diff options
Diffstat (limited to 'src')
| -rw-r--r-- | src/H5D.c | 13 | ||||
| -rw-r--r-- | src/H5Distore.c | 86 | ||||
| -rw-r--r-- | src/H5Fistore.c | 86 | ||||
| -rw-r--r-- | src/H5Fprivate.h | 2 |
4 files changed, 120 insertions, 67 deletions
@@ -3196,10 +3196,12 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) hsize_t addr; /* Offset in dataset */ void *buf = NULL; /* Buffer for fill value writing */ H5O_fill_t fill; /* Fill value information */ + H5D_space_time_t space_time; /* When to allocate space */ H5P_genplist_t *plist; /* Property list */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOINIT(H5D_init_storage); + assert(dset); assert(space); @@ -3208,6 +3210,8 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset creation property list"); if(H5P_get(plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value"); + if(H5P_get(plist, H5D_CRT_SPACE_TIME_NAME, &space_time) < 0) + HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, NULL, "can't retrieve space allocation time"); switch (dset->layout.type) { case H5D_CONTIGUOUS: @@ -3252,12 +3256,15 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) break; case H5D_CHUNKED: -#ifdef H5_HAVE_PARALLEL /* * If the dataset is accessed via parallel I/O, allocate file space * for all chunks now and initialize each chunk with the fill value. */ - if (IS_H5FD_MPIO(dset->ent.file) || IS_H5FD_MPIPOSIX(dset->ent.file)) { + if (space_time==H5D_SPACE_ALLOC_EARLY +#ifdef H5_HAVE_PARALLEL + || (IS_H5FD_MPIO(dset->ent.file) || IS_H5FD_MPIPOSIX(dset->ent.file)) +#endif /*H5_HAVE_PARALLEL*/ + ) { /* We only handle simple data spaces so far */ int ndims; hsize_t dim[H5O_LAYOUT_NDIMS]; @@ -3271,13 +3278,13 @@ H5D_init_storage(H5D_t *dset, const H5S_t *space) &(dset->layout), dim, plist)<0) HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to allocate all chunks of dataset"); } /* end if */ -#endif /*H5_HAVE_PARALLEL*/ break; } /* end switch */ done: if (buf) H5FL_BLK_FREE(type_conv,buf); + FUNC_LEAVE(ret_value); } diff --git a/src/H5Distore.c b/src/H5Distore.c index 2c6a403..c9dc766 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -2320,7 +2320,6 @@ done: * that they should never be written. *------------------------------------------------------------------------- */ -#ifdef H5_HAVE_PARALLEL herr_t H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, const hsize_t *space_dim, H5P_genplist_t *dc_plist) @@ -2334,11 +2333,14 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, void *chunk=NULL; /* Chunk buffer for writing fill values */ H5P_genplist_t *dx_plist; /* Data xfer property list */ double split_ratios[3];/* B-tree node splitting ratios */ - int mpi_rank; /* This process's rank */ - int mpi_size; /* Total # of processes */ +#ifdef H5_HAVE_PARALLEL + 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 */ int mpi_code; /* MPI return code */ unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */ + 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) */ int i; /* Local index variable */ unsigned u; /* Local index variable */ @@ -2369,9 +2371,36 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, if(H5P_get(dx_plist,H5D_XFER_BTREE_SPLIT_RATIO_NAME,split_ratios)<0) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get B-tree split ratios"); +#ifdef H5_HAVE_PARALLEL + /* Retrieve up MPI parameters */ + if(IS_H5FD_MPIO(f)) { + 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) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + else { + if(IS_H5FD_MPIPOSIX(f)) { + /* 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"); + if ((mpi_size=H5FD_mpiposix_mpi_size(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + +#ifdef H5_HAVE_PARALLEL /* Can't use data I/O pipeline in parallel (yet) */ - if (pline.nfilters>0) + 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 @@ -2404,24 +2433,6 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end else */ } /* end if */ - /* Retrieve up MPI parameters */ - if(IS_H5FD_MPIO(f)) { - 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) - HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); - } /* end if */ - else { - /* Sanity Check */ - assert(IS_H5FD_MPIPOSIX(f)); - - /* 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"); - if ((mpi_size=H5FD_mpiposix_mpi_size(f->shared->lf))<0) - HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); - } /* end else */ - /* Loop over all chunks */ carry=0; while (carry==0) { @@ -2441,15 +2452,26 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, /* Check if fill values should be written to blocks */ if(fill_time != H5D_FILL_TIME_NEVER) { - /* Round-robin write the chunks out from only one process */ - if(mpi_round==mpi_rank) { +#ifdef H5_HAVE_PARALLEL + /* Check if this file is accessed with an MPI-capable file driver */ + if(using_mpi) { + /* Round-robin write the chunks out from only one process */ + if(mpi_round==mpi_rank) { + if (H5F_block_write(f, H5FD_MEM_DRAW, udata.addr, udata.key.nbytes, dxpl_id, chunk)<0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); + } /* end if */ + mpi_round=(++mpi_round)%mpi_size; + + /* Indicate that blocks are being written */ + blocks_written=1; + } /* end if */ + else { +#endif /* H5_HAVE_PARALLEL */ if (H5F_block_write(f, H5FD_MEM_DRAW, udata.addr, udata.key.nbytes, dxpl_id, chunk)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); - } /* end if */ - mpi_round=(++mpi_round)%mpi_size; - - /* Indicate that blocks are being written */ - blocks_written=1; +#ifdef H5_HAVE_PARALLEL + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ } /* end if */ } /* end if */ @@ -2463,8 +2485,10 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end for */ } /* end while */ +#ifdef H5_HAVE_PARALLEL /* Only need to block at the barrier if we actually allocated a chunk */ - if(blocks_written) { + /* And if we are using an MPI-capable file driver */ + if(using_mpi && blocks_written) { /* Wait at barrier to avoid race conditions where some processes are * still writing out chunks and other processes race ahead to read * them in, getting bogus data. @@ -2481,6 +2505,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); } /* end else */ } /* end if */ +#endif /* H5_HAVE_PARALLEL */ done: /* Free the chunk for fill values */ @@ -2489,7 +2514,6 @@ done: FUNC_LEAVE(ret_value); } -#endif /* H5_HAVE_PARALLEL */ /*------------------------------------------------------------------------- diff --git a/src/H5Fistore.c b/src/H5Fistore.c index 2c6a403..c9dc766 100644 --- a/src/H5Fistore.c +++ b/src/H5Fistore.c @@ -2320,7 +2320,6 @@ done: * that they should never be written. *------------------------------------------------------------------------- */ -#ifdef H5_HAVE_PARALLEL herr_t H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, const hsize_t *space_dim, H5P_genplist_t *dc_plist) @@ -2334,11 +2333,14 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, void *chunk=NULL; /* Chunk buffer for writing fill values */ H5P_genplist_t *dx_plist; /* Data xfer property list */ double split_ratios[3];/* B-tree node splitting ratios */ - int mpi_rank; /* This process's rank */ - int mpi_size; /* Total # of processes */ +#ifdef H5_HAVE_PARALLEL + 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 */ int mpi_code; /* MPI return code */ unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */ + 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) */ int i; /* Local index variable */ unsigned u; /* Local index variable */ @@ -2369,9 +2371,36 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, if(H5P_get(dx_plist,H5D_XFER_BTREE_SPLIT_RATIO_NAME,split_ratios)<0) HGOTO_ERROR(H5E_STORAGE, H5E_CANTGET, FAIL, "can't get B-tree split ratios"); +#ifdef H5_HAVE_PARALLEL + /* Retrieve up MPI parameters */ + if(IS_H5FD_MPIO(f)) { + 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) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + else { + if(IS_H5FD_MPIPOSIX(f)) { + /* 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"); + if ((mpi_size=H5FD_mpiposix_mpi_size(f->shared->lf))<0) + HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); + + /* Set the MPI-capable file driver flag */ + using_mpi=1; + } /* end if */ + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ + +#ifdef H5_HAVE_PARALLEL /* Can't use data I/O pipeline in parallel (yet) */ - if (pline.nfilters>0) + 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 @@ -2404,24 +2433,6 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end else */ } /* end if */ - /* Retrieve up MPI parameters */ - if(IS_H5FD_MPIO(f)) { - 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) - HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); - } /* end if */ - else { - /* Sanity Check */ - assert(IS_H5FD_MPIPOSIX(f)); - - /* 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"); - if ((mpi_size=H5FD_mpiposix_mpi_size(f->shared->lf))<0) - HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI size"); - } /* end else */ - /* Loop over all chunks */ carry=0; while (carry==0) { @@ -2441,15 +2452,26 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, /* Check if fill values should be written to blocks */ if(fill_time != H5D_FILL_TIME_NEVER) { - /* Round-robin write the chunks out from only one process */ - if(mpi_round==mpi_rank) { +#ifdef H5_HAVE_PARALLEL + /* Check if this file is accessed with an MPI-capable file driver */ + if(using_mpi) { + /* Round-robin write the chunks out from only one process */ + if(mpi_round==mpi_rank) { + if (H5F_block_write(f, H5FD_MEM_DRAW, udata.addr, udata.key.nbytes, dxpl_id, chunk)<0) + HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); + } /* end if */ + mpi_round=(++mpi_round)%mpi_size; + + /* Indicate that blocks are being written */ + blocks_written=1; + } /* end if */ + else { +#endif /* H5_HAVE_PARALLEL */ if (H5F_block_write(f, H5FD_MEM_DRAW, udata.addr, udata.key.nbytes, dxpl_id, chunk)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file"); - } /* end if */ - mpi_round=(++mpi_round)%mpi_size; - - /* Indicate that blocks are being written */ - blocks_written=1; +#ifdef H5_HAVE_PARALLEL + } /* end else */ +#endif /* H5_HAVE_PARALLEL */ } /* end if */ } /* end if */ @@ -2463,8 +2485,10 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, } /* end for */ } /* end while */ +#ifdef H5_HAVE_PARALLEL /* Only need to block at the barrier if we actually allocated a chunk */ - if(blocks_written) { + /* And if we are using an MPI-capable file driver */ + if(using_mpi && blocks_written) { /* Wait at barrier to avoid race conditions where some processes are * still writing out chunks and other processes race ahead to read * them in, getting bogus data. @@ -2481,6 +2505,7 @@ H5F_istore_allocate(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); } /* end else */ } /* end if */ +#endif /* H5_HAVE_PARALLEL */ done: /* Free the chunk for fill values */ @@ -2489,7 +2514,6 @@ done: FUNC_LEAVE(ret_value); } -#endif /* H5_HAVE_PARALLEL */ /*------------------------------------------------------------------------- diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h index a4a2a3d..dd7cbd9 100644 --- a/src/H5Fprivate.h +++ b/src/H5Fprivate.h @@ -391,12 +391,10 @@ __DLL__ herr_t H5F_seq_writev(H5F_t *f, hid_t dxpl_id, /* Functions that operate on indexed storage */ -#ifdef H5_HAVE_PARALLEL __DLL__ herr_t H5F_istore_allocate (H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout, const hsize_t *space_dim, struct H5P_genplist_t *dc_plist); -#endif /* H5_HAVE_PARALLEL */ __DLL__ hsize_t H5F_istore_allocated(H5F_t *f, unsigned ndims, haddr_t addr); __DLL__ herr_t H5F_istore_dump_btree(H5F_t *f, FILE *stream, unsigned ndims, haddr_t addr); |