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authorQuincey Koziol <koziol@lbl.gov>2020-09-03 15:02:14 (GMT)
committerQuincey Koziol <koziol@lbl.gov>2020-09-03 15:02:14 (GMT)
commitcee201a2ea604281694f83c68bdfae41e4505fe6 (patch)
treea72307c522c45ea08a6ada321ade303512d43919
parent3dfc9692f91a944c9e0f17caa5dde79cd3ba23a8 (diff)
parent8b48ddb4c8d02aec2bc5e938fe7b789f6ad9c2b2 (diff)
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Merge pull request #2871 in HDFFV/hdf5 from fix_nil_collective_metadata_write_1_12 to hdf5_1_12
* commit '8b48ddb4c8d02aec2bc5e938fe7b789f6ad9c2b2': Add release note for collective metadata fix Fix mis-merge from develop Update buffer count Revert " Checkin of fix for CGNS bug" Revert "Removed commeted out code from H5C_dump_coll_write_list()"
-rw-r--r--release_docs/RELEASE.txt6
-rw-r--r--src/H5Cdbg.c107
-rw-r--r--src/H5Cmpio.c75
-rw-r--r--src/H5Cprivate.h5
-rw-r--r--src/H5FDmpi.c36
-rw-r--r--src/H5FDmpio.c4
-rw-r--r--src/H5FDprivate.h2
-rw-r--r--src/H5Fmpi.c28
-rw-r--r--src/H5Fprivate.h1
9 files changed, 32 insertions, 232 deletions
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index a7e8735..2e20886 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -143,6 +143,12 @@ Bug Fixes since HDF5-1.12.0 release
==================================
Library
-------
+ - Fix bug and simplify collective metadata write operation when some ranks
+ have no entries to contribute. This fixes parallel regression test
+ failures with IBM SpectrumScale MPI on the Summit system at ORNL.
+
+ (QAK - 2020/09/02)
+
- Avoid setting up complex MPI types with 0-length vectors, which some
MPI implementations don't handle well. (In particular, IBM
SpectrumScale MPI on the Summit system at ORNL)
diff --git a/src/H5Cdbg.c b/src/H5Cdbg.c
index 425bda3..d820ca0 100644
--- a/src/H5Cdbg.c
+++ b/src/H5Cdbg.c
@@ -28,16 +28,12 @@
#include "H5Cmodule.h" /* This source code file is part of the H5C module */
-#define H5AC_FRIEND
-
-
-
/***********/
/* Headers */
/***********/
#include "H5private.h" /* Generic Functions */
-#include "H5ACpkg.h" /* Metadata Cache */
+#include "H5ACprivate.h" /* Metadata Cache */
#include "H5Cpkg.h" /* Cache */
#include "H5Eprivate.h" /* Error Handling */
@@ -341,107 +337,6 @@ H5C_dump_cache_skip_list(H5C_t * cache_ptr, char * calling_fcn)
/*-------------------------------------------------------------------------
- * Function: H5C_dump_coll_write_list
- *
- * Purpose: Debugging routine that prints a summary of the contents of
- * the collective write skip list used by the metadata cache
- * in the parallel case to maintain a list of entries to write
- * collectively at a sync point.
- *
- * Return: Non-negative on success/Negative on failure
- *
- * Programmer: John Mainzer
- * 4/1/17
- *
- *-------------------------------------------------------------------------
- */
-#ifdef H5_HAVE_PARALLEL
-#ifndef NDEBUG
-herr_t
-H5C_dump_coll_write_list(H5C_t * cache_ptr, char * calling_fcn)
-{
- herr_t ret_value = SUCCEED; /* Return value */
- int i;
- int list_len;
- H5AC_aux_t * aux_ptr = NULL;
- H5C_cache_entry_t * entry_ptr = NULL;
- H5SL_node_t * node_ptr = NULL;
-
- FUNC_ENTER_NOAPI_NOERR
-
- HDassert(cache_ptr != NULL);
- HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC);
- HDassert(cache_ptr->aux_ptr);
-
- aux_ptr = (H5AC_aux_t *)cache_ptr->aux_ptr;
-
- HDassert(aux_ptr->magic == H5AC__H5AC_AUX_T_MAGIC);
-
- HDassert(calling_fcn != NULL);
-
- list_len = (int)H5SL_count(cache_ptr->coll_write_list);
-
- HDfprintf(stdout, "\n\nDumping MDC coll write list from %d:%s.\n",
- aux_ptr->mpi_rank, calling_fcn);
- HDfprintf(stdout, " slist len = %u.\n", cache_ptr->slist_len);
-
- if ( list_len > 0 ) {
-
- /* scan the collective write list generating the desired output */
- HDfprintf(stdout,
- "Num: Addr: Len: Prot/Pind: Dirty: Type:\n");
-
- i = 0;
-
- node_ptr = H5SL_first(cache_ptr->coll_write_list);
-
- if ( node_ptr != NULL )
-
- entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr);
-
- else
-
- entry_ptr = NULL;
-
- while ( entry_ptr != NULL ) {
-
- HDassert(entry_ptr->magic == H5C__H5C_CACHE_ENTRY_T_MAGIC);
-
- HDfprintf(stdout,
- "%s%d 0x%016llx %4lld %d/%d %d %s\n",
- cache_ptr->prefix, i,
- (long long)(entry_ptr->addr),
- (long long)(entry_ptr->size),
- (int)(entry_ptr->is_protected),
- (int)(entry_ptr->is_pinned),
- (int)(entry_ptr->is_dirty),
- entry_ptr->type->name);
-
- node_ptr = H5SL_next(node_ptr);
-
- if ( node_ptr != NULL )
-
- entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr);
-
- else
-
- entry_ptr = NULL;
-
- i++;
-
- } /* end while */
- } /* end if */
-
- HDfprintf(stdout, "\n\n");
-
- FUNC_LEAVE_NOAPI(ret_value)
-
-} /* H5C_dump_coll_write_list() */
-#endif /* NDEBUG */
-#endif /* H5_HAVE_PARALLEL */
-
-
-/*-------------------------------------------------------------------------
* Function: H5C_set_prefix
*
* Purpose: Set the values of the prefix field of H5C_t. This
diff --git a/src/H5Cmpio.c b/src/H5Cmpio.c
index 199c494..4989eea 100644
--- a/src/H5Cmpio.c
+++ b/src/H5Cmpio.c
@@ -921,6 +921,7 @@ H5C__collective_write(H5F_t *f)
{
H5AC_t *cache_ptr;
H5FD_mpio_xfer_t orig_xfer_mode = H5FD_MPIO_COLLECTIVE;
+ void *base_buf;
int count;
int *length_array = NULL;
MPI_Aint *buf_array = NULL;
@@ -930,6 +931,8 @@ H5C__collective_write(H5F_t *f)
MPI_Datatype ftype;
hbool_t ftype_created = FALSE;
int mpi_code;
+ char unused = 0; /* Unused, except for non-NULL pointer value */
+ size_t buf_count;
herr_t ret_value = SUCCEED;
FUNC_ENTER_STATIC
@@ -944,20 +947,17 @@ H5C__collective_write(H5F_t *f)
if(H5CX_get_io_xfer_mode(&orig_xfer_mode) < 0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode")
+ /* Set transfer mode */
+ if(H5CX_set_io_xfer_mode(H5FD_MPIO_COLLECTIVE) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode")
+
/* Get number of entries in collective write list */
count = (int)H5SL_count(cache_ptr->coll_write_list);
-
if(count > 0) {
- H5FD_mpio_xfer_t xfer_mode = H5FD_MPIO_COLLECTIVE;
H5SL_node_t *node;
H5C_cache_entry_t *entry_ptr;
- void *base_buf;
int i;
- /* Set new transfer mode */
- if(H5CX_set_io_xfer_mode(xfer_mode) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode")
-
/* Allocate arrays */
if(NULL == (length_array = (int *)H5MM_malloc((size_t)count * sizeof(int))) )
HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for collective write table length array")
@@ -981,7 +981,6 @@ H5C__collective_write(H5F_t *f)
node = H5SL_next(node);
i = 1;
while(node) {
-
if(NULL == (entry_ptr = (H5C_cache_entry_t *)H5SL_item(node)))
HGOTO_ERROR(H5E_CACHE, H5E_NOTFOUND, FAIL, "can't retrieve skip list item")
@@ -998,67 +997,39 @@ H5C__collective_write(H5F_t *f)
/* Create memory MPI type */
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed(count, length_array, buf_array, MPI_BYTE, &btype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
-
btype_created = TRUE;
-
if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&btype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
/* Create file MPI type */
if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed(count, length_array, offset_array, MPI_BYTE, &ftype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
-
ftype_created = TRUE;
-
if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&ftype)))
HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
- /* Pass buf type, file type to the file driver */
- if(H5CX_set_mpi_coll_datatypes(btype, ftype) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_CANTSET, FAIL, "can't set MPI-I/O properties")
-
- /* Write data */
- if(H5F_block_write(f, H5FD_MEM_DEFAULT, (haddr_t)0, (size_t)1, base_buf) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to write entries collectively")
-
+ /* MPI count to write */
+ buf_count = 1;
} /* end if */
else {
- MPI_Status mpi_stat;
- MPI_File *mpi_fh_p;
- MPI_File mpi_fh;
- MPI_Info *info_p;
- MPI_Info info;
-
-/* This should be rewritten to call H5F_block_write, with the correct
- * buffer and file datatypes (null ones). -QAK, 2018/02/21
- */
- if(H5F_get_mpi_handle(f, (MPI_File **)&mpi_fh_p) < 0)
- HGOTO_ERROR(H5E_CACHE, H5E_CANTGET, FAIL, "can't get mpi file handle")
-
- mpi_fh = *(MPI_File*)mpi_fh_p;
-
- if(H5F_get_mpi_info(f, &info_p) < 0)
- HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get mpi file info")
+ /* Pass trivial buf type, file type to the file driver */
+ btype = MPI_BYTE;
+ ftype = MPI_BYTE;
- info = *info_p;
+ /* Set non-NULL pointer for I/O operation */
+ base_buf = &unused;
- /* just to match up with the 1st MPI_File_set_view from
- * H5FD_mpio_write()
- */
- if(MPI_SUCCESS != (mpi_code = MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE, MPI_BYTE, "native", info)))
- HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
+ /* MPI count to write */
+ buf_count = 0;
+ } /* end else */
- /* just to match up with MPI_File_write_at_all from H5FD_mpio_write() */
- HDmemset(&mpi_stat, 0, sizeof(MPI_Status));
- if(MPI_SUCCESS != (mpi_code = MPI_File_write_at_all(mpi_fh, (MPI_Offset)0, NULL, 0, MPI_BYTE, &mpi_stat)))
- HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at_all failed", mpi_code)
+ /* Pass buf type, file type to the file driver */
+ if(H5CX_set_mpi_coll_datatypes(btype, ftype) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTSET, FAIL, "can't set MPI-I/O properties")
- /* just to match up with the 2nd MPI_File_set_view (reset) in
- * H5FD_mpio_write()
- */
- if(MPI_SUCCESS != (mpi_code = MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE, MPI_BYTE, "native", info)))
- HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
- } /* end else */
+ /* Write data */
+ if(H5F_block_write(f, H5FD_MEM_DEFAULT, (haddr_t)0, buf_count, base_buf) < 0)
+ HGOTO_ERROR(H5E_CACHE, H5E_WRITEERROR, FAIL, "unable to write entries collectively")
done:
/* Free arrays */
diff --git a/src/H5Cprivate.h b/src/H5Cprivate.h
index f82f8df..8b42949 100644
--- a/src/H5Cprivate.h
+++ b/src/H5Cprivate.h
@@ -2333,12 +2333,9 @@ H5_DLL herr_t H5C_dump_cache_LRU(H5C_t *cache_ptr, const char *cache_name);
H5_DLL hbool_t H5C_get_serialization_in_progress(const H5C_t *cache_ptr);
H5_DLL hbool_t H5C_cache_is_clean(const H5C_t *cache_ptr, H5C_ring_t inner_ring);
H5_DLL herr_t H5C_dump_cache_skip_list(H5C_t *cache_ptr, char *calling_fcn);
-#ifdef H5_HAVE_PARALLEL
-H5_DLL herr_t H5C_dump_coll_write_list(H5C_t * cache_ptr, char * calling_fcn);
-#endif /* H5_HAVE_PARALLEL */
H5_DLL herr_t H5C_get_entry_ptr_from_addr(H5C_t *cache_ptr, haddr_t addr,
void **entry_ptr_ptr);
-H5_DLL herr_t H5C_flush_dependency_exists(H5C_t *cache_ptr, haddr_t parent_addr,
+H5_DLL herr_t H5C_flush_dependency_exists(H5C_t *cache_ptr, haddr_t parent_addr,
haddr_t child_addr, hbool_t *fd_exists_ptr);
H5_DLL herr_t H5C_verify_entry_type(H5C_t *cache_ptr, haddr_t addr,
const H5C_class_t *expected_type, hbool_t *in_cache_ptr,
diff --git a/src/H5FDmpi.c b/src/H5FDmpi.c
index 43fa340..3cdbc32 100644
--- a/src/H5FDmpi.c
+++ b/src/H5FDmpi.c
@@ -141,42 +141,6 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5FD_get_mpi_info
- *
- * Purpose: Retrieves the file's mpi info
- *
- * Return: Success: SUCCEED
- *
- * Failure: FAIL
- *
- * Programmer: John Mainzer
- * 4/4/17
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5FD_get_mpi_info(H5FD_t *file, void** mpi_info)
-{
- const H5FD_class_mpi_t *cls;
- herr_t ret_value = SUCCEED;
-
- FUNC_ENTER_NOAPI_NOINIT
-
- HDassert(file);
- cls = (const H5FD_class_mpi_t *)(file->cls);
- HDassert(cls);
- HDassert(cls->get_mpi_info); /* All MPI drivers must implement this */
-
- /* Dispatch to driver */
- if((ret_value = (cls->get_mpi_info)(file, mpi_info)) < 0)
- HGOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "driver get_mpi_info request failed")
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5FD_get_mpi_info() */
-
-
-/*-------------------------------------------------------------------------
* Function: H5FD_mpi_MPIOff_to_haddr
*
* Purpose: Convert an MPI_Offset value to haddr_t.
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index 9475093..319e528 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -91,7 +91,6 @@ static herr_t H5FD__mpio_truncate(H5FD_t *_file, hid_t dxpl_id, hbool_t closing)
static int H5FD__mpio_mpi_rank(const H5FD_t *_file);
static int H5FD__mpio_mpi_size(const H5FD_t *_file);
static MPI_Comm H5FD__mpio_communicator(const H5FD_t *_file);
-static herr_t H5FD__mpio_get_info(H5FD_t *_file, void** mpi_info);
/* The MPIO file driver information */
static const H5FD_class_mpi_t H5FD_mpio_g = {
@@ -131,8 +130,7 @@ static const H5FD_class_mpi_t H5FD_mpio_g = {
}, /* End of superclass information */
H5FD__mpio_mpi_rank, /*get_rank */
H5FD__mpio_mpi_size, /*get_size */
- H5FD__mpio_communicator, /*get_comm */
- H5FD__mpio_get_info /*get_info */
+ H5FD__mpio_communicator /*get_comm */
};
#ifdef H5FDmpio_DEBUG
diff --git a/src/H5FDprivate.h b/src/H5FDprivate.h
index 7d5b66d..c5d1be1 100644
--- a/src/H5FDprivate.h
+++ b/src/H5FDprivate.h
@@ -51,7 +51,6 @@ typedef struct H5FD_class_mpi_t {
int (*get_rank)(const H5FD_t *file); /* Get the MPI rank of a process */
int (*get_size)(const H5FD_t *file); /* Get the MPI size of a communicator */
MPI_Comm (*get_comm)(const H5FD_t *file); /* Get the communicator for a file */
- herr_t (*get_mpi_info)(H5FD_t *file, void** mpi_info); /* get MPI_Info for a file */
} H5FD_class_mpi_t;
#endif
@@ -163,7 +162,6 @@ H5_DLL herr_t H5FD_get_mpio_atomicity(H5FD_t *file, hbool_t *flag);
H5_DLL int H5FD_mpi_get_rank(const H5FD_t *file);
H5_DLL int H5FD_mpi_get_size(const H5FD_t *file);
H5_DLL MPI_Comm H5FD_mpi_get_comm(const H5FD_t *_file);
-H5_DLL herr_t H5FD_get_mpi_info(H5FD_t *file, void** file_info);
#endif /* H5_HAVE_PARALLEL */
#endif /* !_H5FDprivate_H */
diff --git a/src/H5Fmpi.c b/src/H5Fmpi.c
index 8189821..02f93f7 100644
--- a/src/H5Fmpi.c
+++ b/src/H5Fmpi.c
@@ -434,33 +434,5 @@ H5F_mpi_retrieve_comm(hid_t loc_id, hid_t acspl_id, MPI_Comm *mpi_comm)
done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5F_mpi_retrieve_comm */
-
-
-/*-------------------------------------------------------------------------
- * Function: H5F_get_mpi_info
- *
- * Purpose: Retrieves MPI File info.
- *
- * Return: Success: The size (positive)
- * Failure: Negative
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5F_get_mpi_info(const H5F_t *f, MPI_Info **f_info)
-{
- herr_t ret_value = SUCCEED;
-
- FUNC_ENTER_NOAPI(FAIL)
-
- HDassert(f && f->shared);
-
- /* Dispatch to driver */
- if ((ret_value = H5FD_get_mpi_info(f->shared->lf, (void **)f_info)) < 0)
- HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get mpi file info")
-
-done:
- FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5F_get_mpi_info() */
#endif /* H5_HAVE_PARALLEL */
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 9deba8c..6e80f4b 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -861,7 +861,6 @@ H5_DLL MPI_Comm H5F_mpi_get_comm(const H5F_t *f);
H5_DLL int H5F_shared_mpi_get_size(const H5F_shared_t *f_sh);
H5_DLL int H5F_mpi_get_size(const H5F_t *f);
H5_DLL herr_t H5F_mpi_retrieve_comm(hid_t loc_id, hid_t acspl_id, MPI_Comm *mpi_comm);
-H5_DLL herr_t H5F_get_mpi_info(const H5F_t *f, MPI_Info **f_info);
H5_DLL herr_t H5F_get_mpi_atomicity(H5F_t *file, hbool_t *flag);
H5_DLL herr_t H5F_set_mpi_atomicity(H5F_t *file, hbool_t flag);
#endif /* H5_HAVE_PARALLEL */