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-rw-r--r--src/H5Fistore.c78
1 files changed, 49 insertions, 29 deletions
diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index 0bba74e..f36b6200 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -1758,7 +1758,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
chunk_addr!=HADDR_UNDEF)
-#ifdef H5_HAVE_PARALLEL
/*
* If MPIO or MPIPOSIX is used and file can be written to, we must bypass the
* chunk-cache scheme because other MPI processes could be writing to
@@ -1766,7 +1765,6 @@ H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
* Do a direct write-through of only the elements requested.
*/
|| ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags))
-#endif /* H5_HAVE_PARALLEL */
) {
H5O_layout_t l; /* temporary layout */
@@ -1942,14 +1940,12 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
chunk_addr!=HADDR_UNDEF)
-#ifdef H5_HAVE_PARALLEL
/*
* If MPIO or MPIPOSIX is used, must bypass the chunk-cache scheme because other
* MPI processes could be writing to other elements in the same chunk.
* Do a direct write-through of only the elements requested.
*/
|| ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f)) && (H5F_ACC_RDWR & f->shared->flags))
-#endif /* H5_HAVE_PARALLEL */
) {
H5O_layout_t l; /* temporary layout */
@@ -2334,6 +2330,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
H5P_genplist_t *dx_plist; /* Data xfer property list */
double split_ratios[3];/* B-tree node splitting ratios */
#ifdef H5_HAVE_PARALLEL
+ MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */
int mpi_rank=(-1); /* This process's rank */
int mpi_size=(-1); /* Total # of processes */
int mpi_round=0; /* Current process responsible for I/O */
@@ -2342,6 +2339,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */
#endif /* H5_HAVE_PARALLEL */
int carry; /* Flag to indicate that chunk increment carrys to higher dimension (sorta) */
+ unsigned chunk_exists; /* Flag to indicate whether a chunk exists already */
int i; /* Local index variable */
unsigned u; /* Local index variable */
herr_t ret_value=SUCCEED; /* Return value */
@@ -2374,6 +2372,11 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
#ifdef H5_HAVE_PARALLEL
/* Retrieve up MPI parameters */
if(IS_H5FD_MPIO(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpio_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
+ /* Get the MPI rank & size */
if ((mpi_rank=H5FD_mpio_mpi_rank(f->shared->lf))<0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
if ((mpi_size=H5FD_mpio_mpi_size(f->shared->lf))<0)
@@ -2384,6 +2387,10 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
} /* end if */
else {
if(IS_H5FD_MPIPOSIX(f)) {
+ /* Get the MPI communicator */
+ if (MPI_COMM_NULL == (mpi_comm=H5FD_mpiposix_communicator(f->shared->lf)))
+ HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator");
+
/* Get the MPI rank & size */
if ((mpi_rank=H5FD_mpiposix_mpi_rank(f->shared->lf))<0)
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank");
@@ -2396,12 +2403,6 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
} /* end else */
#endif /* H5_HAVE_PARALLEL */
-#ifdef H5_HAVE_PARALLEL
- /* Can't use data I/O pipeline in parallel (yet) */
- if (using_mpi && pline.nfilters>0)
- HGOTO_ERROR(H5E_STORAGE, H5E_UNSUPPORTED, FAIL, "can't use data pipeline in parallel");
-#endif /* H5_HAVE_PARALLEL */
-
/*
* Setup indice to go through all chunks. (Future improvement
* should allocate only chunks that have no file space assigned yet.
@@ -2450,8 +2451,32 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
/* Loop over all chunks */
carry=0;
while (carry==0) {
- /* Check if the chunk exists yet */
+ /* Check if the chunk exists yet on disk */
+ chunk_exists=1;
if(H5F_istore_get_addr(f,layout,chunk_offset)==HADDR_UNDEF) {
+ H5F_rdcc_t *rdcc = &(f->shared->rdcc); /*raw data chunk cache */
+ H5F_rdcc_ent_t *ent = NULL; /*cache entry */
+
+ /* Didn't find the chunk on disk */
+ chunk_exists = 0;
+
+ /* Look for chunk in cache */
+ for(ent = rdcc->head; ent && !chunk_exists; ent = ent->next) {
+ /* Make certain we are dealing with the correct B-tree, etc */
+ if (layout->ndims==ent->layout->ndims &&
+ H5F_addr_eq(layout->addr, ent->layout->addr)) {
+
+ /* Assume a match */
+ chunk_exists = 1;
+ for(u = 0; u < layout->ndims && chunk_exists; u++) {
+ if(ent->offset[u] != chunk_offset[u])
+ chunk_exists = 0; /* Reset if no match */
+ } /* end for */
+ } /* end if */
+ } /* end for */
+ } /* end if */
+
+ if(!chunk_exists) {
/* Initialize the chunk information */
udata.mesg = *layout;
udata.key.filter_mask = 0;
@@ -2507,17 +2532,8 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
* still writing out chunks and other processes race ahead to read
* them in, getting bogus data.
*/
- if(IS_H5FD_MPIO(f)) {
- if (MPI_SUCCESS != (mpi_code=MPI_Barrier(H5FD_mpio_communicator(f->shared->lf))))
- HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
- } /* end if */
- else {
- /* Sanity Check */
- assert(IS_H5FD_MPIPOSIX(f));
-
- if (MPI_SUCCESS!=(mpi_code=MPI_Barrier(H5FD_mpiposix_communicator(f->shared->lf))))
- HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
- } /* end else */
+ if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm)))
+ HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code);
} /* end if */
#endif /* H5_HAVE_PARALLEL */
@@ -2662,13 +2678,17 @@ H5F_istore_prune_by_extent(H5F_t *f, const H5O_layout_t *layout, const H5S_t * s
for(ent = rdcc->head; ent; ent = next) {
next = ent->next;
- found = 0;
- for(u = 0; u < ent->layout->ndims - 1; u++) {
- if((hsize_t)ent->offset[u] > curr_dims[u]) {
- found = 1;
- break;
- }
- }
+ /* Make certain we are dealing with the correct B-tree, etc */
+ if (layout->ndims==ent->layout->ndims &&
+ H5F_addr_eq(layout->addr, ent->layout->addr)) {
+ found = 0;
+ for(u = 0; u < ent->layout->ndims - 1; u++) {
+ if((hsize_t)ent->offset[u] > curr_dims[u]) {
+ found = 1;
+ break;
+ }
+ }
+ } /* end if */
if(found) {
#if defined (H5F_ISTORE_DEBUG)
generated by cgit v0.12 at 2024-11-03 11:00:16 (GMT)