count[3];

/* each local array is of size len x len */
buf = (float**) malloc(sizeof(float*) * nvars);
for (i=0; i<nvars; i++) {
buf[i] = (float*) malloc(sizeof(float) * len * len);
for (j=0; j<len*len; j++)
buf[i][j] = i * len + j;
}
varid = (int*) malloc(sizeof(int) * nvars);

switch (kind) {
case(2): cmode = NC_64BIT_OFFSET;
file_kind="Output NetCDF file kind: CDF-2";
break;
case(5): cmode = NC_64BIT_DATA;
file_kind="Output NetCDF file kind: CDF-5";
break;
default: cmode = 0;
file_kind="Output NetCDF file kind: CDF-0";
}

/* start the timer */
timing[0] = wtime();

/* create a new file for writing ----------------------------------------*/
cmode |= NC_CLOBBER;
err = nc_create(filename, cmode, &ncid); ERR

/* add a global attribute */
sprintf(str_att, "Thu Aug 29 14:29:35 2024");
err = nc_put_att_text(ncid, NC_GLOBAL, "history", strlen(str_att),
&str_att[0]); ERR

/* define dimensions x and y */
err = nc_def_dim(ncid, "time", NC_UNLIMITED, &dimid[0]); ERR
err = nc_def_dim(ncid, "Y", len, &dimid[1]); ERR
err = nc_def_dim(ncid, "X", len, &dimid[2]); ERR

/* define 2D variables of float type */
for (i=0; i<nvars; i++) {
sprintf(name, "var_%d", i);
err = nc_def_var(ncid, name, NC_FLOAT, 3, dimid, &varid[i]);
ERR
}

/* add attributes to each variable */
for (i=0; i<nvars; i++) {
short short_att=1234;
float float_att[4];

sprintf(str_att, "some text attribute %d type text.", i);
err = nc_put_att_text(ncid, varid[i], "str_att", strlen(str_att),
str_att); ERR

for (j=0; j<4; j++) float_att[j] = j;
err = nc_put_att_float(ncid, varid[i], "float_att", NC_FLOAT, 4,
float_att); ERR

err = nc_put_att_short(ncid, varid[i], "short_att", NC_SHORT, 1,
&short_att); ERR
}

/* exit define mode */
err = nc_enddef(ncid); ERR

/* set up the access pattern */
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = len;
count[2] = len;

timing[1] = wtime();
for (j=0; j<ntimes; j++) {
start[0] = j;
for (i=0; i<nvars; i++) {
err = nc_put_vara_float(ncid, varid[i], start, count, buf[i]);
ERR
}
}
timing[1] = wtime() - timing[1];

err = nc_close(ncid); ERR
timing[0] = wtime() - timing[0];

free(varid);
for (i=0; i<nvars; i++) free(buf[i]);
free(buf);

if (!verbose) return nerrs;

printf("-----------------------------------------------------------\n");
printf("Output NetCDF file name: %s\n", filename);
printf("%s\n", file_kind);
printf("Total number of variables: %d\n", nvars);
printf("Data type of variables: NC_FLOAT\n");
printf("Each 2D variable size: %d x %d\n",len,len);
printf("Number of time records: %d\n",ntimes);
w_size = sizeof(float) * len * len * nvars * ntimes;
printf("Total write amount: %zd B\n", w_size);
printf(" %.2f MiB\n", (float)w_size/1048576);
printf(" %.2f GiB\n", (float)w_size/1073741824);
bw = (double)w_size / 1048576;
printf("variable write time: %.4f sec\n", timing[1]);
printf("Write bandwidth: %.2f MiB/s\n", bw/timing[1]);
printf(" %.2f GiB/s\n", bw/1024.0/timing[1]);
printf("open-to-close time: %.4f sec\n", timing[0]);
printf("Write bandwidth: %.2f MiB/s\n", bw/timing[0]);
printf(" %.2f GiB/s\n", bw/1024.0/timing[0]);
printf("-----------------------------------------------------------\n");

return nerrs;
}

static void
usage(char *argv0)
{
char *help =
"Usage: %s [-h | -q | -k num |-l num | -n num | -t num] [file_name]\n"
" [-h] Print help\n"
" [-q] Quiet mode (reports when fail)\n"
" [-k format] file format: 1 for CDF-1,\n"
" 2 for CDF-2,\n"
" 5 for CDF-5 (default)\n"
" [-l] X and Y dimension lengths (default 32)\n"
" [-n] number of variables (default 4)\n"
" [-t] number of time iterations (default 1)\n"
" [filename] output netCDF file name\n";
fprintf(stderr, help, argv0);
}

int main(int argc, char** argv)
{
extern int optind;
extern char *optarg;
char filename[512];
int i, kind, nerrs=0;
int nvars, len, ntimes;

verbose = 1;
kind = 5;
nvars = 4;
len = 32;
ntimes = 1;

/* get command-line arguments */
while ((i = getopt(argc, argv, "hqk:l:n:t:")) != EOF)
switch(i) {
case 'q': verbose = 0;
break;
case 'k': kind = atoi(optarg);
break;
case 'l': len = atoi(optarg);
break;
case 'n': nvars = atoi(optarg);
break;
case 't': ntimes = atoi(optarg);
break;
case 'h':
default: usage(argv[0]);
return 1;
}
if (argv[optind] == NULL) strcpy(filename, "testfile.nc");
else snprintf(filename, 512, "%s", argv[optind]);

nerrs += netcdf_io(filename, kind, len, nvars, ntimes);

return (nerrs > 0);
}

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