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authorAlbert Cheng <acheng@hdfgroup.org>2001-12-13 15:29:47 (GMT)
committerAlbert Cheng <acheng@hdfgroup.org>2001-12-13 15:29:47 (GMT)
commit4720897bb99cc6e028f6b0c58df55a974140255e (patch)
tree26984373634f46756528ff03c1dc17469ca37cb9 /perform
parent3037cad73421220f0830feb5074943779ab8ca6a (diff)
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[svn-r4715] Purpose:
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.
Diffstat (limited to 'perform')
-rw-r--r--perform/pio_engine.c327
1 files changed, 302 insertions, 25 deletions
diff --git a/perform/pio_engine.c b/perform/pio_engine.c
index e35276b..0136a7f 100644
--- a/perform/pio_engine.c
+++ b/perform/pio_engine.c
@@ -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);
}