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hdf5/perform/benchpar.c
James Laird 8619af74a4 [svn-r11601] Purpose: 
Added additional targets to build-all

Description:
Surveyed files to find out which ones are not built.
Added test/space_overflow and perform/benchpar to programs built with
--enable-build-all.
Discovered that tools/misc/pdb2hdf5 and tools/misc/h5import were
obsolete and deleted them.

Platforms tested:
mir, modi4, sol

Misc. update:
Update of release file and removal of --enable-pdb2hdf5 to follow.
2005-10-24 13:58:15 -05:00

507 lines
19 KiB
C
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/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
#include <unistd.h>
#include <stdlib.h>
#include <assert.h>
#include <math.h>
#include <float.h>
#include <string.h>
#include "hdf5.h"
/* Local macros */
/*
* HDF Boolean type.
*/
#ifndef FALSE
# define FALSE 0
#endif
#ifndef TRUE
# define TRUE 1
#endif
/* defines for type of VFL driver to use */
#define FACC_DEFAULT 0
#define FACC_MPIO 1
#define FACC_MPIPOSIX 2
/* Defines for computing performance information */
#define ONE_KB 1024
#define ONE_MB (ONE_KB * ONE_KB)
#define ONE_GB (ONE_MB * ONE_KB)
/* report 0.0 in case t is zero too */
#define MB_PER_SEC(bytes,t) ((fabs(t)<0.0000000001) ? 0.0 : ((((double)bytes) / ONE_MB) / (t)))
/* Control default behavior (with no command line arguments) */
#define DEFAULT_RANK 3
#define DEFAULT_DIM 1024
#define DEFAULT_PREFIX "/tmp"
#define DEFAULT_USERNAME "koziol"
#define DEFAULT_FILENAME "benchpar.h5"
#define DEFAULT_SLICE 0
#define DEFAULT_C_TYPE int
#define DEFAULT_HDF5_DATATYPE H5T_NATIVE_INT /* Keep this in sync with the DEFAULT_C_TYPE */
#define DEFAULT_DATASET_NAME "Dataset"
#define DEFAULT_VFL_DRIVER FACC_MPIO
#define DEFAULT_PAR_MODE H5FD_MPIO_COLLECTIVE
#define DEFAULT_CHUNK_STORAGE 0
#define DEFAULT_ITER 3
/* MPI info */
int mpi_rank, mpi_size;
int mpi_namelen;
char mpi_name[MPI_MAX_PROCESSOR_NAME];
/* Usage information */
static void usage(void)
{
printf("usage: benchpar [-d <# of dims>] [-s <dim_size>] [-f <file name>] [-h]\n");
printf(" [-S <slice dim>] [-p] [-I] [-c] [-i <# of iterations>\n");
printf(" -c - Use chunked storage for dataset with 1-1 exact\n");
printf(" mapping of chunks to hyperslabs\n");
printf(" Default: off (i.e. contiguous storage)\n");
printf(" -d <# of dims> - Number of dimensions of the dataset\n");
printf(" Default: 3\n");
printf(" -f <file name> - Set the name of the test file\n");
printf(" Default: /tmp/<login>/benchpar.h5\n");
printf(" -h - Prints usage information\n");
printf(" -i <# of iters> - Set the number of test iterations to perform\n");
printf(" Default: 3\n");
printf(" -I - Use independent parallel I/O\n");
printf(" Default: use collective parallel I/O\n");
printf(" -p - Use MPI-posix VFL driver\n");
printf(" Default: use MPI-I/O VFL driver\n");
printf(" -s <dim_size> - Set the size of each of the dataset's dimensions\n");
printf(" Default: 1024\n");
printf(" -S <slice dim> - Set the dimension to slice the dataset along\n");
printf(" Default: 0\n");
} /* end usage() */
/* Create & initialize file creation property list with appropriate properties */
static hid_t create_fcpl(void)
{
hid_t fcpl; /* File creation property list */
fcpl=H5Pcreate(H5P_FILE_CREATE);
assert(fcpl>0);
return(fcpl);
} /* end create_fcpl() */
/* Create & initialize file access property list with appropriate properties */
static hid_t create_fapl(MPI_Comm comm, MPI_Info info, int acc_type )
{
hid_t fapl; /* File access property list */
hbool_t use_gpfs = FALSE; /* Use GPFS hints */
herr_t ret; /* Generic return value */
fapl = H5Pcreate (H5P_FILE_ACCESS);
assert(fapl>0);
/* set parallel access with communicator, using MPI-I/O driver */
if (acc_type == FACC_MPIO) {
ret = H5Pset_fapl_mpio(fapl, comm, info);
assert(ret>=0);
} /* end if */
/* set parallel access with communicator, using MPI-posix driver */
if (acc_type == FACC_MPIPOSIX) {
ret = H5Pset_fapl_mpiposix(fapl, comm, use_gpfs);
assert(ret>=0);
} /* end if */
return (fapl);
} /* end create_fapl() */
/* Create & initialize dataset creation property list with appropriate properties */
static hid_t create_dcpl(unsigned use_chunks, int rank, hsize_t *dims)
{
hid_t dcpl; /* Dataset creation property list */
herr_t ret; /* Generic return value */
dcpl=H5Pcreate(H5P_DATASET_CREATE);
assert(dcpl>0);
/* Check if the dataset should be chunked */
if(use_chunks) {
ret = H5Pset_chunk(dcpl, rank, dims);
assert(ret>=0);
} /* end if */
return(dcpl);
} /* end create_dcpl() */
/* Create & initialize dataset transfer property list with appropriate properties */
static hid_t create_dxpl(H5FD_mpio_xfer_t par_mode)
{
hid_t dxpl; /* Dataset creation property list */
herr_t ret; /* Generic return value */
dxpl=H5Pcreate(H5P_DATASET_XFER);
assert(dxpl>0);
/* Set collective I/O on this transfer */
ret=H5Pset_dxpl_mpio(dxpl, par_mode);
assert(ret>=0);
return(dxpl);
} /* end create_dcpl() */
int main(int argc, char *argv[])
{
int curr_arg; /* Current command line argument being processed */
int rank; /* Number of dimensions of the dataset */
hsize_t dim_size; /* Dimension size of each dimension */
hsize_t *dims; /* Pointer to array of dimensions */
hssize_t *start; /* Pointer to array of starting locations for hyperslab selection */
hsize_t *count; /* Pointer to array of counts for hyperslab selection */
unsigned slice_dim; /* Dimension to slice up */
char *file_name=NULL; /* Name of file to put data into */
hid_t fcpl; /* HDF5 File creation property list ID */
hid_t fapl; /* HDF5 File access property list ID */
hid_t dcpl; /* HDF5 Dataset creation property list ID */
hid_t dxpl; /* HDF5 Dataset transfer property list ID */
hid_t fid; /* HDF5 file ID */
hid_t dsid; /* HDF5 dataset ID */
hid_t file_sid; /* HDF5 dataspace ID for dataset on disk */
hid_t mem_sid; /* HDF5 dataspace ID for dataset in memory */
DEFAULT_C_TYPE *buf; /* Buffer to write out */
hsize_t buf_size; /* Size of buffer to write */
int i; /* Local index variable */
herr_t ret; /* Generic return value */
double start_write_time, end_write_time, elap_write_time; /* Start, end and elapsed time to write raw data */
double tmp_max_write_time; /* Temporary holders for maximum time for all nodes to perform raw data I/O */
double max_write_time=-DBL_MAX, min_write_time=DBL_MAX; /* Minimum & maximum time for all nodes to perform raw data I/O */
double start_file_time, end_file_time, elap_file_time; /* Start, end and elapsed time from file open to file close */
double tmp_max_file_time; /* Temporary holders for maximum time for all nodes from file open to file close */
double max_file_time=-DBL_MAX, min_file_time=DBL_MAX; /* Minimum & maximum time for all nodes from file open to file close */
int vfl_type; /* Type of VFL driver to use */
H5FD_mpio_xfer_t par_mode; /* Type of parallel I/O to perform */
unsigned use_chunks; /* Whether to use chunks for dataset or not */
unsigned num_iter; /* Number of iterations to perform */
unsigned u; /* Local index variable */
/* Un-buffer the stdout and stderr */
setbuf(stderr, NULL);
setbuf(stdout, NULL);
/* MPI initialization */
MPI_Init(&argc,&argv);
MPI_Comm_size(MPI_COMM_WORLD,&mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
MPI_Get_processor_name(mpi_name,&mpi_namelen);
/* Set some defaults */
rank=DEFAULT_RANK;
dim_size=DEFAULT_DIM;
slice_dim=DEFAULT_SLICE;
vfl_type=DEFAULT_VFL_DRIVER;
par_mode=DEFAULT_PAR_MODE;
use_chunks=DEFAULT_CHUNK_STORAGE;
num_iter=DEFAULT_ITER;
/* Parse command line arguments */
if(argc>1) {
curr_arg=1;
while(curr_arg<argc) {
/* Trap any unknown command line parameters */
if(argv[curr_arg][0]!='-') {
printf("unknown command line parameter: %s\n",argv[curr_arg]);
goto done;
} /* end if */
/* Skip over command line flag */
curr_arg++;
switch(argv[curr_arg-1][1]) {
case 'c': /* Use chunked storage for dataset */
use_chunks=1;
break;
case 'd': /* Change number of dimensions */
/* Get new number of dimensions */
rank=atoi(argv[curr_arg]);
curr_arg++; /* Skip over number of dimensions */
/* Sanity check */
if(rank<=0) {
printf("rank=%d, invalid number of dimensions: %d\n",mpi_rank,rank);
goto done;
} /* end if */
break;
case 'f': /* Change test file name */
/* Get new file name */
file_name=strdup(argv[curr_arg]);
curr_arg++; /* Skip over file name from command line */
break;
case 'h': /* Print usage information */
usage();
goto done;
break;
case 'i': /* Change number of iterations */
/* Get new number of dimensions */
num_iter=atoi(argv[curr_arg]);
curr_arg++; /* Skip over number of iterations */
/* Sanity check */
if(num_iter<1) {
printf("rank=%d, invalid number of iterations: %u\n",mpi_rank,num_iter);
goto done;
} /* end if */
break;
case 'I': /* Use independent I/O for parallel I/O */
par_mode=H5FD_MPIO_INDEPENDENT;
break;
case 'p': /* Use MPI-posix VFL driver */
vfl_type=FACC_MPIPOSIX;
break;
case 's': /* Change dimension size */
/* Get new dimension size */
dim_size=atoi(argv[curr_arg]);
curr_arg++; /* Skip over dimension size from command line */
/* Sanity check */
if(dim_size<=0) {
printf("rank=%d, invalid dimension size: %ld\n",mpi_rank,(long)dim_size);
goto done;
} /* end if */
break;
case 'S': /* Change dimension to slice */
/* Get new dimension to slice */
slice_dim=atoi(argv[curr_arg]);
curr_arg++; /* Skip over slice dimension from command line */
break;
default:
printf("rank=%d, unknown command line parameter: %s\n",mpi_rank,argv[curr_arg-1]);
goto done;
} /* end switch */
} /* end while */
} /* end if */
/* Sanity check */
if(slice_dim>=rank) {
printf("rank=%d, error, slice dim larger than rank: slice_dim=%d, rank=%d\n",mpi_rank,slice_dim,rank);
goto done;
} /* end if */
/* Set rest of defaults */
if(file_name==NULL) {
char *login; /* Pointer to login name */
/* Get the login name for this user */
login=getlogin();
if(login==NULL)
login=DEFAULT_USERNAME;
/* Allocate enough room for the prefix, the login name, two '/'s, the filename and the string terminator */
file_name=malloc(strlen(DEFAULT_PREFIX)+1+strlen(login)+1+strlen(DEFAULT_FILENAME)+1);
strcpy(file_name,DEFAULT_PREFIX);
strcat(file_name,"/");
strcat(file_name,login);
strcat(file_name,"/");
strcat(file_name,DEFAULT_FILENAME);
} /* end if */
/* Allocate memory for this process's portion of dataset */
buf_size=sizeof(DEFAULT_C_TYPE);
for(i=0; i<rank; i++)
buf_size *= dim_size;
buf_size /= mpi_size;
/* Sanity check for overflow */
assert((hsize_t)((size_t)buf_size)==buf_size);
buf=malloc((size_t)buf_size);
assert(buf);
/* Initialize dataset portion to something unique for each process */
memset(buf,mpi_rank,(size_t)buf_size);
for(u=0; u<num_iter; u++) {
/* Create file creation property list */
fcpl=create_fcpl();
assert(fcpl>0);
/* Create file access property list */
fapl=create_fapl(MPI_COMM_WORLD,MPI_INFO_NULL,vfl_type);
assert(fapl>0);
/* Get file start time */
start_file_time = MPI_Wtime();
/* Create file */
fid=H5Fcreate(file_name,H5F_ACC_TRUNC,fcpl,fapl);
assert(fid>0);
/* Close file creation property list */
ret=H5Pclose(fcpl);
assert(ret>=0);
/* Close file access property list */
ret=H5Pclose(fapl);
assert(ret>=0);
/* Create dataspace for dataset on disk */
dims=malloc(sizeof(hsize_t)*rank);
assert(dims);
for(i=0; i<rank; i++)
dims[i]=dim_size;
file_sid=H5Screate_simple(rank,dims,NULL);
assert(file_sid>0);
/* Create dataspace for buffer in memory */
for(i=0; i<rank; i++)
dims[i]=dim_size;
dims[slice_dim] /= mpi_size;
mem_sid=H5Screate_simple(rank,dims,NULL);
assert(mem_sid>0);
/* Create dataset creation property list */
dcpl=create_dcpl(use_chunks,rank,dims);
assert(dcpl>0);
/* Create dataset */
dsid=H5Dcreate(fid,DEFAULT_DATASET_NAME,DEFAULT_HDF5_DATATYPE,file_sid,dcpl);
assert(dsid>0);
/* Close dataset creation property list */
ret=H5Pclose(dcpl);
assert(ret>=0);
/* Select hyperslab for file dataspace */
start=malloc(sizeof(hssize_t)*rank);
assert(start);
count=malloc(sizeof(hsize_t)*rank);
assert(count);
for(i=0; i<rank; i++) {
start[i]=0;
count[i]=dim_size;
} /* end for */
start[slice_dim]=mpi_rank*(dim_size/mpi_size);
count[slice_dim]=dim_size/mpi_size;
ret = H5Sselect_hyperslab(file_sid,H5S_SELECT_SET,start,NULL,count,NULL);
assert(ret>=0);
/* Create dataset transfer property list */
dxpl=create_dxpl(par_mode);
assert(dxpl>0);
/* Get raw data start time */
start_write_time = MPI_Wtime();
/* Write hyperslab to dataset */
ret = H5Dwrite(dsid, DEFAULT_HDF5_DATATYPE, mem_sid,
file_sid, dxpl, buf);
assert(ret>=0);
/* Get stop time for raw data timer */
end_write_time = MPI_Wtime();
/* Close dataset transfer property list */
ret=H5Pclose(dxpl);
assert(ret>=0);
/* Close memory dataspace */
ret=H5Sclose(mem_sid);
assert(ret>=0);
/* Close file dataspace */
ret=H5Sclose(file_sid);
assert(ret>=0);
/* Close dataset */
ret=H5Dclose(dsid);
assert(ret>=0);
/* Close file */
ret=H5Fclose(fid);
assert(ret>=0);
/* Get stop time for file timer */
end_file_time = MPI_Wtime();
/* Compute timing results */
elap_write_time=end_write_time-start_write_time;
elap_file_time=end_file_time-start_file_time;
/* Collect the minimum and maximum times by MPI reduces */
MPI_Allreduce(&elap_write_time, &tmp_max_write_time, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD);
MPI_Allreduce(&elap_file_time, &tmp_max_file_time, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD);
/* Track the fastest & slowest total runs */
if(tmp_max_write_time>max_write_time)
max_write_time=tmp_max_write_time;
if(tmp_max_write_time<min_write_time)
min_write_time=tmp_max_write_time;
if(tmp_max_file_time>max_file_time)
max_file_time=tmp_max_file_time;
if(tmp_max_file_time<min_file_time)
min_file_time=tmp_max_file_time;
} /* end for */
/* Only print information from one node */
if(mpi_rank==0) {
/* Print information about test */
printf("File driver used: %s\n",vfl_type==FACC_MPIO ? "MPI-I/O" : "MPI-posix");
printf("Type of parallel access: %s\n",par_mode==H5FD_MPIO_COLLECTIVE ? "Collective" : "Independent");
printf("Type of dataset storage: %s\n",use_chunks ? "Chunked" : "Contiguous");
printf("Number of processes: %d\n",mpi_size);
printf("Element size: %u\n",(unsigned)sizeof(DEFAULT_C_TYPE));
printf("# of dimensions: %d\n",rank);
printf("Dimension size: %ld\n",(long)dim_size);
printf("Dimension sliced: %u\n",slice_dim);
printf("Number of elements: %lu\n",(unsigned long)((buf_size/sizeof(DEFAULT_C_TYPE))*mpi_size));
printf("Total dataset size (bytes): %lu\n",(unsigned long)(buf_size*mpi_size));
printf("Dataset size per process (bytes): %lu\n",(unsigned long)buf_size);
/* Print timing results */
printf("# of iterations: %u\n",num_iter);
printf("Maximum raw data write throughput=%6.2f MB/s (%7.3f s)\n",MB_PER_SEC((buf_size*mpi_size),min_write_time),min_write_time);
printf("Minimum raw data write throughput=%6.2f MB/s (%7.3f s)\n",MB_PER_SEC((buf_size*mpi_size),max_write_time),max_write_time);
printf("Maximum file throughput=%6.2f MB/s (%7.3f s)\n",MB_PER_SEC((buf_size*mpi_size),min_file_time),min_file_time);
printf("Minimum file throughput=%6.2f MB/s (%7.3f s)\n",MB_PER_SEC((buf_size*mpi_size),max_file_time),max_file_time);
} /* end if */
done:
/* Free buffers allocated */
if(file_name)
free(file_name);
if(buf)
free(buf);
if(dims)
free(dims);
if(start)
free(start);
if(count)
free(count);
/* MPI termination */
MPI_Finalize();
return(0);
} /* end main() */
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