Exodus 7.22

/test/rd_wt_mesh.c
/*
* Copyright (c) 2005-2017 National Technology & Engineering Solutions
* of Sandia, LLC (NTESS). Under the terms of Contract DE-NA0003525 with
* NTESS, the U.S. Government retains certain rights in this software.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
*
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
*
* * Neither the name of NTESS nor the names of its
* contributors may be used to endorse or promote products derived
* from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
#define _FILE_OFFSET_BITS 64
#define _LARGEFILE_SOURCE
#define _LARGE_FILES 1
#ifdef PARALLEL_AWARE_EXODUS
#include <mpi.h>
#else
#include <string.h>
#include <time.h>
#endif
#include <assert.h>
#include <float.h>
#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <sys/types.h>
#include <unistd.h>
#include "exodusII.h"
#define DEFAULT_NUM_FIELDS 0
#define DEFAULT_FILE_NAME "mesh"
#define DEFAULT_NUM_ITERATIONS 1
#define EXODUS_FILE_TYPE "e"
#define MBYTES (1024 * 1024)
#define MAX_STRING_LEN 128
#define NUM_NODES_PER_ELEM 8
#define QUIT EX_FALSE
#define WRITE_FILE_TYPE "new"
#define EBLK_ID 100000
/*
* Prototypes
*/
typedef double realtyp;
void get_file_name(const char *base, const char *ext, int rank, int nprocs, const char *other,
char *output);
int parse_input(int argc, char *argv[], int *exodus, int *close_files, char *file_name,
int *num_nodal_fields, int *num_global_fields, int *num_element_fields,
int *files_per_domain, int *num_iterations, int *sleep_time);
int read_exo_mesh(char *file_name, int rank, int *num_dim, int num_domains, int *num_nodal_fields,
int *num_global_fields, int *num_element_fields, int *num_timesteps,
int sleep_time, int num_iterations, int *num_nodes, int **node_map,
int *num_elems, int **elem_map, realtyp **x_coords, realtyp **y_coords,
realtyp **z_coords, int **connect);
int write_exo_mesh(char *file_name, int rank, int num_dim, int num_domains, int num_nodal_fields,
int num_global_fields, int num_element_fields, int num_timesteps,
int files_per_domain, int sleep_time, int num_iterations, int num_nodes,
int *node_map, int num_elems, int *elem_map, realtyp *x_coords,
realtyp *y_coords, realtyp *z_coords, int *connect, int close_files);
double my_timer()
{
#ifdef PARALLEL_AWARE_EXODUS
double t1 = MPI_Wtime();
#else
clock_t ctime = clock();
double t1 = ctime / (double)CLOCKS_PER_SEC;
#endif
return t1;
}
/***********************************************************************
*
* Main function
*
***********************************************************************/
int main(int argc, char **argv)
{
int rank, num_domains;
int quit = EX_FALSE;
int loc_num_nodes, loc_num_elems;
int *loc_connect = NULL;
#ifdef PARALLEL_AWARE_EXODUS
MPI_Info mpi_info_object = MPI_INFO_NULL; /* Copy of MPI Info object. */
#endif
int *elem_map = NULL;
int exodus = EX_TRUE; /* EX_TRUE, perform EXODUS benchmark; EX_FALSE don't */
int close_files = EX_FALSE;
char file_name[MAX_STRING_LEN] = DEFAULT_FILE_NAME; /* Input file name. */
/* object, EX_FALSE otherwise. Should always be */
/* EX_TRUE in the current implementation. */
int num_nodal_fields = DEFAULT_NUM_FIELDS;
int num_global_fields = DEFAULT_NUM_FIELDS;
int num_element_fields = DEFAULT_NUM_FIELDS;
int num_timesteps = 0;
int sleep_time = 0;
int files_per_domain = 1;
int num_iterations = DEFAULT_NUM_ITERATIONS;
#ifdef PARALLEL_AWARE_EXODUS
static const char *hints[] = {/* List of MPI Info hints that if defined in */
"cb_buffer_size", /* the environment process 0, will be used to */
"cb_nodes", /* set key/value pairs in the MPI */
"ind_rd_buffer_size", /* Info object. */
"ind_wr_buffer_size", "cb_config_list", "romio_cb_read",
"romio_cb_write", "romio_ds_read", "romio_ds_write",
"romio_no_indep_rw"};
char key_name[MAX_STRING_LEN]; /* MPI Info object key name. */
int key; /* MPI Info object key index. */
int key_exists; /* EX_TRUE, if the key exists in the MPI Info */
const int nhints = 10; /* Number of items in hints list. */
int nkeys; /* Number of keys in a MPI Info object. */
char value[MAX_STRING_LEN]; /* Value of a key/value pair in a MPI Info */
#endif
/* object. */
realtyp *x_coords = NULL;
realtyp *y_coords = NULL;
realtyp *z_coords = NULL;
int ndim;
/*
* Initialize Stuff
*/
ex_opts(EX_VERBOSE | EX_ABORT);
#if defined(__LIBCATAMOUNT__)
setlinebuf(stderr);
#endif
#ifdef PARALLEL_AWARE_EXODUS
MPI_Init(&argc, &argv);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &num_domains);
#else
rank = 0;
num_domains = 1;
#endif
/*
* Processor 0: parse the command line arguments.
*/
if (rank == 0) {
quit = (1 == parse_input(argc, argv, &exodus, &close_files, file_name, &num_nodal_fields,
&num_global_fields, &num_element_fields, &files_per_domain,
&num_iterations, &sleep_time));
}
/*
* Broadcast Input
*/
#ifdef PARALLEL_AWARE_EXODUS
MPI_Bcast(&quit, 1, MPI_INT, 0, MPI_COMM_WORLD);
#endif
if (quit) {
#ifdef PARALLEL_AWARE_EXODUS
MPI_Finalize();
#endif
exit(0);
}
#ifdef PARALLEL_AWARE_EXODUS
MPI_Bcast(&exodus, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&close_files, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(file_name, MAX_STRING_LEN, MPI_CHAR, 0, MPI_COMM_WORLD);
MPI_Bcast(&num_nodal_fields, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&num_global_fields, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&num_element_fields, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&num_iterations, 1, MPI_INT, 0, MPI_COMM_WORLD);
MPI_Bcast(&files_per_domain, 1, MPI_INT, 0, MPI_COMM_WORLD);
/* env_mpi_hints( nhints, hints ); */
{
char *env; /* Contents of environmental variable. */
int hint; /* ROMIO hint index. */
char hint_value[MAX_STRING_LEN]; /* ROMIO hint value. */
int rank; /* MPI process rank. */
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
/* The "value" of the hint is obtained from the environment of
* processor 0 only. The value is broadcast to the other
* processors.
*/
for (hint = 0; hint < nhints; hint++) {
if (rank == 0) {
env = getenv(hints[hint]);
if (env != NULL)
ex_copy_string(hint_value, env, MAX_STRING_LEN);
else
hint_value[0] = 0;
}
MPI_Bcast(hint_value, MAX_STRING_LEN, MPI_CHAR, 0, MPI_COMM_WORLD);
if (hint_value[0]) {
if (mpi_info_object == MPI_INFO_NULL)
MPI_Info_create(&mpi_info_object);
MPI_Info_set(mpi_info_object, hints[hint], hint_value);
}
}
}
#endif
if (rank == 0) {
fprintf(stderr, "\nEXODUSII 3D Benchmark\n\n");
fprintf(stderr, " Number of Domains\t\t%8d\n", num_domains);
fprintf(stderr, " Number of Files/Domain\t%8d\n", files_per_domain);
fprintf(stderr, " Number of Iterations\t\t%8d\n", num_iterations);
#ifdef PARALLEL_AWARE_EXODUS
if (mpi_info_object != MPI_INFO_NULL) {
fprintf(stderr, " MPI Hint Status\n");
MPI_Info_get_nkeys(mpi_info_object, &nkeys);
for (key = 0; key < nkeys; key++) {
MPI_Info_get_nthkey(mpi_info_object, key, key_name);
MPI_Info_get(mpi_info_object, key_name, MAX_STRING_LEN, value, &key_exists);
fprintf(stderr, " %s\t\t\t%s\n", key_name, value);
}
MPI_Info_free(&mpi_info_object);
}
else
fprintf(stderr, " MPI Hint Status\tMPI_INFO_NULL\n");
#endif
}
if (exodus) {
int *node_map = NULL;
if (0 == read_exo_mesh(file_name, rank, &ndim, num_domains, &num_nodal_fields,
&num_global_fields, &num_element_fields, &num_timesteps, sleep_time,
num_iterations, &loc_num_nodes, &node_map, &loc_num_elems, &elem_map,
&x_coords, &y_coords, &z_coords, &loc_connect)) {
write_exo_mesh(file_name, rank, ndim, num_domains, num_nodal_fields, num_global_fields,
num_element_fields, num_timesteps, files_per_domain, sleep_time,
num_iterations, loc_num_nodes, node_map, loc_num_elems, elem_map, x_coords,
y_coords, z_coords, loc_connect, close_files);
free(elem_map);
free(loc_connect);
free(node_map);
free(x_coords);
free(y_coords);
free(z_coords);
}
}
#ifdef PARALLEL_AWARE_EXODUS
MPI_Finalize();
#endif
return (0);
}
/***********************************************************************
*
* Parse Input
*
***********************************************************************/
int parse_input(int argc, char *argv[], int *exodus, int *close_files, char *file_name,
int *num_nodal_fields, int *num_global_fields, int *num_element_fields,
int *files_per_domain, int *num_iterations, int *sleep_time)
{
int arg = 0; /* Argument index. */
while (++arg < argc) {
if (strcmp("-c", argv[arg]) == 0) {
if (++arg < argc) {
*num_nodal_fields = atoi(argv[arg]);
}
}
else if (strcmp("-nv", argv[arg]) == 0) {
if (++arg < argc) {
*num_nodal_fields = atoi(argv[arg]);
}
}
else if (strcmp("-gv", argv[arg]) == 0) {
if (++arg < argc) {
*num_global_fields = atoi(argv[arg]);
}
}
else if (strcmp("-ev", argv[arg]) == 0) {
if (++arg < argc) {
*num_element_fields = atoi(argv[arg]);
}
}
else if (strcmp("-f", argv[arg]) == 0) {
if (++arg < argc) {
ex_copy_string(file_name, argv[arg], MAX_STRING_LEN);
}
}
else if (strcmp("-M", argv[arg]) == 0) {
if (++arg < argc) {
*files_per_domain = atoi(argv[arg]);
}
}
else if (strcmp("-i", argv[arg]) == 0) {
if (++arg < argc) {
*num_iterations = atoi(argv[arg]);
}
}
else if (strcmp("-w", argv[arg]) == 0) {
if (++arg < argc) {
*sleep_time = atoi(argv[arg]);
}
}
else if (strcmp("-x", argv[arg]) == 0) {
*exodus = EX_TRUE;
}
else if (strcmp("-C", argv[arg]) == 0) {
*close_files = EX_TRUE;
}
else if ((strcmp("-h", argv[arg]) == 0) || (strcmp("-u", argv[arg]) == 0)) {
fprintf(stderr, " \n");
fprintf(stderr, "NAME \n");
fprintf(stderr, " \n");
fprintf(stderr, "rd_wt_mesh - reads and writes a mesh in parallel for performance\n");
fprintf(stderr, " benchmarking. \n");
fprintf(stderr, " \n");
fprintf(stderr, "SYNOPSIS \n");
fprintf(stderr, " \n");
fprintf(stderr, "rd_wt_mesh [-S] [-c fields] [-f file_name] [-h] [-i iterations] \n");
fprintf(stderr, " [-s] [-u] [-x] [-w] \n");
fprintf(stderr, " \n");
fprintf(stderr, "DESCRIPTION \n");
fprintf(stderr, " \n");
fprintf(stderr, "This program reads and writes a mesh in parallel for performance\n");
fprintf(stderr, "benchmarking. The first Exodus database file read by \n");
fprintf(stderr, "this program is created by create_mesh. Performance summaries \n");
fprintf(stderr, "are written to stdout. \n");
fprintf(stderr, " \n");
fprintf(stderr, "OPTIONS \n");
fprintf(stderr, " \n");
fprintf(stderr, "-c fields number of fields. Default: %d \n",
DEFAULT_NUM_FIELDS);
fprintf(stderr, "-f file_name file name prefix for all read files: \n");
fprintf(stderr, " \n");
fprintf(stderr, " 'file_name'%s.nproc.rank [EXODUS II file] \n",
EXODUS_FILE_TYPE);
fprintf(stderr, " \n");
fprintf(stderr, " Default: %s \n",
DEFAULT_FILE_NAME);
fprintf(stderr, "-M files number of files/domain. Default: 1 \n");
fprintf(stderr, "-h display help/usage information \n");
fprintf(stderr, "-i iterations number of iterations. Default: %d \n",
DEFAULT_NUM_ITERATIONS);
fprintf(stderr, "-C minimize open files. \n");
fprintf(stderr, "-u display help/usage information \n");
fprintf(stderr, "-w time wait (sleep) specified time between timesteps.\n");
return (1);
}
else {
fprintf(stderr, "Unknown option: %s\n", argv[arg]);
fprintf(stderr, "Enter rd_wt_mesh -h for description of valid options.\n");
return (1);
}
}
return (0);
}
/***********************************************************************
***********************************************************************/
int read_exo_mesh(char *file_name, int rank, int *num_dim, int num_domains, int *num_nodal_fields,
int *num_global_fields, int *num_element_fields, int *num_timesteps,
int sleep_time, int num_iterations, int *num_nodes, int **node_map,
int *num_elems, int **elem_map, realtyp **x_coords, realtyp **y_coords,
realtyp **z_coords, int **connect)
{
int CPU_word_size = sizeof(realtyp);
int IO_word_size = 0;
int exoid, err, num_elem_blk, num_node_sets, num_side_sets;
int num_nodes_per_elem, num_attrs, num_vars, i, iter;
size_t len_connect;
size_t file_size;
struct stat file_status;
size_t glob_file_size;
size_t glob_raw_data_vol;
size_t raw_data_vol = 0;
float version;
realtyp *globals = NULL;
double tstart, tend, t_tmp1, t_tmp2;
double raw_read_time, max_raw_read_time = 0.0, min_raw_read_time = DBL_MAX;
double cum_raw_read_time = 0.0;
double total_time, max_total_time = 0.0, min_total_time = DBL_MAX;
double raw_sleep_time = 0.0;
double cum_total_time = 0.0;
char tmp_name[MAX_STRING_LEN], title[MAX_STRING_LEN + 1];
char type[MAX_STRING_LEN + 1];
for (iter = 0; iter < num_iterations; iter++) {
/* open the EXODUS file */
get_file_name(file_name, EXODUS_FILE_TYPE, rank, num_domains, NULL, tmp_name);
exoid = ex_open(tmp_name, EX_READ, &CPU_word_size, &IO_word_size, &version);
if (exoid < 0) {
printf("after ex_open\n");
return (1);
}
raw_read_time = 0.0;
raw_data_vol = 0;
tstart = my_timer();
err = ex_get_init(exoid, title, num_dim, num_nodes, num_elems, &num_elem_blk, &num_node_sets,
&num_side_sets);
if (err) {
printf("after ex_get_init, error = %d\n", err);
ex_close(exoid);
return (1);
}
len_connect = (size_t)NUM_NODES_PER_ELEM * (*num_elems);
/* malloc things we need */
if (iter == 0) {
*elem_map = malloc(sizeof(int) * (*num_elems));
assert(elem_map);
*connect = malloc(sizeof(int) * len_connect);
assert(connect);
*node_map = malloc(sizeof(int) * (*num_nodes));
assert(node_map);
*x_coords = malloc(sizeof(realtyp) * (*num_nodes));
assert(x_coords);
*y_coords = malloc(sizeof(realtyp) * (*num_nodes));
assert(y_coords);
*z_coords = malloc(sizeof(realtyp) * (*num_nodes));
assert(z_coords);
}
t_tmp1 = my_timer();
err = ex_get_coord(exoid, *x_coords, *y_coords, *z_coords);
t_tmp2 = my_timer();
raw_read_time += t_tmp2 - t_tmp1;
raw_data_vol += sizeof(realtyp) * 3 * (*num_nodes);
if (err) {
printf("after ex_get_coord, error = %d\n", err);
ex_close(exoid);
return (1);
}
err = ex_get_block(exoid, EX_ELEM_BLOCK, EBLK_ID, type, num_elems, &num_nodes_per_elem, 0, 0,
&num_attrs);
if (err) {
printf("after ex_get_elem_block, error = %d\n", err);
ex_close(exoid);
return (1);
}
t_tmp1 = my_timer();
err = ex_get_conn(exoid, EX_ELEM_BLOCK, EBLK_ID, *connect, 0, 0);
t_tmp2 = my_timer();
raw_read_time += t_tmp2 - t_tmp1;
raw_data_vol += sizeof(int) * len_connect;
if (err) {
printf("after ex_get_elem_conn, error = %d\n", err);
ex_close(exoid);
return (1);
}
/* read element and node maps */
t_tmp1 = my_timer();
ex_get_id_map(exoid, EX_NODE_MAP, *node_map);
t_tmp2 = my_timer();
raw_data_vol += sizeof(int) * (*num_nodes);
raw_read_time += t_tmp2 - t_tmp1;
t_tmp1 = my_timer();
ex_get_id_map(exoid, EX_ELEM_MAP, *elem_map);
t_tmp2 = my_timer();
raw_data_vol += sizeof(int) * (*num_elems);
raw_read_time += t_tmp2 - t_tmp1;
/* read results variables */
err = ex_get_variable_param(exoid, EX_NODAL, &num_vars);
if (err) {
printf("after ex_get_variable_param, error = %d\n", err);
ex_close(exoid);
return (1);
}
*num_nodal_fields = num_vars;
err = ex_get_variable_param(exoid, EX_GLOBAL, &num_vars);
if (err) {
printf("after ex_get_variable_param, error = %d\n", err);
ex_close(exoid);
return (1);
}
*num_global_fields = num_vars;
if (*num_global_fields > 0) {
globals = malloc(*num_global_fields * sizeof(realtyp));
assert(globals);
}
err = ex_get_variable_param(exoid, EX_ELEM_BLOCK, &num_vars);
if (err) {
printf("after ex_get_variable_param, error = %d\n", err);
ex_close(exoid);
if (globals)
free(globals);
return (1);
}
*num_element_fields = num_vars;
/* read number of timesteps */
*num_timesteps = ex_inquire_int(exoid, EX_INQ_TIME);
if (rank == 0) {
fprintf(stderr, " Number of Elements\t\t%8d (per domain)\n", *num_elems);
fprintf(stderr, " Number of Nodes\t\t%8d (per domain)\n", *num_nodes);
fprintf(stderr, " Number of Global Fields\t%8d\n", *num_global_fields);
fprintf(stderr, " Number of Nodal Fields\t%8d\n", *num_nodal_fields);
fprintf(stderr, " Number of Element Fields\t%8d\n", *num_element_fields);
fprintf(stderr, " Number of Timesteps\t\t%8d\n", *num_timesteps);
if (sleep_time > 0) {
fprintf(stderr, " Timestep Sleep time\t%8d\n", sleep_time);
}
}
if (*num_nodal_fields + *num_global_fields + *num_element_fields > 0) {
int t;
if (rank == 0) {
fprintf(stderr, "\nReading Timestep: ");
}
for (t = 0; t < *num_timesteps; t++) {
if (sleep_time > 0) {
t_tmp1 = my_timer();
sleep(sleep_time);
t_tmp2 = my_timer();
raw_sleep_time += t_tmp2 - t_tmp1;
}
if (rank == 0) {
fprintf(stderr, " %d,", t + 1);
}
for (i = 1; i <= *num_nodal_fields; i++) {
t_tmp1 = my_timer();
err = ex_get_var(exoid, t + 1, EX_NODAL, i, 0, *num_nodes, *x_coords);
t_tmp2 = my_timer();
raw_read_time += t_tmp2 - t_tmp1;
raw_data_vol += sizeof(realtyp) * (*num_nodes);
if (err) {
printf("after ex_get_nodal_var, error = %d\n", err);
ex_close(exoid);
return (1);
}
}
t_tmp1 = my_timer();
err = ex_get_var(exoid, t + 1, EX_GLOBAL, 0, 0, *num_global_fields, globals);
t_tmp2 = my_timer();
raw_read_time += t_tmp2 - t_tmp1;
raw_data_vol += sizeof(realtyp) * *num_global_fields;
if (err) {
printf("after ex_get_glob_vars, error = %d\n", err);
ex_close(exoid);
return (1);
}
for (i = 1; i <= *num_element_fields; i++) {
t_tmp1 = my_timer();
err = ex_get_var(exoid, t + 1, EX_ELEM_BLOCK, i, EBLK_ID, *num_elems, *x_coords);
t_tmp2 = my_timer();
raw_read_time += t_tmp2 - t_tmp1;
raw_data_vol += sizeof(realtyp) * (*num_elems);
if (err) {
printf("after ex_get_elem_var, error = %d\n", err);
ex_close(exoid);
return (1);
}
}
}
if (rank == 0) {
fprintf(stderr, "\n");
}
}
err = ex_close(exoid);
if (err) {
printf("after ex_close, error = %d\n", err);
return (1);
}
tend = my_timer();
total_time = tend - tstart - raw_sleep_time;
if (total_time > max_total_time) {
max_total_time = total_time;
}
if (total_time < min_total_time) {
min_total_time = total_time;
}
cum_total_time += total_time;
if (raw_read_time > max_raw_read_time) {
max_raw_read_time = raw_read_time;
}
if (raw_read_time < min_raw_read_time) {
min_raw_read_time = raw_read_time;
}
cum_raw_read_time += raw_read_time;
} /* end of for (iter...) */
#ifdef PARALLEL_AWARE_EXODUS
MPI_Allreduce(&raw_data_vol, &glob_raw_data_vol, 1, MPI_LONG, MPI_SUM, MPI_COMM_WORLD);
#else
glob_raw_data_vol = raw_data_vol;
#endif
/*
* Get File Sizes
*
* Note: On ASCI Red, a specialized "stat", named "estat", was added to
* accommodate file sizes up to 16GB. 3/27/2002
*/
if (stat(tmp_name, &file_status)) {
if (rank == 0) {
fprintf(stderr, "Exodus Read: cannot get %s file size.\n", tmp_name);
}
return (1);
}
{
file_size = file_status.st_size;
}
#ifdef PARALLEL_AWARE_EXODUS
MPI_Allreduce(&file_size, &glob_file_size, 1, MPI_LONG, MPI_SUM, MPI_COMM_WORLD);
#else
glob_file_size = file_size;
#endif
if (rank == 0) {
fprintf(stderr, " \n");
fprintf(stderr, " Exodus Read Results \n");
fprintf(stderr, " \n");
fprintf(stderr, " Sizes (bytes) \n");
fprintf(stderr, " File %14ld \n",
(long)glob_file_size);
fprintf(stderr, " Raw Data %14ld \n",
(long)glob_raw_data_vol);
fprintf(stderr, " Difference %14ld (%5.2f%%) \n",
(long)(glob_file_size - glob_raw_data_vol),
(1.0 * glob_file_size - 1.0 * glob_raw_data_vol) / (0.01 * glob_file_size));
fprintf(stderr, " \n");
fprintf(stderr, " Times (sec) \t Minimum\t Maximum\t Average\n");
fprintf(stderr, " Raw Data Read (sec) \t%8.4g\t%8.4g\t%8.4g \n",
min_raw_read_time, max_raw_read_time, cum_raw_read_time / num_iterations);
fprintf(stderr, " All Other Read (sec) \t \t \t%8.4g \n",
(cum_total_time - cum_raw_read_time) / num_iterations);
fprintf(stderr, " Total Read (sec) \t \t \t%8.4g \n",
cum_total_time / num_iterations);
fprintf(stderr, " \n");
fprintf(stderr, " Input Bandwidths (MiB/sec) \t Minimum\t Maximum\t Average\n");
fprintf(stderr, " Raw Data Read (MiB/sec) \t%8.4g\t%8.4g\t%8.4g \n",
(double)glob_raw_data_vol / max_raw_read_time / MBYTES,
(double)glob_raw_data_vol / min_raw_read_time / MBYTES,
(double)glob_raw_data_vol / cum_raw_read_time / MBYTES * num_iterations);
fprintf(stderr, " Raw + Meta Data Read (MiB/sec)\t \t \t%8.4g \n",
(double)glob_file_size / cum_total_time / MBYTES * num_iterations);
}
if (*num_global_fields > 0) {
free(globals);
}
return (0);
}
/***********************************************************************
***********************************************************************/
int write_exo_mesh(char *file_name, int rank, int num_dim, int num_domains, int num_nodal_fields,
int num_global_fields, int num_element_fields, int num_timesteps,
int files_per_domain, int sleep_time, int num_iterations, int num_nodes,
int *node_map, int num_elems, int *elem_map, realtyp *x_coords,
realtyp *y_coords, realtyp *z_coords, int *connect, int close_files)
{
int CPU_word_size = sizeof(realtyp);
int IO_word_size = sizeof(realtyp);
int j, t, npd, err, num_elem_blk, num_node_sets, num_side_sets;
int iter;
int * elem_var_tab = NULL;
size_t file_size;
struct stat file_status;
size_t glob_file_size;
size_t glob_raw_data_vol;
size_t raw_data_vol = 0;
realtyp *globals = NULL;
double raw_open_close_time = 0.0;
double cum_open_close_time = 0.0;
double min_raw_open_close_time = DBL_MAX;
double max_raw_open_close_time = 0.0;
double tstart, tend, t_tmp1, t_tmp2;
double raw_write_time, max_raw_write_time = 0.0, min_raw_write_time = DBL_MAX;
double cum_raw_write_time = 0.0;
double total_time, max_total_time = 0.0, min_total_time = DBL_MAX;
double cum_total_time = 0.0;
double raw_sleep_time = 0.0;
double put_time_time = 0.0;
char tmp_name[MAX_STRING_LEN];
char base_name[MAX_STRING_LEN];
char **gvar_name = NULL;
char **nvar_name = NULL;
char **evar_name = NULL;
int *exoid = malloc(files_per_domain * sizeof(int));
for (iter = 0; iter < num_iterations; iter++) {
if (!close_files) {
t_tmp1 = my_timer();
for (npd = 0; npd < files_per_domain; npd++) {
/* create the EXODUS file */
sprintf(base_name, "%s_%d", file_name, npd);
get_file_name(base_name, EXODUS_FILE_TYPE, rank, num_domains, WRITE_FILE_TYPE, tmp_name);
exoid[npd] = ex_create(tmp_name, EX_CLOBBER, &CPU_word_size, &IO_word_size);
if (exoid[npd] < 0) {
printf("after ex_create\n");
free(exoid);
return (1);
}
}
t_tmp2 = my_timer();
raw_open_close_time += (t_tmp2 - t_tmp1);
}
raw_write_time = 0.0;
raw_data_vol = 0;
tstart = my_timer();
num_elem_blk = 1;
num_node_sets = 0;
num_side_sets = 0;
for (npd = 0; npd < files_per_domain; npd++) {
if (close_files) {
/* create the EXODUS file */
sprintf(base_name, "%s_%d", file_name, npd);
get_file_name(base_name, EXODUS_FILE_TYPE, rank, num_domains, WRITE_FILE_TYPE, tmp_name);
exoid[npd] = ex_create(tmp_name, EX_CLOBBER, &CPU_word_size, &IO_word_size);
if (exoid[npd] < 0) {
printf("after ex_create\n");
free(exoid);
return (1);
}
}
err = ex_put_init(exoid[npd], "This is an EXODUSII performance test.", num_dim, num_nodes,
num_elems, num_elem_blk, num_node_sets, num_side_sets);
if (err) {
printf("after ex_put_init, error = %d\n", err);
ex_close(exoid[npd]);
free(exoid);
return (1);
}
#if 0
{
int ids[1] = {EBLK_ID};
int num_elem_per_block[1];
char *names[1] = {"hex"};
int num_node_per_elem[1];
int num_attr_per_block[1];
int write_map = num_domains > 1 ? EX_TRUE : EX_FALSE;
num_elem_per_block[0] = num_elems;
num_node_per_elem[0] = NUM_NODES_PER_ELEM;
num_attr_per_block[0] = 0;
err = ex_put_concat_elem_block (exoid[npd], ids, names, num_elem_per_block,
num_node_per_elem, num_attr_per_block, write_map);
}
#else
err = ex_put_block(exoid[npd], EX_ELEM_BLOCK, EBLK_ID, "hex", num_elems, NUM_NODES_PER_ELEM,
0, 0, 0);
#endif
if (err) {
printf("after ex_put_elem_block, error = %d\n", err);
ex_close(exoid[npd]);
free(exoid);
return (1);
}
t_tmp1 = my_timer();
err = ex_put_coord(exoid[npd], x_coords, y_coords, z_coords);
t_tmp2 = my_timer();
raw_write_time += t_tmp2 - t_tmp1;
raw_data_vol += sizeof(realtyp) * num_dim * num_nodes;
if (err) {
printf("after ex_put_coord, error = %d\n", err);
ex_close(exoid[npd]);
free(exoid);
return (1);
}
t_tmp1 = my_timer();
err = ex_put_conn(exoid[npd], EX_ELEM_BLOCK, EBLK_ID, connect, NULL, NULL);
t_tmp2 = my_timer();
raw_write_time += t_tmp2 - t_tmp1;
raw_data_vol += sizeof(int) * num_elems * NUM_NODES_PER_ELEM;
if (err) {
printf("after ex_put_elem_conn, error = %d\n", err);
ex_close(exoid[npd]);
free(exoid);
return (1);
}
/* write out element and node maps */
t_tmp1 = my_timer();
err = ex_put_id_map(exoid[npd], EX_NODE_MAP, node_map);
t_tmp2 = my_timer();
raw_write_time += t_tmp2 - t_tmp1;
raw_data_vol += sizeof(int) * num_nodes;
if (err) {
printf("after ex_put_id_map, error = %d\n", err);
ex_close(exoid[npd]);
free(exoid);
return (1);
}
t_tmp1 = my_timer();
err = ex_put_id_map(exoid[npd], EX_ELEM_MAP, elem_map);
t_tmp2 = my_timer();
raw_write_time += t_tmp2 - t_tmp1;
raw_data_vol += sizeof(int) * num_elems;
if (err) {
printf("after ex_put_id_map, error = %d\n", err);
ex_close(exoid[npd]);
free(exoid);
return (1);
}
/* write out simulated results fields;
we'll just write out the x coordinate field 'num_element_fields' times */
if (num_element_fields > 0) {
if (npd == 0) {
elem_var_tab = malloc(num_element_fields * sizeof(int));
assert(elem_var_tab);
for (j = 0; j < num_element_fields; j++) {
elem_var_tab[j] = 1;
}
}
}
else {
elem_var_tab = 0;
}
err = ex_put_all_var_param(exoid[npd], num_global_fields, num_nodal_fields,
num_element_fields, elem_var_tab, 0, 0, 0, 0);
if (err) {
fprintf(stderr, "after ex_put_all_var_param, error = %d\n", err);
ex_close(exoid[npd]);
exit(1);
}
if (num_nodal_fields > 0) {
if (npd == 0) {
nvar_name = malloc(num_nodal_fields * sizeof(char *));
assert(nvar_name);
for (j = 0; j < num_nodal_fields; j++) {
nvar_name[j] = malloc((MAX_STRING_LEN + 1) * sizeof(char));
sprintf(nvar_name[j], "node_field_%d", j + 1);
}
}
err = ex_put_variable_names(exoid[npd], EX_NODAL, num_nodal_fields, nvar_name);
if (npd == files_per_domain - 1) {
for (j = 0; j < num_nodal_fields; j++) {
free(nvar_name[j]);
}
free(nvar_name);
}
}
if (num_global_fields > 0) {
if (npd == 0) {
globals = malloc(num_global_fields * sizeof(realtyp));
gvar_name = malloc(num_global_fields * sizeof(char *));
for (j = 0; j < num_global_fields; j++) {
gvar_name[j] = malloc((MAX_STRING_LEN + 1) * sizeof(char));
sprintf(gvar_name[j], "global_field_%d", j + 1);
globals[j] = j;
}
}
err = ex_put_variable_names(exoid[npd], EX_GLOBAL, num_global_fields, gvar_name);
if (npd == files_per_domain - 1) {
for (j = 0; j < num_global_fields; j++) {
free(gvar_name[j]);
}
free(gvar_name);
}
}
if (num_element_fields > 0) {
if (npd == 0) {
evar_name = malloc(num_element_fields * sizeof(char *));
for (j = 0; j < num_element_fields; j++) {
evar_name[j] = malloc((MAX_STRING_LEN + 1) * sizeof(char));
sprintf(evar_name[j], "element_field_%d", j + 1);
}
}
err = ex_put_variable_names(exoid[npd], EX_ELEM_BLOCK, num_element_fields, evar_name);
if (npd == files_per_domain - 1) {
free(elem_var_tab);
for (j = 0; j < num_element_fields; j++) {
free(evar_name[j]);
}
free(evar_name);
}
}
if (close_files) {
t_tmp1 = my_timer();
ex_close(exoid[npd]);
t_tmp2 = my_timer();
raw_open_close_time += (t_tmp2 - t_tmp1);
}
}
if (num_nodal_fields + num_global_fields + num_element_fields > 0) {
if (rank == 0) {
fprintf(stderr, "\nWriting Timestep: ");
}
for (t = 0; t < num_timesteps; t++) {
for (npd = 0; npd < files_per_domain; npd++) {
realtyp time = t;
if (close_files) {
float version;
sprintf(base_name, "%s_%d", file_name, npd);
t_tmp1 = my_timer();
get_file_name(base_name, EXODUS_FILE_TYPE, rank, num_domains, WRITE_FILE_TYPE,
tmp_name);
exoid[npd] = ex_open(tmp_name, EX_WRITE, &CPU_word_size, &IO_word_size, &version);
t_tmp2 = my_timer();
raw_open_close_time += (t_tmp2 - t_tmp1);
}
if (sleep_time > 0) {
t_tmp1 = my_timer();
sleep(sleep_time);
t_tmp2 = my_timer();
raw_sleep_time += t_tmp2 - t_tmp1;
}
t_tmp1 = my_timer();
ex_put_time(exoid[npd], t + 1, &time);
t_tmp2 = my_timer();
put_time_time += t_tmp2 - t_tmp1;
if (rank == 0) {
if (npd == 0) {
fprintf(stderr, " %d", t + 1);
}
else {
fprintf(stderr, ".");
}
}
if (num_global_fields > 0) {
t_tmp1 = my_timer();
err = ex_put_var(exoid[npd], t + 1, EX_GLOBAL, 1, 0, num_global_fields, globals);
t_tmp2 = my_timer();
raw_write_time += t_tmp2 - t_tmp1;
if (err) {
fprintf(stderr, "after ex_put_global_var, error = %d\n", err);
ex_close(exoid[npd]);
exit(1);
}
}
for (j = 0; j < num_nodal_fields; j++) {
t_tmp1 = my_timer();
err = ex_put_var(exoid[npd], t + 1, EX_NODAL, j + 1, 0, num_nodes, x_coords);
t_tmp2 = my_timer();
raw_write_time += t_tmp2 - t_tmp1;
if (err) {
fprintf(stderr, "after ex_put_nodal_var, error = %d\n", err);
ex_close(exoid[npd]);
exit(1);
}
}
for (j = 0; j < num_element_fields; j++) {
t_tmp1 = my_timer();
err = ex_put_var(exoid[npd], t + 1, EX_ELEM_BLOCK, j + 1, EBLK_ID, num_elems, x_coords);
t_tmp2 = my_timer();
raw_write_time += t_tmp2 - t_tmp1;
if (err) {
fprintf(stderr, "after ex_put_element_var, error = %d\n", err);
ex_close(exoid[npd]);
exit(1);
}
}
if (close_files) {
t_tmp1 = my_timer();
ex_close(exoid[npd]);
t_tmp2 = my_timer();
raw_open_close_time += (t_tmp2 - t_tmp1);
}
}
}
if (rank == 0) {
fprintf(stderr, "\n");
}
}
t_tmp1 = my_timer();
if (!close_files) {
if (rank == 0) {
fprintf(stderr, "Closing database...");
}
for (npd = 0; npd < files_per_domain; npd++) {
err = ex_close(exoid[npd]);
if (err) {
printf("after ex_close, error = %d\n", err);
free(exoid);
return (1);
}
}
if (rank == 0) {
fprintf(stderr, "\n");
}
}
t_tmp2 = my_timer();
raw_open_close_time += (t_tmp2 - t_tmp1);
if (rank == 0) {
fprintf(stderr, "ex_put_time = %5.2f seconds\n", put_time_time);
}
tend = my_timer();
total_time = tend - tstart - raw_sleep_time;
if (total_time > max_total_time) {
max_total_time = total_time;
}
if (total_time < min_total_time) {
min_total_time = total_time;
}
cum_total_time += total_time;
if (raw_write_time > max_raw_write_time) {
max_raw_write_time = raw_write_time;
}
if (raw_write_time < min_raw_write_time) {
min_raw_write_time = raw_write_time;
}
cum_raw_write_time += raw_write_time;
if (raw_open_close_time > max_raw_open_close_time) {
max_raw_open_close_time = raw_open_close_time;
}
if (raw_open_close_time < min_raw_open_close_time) {
min_raw_open_close_time = raw_open_close_time;
}
cum_open_close_time += raw_open_close_time;
raw_data_vol += sizeof(realtyp) *
(((size_t)num_nodes * num_nodal_fields) + (num_elems * num_element_fields) +
(num_global_fields)) *
num_timesteps * files_per_domain;
} /* end of for (iter...) */
#ifdef PARALLEL_AWARE_EXODUS
MPI_Allreduce(&raw_data_vol, &glob_raw_data_vol, 1, MPI_LONG, MPI_SUM, MPI_COMM_WORLD);
#else
glob_raw_data_vol = raw_data_vol;
#endif
/*
* Get File Sizes
*
* Note: On ASCI Red, a specialized "stat", named "estat", was added to
* accommodate file sizes up to 16GB. 3/27/2002
*/
if (stat(tmp_name, &file_status)) {
if (rank == 0) {
fprintf(stderr, "Exodus Write: cannot get %s file size.\n", tmp_name);
}
free(exoid);
return (1);
}
{
file_size = file_status.st_size * files_per_domain;
}
#ifdef PARALLEL_AWARE_EXODUS
MPI_Allreduce(&file_size, &glob_file_size, 1, MPI_LONG, MPI_SUM, MPI_COMM_WORLD);
#else
glob_file_size = file_size;
#endif
if (rank == 0) {
fprintf(stderr, " \n");
fprintf(stderr, " Exodus Write Results \n");
fprintf(stderr, " \n");
fprintf(stderr, " Sizes (bytes) \n");
fprintf(stderr, " File %14ld \n",
(long)glob_file_size);
fprintf(stderr, " Raw Data %14ld \n",
(long)glob_raw_data_vol);
fprintf(stderr, " Difference %14ld (%5.2f%%) \n",
(long)(glob_file_size - glob_raw_data_vol),
(1.0 * glob_file_size - 1.0 * glob_raw_data_vol) / (0.01 * glob_file_size));
fprintf(stderr, " \n");
fprintf(stderr, " Times \t Minimum\t Maximum\t Average\n");
fprintf(stderr, " Raw Data Write (sec) \t%8.4g\t%8.4g\t%8.4g \n",
min_raw_write_time, max_raw_write_time, cum_raw_write_time / num_iterations);
fprintf(stderr, " All Other Write (sec) \t \t \t%8.4g \n",
(cum_total_time - cum_raw_write_time) / num_iterations);
fprintf(stderr, " Open/Close Time (sec) \t \t \t%8.4g \n",
cum_open_close_time / num_iterations);
fprintf(stderr, " Total Write (sec) \t \t \t%8.4g \n",
cum_total_time / num_iterations);
fprintf(stderr, " \n");
fprintf(stderr, " Output Bandwidths \t Minimum\t Maximum\t Average\n");
fprintf(stderr, " Raw Data Write (MiB/sec) \t%8.4g\t%8.4g\t%8.4g \n",
(double)glob_raw_data_vol / max_raw_write_time / MBYTES,
(double)glob_raw_data_vol / min_raw_write_time / MBYTES,
(double)glob_raw_data_vol / cum_raw_write_time / MBYTES * num_iterations);
fprintf(stderr, " Raw + Meta Data Write (MiB/sec) \t \t%8.4g\n",
(double)glob_file_size / cum_total_time / MBYTES * num_iterations);
}
free(exoid);
if (num_global_fields > 0) {
free(globals);
}
return (0);
}
/*****************************************************************************/
void get_file_name(const char *base, const char *ext, int rank, int nprocs, const char *other,
char *output)
{
int i1, iTemp1;
int iMaxDigit = 0, iMyDigit = 0;
char cTemp[128];
output[0] = '\0';
ex_copy_string(output, base, MAX_STRING_LEN);
strcat(output, ".");
strcat(output, ext);
if (other != NULL) {
strcat(output, ".");
strcat(output, other);
}
if (nprocs > 1) {
/*
* Find out the number of digits needed to specify the processor ID.
* This allows numbers like 01-99, i.e., prepending zeros to the
* name to preserve proper alphabetic sorting of the files.
*/
iTemp1 = nprocs;
do {
iTemp1 /= 10;
iMaxDigit++;
} while (iTemp1 >= 1);
iTemp1 = rank;
do {
iTemp1 /= 10;
iMyDigit++;
} while (iTemp1 >= 1);
strcat(output, ".");
sprintf(cTemp, "%d", nprocs);
strcat(output, cTemp);
strcat(output, ".");
/*
* Append the proper number of zeros to the filename.
*/
for (i1 = 0; i1 < iMaxDigit - iMyDigit; i1++) {
strcat(output, "0");
}
sprintf(cTemp, "%d", rank);
strcat(output, cTemp);
}
}
ex_get_block
int ex_get_block(int exoid, ex_entity_type blk_type, ex_entity_id blk_id, char *elem_type, void_int *num_entries_this_blk, void_int *num_nodes_per_entry, void_int *num_edges_per_entry, void_int *num_faces_per_entry, void_int *num_attr_per_entry)
Definition: ex_get_block.c:63
ex_put_block
int ex_put_block(int exoid, ex_entity_type blk_type, ex_entity_id blk_id, const char *entry_descrip, int64_t num_entries_this_blk, int64_t num_nodes_per_entry, int64_t num_edges_per_entry, int64_t num_faces_per_entry, int64_t num_attr_per_entry)
Definition: ex_put_block.c:73
ex_inquire_int
int64_t ex_inquire_int(int exoid, ex_inquiry req_info)
Definition: ex_inquire.c:956
ex_opts
int ex_opts(int options)
Definition: ex_opts.c:83
EX_FALSE
#define EX_FALSE
Definition: exodusII.h:102
ex_put_all_var_param
int ex_put_all_var_param(int exoid, int num_g, int num_n, int num_e, int *elem_var_tab, int num_m, int *nset_var_tab, int num_s, int *sset_var_tab)
Definition: ex_put_all_var_param.c:71
ex_put_time
int ex_put_time(int exoid, int time_step, const void *time_value)
Definition: ex_put_time.c:78
ex_open
#define ex_open(path, mode, comp_ws, io_ws, version)
Definition: exodusII.h:474
ex_get_conn
int ex_get_conn(int exoid, ex_entity_type blk_type, ex_entity_id blk_id, void_int *nodeconn, void_int *edgeconn, void_int *faceconn)
Definition: ex_get_conn.c:56
ex_put_concat_elem_block
int ex_put_concat_elem_block(int exoid, const void_int *elem_blk_id, char *elem_type[], const void_int *num_elem_this_blk, const void_int *num_nodes_per_elem, const void_int *num_attr_this_blk, int define_maps)
Definition: ex_put_concat_elem_block.c:62
EX_NODE_MAP
Definition: exodusII.h:267
ex_create
#define ex_create(path, mode, comp_ws, io_ws)
Definition: exodusII.h:444
ex_put_id_map
int ex_put_id_map(int exoid, ex_entity_type map_type, const void_int *map)
Definition: ex_put_id_map.c:63
EX_TRUE
#define EX_TRUE
Definition: exodusII.h:98
ex_close
int ex_close(int exoid)
Definition: ex_close.c:73
ex_get_variable_param
int ex_get_variable_param(int exoid, ex_entity_type obj_type, int *num_vars)
Definition: ex_get_variable_param.c:99
EX_GLOBAL
Definition: exodusII.h:271
EX_WRITE
#define EX_WRITE
Definition: exodusII.h:110
ex_get_var
int ex_get_var(int exoid, int time_step, ex_entity_type var_type, int var_index, ex_entity_id obj_id, int64_t num_entry_this_obj, void *var_vals)
Definition: ex_get_var.c:95
EX_ABORT
Definition: exodusII.h:284
EX_ELEM_MAP
Definition: exodusII.h:266
ex_put_variable_names
int ex_put_variable_names(int exoid, ex_entity_type obj_type, int num_vars, char *var_names[])
Definition: ex_put_variable_names.c:151
EX_CLOBBER
#define EX_CLOBBER
Definition: exodusII.h:114
EX_NODAL
Definition: exodusII.h:254
ex_get_coord
int ex_get_coord(int exoid, void *x_coor, void *y_coor, void *z_coor)
Definition: ex_get_coord.c:98
ex_put_conn
int ex_put_conn(int exoid, ex_entity_type blk_type, ex_entity_id blk_id, const void_int *node_conn, const void_int *elem_edge_conn, const void_int *elem_face_conn)
Definition: ex_put_conn.c:71
EX_READ
#define EX_READ
Definition: exodusII.h:111
exodusII.h
EX_INQ_TIME
Definition: exodusII.h:172
ex_put_init
int ex_put_init(int exoid, const char *title, int64_t num_dim, int64_t num_nodes, int64_t num_elem, int64_t num_elem_blk, int64_t num_node_sets, int64_t num_side_sets)
Definition: ex_put_init.c:80
ex_put_coord
int ex_put_coord(int exoid, const void *x_coor, const void *y_coor, const void *z_coor)
Definition: ex_put_coord.c:113
EX_ELEM_BLOCK
Definition: exodusII.h:261
ex_get_id_map
int ex_get_id_map(int exoid, ex_entity_type map_type, void_int *map)
Definition: ex_get_id_map.c:55
ex_get_init
int ex_get_init(int exoid, char *title, void_int *num_dim, void_int *num_nodes, void_int *num_elem, void_int *num_elem_blk, void_int *num_node_sets, void_int *num_side_sets)
Definition: ex_get_init.c:101
EX_VERBOSE
Definition: exodusII.h:282
ex_put_var
int ex_put_var(int exoid, int time_step, ex_entity_type var_type, int var_index, ex_entity_id obj_id, int64_t num_entries_this_obj, const void *var_vals)
Definition: ex_put_var.c:238
ex_copy_string
char * ex_copy_string(char *dest, char const *source, size_t elements)
Definition: ex_utils.c:2170