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Skip atomicity tests for OpenMPI major versions < 5
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@jhendersonHDF
jhendersonHDF committed Aug 24, 2023
1 parent 755dd4e commit 196bb2a
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9 changes: 9 additions & 0 deletions release_docs/RELEASE.txt
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Expand Up @@ -759,6 +759,15 @@ Bug Fixes since HDF5-1.14.0 release

Testing
-------
- Disabled running of MPI Atomicity tests for OpenMPI major versions < 5

Support for MPI atomicity operations is not implemented for major
versions of OpenMPI less than version 5. This would cause the MPI
atomicity tests for parallel HDF5 to sporadically fail when run
with OpenMPI. Testphdf5 now checks if OpenMPI is being used and will
skip running the atomicity tests if the major version of OpenMPI is
< 5.

- Fixed a testing failure in testphdf5 on Cray machines

On some Cray machines, what appears to be a bug in Cray MPICH was causing
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338 changes: 0 additions & 338 deletions testpar/t_2Gio.c
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Expand Up @@ -4200,344 +4200,6 @@ no_collective_cause_tests(void)
return;
}

/*
* Test consistency semantics of atomic mode
*/

/*
* Example of using the parallel HDF5 library to create a dataset,
* where process 0 writes and the other processes read at the same
* time. If atomic mode is set correctly, the other processes should
* read the old values in the dataset or the new ones.
*/

void
dataset_atomicity(void)
{
hid_t fid; /* HDF5 file ID */
hid_t acc_tpl; /* File access templates */
hid_t sid; /* Dataspace ID */
hid_t dataset1; /* Dataset IDs */
hsize_t dims[MAX_RANK]; /* dataset dim sizes */
int *write_buf = NULL; /* data buffer */
int *read_buf = NULL; /* data buffer */
int buf_size;
hid_t dataset2;
hid_t file_dataspace; /* File dataspace ID */
hid_t mem_dataspace; /* Memory dataspace ID */
hsize_t start[MAX_RANK];
hsize_t stride[MAX_RANK];
hsize_t count[MAX_RANK];
hsize_t block[MAX_RANK];
const char *filename;
herr_t ret; /* Generic return value */
int mpi_size, mpi_rank;
int i, j, k;
hbool_t atomicity = FALSE;
MPI_Comm comm = test_comm;
MPI_Info info = MPI_INFO_NULL;

dim0 = 64;
dim1 = 32;
filename = GetTestParameters();
if (facc_type != FACC_MPIO) {
printf("Atomicity tests will not work without the MPIO VFD\n");
return;
}
if (VERBOSE_MED)
printf("atomic writes to file %s\n", filename);

/* set up MPI parameters */
MPI_Comm_size(test_comm, &mpi_size);
MPI_Comm_rank(test_comm, &mpi_rank);

buf_size = dim0 * dim1;
/* allocate memory for data buffer */
write_buf = (int *)calloc((size_t)buf_size, sizeof(int));
VRFY((write_buf != NULL), "write_buf calloc succeeded");
/* allocate memory for data buffer */
read_buf = (int *)calloc((size_t)buf_size, sizeof(int));
VRFY((read_buf != NULL), "read_buf calloc succeeded");

/* setup file access template */
acc_tpl = create_faccess_plist(comm, info, facc_type);
VRFY((acc_tpl >= 0), "");

/* create the file collectively */
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
VRFY((fid >= 0), "H5Fcreate succeeded");

/* Release file-access template */
ret = H5Pclose(acc_tpl);
VRFY((ret >= 0), "H5Pclose succeeded");

/* setup dimensionality object */
dims[0] = (hsize_t)dim0;
dims[1] = (hsize_t)dim1;
sid = H5Screate_simple(MAX_RANK, dims, NULL);
VRFY((sid >= 0), "H5Screate_simple succeeded");

/* create datasets */
dataset1 = H5Dcreate2(fid, DATASETNAME5, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dataset1 >= 0), "H5Dcreate2 succeeded");

dataset2 = H5Dcreate2(fid, DATASETNAME6, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
VRFY((dataset2 >= 0), "H5Dcreate2 succeeded");

/* initialize datasets to 0s */
if (0 == mpi_rank) {
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf);
VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");

ret = H5Dwrite(dataset2, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf);
VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
}

ret = H5Dclose(dataset1);
VRFY((ret >= 0), "H5Dclose succeeded");
ret = H5Dclose(dataset2);
VRFY((ret >= 0), "H5Dclose succeeded");
ret = H5Sclose(sid);
VRFY((ret >= 0), "H5Sclose succeeded");
ret = H5Fclose(fid);
VRFY((ret >= 0), "H5Fclose succeeded");

MPI_Barrier(comm);

/* make sure setting atomicity fails on a serial file ID */
/* file locking allows only one file open (serial) for writing */
if (MAINPROCESS) {
fid = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
VRFY((fid >= 0), "H5Fopen succeeded");
}

/* should fail */
ret = H5Fset_mpi_atomicity(fid, TRUE);
VRFY((ret == FAIL), "H5Fset_mpi_atomicity failed");

if (MAINPROCESS) {
ret = H5Fclose(fid);
VRFY((ret >= 0), "H5Fclose succeeded");
}

MPI_Barrier(comm);

/* setup file access template */
acc_tpl = create_faccess_plist(comm, info, facc_type);
VRFY((acc_tpl >= 0), "");

/* open the file collectively */
fid = H5Fopen(filename, H5F_ACC_RDWR, acc_tpl);
VRFY((fid >= 0), "H5Fopen succeeded");

/* Release file-access template */
ret = H5Pclose(acc_tpl);
VRFY((ret >= 0), "H5Pclose succeeded");

ret = H5Fset_mpi_atomicity(fid, TRUE);
VRFY((ret >= 0), "H5Fset_mpi_atomicity succeeded");

/* open dataset1 (contiguous case) */
dataset1 = H5Dopen2(fid, DATASETNAME5, H5P_DEFAULT);
VRFY((dataset1 >= 0), "H5Dopen2 succeeded");

if (0 == mpi_rank) {
for (i = 0; i < buf_size; i++) {
write_buf[i] = 5;
}
}
else {
for (i = 0; i < buf_size; i++) {
read_buf[i] = 8;
}
}

/* check that the atomicity flag is set */
ret = H5Fget_mpi_atomicity(fid, &atomicity);
VRFY((ret >= 0), "atomcity get failed");
VRFY((atomicity == TRUE), "atomcity set failed");

MPI_Barrier(comm);

/* Process 0 writes contiguously to the entire dataset */
if (0 == mpi_rank) {
ret = H5Dwrite(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, write_buf);
VRFY((ret >= 0), "H5Dwrite dataset1 succeeded");
}
/* The other processes read the entire dataset */
else {
ret = H5Dread(dataset1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, read_buf);
VRFY((ret >= 0), "H5Dwrite() dataset multichunk write succeeded");
}

if (VERBOSE_MED) {
i = 0;
j = 0;
k = 0;
for (i = 0; i < dim0; i++) {
printf("\n");
for (j = 0; j < dim1; j++)
printf("%d ", read_buf[k++]);
}
}

/* The processes that read the dataset must either read all values
as 0 (read happened before process 0 wrote to dataset 1), or 5
(read happened after process 0 wrote to dataset 1) */
if (0 != mpi_rank) {
int compare = read_buf[0];

VRFY((compare == 0 || compare == 5),
"Atomicity Test Failed Process %d: Value read should be 0 or 5\n");
for (i = 1; i < buf_size; i++) {
if (read_buf[i] != compare) {
printf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank, i,
read_buf[i], compare);
nerrors++;
}
}
}

ret = H5Dclose(dataset1);
VRFY((ret >= 0), "H5D close succeeded");

/* release data buffers */
if (write_buf)
free(write_buf);
if (read_buf)
free(read_buf);

/* open dataset2 (non-contiguous case) */
dataset2 = H5Dopen2(fid, DATASETNAME6, H5P_DEFAULT);
VRFY((dataset2 >= 0), "H5Dopen2 succeeded");

/* allocate memory for data buffer */
write_buf = (int *)calloc((size_t)buf_size, sizeof(int));
VRFY((write_buf != NULL), "write_buf calloc succeeded");
/* allocate memory for data buffer */
read_buf = (int *)calloc((size_t)buf_size, sizeof(int));
VRFY((read_buf != NULL), "read_buf calloc succeeded");

for (i = 0; i < buf_size; i++) {
write_buf[i] = 5;
}
for (i = 0; i < buf_size; i++) {
read_buf[i] = 8;
}

atomicity = FALSE;
/* check that the atomicity flag is set */
ret = H5Fget_mpi_atomicity(fid, &atomicity);
VRFY((ret >= 0), "atomcity get failed");
VRFY((atomicity == TRUE), "atomcity set failed");

block[0] = (hsize_t)(dim0 / mpi_size) - 1;
block[1] = (hsize_t)(dim1 / mpi_size) - 1;
stride[0] = block[0] + 1;
stride[1] = block[1] + 1;
count[0] = (hsize_t)mpi_size;
count[1] = (hsize_t)mpi_size;
start[0] = 0;
start[1] = 0;

/* create a file dataspace */
file_dataspace = H5Dget_space(dataset2);
VRFY((file_dataspace >= 0), "H5Dget_space succeeded");
ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");

/* create a memory dataspace */
mem_dataspace = H5Screate_simple(MAX_RANK, dims, NULL);
VRFY((mem_dataspace >= 0), "");

ret = H5Sselect_hyperslab(mem_dataspace, H5S_SELECT_SET, start, stride, count, block);
VRFY((ret >= 0), "H5Sset_hyperslab succeeded");

MPI_Barrier(comm);

/* Process 0 writes to the dataset */
if (0 == mpi_rank) {
ret = H5Dwrite(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, write_buf);
VRFY((ret >= 0), "H5Dwrite dataset2 succeeded");
}
/* All processes wait for the write to finish. This works because
atomicity is set to true */
MPI_Barrier(comm);
/* The other processes read the entire dataset */
if (0 != mpi_rank) {
ret = H5Dread(dataset2, H5T_NATIVE_INT, mem_dataspace, file_dataspace, H5P_DEFAULT, read_buf);
VRFY((ret >= 0), "H5Dread dataset2 succeeded");
}

if (VERBOSE_MED) {
if (mpi_rank == 1) {
i = 0;
j = 0;
k = 0;
for (i = 0; i < dim0; i++) {
printf("\n");
for (j = 0; j < dim1; j++)
printf("%d ", read_buf[k++]);
}
printf("\n");
}
}

/* The processes that read the dataset must either read all values
as 5 (read happened after process 0 wrote to dataset 1) */
if (0 != mpi_rank) {
int compare;
i = 0;
j = 0;
k = 0;

compare = 5;

for (i = 0; i < dim0; i++) {
if ((hsize_t)i >= (hsize_t)mpi_rank * (block[0] + 1)) {
break;
}
if (((hsize_t)i + 1) % (block[0] + 1) == 0) {
k += dim1;
continue;
}
for (j = 0; j < dim1; j++) {
if ((hsize_t)j >= (hsize_t)mpi_rank * (block[1] + 1)) {
H5_CHECKED_ASSIGN(k, int, (hsize_t)dim1 - (hsize_t)mpi_rank * (block[1] + 1) + (hsize_t)k,
hsize_t);
break;
}
if (((hsize_t)j + 1) % (block[1] + 1) == 0) {
k++;
continue;
}
else if (compare != read_buf[k]) {
printf("Atomicity Test Failed Process %d: read_buf[%d] is %d, should be %d\n", mpi_rank,
k, read_buf[k], compare);
nerrors++;
}
k++;
}
}
}

ret = H5Dclose(dataset2);
VRFY((ret >= 0), "H5Dclose succeeded");
ret = H5Sclose(file_dataspace);
VRFY((ret >= 0), "H5Sclose succeeded");
ret = H5Sclose(mem_dataspace);
VRFY((ret >= 0), "H5Sclose succeeded");

/* release data buffers */
if (write_buf)
free(write_buf);
if (read_buf)
free(read_buf);

ret = H5Fclose(fid);
VRFY((ret >= 0), "H5Fclose succeeded");
}

/* Function: dense_attr_test
*
* Purpose: Test cases for writing dense attributes in parallel
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8 changes: 8 additions & 0 deletions testpar/testphdf5.c
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Expand Up @@ -487,6 +487,13 @@ main(int argc, char **argv)
AddTest((mpi_size < 2) ? "-fiodc" : "fiodc", file_image_daisy_chain_test, NULL,
"file image ops daisy chain", NULL);

/* Atomicity operations are not supported for OpenMPI versions < major
* version 5 and will sporadically fail.
*/
#if defined(OPEN_MPI) && defined(OMPI_MAJOR_VERSION) && (OMPI_MAJOR_VERSION < 5)
if (MAINPROCESS)
printf("OpenMPI major version is < 5. Atomicity tests will be skipped due to support for atomicity operations not being implemented.\n");
#else
if ((mpi_size < 2) && MAINPROCESS) {
printf("Atomicity tests need at least 2 processes to participate\n");
printf("8 is more recommended.. Atomicity tests will be skipped \n");
Expand All @@ -497,6 +504,7 @@ main(int argc, char **argv)
else if (mpi_size >= 2 && facc_type == FACC_MPIO) {
AddTest("atomicity", dataset_atomicity, NULL, "dataset atomic updates", PARATESTFILE);
}
#endif

AddTest("denseattr", test_dense_attr, NULL, "Store Dense Attributes", PARATESTFILE);

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