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https://github.com/HDFGroup/hdf5.git
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c857aa12c1
Description: Program would crash, complaining MPI calls were invoked after MPI_Finalize() has occurred. Previously, H5close() before MPI_Finalize() would remove the crash. Solution: It turned out that two H5 property objects (mpio_pl and acc_tpl) were not closed before MPI_Finalize(). In the at_exit code, HDF5 library attempted to close them by releasing the MPI Communicators in them too. That was the error. Adding code to close them properly before MPI_Finalize() took care things. Tested: Only in kagiso parallel. Did not run h5committest since kagiso would have been the one running parallel test. This part of code would not be compiled at all in non-phdf5 mode.
472 lines
15 KiB
C
472 lines
15 KiB
C
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
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* Copyright by The HDF Group. *
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* Copyright by the Board of Trustees of the University of Illinois. *
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* All rights reserved. *
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* *
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* This file is part of HDF5. The full HDF5 copyright notice, including *
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* terms governing use, modification, and redistribution, is contained in *
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* the files COPYING and Copyright.html. COPYING can be found at the root *
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* of the source code distribution tree; Copyright.html can be found at the *
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* root level of an installed copy of the electronic HDF5 document set and *
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* is linked from the top-level documents page. It can also be found at *
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* http://hdfgroup.org/HDF5/doc/Copyright.html. If you do not have *
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* access to either file, you may request a copy from help@hdfgroup.org. *
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* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
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/*
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* Author: Albert Cheng of NCSA, May 1, 2001.
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* This is derived from code given to me by Robert Ross.
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*
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* NOTE: This code assumes that all command line arguments make it out to all
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* the processes that make up the parallel job, which isn't always the case.
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* So if it doesn't work on some platform, that might be why.
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*/
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#include "hdf5.h"
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#include "H5private.h"
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#ifdef H5_HAVE_PARALLEL
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#include <stdio.h>
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#include <stdlib.h>
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#include <fcntl.h>
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#include <unistd.h>
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#include <errno.h>
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#include <string.h>
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#include <sys/time.h>
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#include <mpi.h>
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#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */
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# include <mpio.h>
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#endif
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/* Macro definitions */
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/* Verify:
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* if val is false (0), print mesg and if fatal is true (non-zero), die.
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*/
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#define H5FATAL 1
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#define VRFY(val, mesg, fatal) do { \
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if (!val) { \
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printf("Proc %d: ", mynod); \
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printf("*** Assertion failed (%s) at line %4d in %s\n", \
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mesg, (int)__LINE__, __FILE__); \
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if (fatal){ \
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fflush(stdout); \
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goto die_jar_jar_die; \
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} \
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} \
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} while(0)
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#define RANK 1
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hsize_t dims[RANK]; /* dataset dim sizes */
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hsize_t block[RANK], stride[RANK], count[RANK];
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hssize_t start[RANK];
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hid_t fid; /* HDF5 file ID */
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hid_t acc_tpl; /* File access templates */
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hid_t sid; /* Dataspace ID */
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hid_t file_dataspace; /* File dataspace ID */
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hid_t mem_dataspace; /* memory dataspace ID */
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hid_t dataset; /* Dataset ID */
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hsize_t opt_alignment = 1;
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hsize_t opt_threshold = 1;
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int opt_split_vfd = 0;
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char *meta_ext, *raw_ext; /* holds the meta and raw file extension if */
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/* opt_split_vfd is set */
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/* DEFAULT VALUES FOR OPTIONS */
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int64_t opt_block = 1048576*16;
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int opt_iter = 1;
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int opt_stripe = -1;
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int opt_correct = 0;
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int amode = O_RDWR | O_CREAT;
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char opt_file[256] = "perftest.out";
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char opt_pvfstab[256] = "notset";
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int opt_pvfstab_set = 0;
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/* function prototypes */
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int parse_args(int argc, char **argv);
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double Wtime(void);
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extern int errno;
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extern int debug_on;
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/* globals needed for getopt */
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extern char *optarg;
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extern int optind, opterr;
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int main(int argc, char **argv)
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{
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char *buf, *tmp, *buf2, *tmp2, *check;
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int i, j, mynod=0, nprocs=1, err, my_correct = 1, correct, myerrno;
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double stim, etim;
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double write_tim = 0;
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double read_tim = 0;
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double read_bw, write_bw;
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double max_read_tim, max_write_tim;
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double min_read_tim, min_write_tim;
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double ave_read_tim, ave_write_tim;
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int64_t iter_jump = 0;
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int64_t seek_position = 0;
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MPI_File fh;
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MPI_Status status;
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int nchars;
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herr_t ret; /* Generic return value */
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/* startup MPI and determine the rank of this process */
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MPI_Init(&argc,&argv);
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MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
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MPI_Comm_rank(MPI_COMM_WORLD, &mynod);
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/* parse the command line arguments */
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parse_args(argc, argv);
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if (mynod == 0) printf("# Using hdf5-io calls.\n");
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/* kindof a weird hack- if the location of the pvfstab file was
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* specified on the command line, then spit out this location into
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* the appropriate environment variable: */
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#if H5_HAVE_SETENV
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/* no setenv or unsetenv */
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if (opt_pvfstab_set) {
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if((setenv("PVFSTAB_FILE", opt_pvfstab, 1)) < 0){
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perror("setenv");
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goto die_jar_jar_die;
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}
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}
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#endif
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/* this is how much of the file data is covered on each iteration of
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* the test. used to help determine the seek offset on each
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* iteration */
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iter_jump = nprocs * opt_block;
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/* setup a buffer of data to write */
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if (!(tmp = (char *) malloc(opt_block + 256))) {
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perror("malloc");
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goto die_jar_jar_die;
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}
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buf = tmp + 128 - (((long)tmp) % 128); /* align buffer */
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if (opt_correct) {
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/* do the same buffer setup for verifiable data */
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if (!(tmp2 = (char *) malloc(opt_block + 256))) {
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perror("malloc2");
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goto die_jar_jar_die;
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}
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buf2 = tmp + 128 - (((long)tmp) % 128);
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}
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/* setup file access template with parallel IO access. */
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if (opt_split_vfd){
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hid_t mpio_pl;
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mpio_pl = H5Pcreate (H5P_FILE_ACCESS);
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VRFY((acc_tpl >= 0), "", H5FATAL);
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ret = H5Pset_fapl_mpio(mpio_pl, MPI_COMM_WORLD, MPI_INFO_NULL);
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VRFY((ret >= 0), "", H5FATAL);
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/* set optional allocation alignment */
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if (opt_alignment*opt_threshold != 1){
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ret = H5Pset_alignment(acc_tpl, opt_threshold, opt_alignment );
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VRFY((ret >= 0), "H5Pset_alignment succeeded", !H5FATAL);
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}
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/* setup file access template */
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acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
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VRFY((acc_tpl >= 0), "", H5FATAL);
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ret = H5Pset_fapl_split(acc_tpl, meta_ext, mpio_pl, raw_ext, mpio_pl);
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VRFY((ret >= 0), "H5Pset_fapl_split succeeded", H5FATAL);
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ret = H5Pclose(mpio_pl);
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VRFY((ret >= 0), "H5Pclose mpio_pl succeeded", H5FATAL);
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}else{
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/* setup file access template */
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acc_tpl = H5Pcreate (H5P_FILE_ACCESS);
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VRFY((acc_tpl >= 0), "", H5FATAL);
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ret = H5Pset_fapl_mpio(acc_tpl, MPI_COMM_WORLD, MPI_INFO_NULL);
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VRFY((ret >= 0), "", H5FATAL);
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/* set optional allocation alignment */
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if (opt_alignment*opt_threshold != 1){
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ret = H5Pset_alignment(acc_tpl, opt_threshold, opt_alignment );
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VRFY((ret >= 0), "H5Pset_alignment succeeded", !H5FATAL);
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}
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}
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/* create the parallel file */
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fid = H5Fcreate(opt_file, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
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VRFY((fid >= 0), "H5Fcreate succeeded", H5FATAL);
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/* define a contiquous dataset of opt_iter*nprocs*opt_block chars */
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dims[0] = opt_iter * nprocs * opt_block;
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sid = H5Screate_simple(RANK, dims, NULL);
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VRFY((sid >= 0), "H5Screate_simple succeeded", H5FATAL);
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dataset = H5Dcreate2(fid, "Dataset1", H5T_NATIVE_CHAR, sid,
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H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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VRFY((dataset >= 0), "H5Dcreate2 succeeded", H5FATAL);
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/* create the memory dataspace and the file dataspace */
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dims[0] = opt_block;
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mem_dataspace = H5Screate_simple(RANK, dims, NULL);
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VRFY((mem_dataspace >= 0), "", H5FATAL);
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file_dataspace = H5Dget_space(dataset);
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VRFY((file_dataspace >= 0), "H5Dget_space succeeded", H5FATAL);
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/* now each process writes a block of opt_block chars in round robbin
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* fashion until the whole dataset is covered.
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*/
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for(j=0; j < opt_iter; j++) {
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/* setup a file dataspace selection */
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start[0] = (j*iter_jump)+(mynod*opt_block);
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stride[0] = block[0] = opt_block;
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count[0]= 1;
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
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VRFY((ret >= 0), "H5Sset_hyperslab succeeded", H5FATAL);
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if (opt_correct) /* fill in buffer for iteration */ {
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for (i=mynod+j, check=buf; i<opt_block; i++,check++) *check=(char)i;
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}
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/* discover the starting time of the operation */
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MPI_Barrier(MPI_COMM_WORLD);
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stim = MPI_Wtime();
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/* write data */
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ret = H5Dwrite(dataset, H5T_NATIVE_CHAR, mem_dataspace, file_dataspace,
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H5P_DEFAULT, buf);
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VRFY((ret >= 0), "H5Dwrite dataset1 succeeded", !H5FATAL);
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/* discover the ending time of the operation */
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etim = MPI_Wtime();
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write_tim += (etim - stim);
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/* we are done with this "write" iteration */
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}
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/* close dataset and file */
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ret=H5Dclose(dataset);
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VRFY((ret >= 0), "H5Dclose succeeded", H5FATAL);
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ret=H5Fclose(fid);
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VRFY((ret >= 0), "H5Fclose succeeded", H5FATAL);
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/* wait for everyone to synchronize at this point */
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MPI_Barrier(MPI_COMM_WORLD);
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/* reopen the file for reading */
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fid=H5Fopen(opt_file,H5F_ACC_RDONLY,acc_tpl);
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VRFY((fid >= 0), "", H5FATAL);
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/* open the dataset */
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dataset = H5Dopen2(fid, "Dataset1", H5P_DEFAULT);
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VRFY((dataset >= 0), "H5Dopen succeeded", H5FATAL);
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/* we can re-use the same mem_dataspace and file_dataspace
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* the H5Dwrite used since the dimension size is the same.
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*/
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/* we are going to repeat the read the same pattern the write used */
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for (j=0; j < opt_iter; j++) {
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/* setup a file dataspace selection */
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start[0] = (j*iter_jump)+(mynod*opt_block);
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stride[0] = block[0] = opt_block;
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count[0]= 1;
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ret=H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
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VRFY((ret >= 0), "H5Sset_hyperslab succeeded", H5FATAL);
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/* seek to the appropriate spot give the current iteration and
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* rank within the MPI processes */
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/* discover the start time */
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MPI_Barrier(MPI_COMM_WORLD);
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stim = MPI_Wtime();
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/* read in the file data */
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if (!opt_correct){
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ret = H5Dread(dataset, H5T_NATIVE_CHAR, mem_dataspace, file_dataspace, H5P_DEFAULT, buf);
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}
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else{
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ret = H5Dread(dataset, H5T_NATIVE_CHAR, mem_dataspace, file_dataspace, H5P_DEFAULT, buf2);
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}
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myerrno = errno;
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/* discover the end time */
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etim = MPI_Wtime();
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read_tim += (etim - stim);
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VRFY((ret >= 0), "H5Dwrite dataset1 succeeded", !H5FATAL);
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if (ret < 0) fprintf(stderr, "node %d, read error, loc = %Ld: %s\n",
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mynod, mynod*opt_block, strerror(myerrno));
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/* if the user wanted to check correctness, compare the write
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* buffer to the read buffer */
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if (opt_correct && memcmp(buf, buf2, opt_block)) {
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fprintf(stderr, "node %d, correctness test failed\n", mynod);
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my_correct = 0;
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MPI_Allreduce(&my_correct, &correct, 1, MPI_INT, MPI_MIN,
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MPI_COMM_WORLD);
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}
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/* we are done with this read iteration */
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}
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/* close dataset and file */
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ret=H5Dclose(dataset);
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VRFY((ret >= 0), "H5Dclose succeeded", H5FATAL);
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ret=H5Fclose(fid);
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VRFY((ret >= 0), "H5Fclose succeeded", H5FATAL);
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ret=H5Pclose(acc_tpl);
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VRFY((ret >= 0), "H5Pclose succeeded", H5FATAL);
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/* compute the read and write times */
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MPI_Allreduce(&read_tim, &max_read_tim, 1, MPI_DOUBLE, MPI_MAX,
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MPI_COMM_WORLD);
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MPI_Allreduce(&read_tim, &min_read_tim, 1, MPI_DOUBLE, MPI_MIN,
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MPI_COMM_WORLD);
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MPI_Allreduce(&read_tim, &ave_read_tim, 1, MPI_DOUBLE, MPI_SUM,
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MPI_COMM_WORLD);
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/* calculate the average from the sum */
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ave_read_tim = ave_read_tim / nprocs;
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MPI_Allreduce(&write_tim, &max_write_tim, 1, MPI_DOUBLE, MPI_MAX,
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MPI_COMM_WORLD);
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MPI_Allreduce(&write_tim, &min_write_tim, 1, MPI_DOUBLE, MPI_MIN,
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MPI_COMM_WORLD);
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MPI_Allreduce(&write_tim, &ave_write_tim, 1, MPI_DOUBLE, MPI_SUM,
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MPI_COMM_WORLD);
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/* calculate the average from the sum */
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ave_write_tim = ave_write_tim / nprocs;
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/* print out the results on one node */
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if (mynod == 0) {
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read_bw = ((int64_t)(opt_block*nprocs*opt_iter))/(max_read_tim*1000000.0);
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write_bw = ((int64_t)(opt_block*nprocs*opt_iter))/(max_write_tim*1000000.0);
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printf("nr_procs = %d, nr_iter = %d, blk_sz = %ld\n", nprocs,
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opt_iter, (long)opt_block);
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printf("# total_size = %ld\n", (long)(opt_block*nprocs*opt_iter));
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printf("# Write: min_time = %f, max_time = %f, mean_time = %f\n",
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min_write_tim, max_write_tim, ave_write_tim);
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printf("# Read: min_time = %f, max_time = %f, mean_time = %f\n",
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min_read_tim, max_read_tim, ave_read_tim);
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printf("Write bandwidth = %f Mbytes/sec\n", write_bw);
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printf("Read bandwidth = %f Mbytes/sec\n", read_bw);
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if (opt_correct) {
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printf("Correctness test %s.\n", correct ? "passed" : "failed");
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}
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}
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die_jar_jar_die:
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#if H5_HAVE_SETENV
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/* no setenv or unsetenv */
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/* clear the environment variable if it was set earlier */
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if (opt_pvfstab_set){
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unsetenv("PVFSTAB_FILE");
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}
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#endif
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free(tmp);
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if (opt_correct) free(tmp2);
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MPI_Finalize();
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return(0);
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}
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int parse_args(int argc, char **argv)
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{
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int c;
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while ((c = getopt(argc, argv, "s:b:i:f:p:a:2:c")) != EOF) {
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switch (c) {
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case 's': /* stripe */
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opt_stripe = atoi(optarg);
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break;
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case 'b': /* block size */
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opt_block = atoi(optarg);
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break;
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case 'i': /* iterations */
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opt_iter = atoi(optarg);
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break;
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case 'f': /* filename */
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strncpy(opt_file, optarg, 255);
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break;
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case 'p': /* pvfstab file */
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strncpy(opt_pvfstab, optarg, 255);
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opt_pvfstab_set = 1;
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break;
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case 'a': /* aligned allocation.
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* syntax: -a<alignment>/<threshold>
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* e.g., -a4096/512 allocate at 4096 bytes
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* boundary if request size >= 512.
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*/
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{char *p;
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opt_alignment = atoi(optarg);
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if (p=(char*)strchr(optarg, '/'))
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opt_threshold = atoi(p+1);
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}
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HDfprintf(stdout,
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"alignment/threshold=%Hu/%Hu\n",
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opt_alignment, opt_threshold);
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break;
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case '2': /* use 2-files, i.e., split file driver */
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opt_split_vfd=1;
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/* get meta and raw file extension. */
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/* syntax is <raw_ext>,<meta_ext> */
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meta_ext = raw_ext = optarg;
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while (*raw_ext != '\0'){
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if (*raw_ext == ','){
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*raw_ext = '\0';
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raw_ext++;
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break;
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}
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raw_ext++;
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}
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printf("split-file-vfd used: %s,%s\n",
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meta_ext, raw_ext);
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break;
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case 'c': /* correctness */
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opt_correct = 1;
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break;
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case '?': /* unknown */
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default:
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break;
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}
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}
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return(0);
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}
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/* Wtime() - returns current time in sec., in a double */
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double Wtime()
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{
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struct timeval t;
|
|
|
|
gettimeofday(&t, NULL);
|
|
return((double)t.tv_sec + (double)t.tv_usec / 1000000);
|
|
}
|
|
|
|
/*
|
|
* Local variables:
|
|
* c-indent-level: 3
|
|
* c-basic-offset: 3
|
|
* tab-width: 3
|
|
* End:
|
|
*/
|
|
|
|
#else /* H5_HAVE_PARALLEL */
|
|
/* dummy program since H5_HAVE_PARALLE is not configured in */
|
|
int
|
|
main(int UNUSED argc, char UNUSED **argv)
|
|
{
|
|
printf("No parallel performance because parallel is not configured in\n");
|
|
return(0);
|
|
}
|
|
#endif /* H5_HAVE_PARALLEL */
|