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[svn-r4715] Purpose:

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bug fix, new feature
Description:
    Added HDF5 write in do_write.
    Added a complete do_read.
    Still need timing code for the read part.
Platforms tested:
    eirene (pp), modi4(pp).
    Did not test serial since all changes were done in parallel area.
This commit is contained in:
Albert Cheng 2001-12-13 10:29:47 -05:00
parent 3037cad734
commit 4720897bb9
1 changed files with 302 additions and 25 deletions
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327
perform/pio_engine.c
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@ -133,12 +133,21 @@ typedef union _file_descr {
static char *pio_create_filename(iotype iot, const char *base_name,
char *fullname, size_t size);
static herr_t do_write(file_descr *fd, iotype iot, long ndsets,
long nelmts, long buf_size, char *buffer);
long nelmts, long buf_size, void *buffer);
static herr_t do_read(file_descr *fd, iotype iot, long ndsets,
long nelmts, long buf_size, void *buffer /*out*/);
static herr_t do_fopen(iotype iot, char *fname, file_descr *fd /*out*/,
int flags);
static herr_t do_fclose(iotype iot, file_descr *fd);
static void do_cleanupfile(char *fname);
/*
* Function: do_pio
* Purpose: PIO Engine where Parallel IO are executed.
* Return: results
* Programmer: Albert Cheng, Bill Wendling 2001/12/12
* Modifications:
*/
results
do_pio(parameters param)
{
@ -228,7 +237,7 @@ do_pio(parameters param)
GOTOERROR(FAIL);
}
#if 1
#if AKCDEBUG
/* DEBUG*/
fprintf(stderr, "nfiles=%d\n", nfiles);
fprintf(stderr, "ndsets=%ld\n", ndsets);
@ -236,8 +245,9 @@ fprintf(stderr, "nelmts=%ld\n", nelmts);
fprintf(stderr, "niters=%d\n", niters);
fprintf(stderr, "maxprocs=%d\n", maxprocs);
fprintf(stderr, "buffer size=%ld\n", buf_size);
fprintf(stderr, "total data size=%ld\n", ndsets*nelmts*sizeof(int));
nfiles=MIN(3, nfiles);
ndsets=MIN(5, ndsets);
/*ndsets=MIN(5, ndsets);*/
/*nelmts=MIN(1000, nelmts);*/
buf_size=MIN(1024*1024, buf_size);
/* DEBUG END */
@ -282,7 +292,9 @@ buf_size=MIN(1024*1024, buf_size);
sprintf(base_name, "#pio_tmp_%u", nf);
pio_create_filename(iot, base_name, fname, sizeof(fname));
#if AKCDEBUG
fprintf(stderr, "filename=%s\n", fname);
#endif
set_time(res.timers, HDF5_FILE_OPENCLOSE, START);
hrc = do_fopen(iot, fname, &fd, PIO_CREATE | PIO_WRITE);
@ -310,11 +322,8 @@ fprintf(stderr, "filename=%s\n", fname);
hrc = do_fopen(iot, fname, &fd, PIO_READ);
VRFY((hrc == SUCCESS), "do_fopen failed");
/*
hrc = do_read(&fd, iot, ndsets, nelmts, buffer);
hrc = do_read(&fd, iot, ndsets, nelmts, buf_size, buffer);
VRFY((hrc == SUCCESS), "do_read failed");
*/
/* Close file for read */
hrc = do_fclose(iot, &fd);
@ -473,12 +482,12 @@ pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t si
* Function: do_write
* Purpose: Write the required amount of data to the file.
* Return: SUCCESS or FAIL
* Programmer: Bill Wendling, 14. November 2001
* Programmer: Albert Cheng, Bill Wendling, 2001/12/13
* Modifications:
*/
static herr_t
do_write(file_descr *fd, iotype iot, long ndsets,
long nelmts, long buf_size, char *buffer)
long nelmts, long buf_size, void *buffer)
{
int ret_code = SUCCESS;
int rc; /*routine return code */
@ -502,18 +511,24 @@ do_write(file_descr *fd, iotype iot, long ndsets,
hid_t h5mem_space_id = -1; /*memory dataspace ID */
hid_t h5ds_id = -1; /* dataset handle */
#if AKCDEBUG
fprintf(stderr, "In do_write\n");
fprintf(stderr, "ndsets=%ld\n", ndsets);
fprintf(stderr, "nelmts=%ld\n", nelmts);
fprintf(stderr, "buffer size=%ld\n", buf_size);
#endif
/* calculate dataset parameters. data type is always native C int */
dset_size = nelmts * ELMT_SIZE;
nelmts_in_buf = buf_size/ELMT_SIZE;
/* hdf5 dataset setup */
/* hdf5 data space setup */
if (iot == PHDF5){
/* define a contiquous dataset of nelmts native ints */
h5dims[0] = nelmts;
h5dset_space_id = H5Screate_simple(1, h5dims, NULL);
VRFY((h5dset_space_id >= 0), "H5Screate_simple");
/* create the memory dataspace */
/* create the memory dataspace that corresponds to the xfer buffer */
h5dims[0] = nelmts_in_buf;
h5mem_space_id = H5Screate_simple(1, h5dims, NULL);
VRFY((h5mem_space_id >= 0), "H5Screate_simple");
@ -549,18 +564,21 @@ do_write(file_descr *fd, iotype iot, long ndsets,
* and the next process. Count of elements is the difference between
* these two beginnings. This way, it avoids any rounding errors.
*/
elmts_begin = (nelmts * 1.0)/pio_mpi_nprocs_g*pio_mpi_rank_g;
elmts_begin = (nelmts*1.0)/pio_mpi_nprocs_g*pio_mpi_rank_g;
if (pio_mpi_rank_g < (pio_mpi_nprocs_g - 1)){
elmts_count = ((nelmts * 1.0)/pio_mpi_nprocs_g*(pio_mpi_rank_g+1)) - elmts_begin;
elmts_count = ((nelmts*1.0)/pio_mpi_nprocs_g*(pio_mpi_rank_g+1)) -
elmts_begin;
}else{
/* last process. Take whatever are left */
elmts_count = nelmts - elmts_begin;
}
#if AKCDEBUG
fprintf(stderr, "proc %d: elmts_begin=%ld, elmts_count=%ld\n",
pio_mpi_rank_g, elmts_begin, elmts_count);
#endif
nelmts_written = 0 ;
while (nelmts_written < elmts_count){
nelmts_towrite = elmts_count - nelmts_written;
@ -570,8 +588,8 @@ fprintf(stderr, "proc %d: elmts_begin=%ld, elmts_count=%ld\n",
/* last write of a partial buffer */
nelmts_towrite = elmts_count - nelmts_written;
}
file_offset = dset_offset + (elmts_begin + nelmts_written)*ELMT_SIZE;
#if AKCDEBUG
/*Prepare write data*/
{
int *intptr = (int *)buffer;
@ -580,13 +598,18 @@ fprintf(stderr, "proc %d: elmts_begin=%ld, elmts_count=%ld\n",
for (i = 0; i < nelmts_towrite; ++i)
*intptr++ = nelmts_towrite + i;
}
#endif
/* Write */
fprintf(stderr, "proc %d: writes %ld bytes at file-offset %ld\n",
pio_mpi_rank_g, nelmts_towrite*ELMT_SIZE, file_offset);
/* Calculate offset of write within a dataset/file */
switch (iot){
case RAW:
file_offset = dset_offset +
(elmts_begin + nelmts_written)*ELMT_SIZE;
#if AKCDEBUG
fprintf(stderr, "proc %d: writes %ld bytes at file-offset %ld\n",
pio_mpi_rank_g, nelmts_towrite*ELMT_SIZE, file_offset);
#endif
rc = RAWSEEK(fd->rawfd, file_offset);
VRFY((rc>=0), "RAWSEEK");
rc = RAWWRITE(fd->rawfd, buffer, nelmts_towrite*ELMT_SIZE);
@ -594,12 +617,41 @@ fprintf(stderr, "proc %d: writes %ld bytes at file-offset %ld\n",
break;
case MPIO:
mpi_offset = file_offset;
mpi_offset = dset_offset +
(elmts_begin + nelmts_written)*ELMT_SIZE;
#if AKCDEBUG
fprintf(stderr, "proc %d: writes %ld bytes at mpi-offset %ld\n",
pio_mpi_rank_g, nelmts_towrite*ELMT_SIZE, mpi_offset);
#endif
mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buffer,
nelmts_towrite*ELMT_SIZE, MPI_CHAR, &mpi_status);
VRFY((mrc==MPI_SUCCESS), "MPIO_WRITE");
break;
case PHDF5:
/*set up the dset space id to select the segment to process */
{
hsize_t block[1], stride[1], count[1];
hssize_t start[1];
start[0] = elmts_begin + nelmts_written;
stride[0] = block[0] = nelmts_towrite;
count[0] = 1;
hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
start, stride, count, block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
/*setup the memory space id too. Only start is different */
start[0] = 0;
hrc = H5Sselect_hyperslab(h5mem_space_id, H5S_SELECT_SET,
start, stride, count, block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
}
MPI_Barrier(pio_comm_g);
/* set write time here */
hrc = H5Dwrite(h5ds_id, H5T_NATIVE_INT, h5mem_space_id,
h5dset_space_id, H5P_DEFAULT, buffer);
VRFY((hrc >= 0), "H5Dwrite");
break;
}
@ -646,11 +698,232 @@ done:
return ret_code;
}
/*
* Function: do_read
* Purpose: read the required amount of data from the file.
* Return: SUCCESS or FAIL
* Programmer: Albert Cheng 2001/12/13
* Modifications:
*/
static herr_t
do_read(file_descr *fd, iotype iot, long ndsets,
long nelmts, long buf_size, void *buffer /*out*/)
{
int ret_code = SUCCESS;
int rc; /*routine return code */
int mrc; /*MPI return code */
MPI_Offset mpi_offset;
MPI_Status mpi_status;
long ndset;
long nelmts_toread, nelmts_read;
char dname[64];
off_t dset_offset; /*dataset offset in a file */
off_t file_offset; /*file offset of the next transfer */
long dset_size; /*one dataset size in bytes */
long nelmts_in_buf;
long elmts_begin; /*first elmt this process transfer */
long elmts_count; /*number of elmts this process transfer */
/* HDF5 variables */
herr_t hrc; /*HDF5 return code */
hsize_t h5dims[1]; /*dataset dim sizes */
hid_t h5dset_space_id = -1; /*dataset space ID */
hid_t h5mem_space_id = -1; /*memory dataspace ID */
hid_t h5ds_id = -1; /* dataset handle */
#if AKCDEBUG
fprintf(stderr, "In do_read\n");
fprintf(stderr, "ndsets=%ld\n", ndsets);
fprintf(stderr, "nelmts=%ld\n", nelmts);
fprintf(stderr, "buffer size=%ld\n", buf_size);
#endif
/* calculate dataset parameters. data type is always native C int */
dset_size = nelmts * ELMT_SIZE;
nelmts_in_buf = buf_size/ELMT_SIZE;
/* hdf5 data space setup */
if (iot == PHDF5){
/* define a contiquous dataset of nelmts native ints */
h5dims[0] = nelmts;
h5dset_space_id = H5Screate_simple(1, h5dims, NULL);
VRFY((h5dset_space_id >= 0), "H5Screate_simple");
/* create the memory dataspace that corresponds to the xfer buffer */
h5dims[0] = nelmts_in_buf;
h5mem_space_id = H5Screate_simple(1, h5dims, NULL);
VRFY((h5mem_space_id >= 0), "H5Screate_simple");
}
for (ndset = 1; ndset <= ndsets; ++ndset) {
/* Calculate dataset offset within a file */
/* create dataset */
switch (iot) {
case RAW:
case MPIO:
/* both raw and mpi io just need dataset offset in file*/
dset_offset = (ndset - 1) * dset_size;
break;
case PHDF5:
sprintf(dname, "Dataset_%ld", ndset);
h5ds_id = H5Dopen(fd->h5fd, dname);
if (h5ds_id < 0) {
fprintf(stderr, "HDF5 Dataset open failed\n");
GOTOERROR(FAIL);
}
break;
}
/* Calculate the first element and how many elements this process
* transfer. First calculate the beginning element of this process
* and the next process. Count of elements is the difference between
* these two beginnings. This way, it avoids any rounding errors.
*/
elmts_begin = (nelmts*1.0)/pio_mpi_nprocs_g*pio_mpi_rank_g;
if (pio_mpi_rank_g < (pio_mpi_nprocs_g - 1)){
elmts_count = ((nelmts*1.0)/pio_mpi_nprocs_g*(pio_mpi_rank_g+1)) -
elmts_begin;
}else{
/* last process. Take whatever are left */
elmts_count = nelmts - elmts_begin;
}
#if AKCDEBUG
fprintf(stderr, "proc %d: elmts_begin=%ld, elmts_count=%ld\n",
pio_mpi_rank_g, elmts_begin, elmts_count);
#endif
nelmts_read = 0 ;
while (nelmts_read < elmts_count){
nelmts_toread = elmts_count - nelmts_read;
if (elmts_count - nelmts_read >= nelmts_in_buf) {
nelmts_toread = nelmts_in_buf;
} else {
/* last read of a partial buffer */
nelmts_toread = elmts_count - nelmts_read;
}
/* read */
/* Calculate offset of read within a dataset/file */
switch (iot){
case RAW:
file_offset = dset_offset +
(elmts_begin + nelmts_read)*ELMT_SIZE;
#if AKCDEBUG
fprintf(stderr, "proc %d: read %ld bytes at file-offset %ld\n",
pio_mpi_rank_g, nelmts_toread*ELMT_SIZE, file_offset);
#endif
rc = RAWSEEK(fd->rawfd, file_offset);
VRFY((rc>=0), "RAWSEEK");
rc = RAWREAD(fd->rawfd, buffer, nelmts_toread*ELMT_SIZE);
VRFY((rc==(nelmts_toread*ELMT_SIZE)), "RAWREAD");
break;
case MPIO:
mpi_offset = dset_offset +
(elmts_begin + nelmts_read)*ELMT_SIZE;
#if AKCDEBUG
fprintf(stderr, "proc %d: read %ld bytes at mpi-offset %ld\n",
pio_mpi_rank_g, nelmts_toread*ELMT_SIZE, mpi_offset);
#endif
mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buffer,
nelmts_toread*ELMT_SIZE, MPI_CHAR, &mpi_status);
VRFY((mrc==MPI_SUCCESS), "MPIO_read");
break;
case PHDF5:
/*set up the dset space id to select the segment to process */
{
hsize_t block[1], stride[1], count[1];
hssize_t start[1];
start[0] = elmts_begin + nelmts_read;
stride[0] = block[0] = nelmts_toread;
count[0] = 1;
hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET,
start, stride, count, block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
/*setup the memory space id too. Only start is different */
start[0] = 0;
hrc = H5Sselect_hyperslab(h5mem_space_id, H5S_SELECT_SET,
start, stride, count, block);
VRFY((hrc >= 0), "H5Sset_hyperslab");
}
MPI_Barrier(pio_comm_g);
/* set read time here */
hrc = H5Dread(h5ds_id, H5T_NATIVE_INT, h5mem_space_id,
h5dset_space_id, H5P_DEFAULT, buffer);
VRFY((hrc >= 0), "H5Dread");
break;
}
#if AKCDEBUG & 0
/*verify read data*/
{
int *intptr = (int *)buffer;
register int i;
for (i = 0; i < nelmts_towrite; ++i)
/* TO BE IMPLEMENTED */
;
}
#endif
nelmts_read += nelmts_toread;
}
/* Calculate read time */
/* Close dataset. Only HDF5 needs to do an explicit close. */
if (iot == PHDF5){
hrc = H5Dclose(h5ds_id);
if (hrc < 0) {
fprintf(stderr, "HDF5 Dataset Close failed\n");
GOTOERROR(FAIL);
}
h5ds_id = -1;
}
}
done:
/* release HDF5 objects */
if (h5dset_space_id != -1) {
hrc = H5Sclose(h5dset_space_id);
if (hrc < 0){
fprintf(stderr, "HDF5 Dataset Space Close failed\n");
ret_code = FAIL;
} else {
h5dset_space_id = -1;
}
}
if (h5mem_space_id != -1) {
hrc = H5Sclose(h5mem_space_id);
if (hrc < 0) {
fprintf(stderr, "HDF5 Memory Space Close failed\n");
ret_code = FAIL;
} else {
h5mem_space_id = -1;
}
}
return ret_code;
}
/*
* Function: do_fopen
* Purpose: Open the specified file.
* Return: SUCCESS or FAIL
* Programmer: Bill Wendling, 14. November 2001
* Programmer: Albert Cheng, Bill Wendling, 2001/12/13
* Modifications:
*/
static herr_t
@ -737,7 +1010,7 @@ done:
* Function: do_fclose
* Purpose: Close the specified file descriptor.
* Return: SUCCESS or FAIL
* Programmer: Bill Wendling, 14. November 2001
* Programmer: Albert Cheng, Bill Wendling, 2001/12/13
* Modifications:
*/
static herr_t
@ -787,11 +1060,16 @@ done:
/*
* Cleanup temporary file, fname unless HDF5_NOCLEANUP is set.
* Only Proc 0 of the PIO communicator will do the cleanup. Other processes
* just returns.
* Function: do_fclose
* Purpose: Cleanup temporary file unless HDF5_NOCLEANUP is set.
* Only Proc 0 of the PIO communicator will do the cleanup.
* Other processes just return.
* Return: void
* Programmer: Albert Cheng 2001/12/12
* Modifications:
*/
static void do_cleanupfile(char *fname)
static void
do_cleanupfile(char *fname)
{
if (pio_mpi_rank_g != 0)
return;
@ -799,7 +1077,6 @@ static void do_cleanupfile(char *fname)
if (clean_file_g == -1)
clean_file_g = (getenv("HDF5_NOCLEANUP")==NULL) ? 1 : 0;
fprintf(stderr, "clean_file_g=%d\n", clean_file_g);
if (clean_file_g)
remove(fname);
}