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Fix for HDFFV-11109 - Copy MPI comm and info object into output FAPL from H5F_get_access_plist (#342)

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* Avoid freeing MPI_COMM_WORLD in H5_mpi_comm_free

* Copy MPI Comm and Info to new FAPL in H5F_get_access_plist
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jhendersonHDF 2021-02-17 06:37:23 -06:00 committed by GitHub
parent 2359a9b020
commit afdb7903c6
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6 changed files with 224 additions and 7 deletions
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9
release_docs/RELEASE.txt
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@ -696,6 +696,15 @@ Bug Fixes since HDF5-1.12.0 release
==================================
Library
-------
- Fixed issue with MPI communicator and info object not being
copied into new FAPL retrieved from H5F_get_access_plist
Added logic to copy the MPI communicator and info object into
the output FAPL. MPI communicator is retrieved from the VFD, while
the MPI info object is retrieved from the file's original FAPL.
(JTH - 2021/02/15, HDFFV-11109)
- Fixed problems with vlens and refs inside compound using
H5VLget_file_type()

28
src/H5Fint.c
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@ -413,24 +413,40 @@ H5F_get_access_plist(H5F_t *f, hbool_t app_ref)
if (f->shared->efc)
efc_size = H5F__efc_max_nfiles(f->shared->efc);
if (H5P_set(new_plist, H5F_ACS_EFC_SIZE_NAME, &efc_size) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, H5I_INVALID_HID, "can't set elink file cache size")
HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set elink file cache size")
if (f->shared->page_buf != NULL) {
if (H5P_set(new_plist, H5F_ACS_PAGE_BUFFER_SIZE_NAME, &(f->shared->page_buf->max_size)) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, H5I_INVALID_HID, "can't set page buffer size")
HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set page buffer size")
if (H5P_set(new_plist, H5F_ACS_PAGE_BUFFER_MIN_META_PERC_NAME,
&(f->shared->page_buf->min_meta_perc)) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, H5I_INVALID_HID,
HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID,
"can't set minimum metadata fraction of page buffer")
if (H5P_set(new_plist, H5F_ACS_PAGE_BUFFER_MIN_RAW_PERC_NAME, &(f->shared->page_buf->min_raw_perc)) <
0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, H5I_INVALID_HID,
HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID,
"can't set minimum raw data fraction of page buffer")
} /* end if */
#ifdef H5_HAVE_PARALLEL
if (H5P_set(new_plist, H5_COLL_MD_READ_FLAG_NAME, &(f->shared->coll_md_read)) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, H5I_INVALID_HID, "can't set collective metadata read flag")
HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set collective metadata read flag")
if (H5P_set(new_plist, H5F_ACS_COLL_MD_WRITE_FLAG_NAME, &(f->shared->coll_md_write)) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, H5I_INVALID_HID, "can't set collective metadata read flag")
HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set collective metadata read flag")
if (H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) {
MPI_Comm mpi_comm;
MPI_Info mpi_info;
/* Retrieve and set MPI communicator */
if (MPI_COMM_NULL == (mpi_comm = H5F_mpi_get_comm(f)))
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, H5I_INVALID_HID, "can't get MPI communicator")
if (H5P_set(new_plist, H5F_ACS_MPI_PARAMS_COMM_NAME, &mpi_comm) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set MPI communicator")
/* Retrieve and set MPI info object */
if (H5P_get(old_plist, H5F_ACS_MPI_PARAMS_INFO_NAME, &mpi_info) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTGET, H5I_INVALID_HID, "can't get MPI info object")
if (H5P_set(new_plist, H5F_ACS_MPI_PARAMS_INFO_NAME, &mpi_info) < 0)
HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set MPI info object")
}
#endif /* H5_HAVE_PARALLEL */
if (H5P_set(new_plist, H5F_ACS_META_CACHE_INIT_IMAGE_CONFIG_NAME, &(f->shared->mdc_initCacheImageCfg)) <
0)

2
src/H5mpi.c
View File

@ -210,7 +210,7 @@ H5_mpi_comm_free(MPI_Comm *comm)
HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "comm pointer cannot be NULL")
/* Free the communicator */
if (MPI_COMM_NULL != *comm)
if (MPI_COMM_WORLD != *comm && MPI_COMM_NULL != *comm)
MPI_Comm_free(comm);
*comm = MPI_COMM_NULL;

189
testpar/t_prop.c
View File

@ -441,3 +441,192 @@ test_plist_ed(void)
ret = H5Pclose(acpl);
VRFY((ret >= 0), "H5Pclose succeeded");
}
void
external_links(void)
{
hid_t lcpl = H5I_INVALID_HID; /* link create prop. list */
hid_t lapl = H5I_INVALID_HID; /* link access prop. list */
hid_t fapl = H5I_INVALID_HID; /* file access prop. list */
hid_t gapl = H5I_INVALID_HID; /* group access prop. list */
hid_t fid = H5I_INVALID_HID; /* file id */
hid_t group = H5I_INVALID_HID; /* group id */
int mpi_size, mpi_rank;
MPI_Comm comm;
int doIO;
int i, mrc;
herr_t ret; /* Generic return value */
htri_t tri_status; /* tri return value */
const char *filename = "HDF5test.h5";
const char *filename_ext = "HDF5test_ext.h5";
const char *group_path = "/Base/Block/Step";
const char *link_name = "link"; /* external link */
char link_path[50];
if (VERBOSE_MED)
HDprintf("Check external links\n");
/* set up MPI parameters */
MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
/* Check MPI communicator access properties are passed to
linked external files */
if (mpi_rank == 0) {
lcpl = H5Pcreate(H5P_LINK_CREATE);
VRFY((lcpl >= 0), "H5Pcreate succeeded");
ret = H5Pset_create_intermediate_group(lcpl, 1);
VRFY((ret >= 0), "H5Pset_create_intermediate_group succeeded");
/* Create file to serve as target for external link.*/
fid = H5Fcreate(filename_ext, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
VRFY((fid >= 0), "H5Fcreate succeeded");
group = H5Gcreate2(fid, group_path, lcpl, H5P_DEFAULT, H5P_DEFAULT);
VRFY((group >= 0), "H5Gcreate succeeded");
ret = H5Gclose(group);
VRFY((ret >= 0), "H5Gclose succeeded");
ret = H5Fclose(fid);
VRFY((ret >= 0), "H5Fclose succeeded");
fapl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl >= 0), "H5Pcreate succeeded");
/* Create a new file using the file access property list. */
fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
VRFY((fid >= 0), "H5Fcreate succeeded");
ret = H5Pclose(fapl);
VRFY((ret >= 0), "H5Pclose succeeded");
group = H5Gcreate2(fid, group_path, lcpl, H5P_DEFAULT, H5P_DEFAULT);
VRFY((group >= 0), "H5Gcreate succeeded");
/* Create external links to the target files. */
ret = H5Lcreate_external(filename_ext, group_path, group, link_name, H5P_DEFAULT, H5P_DEFAULT);
VRFY((ret >= 0), "H5Lcreate_external succeeded");
/* Close and release resources. */
ret = H5Pclose(lcpl);
VRFY((ret >= 0), "H5Pclose succeeded");
ret = H5Gclose(group);
VRFY((ret >= 0), "H5Gclose succeeded");
ret = H5Fclose(fid);
VRFY((ret >= 0), "H5Fclose succeeded");
}
MPI_Barrier(MPI_COMM_WORLD);
/*
* For the first case, use all the processes. For the second case
* use a sub-communicator to verify the correct communicator is
* being used for the externally linked files.
* There is no way to determine if MPI info is being used for the
* externally linked files.
*/
for (i = 0; i < 2; i++) {
if (i == 0) {
doIO = 1;
comm = MPI_COMM_WORLD;
}
else {
doIO = mpi_rank % 2;
mrc = MPI_Comm_split(MPI_COMM_WORLD, doIO, mpi_rank, &comm);
VRFY((mrc == MPI_SUCCESS), "");
}
if (doIO) {
fapl = H5Pcreate(H5P_FILE_ACCESS);
VRFY((fapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_fapl_mpio(fapl, comm, MPI_INFO_NULL);
VRFY((fapl >= 0), "H5Pset_fapl_mpio succeeded");
fid = H5Fopen(filename, H5F_ACC_RDWR, fapl);
VRFY((fid >= 0), "H5Fopen succeeded");
/* test opening a group that is to an external link, the external linked
file should inherit the source file's access properties */
HDsprintf(link_path, "%s%s%s", group_path, "/", link_name);
group = H5Gopen2(fid, link_path, H5P_DEFAULT);
VRFY((group >= 0), "H5Gopen succeeded");
ret = H5Gclose(group);
VRFY((ret >= 0), "H5Gclose succeeded");
/* test opening a group that is external link by setting group
creation property */
gapl = H5Pcreate(H5P_GROUP_ACCESS);
VRFY((gapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_elink_fapl(gapl, fapl);
VRFY((ret >= 0), "H5Pset_elink_fapl succeeded");
group = H5Gopen2(fid, link_path, gapl);
VRFY((group >= 0), "H5Gopen succeeded");
ret = H5Gclose(group);
VRFY((ret >= 0), "H5Gclose succeeded");
ret = H5Pclose(gapl);
VRFY((ret >= 0), "H5Pclose succeeded");
/* test link APIs */
lapl = H5Pcreate(H5P_LINK_ACCESS);
VRFY((lapl >= 0), "H5Pcreate succeeded");
ret = H5Pset_elink_fapl(lapl, fapl);
VRFY((ret >= 0), "H5Pset_elink_fapl succeeded");
tri_status = H5Lexists(fid, link_path, H5P_DEFAULT);
VRFY((tri_status == TRUE), "H5Lexists succeeded");
tri_status = H5Lexists(fid, link_path, lapl);
VRFY((tri_status == TRUE), "H5Lexists succeeded");
group = H5Oopen(fid, link_path, H5P_DEFAULT);
VRFY((group >= 0), "H5Oopen succeeded");
ret = H5Oclose(group);
VRFY((ret >= 0), "H5Oclose succeeded");
group = H5Oopen(fid, link_path, lapl);
VRFY((group >= 0), "H5Oopen succeeded");
ret = H5Oclose(group);
VRFY((ret >= 0), "H5Oclose succeeded");
ret = H5Pclose(lapl);
VRFY((ret >= 0), "H5Pclose succeeded");
/* close the remaining resources */
ret = H5Pclose(fapl);
VRFY((ret >= 0), "H5Pclose succeeded");
ret = H5Fclose(fid);
VRFY((ret >= 0), "H5Fclose succeeded");
if (i == 1) {
mrc = MPI_Comm_free(&comm);
VRFY((mrc == MPI_SUCCESS), "MPI_Comm_free succeeded");
}
}
}
MPI_Barrier(MPI_COMM_WORLD);
/* delete the test files */
if (mpi_rank == 0) {
MPI_File_delete(filename, MPI_INFO_NULL);
MPI_File_delete(filename_ext, MPI_INFO_NULL);
}
}

2
testpar/testphdf5.c
View File

@ -467,6 +467,8 @@ main(int argc, char **argv)
AddTest("edpl", test_plist_ed, NULL, "encode/decode Property Lists", NULL);
AddTest("extlink", external_links, NULL, "test external links", NULL);
if ((mpi_size < 2) && MAINPROCESS) {
HDprintf("File Image Ops daisy chain test needs at least 2 processes.\n");
HDprintf("File Image Ops daisy chain test will be skipped \n");

1
testpar/testphdf5.h
View File

@ -235,6 +235,7 @@ extern int dxfer_coll_type;
/* Test program prototypes */
void test_plist_ed(void);
void external_links(void);
void zero_dim_dset(void);
void test_file_properties(void);
void multiple_dset_write(void);