diff options
Diffstat (limited to 'src')
-rw-r--r-- | src/Dependencies | 92 | ||||
-rw-r--r-- | src/H5Dio.c | 57 | ||||
-rw-r--r-- | src/H5Distore.c | 4 | ||||
-rw-r--r-- | src/H5Dmpio.c | 10 | ||||
-rw-r--r-- | src/H5Dpkg.h | 2 | ||||
-rw-r--r-- | src/H5Dprivate.h | 31 | ||||
-rw-r--r-- | src/H5S.c | 50 | ||||
-rw-r--r-- | src/H5Shyper.c | 62 | ||||
-rw-r--r-- | src/H5Smpio.c | 355 | ||||
-rw-r--r-- | src/H5Spkg.h | 18 | ||||
-rw-r--r-- | src/H5Sprivate.h | 14 | ||||
-rw-r--r-- | src/H5config.h.in | 10 | ||||
-rw-r--r-- | src/Makefile.in | 26 |
13 files changed, 366 insertions, 365 deletions
diff --git a/src/Dependencies b/src/Dependencies index 80d76d4..0d4a162 100644 --- a/src/Dependencies +++ b/src/Dependencies @@ -430,6 +430,49 @@ H5Distore.lo: \ $(srcdir)/H5MFprivate.h \ $(srcdir)/H5MMprivate.h \ $(srcdir)/H5Vprivate.h +H5Dmpio.lo: \ + $(srcdir)/H5Dmpio.c \ + $(srcdir)/H5private.h \ + $(srcdir)/H5public.h \ + H5pubconf.h \ + $(srcdir)/H5api_adpt.h \ + $(srcdir)/H5MPprivate.h \ + $(srcdir)/H5Dpkg.h \ + $(srcdir)/H5Dprivate.h \ + $(srcdir)/H5Dpublic.h \ + $(srcdir)/H5Ipublic.h \ + $(srcdir)/H5FDprivate.h \ + $(srcdir)/H5FDpublic.h \ + $(srcdir)/H5Fpublic.h \ + $(srcdir)/H5FDmpi.h \ + $(srcdir)/H5FDmpio.h \ + $(srcdir)/H5FDmpiposix.h \ + $(srcdir)/H5Oprivate.h \ + $(srcdir)/H5Opublic.h \ + $(srcdir)/H5Spublic.h \ + $(srcdir)/H5HGprivate.h \ + $(srcdir)/H5HGpublic.h \ + $(srcdir)/H5Fprivate.h \ + $(srcdir)/H5RCprivate.h \ + $(srcdir)/H5Tprivate.h \ + $(srcdir)/H5Tpublic.h \ + $(srcdir)/H5MMpublic.h \ + $(srcdir)/H5Gprivate.h \ + $(srcdir)/H5Gpublic.h \ + $(srcdir)/H5Bprivate.h \ + $(srcdir)/H5Bpublic.h \ + $(srcdir)/H5ACprivate.h \ + $(srcdir)/H5ACpublic.h \ + $(srcdir)/H5RSprivate.h \ + $(srcdir)/H5Rprivate.h \ + $(srcdir)/H5Rpublic.h \ + $(srcdir)/H5Zprivate.h \ + $(srcdir)/H5Zpublic.h \ + $(srcdir)/H5Sprivate.h \ + $(srcdir)/H5Pprivate.h \ + $(srcdir)/H5Ppublic.h \ + $(srcdir)/H5Eprivate.h \ + $(srcdir)/H5Epublic.h H5Dseq.lo: \ $(srcdir)/H5Dseq.c \ $(srcdir)/H5private.h \ @@ -2468,8 +2511,8 @@ H5S.lo: \ $(srcdir)/H5Eprivate.h \ $(srcdir)/H5Epublic.h \ $(srcdir)/H5Ipublic.h \ - $(srcdir)/H5Iprivate.h \ $(srcdir)/H5FLprivate.h \ + $(srcdir)/H5Iprivate.h \ $(srcdir)/H5MMprivate.h \ $(srcdir)/H5MMpublic.h \ $(srcdir)/H5Oprivate.h \ @@ -2602,46 +2645,43 @@ H5Smpio.lo: \ H5pubconf.h \ $(srcdir)/H5api_adpt.h \ $(srcdir)/H5MPprivate.h \ - $(srcdir)/H5Eprivate.h \ - $(srcdir)/H5Epublic.h \ + $(srcdir)/H5Dprivate.h \ + $(srcdir)/H5Dpublic.h \ $(srcdir)/H5Ipublic.h \ - $(srcdir)/H5Fpkg.h \ - $(srcdir)/H5Fprivate.h \ - $(srcdir)/H5Fpublic.h \ - $(srcdir)/H5FDpublic.h \ - $(srcdir)/H5Bpublic.h \ - $(srcdir)/H5FOprivate.h \ - $(srcdir)/H5TBprivate.h \ - $(srcdir)/H5Gprivate.h \ - $(srcdir)/H5Gpublic.h \ - $(srcdir)/H5Opublic.h \ - $(srcdir)/H5Bprivate.h \ - $(srcdir)/H5ACprivate.h \ - $(srcdir)/H5ACpublic.h \ - $(srcdir)/H5RCprivate.h \ - $(srcdir)/H5RSprivate.h \ $(srcdir)/H5FDprivate.h \ + $(srcdir)/H5FDpublic.h \ + $(srcdir)/H5Fpublic.h \ $(srcdir)/H5FDmpi.h \ $(srcdir)/H5FDmpio.h \ $(srcdir)/H5FDmpiposix.h \ - $(srcdir)/H5Iprivate.h \ - $(srcdir)/H5Pprivate.h \ - $(srcdir)/H5Ppublic.h \ - $(srcdir)/H5Dpublic.h \ - $(srcdir)/H5MMpublic.h \ - $(srcdir)/H5Zpublic.h \ $(srcdir)/H5Oprivate.h \ + $(srcdir)/H5Opublic.h \ $(srcdir)/H5Spublic.h \ $(srcdir)/H5HGprivate.h \ $(srcdir)/H5HGpublic.h \ + $(srcdir)/H5Fprivate.h \ + $(srcdir)/H5RCprivate.h \ $(srcdir)/H5Tprivate.h \ $(srcdir)/H5Tpublic.h \ + $(srcdir)/H5MMpublic.h \ + $(srcdir)/H5Gprivate.h \ + $(srcdir)/H5Gpublic.h \ + $(srcdir)/H5Bprivate.h \ + $(srcdir)/H5Bpublic.h \ + $(srcdir)/H5ACprivate.h \ + $(srcdir)/H5ACpublic.h \ + $(srcdir)/H5RSprivate.h \ $(srcdir)/H5Rprivate.h \ $(srcdir)/H5Rpublic.h \ $(srcdir)/H5Zprivate.h \ + $(srcdir)/H5Zpublic.h \ + $(srcdir)/H5Eprivate.h \ + $(srcdir)/H5Epublic.h \ + $(srcdir)/H5Iprivate.h \ + $(srcdir)/H5Pprivate.h \ + $(srcdir)/H5Ppublic.h \ $(srcdir)/H5Spkg.h \ - $(srcdir)/H5Sprivate.h \ - $(srcdir)/H5Dprivate.h + $(srcdir)/H5Sprivate.h H5Snone.lo: \ $(srcdir)/H5Snone.c \ $(srcdir)/H5private.h \ diff --git a/src/H5Dio.c b/src/H5Dio.c index 32e6a28..b59a11f 100644 --- a/src/H5Dio.c +++ b/src/H5Dio.c @@ -21,7 +21,6 @@ #include "H5private.h" /* Generic Functions */ #include "H5Dpkg.h" /* Dataset functions */ #include "H5Eprivate.h" /* Error handling */ -#include "H5FDprivate.h" /* File drivers */ #include "H5FLprivate.h" /* Free Lists */ #include "H5Iprivate.h" /* IDs */ #include "H5MMprivate.h" /* Memory management */ @@ -644,6 +643,8 @@ H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, hbool_t use_par_opt_io=FALSE; /* Whether the 'optimized' I/O routines with be parallel */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed=FALSE; /* Whether the transfer mode was changed */ + int prop_value,new_value; + htri_t check_prop; #endif /*H5_HAVE_PARALLEL*/ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ @@ -756,10 +757,33 @@ H5D_read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, } /* end switch */ /* Get dataspace functions */ - if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags, &use_par_opt_io))) + if (NULL==(sconv=H5S_find(dataset->ent.file, mem_space, file_space, sconv_flags, &use_par_opt_io, &dataset->layout))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from file to memory data space") #ifdef H5_HAVE_PARALLEL +#ifdef H5_HAVE_INSTRUMENTED_LIBRARY + /**** Test for collective chunk IO + notice the following code should be removed after + a more general collective chunk IO algorithm is applied. + */ + + if(dataset->layout.type == H5D_CHUNKED) { /*only check for chunking storage */ + check_prop = H5Pexist(dxpl_id,H5D_XFER_COLL_CHUNK_NAME); + if(check_prop < 0) + HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to check property list"); + if(check_prop > 0) { + if(H5Pget(dxpl_id,H5D_XFER_COLL_CHUNK_NAME,&prop_value)<0) + HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to get property value"); + if(!use_par_opt_io) { + new_value = 0; + if(H5Pset(dxpl_id,H5D_XFER_COLL_CHUNK_NAME,&new_value)<0) + HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to set property value"); + } + } + } + /* end Test for collective chunk IO */ +#endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ + /* Don't reset the transfer mode if we can't or won't use it */ if(!use_par_opt_io || !H5T_path_noop(tpath)) H5D_io_assist_mpio(dxpl_id, dxpl_cache, &xfer_mode_changed); @@ -846,6 +870,8 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, hbool_t use_par_opt_io=FALSE; /* Whether the 'optimized' I/O routines with be parallel */ #ifdef H5_HAVE_PARALLEL hbool_t xfer_mode_changed=FALSE; /* Whether the transfer mode was changed */ + int prop_value,new_value; + htri_t check_prop; #endif /*H5_HAVE_PARALLEL*/ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */ H5D_dxpl_cache_t *dxpl_cache=&_dxpl_cache; /* Data transfer property cache */ @@ -978,10 +1004,33 @@ H5D_write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space, } /* end switch */ /* Get dataspace functions */ - if (NULL==(sconv=H5S_find(mem_space, file_space, sconv_flags, &use_par_opt_io))) + if (NULL==(sconv=H5S_find(dataset->ent.file, mem_space, file_space, sconv_flags, &use_par_opt_io, &dataset->layout))) HGOTO_ERROR (H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert from memory to file data space") #ifdef H5_HAVE_PARALLEL +#ifdef H5_HAVE_INSTRUMENTED_LIBRARY + /**** Test for collective chunk IO + notice the following code should be removed after + a more general collective chunk IO algorithm is applied. + */ + + if(dataset->layout.type == H5D_CHUNKED) { /*only check for chunking storage */ + + check_prop = H5Pexist(dxpl_id,H5D_XFER_COLL_CHUNK_NAME); + if(check_prop < 0) + HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to check property list"); + if(check_prop > 0) { + if(H5Pget(dxpl_id,H5D_XFER_COLL_CHUNK_NAME,&prop_value)<0) + HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to get property value"); + if(!use_par_opt_io) { + new_value = 0; + if(H5Pset(dxpl_id,H5D_XFER_COLL_CHUNK_NAME,&new_value)<0) + HGOTO_ERROR(H5E_PLIST, H5E_UNSUPPORTED, FAIL, "unable to set property value"); + } + } + } +#endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ + /* Don't reset the transfer mode if we can't or won't use it */ if(!use_par_opt_io || !H5T_path_noop(tpath)) H5D_io_assist_mpio(dxpl_id, dxpl_cache, &xfer_mode_changed); @@ -2494,7 +2543,7 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp } /* end if */ } /* end else */ -#ifdef QAK +#ifdef QAK { int mpi_rank; double time; diff --git a/src/H5Distore.c b/src/H5Distore.c index 136ed69..daa2582 100644 --- a/src/H5Distore.c +++ b/src/H5Distore.c @@ -146,8 +146,6 @@ typedef struct H5D_istore_ud1_t { #define H5D_HASH(D,ADDR) H5F_addr_hash(ADDR,(D)->cache.chunk.nslots) /* Private prototypes */ -static haddr_t H5D_istore_get_addr(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, - const hssize_t offset[], H5D_istore_ud1_t *_udata); static void *H5D_istore_chunk_alloc(size_t size, const H5O_pline_t *pline); static void *H5D_istore_chunk_xfree(void *chk, const H5O_pline_t *pline); static herr_t H5D_istore_shared_free (void *page); @@ -2164,7 +2162,7 @@ done: * *------------------------------------------------------------------------- */ -static haddr_t +haddr_t H5D_istore_get_addr(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, const hssize_t offset[], H5D_istore_ud1_t *_udata) { diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c index 581a20a..e8da931 100644 --- a/src/H5Dmpio.c +++ b/src/H5Dmpio.c @@ -39,6 +39,10 @@ #ifdef H5_HAVE_PARALLEL +/* Interface initialization */ +#define INTERFACE_INIT NULL +static int interface_initialize_g = 0; + static herr_t H5D_mpio_spaces_xfer(H5F_t *f, const H5D_t *dset, size_t elmt_size, const H5S_t *file_space, const H5S_t *mem_space, @@ -219,11 +223,12 @@ H5D_mpio_spaces_read(H5F_t *f, const H5D_dxpl_cache_t UNUSED *dxpl_cache, hid_t { herr_t ret_value; - FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_spaces_read); + FUNC_ENTER_NOAPI(H5D_mpio_spaces_read, FAIL); ret_value = H5D_mpio_spaces_xfer(f, dset, elmt_size, file_space, mem_space, dxpl_id, buf, store, 0/*read*/); +done: FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_mpio_spaces_read() */ @@ -257,12 +262,13 @@ H5D_mpio_spaces_write(H5F_t *f, const H5D_dxpl_cache_t UNUSED *dxpl_cache, hid_t { herr_t ret_value; - FUNC_ENTER_NOAPI_NOFUNC(H5D_mpio_spaces_write); + FUNC_ENTER_NOAPI(H5D_mpio_spaces_write, FAIL); /*OKAY: CAST DISCARDS CONST QUALIFIER*/ ret_value = H5D_mpio_spaces_xfer(f, dset, elmt_size, file_space, mem_space, dxpl_id, (void*)buf, store, 1/*write*/); +done: FUNC_LEAVE_NOAPI(ret_value); } /* end H5D_mpio_spaces_write() */ #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h index e1d4b71..30183c3 100644 --- a/src/H5Dpkg.h +++ b/src/H5Dpkg.h @@ -33,7 +33,7 @@ /* Other private headers needed by this file */ #include "H5Gprivate.h" /* Groups */ #include "H5Oprivate.h" /* Object headers */ -#include "H5Sprivate.h" /* Dataspace functions */ +#include "H5Sprivate.h" /* Dataspaces */ #include "H5Tprivate.h" /* Datatype functions */ /**************************/ diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h index 163c1a6..f8fef09 100644 --- a/src/H5Dprivate.h +++ b/src/H5Dprivate.h @@ -154,6 +154,12 @@ #define H5D_XFER_FILTER_CB_NAME "filter_cb" #define H5D_XFER_FILTER_CB_SIZE sizeof(H5Z_cb_t) #define H5D_XFER_FILTER_CB_DEF {NULL,NULL} +#ifdef H5_HAVE_INSTRUMENTED_LIBRARY +/* Definitions for collective chunk I/O property */ +#define H5D_XFER_COLL_CHUNK_NAME "coll_chunk" +#define H5D_XFER_COLL_CHUNK_SIZE sizeof(unsigned) +#define H5D_XFER_COLL_CHUNK_DEF 1 +#endif /* H5_HAVE_INSTRUMENTED_LIBRARY */ /****************************/ /* Library Private Typedefs */ @@ -247,6 +253,9 @@ H5_DLL ssize_t H5D_compact_writevv(H5F_t *f, hid_t dxpl_id, H5D_t *dset, size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_size_arr[], hsize_t mem_offset_arr[], const void *buf); +/* forward reference for collective-chunk IO use */ +struct H5D_istore_ud1_t; /*define at H5Distore.c*/ + /* Functions that operate on indexed storage */ H5_DLL herr_t H5D_istore_delete(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout); @@ -260,7 +269,29 @@ H5_DLL ssize_t H5D_istore_writevv(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[], size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[], const void *buf); +H5_DLL haddr_t H5D_istore_get_addr(H5F_t *f, hid_t dxpl_id, + const H5O_layout_t *layout, const hssize_t offset[], + struct H5D_istore_ud1_t *_udata); H5_DLL herr_t H5D_istore_debug(H5F_t *f, hid_t dxpl_id, haddr_t addr, FILE * stream, int indent, int fwidth, int ndims); +#ifdef H5_HAVE_PARALLEL +/* Forward references */ +struct H5S_t; + +/* MPI-IO function to read directly from app buffer to file rky980813 */ +H5_DLL herr_t H5D_mpio_spaces_read(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, + H5D_t *dset, const H5D_storage_t *store, + size_t nelmts, size_t elmt_size, + const struct H5S_t *file_space, const struct H5S_t *mem_space, + void *buf/*out*/); + +/* MPI-IO function to write directly from app buffer to file rky980813 */ +H5_DLL herr_t H5D_mpio_spaces_write(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, + H5D_t *dset, const H5D_storage_t *store, + size_t nelmts, size_t elmt_size, + const struct H5S_t *file_space, const struct H5S_t *mem_space, + const void *buf); +#endif /* H5_HAVE_PARALLEL */ + #endif @@ -14,14 +14,18 @@ #define H5S_PACKAGE /*suppress error about including H5Spkg */ +/* Pablo information */ +/* (Put before include files to avoid problems with inline functions) */ +#define PABLO_MASK H5S_mask + #define _H5S_IN_H5S_C -#include "H5private.h" /* Generic Functions */ -#include "H5Eprivate.h" /* Error handling */ -#include "H5Iprivate.h" /* ID Functions */ -#include "H5FLprivate.h" /* Free Lists */ -#include "H5MMprivate.h" /* Memory Management functions */ -#include "H5Oprivate.h" /* object headers */ -#include "H5Spkg.h" /* Dataspace functions */ +#include "H5private.h" /* Generic Functions */ +#include "H5Eprivate.h" /* Error handling */ +#include "H5FLprivate.h" /* Free lists */ +#include "H5Iprivate.h" /* IDs */ +#include "H5MMprivate.h" /* Memory management */ +#include "H5Oprivate.h" /* Object headers */ +#include "H5Spkg.h" /* Dataspaces */ /* Local static function prototypes */ static H5S_t * H5S_create(H5S_class_t type); @@ -30,7 +34,6 @@ static herr_t H5S_set_extent_simple (H5S_t *space, unsigned rank, static htri_t H5S_is_simple(const H5S_t *sdim); /* Interface initialization */ -#define PABLO_MASK H5S_mask #define INTERFACE_INIT H5S_init_interface static int interface_initialize_g = 0; static herr_t H5S_init_interface(void); @@ -1403,7 +1406,12 @@ done: *------------------------------------------------------------------------- */ H5S_conv_t * -H5S_find (const H5S_t *mem_space, const H5S_t *file_space, unsigned +H5S_find (const H5F_t +#ifndef H5_HAVE_PARALLEL +UNUSED +#endif/* H5_HAVE_PARALLEL*/ +*file, +const H5S_t *mem_space, const H5S_t *file_space, unsigned #ifndef H5_HAVE_PARALLEL UNUSED #endif /* H5_HAVE_PARALLEL */ @@ -1411,7 +1419,13 @@ flags, hbool_t #ifndef H5_HAVE_PARALLEL UNUSED #endif /* H5_HAVE_PARALLEL */ -*use_par_opt_io) +*use_par_opt_io, +#ifndef H5_HAVE_PARALLEL +UNUSED +#endif +const H5O_layout_t *layout + +) { H5S_conv_t *path=NULL; /* Space conversion path */ #ifdef H5_HAVE_PARALLEL @@ -1441,15 +1455,15 @@ UNUSED /* * Check if we can set direct MPI-IO read/write functions */ - opt=H5S_mpio_opt_possible(mem_space,file_space,flags); + opt=H5S_mpio_opt_possible(file,mem_space,file_space,flags,layout); if(opt==FAIL) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, NULL, "invalid check for contiguous dataspace "); + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, NULL, "invalid check for direct IO dataspace "); /* Check if we can use the optimized parallel I/O routines */ if(opt==TRUE) { /* Set the pointers to the MPI-specific routines */ - H5S_conv_g[i]->read = H5S_mpio_spaces_read; - H5S_conv_g[i]->write = H5S_mpio_spaces_write; + H5S_conv_g[i]->read = H5D_mpio_spaces_read; + H5S_conv_g[i]->write = H5D_mpio_spaces_write; /* Indicate that the I/O will be parallel */ *use_par_opt_io=TRUE; @@ -1483,15 +1497,15 @@ UNUSED /* * Check if we can set direct MPI-IO read/write functions */ - opt=H5S_mpio_opt_possible(mem_space,file_space,flags); + opt=H5S_mpio_opt_possible(file,mem_space,file_space,flags,layout); if(opt==FAIL) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, NULL, "invalid check for contiguous dataspace "); + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, NULL, "invalid check for direct IO dataspace "); /* Check if we can use the optimized parallel I/O routines */ if(opt==TRUE) { /* Set the pointers to the MPI-specific routines */ - path->read = H5S_mpio_spaces_read; - path->write = H5S_mpio_spaces_write; + path->read = H5D_mpio_spaces_read; + path->write = H5D_mpio_spaces_write; /* Indicate that the I/O will be parallel */ *use_par_opt_io=TRUE; diff --git a/src/H5Shyper.c b/src/H5Shyper.c index f468db0..735a339 100644 --- a/src/H5Shyper.c +++ b/src/H5Shyper.c @@ -2295,7 +2295,7 @@ H5S_hyper_span_blocklist(H5S_hyper_span_info_t *spans, hssize_t start[], hssize_ hsize_t u; /* Index variable */ herr_t ret_value=SUCCEED; /* return value */ - FUNC_ENTER_NOAPI(H5S_hyper_span_blocklist, FAIL); + FUNC_ENTER_NOAPI_NOINIT(H5S_hyper_span_blocklist); /* Sanity checks */ assert(spans); @@ -2389,7 +2389,7 @@ done: EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ -herr_t +static herr_t H5S_get_select_hyper_blocklist(H5S_t *space, hbool_t internal, hsize_t startblock, hsize_t numblocks, hsize_t *buf) { H5S_hyper_dim_t *diminfo; /* Alias for dataspace's diminfo information */ @@ -2621,16 +2621,15 @@ H5S_hyper_bounds_helper (const H5S_hyper_span_info_t *spans, const hssize_t *off /* Recurse if this node has down spans */ if(curr->down!=NULL) { - if(H5S_hyper_bounds_helper(curr->down,offset,rank+1,start,end)<0) { - ret_value=FAIL; - break; - } /* end if */ + if(H5S_hyper_bounds_helper(curr->down,offset,rank+1,start,end)<0) + HGOTO_DONE(FAIL) } /* end if */ /* Advance to next node */ curr=curr->next; } /* end while */ +done: FUNC_LEAVE_NOAPI(ret_value); } /* end H5S_hyper_bounds_helper() */ @@ -2913,7 +2912,7 @@ H5S_hyper_is_single(const H5S_t *space) H5S_hyper_span_info_t *spans; /* Hyperslab span info node */ H5S_hyper_span_t *span; /* Hyperslab span node */ unsigned u; /* index variable */ - htri_t ret_value=FALSE; /* return value */ + htri_t ret_value=TRUE; /* return value */ FUNC_ENTER_NOAPI(H5S_hyper_is_single, FAIL); @@ -2926,24 +2925,16 @@ H5S_hyper_is_single(const H5S_t *space) * block (i.e. count==1 in all dimensions) */ - /* Initialize flags */ - ret_value=TRUE; /* assume true and reset if the dimensions don't match */ - /* Check for a single block */ for(u=0; u<space->extent.rank; u++) { - if(space->select.sel_info.hslab->opt_diminfo[u].count>1) { - ret_value=FALSE; - break; - } /* end if */ + if(space->select.sel_info.hslab->opt_diminfo[u].count>1) + HGOTO_DONE(FALSE) } /* end for */ } /* end if */ else { /* * For a region to be single, it must have only one block */ - /* Initialize flags */ - ret_value=TRUE; /* assume true and reset if the dimensions don't match */ - /* Get information for slowest changing information */ spans=space->select.sel_info.hslab->span_lst; @@ -2952,14 +2943,11 @@ H5S_hyper_is_single(const H5S_t *space) span=spans->head; /* Check that this is the only span and it spans the entire dimension */ - if(span->next!=NULL) { - ret_value=FALSE; - break; - } /* end if */ - else { + if(span->next!=NULL) + HGOTO_DONE(FALSE) + else /* Walk down to the next span */ spans=span->down; - } /* end else */ } /* end while */ } /* end else */ @@ -3809,7 +3797,6 @@ static herr_t H5S_hyper_adjust_helper (H5S_hyper_span_info_t *spans, const hssize_t *offset) { H5S_hyper_span_t *span; /* Pointer to current span in span tree */ - herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5S_hyper_adjust_helper); @@ -3834,18 +3821,15 @@ H5S_hyper_adjust_helper (H5S_hyper_span_info_t *spans, const hssize_t *offset) assert(span->high>=0); /* Recursively adjust spans in next dimension down */ - if(span->down!=NULL) { - if(H5S_hyper_adjust_helper(span->down,offset+1)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADSELECT, FAIL, "can't perform hyperslab adjustment"); - } /* end if */ + if(span->down!=NULL) + H5S_hyper_adjust_helper(span->down,offset+1); /* Advance to next span in this dimension */ span=span->next; } /* end while */ } /* end if */ -done: - FUNC_LEAVE_NOAPI(ret_value); + FUNC_LEAVE_NOAPI(SUCCEED); } /* H5S_hyper_adjust_helper() */ @@ -3924,7 +3908,6 @@ static herr_t H5S_hyper_move_helper (H5S_hyper_span_info_t *spans, const hssize_t *offset) { H5S_hyper_span_t *span; /* Pointer to current span in span tree */ - herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT(H5S_hyper_move_helper); @@ -3949,18 +3932,15 @@ H5S_hyper_move_helper (H5S_hyper_span_info_t *spans, const hssize_t *offset) assert(span->low>=0); /* Recursively move spans in next dimension down */ - if(span->down!=NULL) { - if(H5S_hyper_move_helper(span->down,offset+1)<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADSELECT, FAIL, "can't perform hyperslab movement"); - } /* end if */ + if(span->down!=NULL) + H5S_hyper_move_helper(span->down,offset+1); /* Advance to next span in this dimension */ span=span->next; } /* end while */ } /* end if */ -done: - FUNC_LEAVE_NOAPI(ret_value); + FUNC_LEAVE_NOAPI(SUCCEED); } /* H5S_hyper_move_helper() */ @@ -5280,7 +5260,6 @@ H5S_hyper_rebuild (H5S_t *space) H5S_hyper_dim_t *app_diminfo; /* "Application view" per-dimension for the selection */ H5S_hyper_span_t *span; /* Current hyperslab span */ unsigned curr_dim; /* Current dimension being worked on */ - herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5S_hyper_rebuild); @@ -5321,7 +5300,7 @@ H5S_hyper_rebuild (H5S_t *space) space->select.sel_info.hslab->diminfo_valid=TRUE; } /* end if */ - FUNC_LEAVE_NOAPI(ret_value); + FUNC_LEAVE_NOAPI(SUCCEED); } /* H5S_hyper_rebuild() */ @@ -6828,14 +6807,14 @@ H5S_hyper_get_seq_list_opt(const H5S_t *space,H5S_sel_iter_t *iter, EXAMPLES REVISION LOG --------------------------------------------------------------------------*/ -herr_t +static herr_t H5S_hyper_get_seq_list(const H5S_t *space, unsigned UNUSED flags, H5S_sel_iter_t *iter, size_t maxseq, size_t maxelem, size_t *nseq, size_t *nelem, hsize_t *off, size_t *len) { herr_t ret_value; /* return value */ - FUNC_ENTER_NOAPI (H5S_hyper_get_seq_list, FAIL); + FUNC_ENTER_NOAPI_NOINIT(H5S_hyper_get_seq_list); /* Check args */ assert(space); @@ -6855,7 +6834,6 @@ H5S_hyper_get_seq_list(const H5S_t *space, unsigned UNUSED flags, H5S_sel_iter_t /* Call the general sequence generator routine */ ret_value=H5S_hyper_get_seq_list_gen(space,iter,maxseq,maxelem,nseq,nelem,off,len); -done: FUNC_LEAVE_NOAPI(ret_value); } /* end H5S_hyper_get_seq_list() */ diff --git a/src/H5Smpio.c b/src/H5Smpio.c index c8aab2d..bf8f717 100644 --- a/src/H5Smpio.c +++ b/src/H5Smpio.c @@ -21,7 +21,6 @@ * I didn't make them portable. */ -#define H5F_PACKAGE /*suppress error about including H5Fpkg */ #define H5S_PACKAGE /*suppress error about including H5Spkg */ /* Pablo information */ @@ -29,10 +28,12 @@ #define PABLO_MASK H5S_mpio_mask #include "H5private.h" /* Generic Functions */ +#include "H5Dprivate.h" /* Datasets */ #include "H5Eprivate.h" /* Error handling */ -#include "H5Fpkg.h" /* Files */ +#include "H5Fprivate.h" /* File access */ #include "H5FDprivate.h" /* File drivers */ #include "H5Iprivate.h" /* IDs */ +#include "H5Oprivate.h" /* Object headers */ #include "H5Pprivate.h" /* Property lists */ #include "H5Spkg.h" /* Dataspaces */ @@ -63,17 +64,6 @@ H5S_mpio_hyper_type( const H5S_t *space, size_t elmt_size, size_t *count, hsize_t *extra_offset, hbool_t *is_derived_type ); -static herr_t -H5S_mpio_space_type( const H5S_t *space, size_t elmt_size, - /* out: */ - MPI_Datatype *new_type, - size_t *count, - hsize_t *extra_offset, - hbool_t *is_derived_type ); -static herr_t -H5S_mpio_spaces_xfer(H5F_t *f, const H5D_t *dset, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - hid_t dxpl_id, void *buf/*out*/, hbool_t do_write); /*------------------------------------------------------------------------- @@ -522,7 +512,7 @@ done: * *------------------------------------------------------------------------- */ -static herr_t +herr_t H5S_mpio_space_type( const H5S_t *space, size_t elmt_size, /* out: */ MPI_Datatype *new_type, @@ -586,221 +576,6 @@ done: /*------------------------------------------------------------------------- - * Function: H5S_mpio_spaces_xfer - * - * Purpose: Use MPI-IO to transfer data efficiently - * directly between app buffer and file. - * - * Return: non-negative on success, negative on failure. - * - * Programmer: rky 980813 - * - * Notes: - * For collective data transfer only since this would eventually call - * H5FD_mpio_setup to do setup to eveually call MPI_File_set_view in - * H5FD_mpio_read or H5FD_mpio_write. MPI_File_set_view is a collective - * call. Letting independent data transfer use this route would result in - * hanging. - * - * The preconditions for calling this routine are located in the - * H5S_mpio_opt_possible() routine, which determines whether this routine - * can be called for a given dataset transfer. - * - * Modifications: - * rky 980918 - * Added must_convert parameter to let caller know we can't optimize - * the xfer. - * - * Albert Cheng, 001123 - * Include the MPI_type freeing as part of cleanup code. - * - * QAK - 2002/04/02 - * Removed the must_convert parameter and move preconditions to - * H5S_mpio_opt_possible() routine - * - * QAK - 2002/06/17 - * Removed 'disp' parameter from H5FD_mpio_setup routine and use the - * address of the dataset in MPI_File_set_view() calls, as necessary. - * - * QAK - 2002/06/18 - * Removed 'dc_plist' parameter, since it was not used. Also, switch to - * getting the 'extra_offset' setting for each selection. - * - *------------------------------------------------------------------------- - */ -static herr_t -H5S_mpio_spaces_xfer(H5F_t *f, const H5D_t *dset, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - hid_t dxpl_id, void *_buf /*out*/, - hbool_t do_write ) -{ - haddr_t addr; /* Address of dataset (or selection) within file */ - size_t mpi_buf_count, mpi_file_count; /* Number of "objects" to transfer */ - hsize_t mpi_buf_offset, mpi_file_offset; /* Offset within dataset where selection (ie. MPI type) begins */ - MPI_Datatype mpi_buf_type, mpi_file_type; /* MPI types for buffer (memory) and file */ - hbool_t mbt_is_derived=0, /* Whether the buffer (memory) type is derived and needs to be free'd */ - mft_is_derived=0; /* Whether the file type is derived and needs to be free'd */ - hbool_t plist_is_setup=0; /* Whether the dxpl has been customized */ - uint8_t *buf=(uint8_t *)_buf; /* Alias for pointer arithmetic */ - int mpi_code; /* MPI return code */ - herr_t ret_value = SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI_NOINIT(H5S_mpio_spaces_xfer); - - /* Check args */ - assert (f); - assert (dset); - assert (file_space); - assert (mem_space); - assert (buf); - assert (IS_H5FD_MPIO(f)); - /* Make certain we have the correct type of property list */ - assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); - - /* create the MPI buffer type */ - if (H5S_mpio_space_type( mem_space, elmt_size, - /* out: */ - &mpi_buf_type, - &mpi_buf_count, - &mpi_buf_offset, - &mbt_is_derived )<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI buf type"); - - /* create the MPI file type */ - if ( H5S_mpio_space_type( file_space, elmt_size, - /* out: */ - &mpi_file_type, - &mpi_file_count, - &mpi_file_offset, - &mft_is_derived )<0) - HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't create MPI file type"); - - addr = H5D_contig_get_addr(dset) + mpi_file_offset; -#ifdef H5Smpi_DEBUG - HDfprintf(stderr, "spaces_xfer: relative addr=%a\n", addr ); -#endif - - /* - * Pass buf type, file type to the file driver. Request an MPI type - * transfer (instead of an elementary byteblock transfer). - */ - if(H5FD_mpi_setup_collective(dxpl_id, mpi_buf_type, mpi_file_type)<0) - HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set MPI-I/O properties"); - plist_is_setup=1; - - /* Adjust the buffer pointer to the beginning of the selection */ - buf+=mpi_buf_offset; - - /* transfer the data */ - if (do_write) { - if (H5F_block_write(f, H5FD_MEM_DRAW, addr, mpi_buf_count, dxpl_id, buf) <0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,"MPI write failed"); - } else { - if (H5F_block_read (f, H5FD_MEM_DRAW, addr, mpi_buf_count, dxpl_id, buf) <0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,"MPI read failed"); - } - -done: - /* Reset the dxpl settings */ - if(plist_is_setup) { - if(H5FD_mpi_teardown_collective(dxpl_id)<0) - HDONE_ERROR(H5E_DATASPACE, H5E_CANTFREE, FAIL, "unable to reset dxpl values"); - } /* end if */ - - /* free the MPI buf and file types */ - if (mbt_is_derived) { - if (MPI_SUCCESS != (mpi_code= MPI_Type_free( &mpi_buf_type ))) - HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code); - } - if (mft_is_derived) { - if (MPI_SUCCESS != (mpi_code= MPI_Type_free( &mpi_file_type ))) - HMPI_DONE_ERROR(FAIL, "MPI_Type_free failed", mpi_code); - } - - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5S_mpio_spaces_xfer() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_mpio_spaces_read - * - * Purpose: MPI-IO function to read directly from app buffer to file. - * - * Return: non-negative on success, negative on failure. - * - * Programmer: rky 980813 - * - * Modifications: - * - * rky 980918 - * Added must_convert parameter to let caller know we can't optimize the xfer. - * - * QAK - 2002/04/02 - * Removed the must_convert parameter and move preconditions to - * H5S_mpio_opt_possible() routine - * - *------------------------------------------------------------------------- - */ -herr_t -H5S_mpio_spaces_read(H5F_t *f, const H5D_dxpl_cache_t UNUSED *dxpl_cache, hid_t dxpl_id, - H5D_t *dset, const H5D_storage_t UNUSED *store, - size_t UNUSED nelmts, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - void *buf/*out*/) -{ - herr_t ret_value; - - FUNC_ENTER_NOAPI(H5S_mpio_spaces_read, FAIL); - - ret_value = H5S_mpio_spaces_xfer(f, dset, elmt_size, file_space, - mem_space, dxpl_id, buf, 0/*read*/); - -done: - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5S_mpio_spaces_read() */ - - -/*------------------------------------------------------------------------- - * Function: H5S_mpio_spaces_write - * - * Purpose: MPI-IO function to write directly from app buffer to file. - * - * Return: non-negative on success, negative on failure. - * - * Programmer: rky 980813 - * - * Modifications: - * - * rky 980918 - * Added must_convert parameter to let caller know we can't optimize the xfer. - * - * QAK - 2002/04/02 - * Removed the must_convert parameter and move preconditions to - * H5S_mpio_opt_possible() routine - * - *------------------------------------------------------------------------- - */ -herr_t -H5S_mpio_spaces_write(H5F_t *f, const H5D_dxpl_cache_t UNUSED *dxpl_cache, hid_t dxpl_id, - H5D_t *dset, const H5D_storage_t UNUSED *store, - size_t UNUSED nelmts, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - const void *buf) -{ - herr_t ret_value; - - FUNC_ENTER_NOAPI(H5S_mpio_spaces_write, FAIL); - - /*OKAY: CAST DISCARDS CONST QUALIFIER*/ - ret_value = H5S_mpio_spaces_xfer(f, dset, elmt_size, file_space, - mem_space, dxpl_id, (void*)buf, 1/*write*/); - -done: - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5S_mpio_spaces_write() */ - - -/*------------------------------------------------------------------------- * Function: H5S_mpio_opt_possible * * Purpose: Checks if an direct I/O transfer is possible between memory and @@ -817,7 +592,7 @@ done: *------------------------------------------------------------------------- */ htri_t -H5S_mpio_opt_possible( const H5S_t *mem_space, const H5S_t *file_space, const unsigned flags) +H5S_mpio_opt_possible( const H5F_t *file, const H5S_t *mem_space, const H5S_t *file_space, const unsigned flags,const H5O_layout_t *layout) { htri_t c1,c2; /* Flags whether a selection is optimizable */ htri_t ret_value=TRUE; @@ -849,12 +624,126 @@ H5S_mpio_opt_possible( const H5S_t *mem_space, const H5S_t *file_space, const un if (H5S_SEL_POINTS==H5S_GET_SELECT_TYPE(mem_space) || H5S_SEL_POINTS==H5S_GET_SELECT_TYPE(file_space)) HGOTO_DONE(FALSE); - /* Dataset storage must be contiguous currently */ - if ((flags&H5S_CONV_STORAGE_MASK)!=H5S_CONV_STORAGE_CONTIGUOUS) + /* Dataset storage must be contiguous or chunked */ + if ((flags&H5S_CONV_STORAGE_MASK)!=H5S_CONV_STORAGE_CONTIGUOUS && + (flags&H5S_CONV_STORAGE_MASK)!=H5S_CONV_STORAGE_CHUNKED) HGOTO_DONE(FALSE); + if ((flags&H5S_CONV_STORAGE_MASK)==H5S_CONV_STORAGE_CHUNKED) { + hsize_t chunk_dim[H5O_LAYOUT_NDIMS]; /* Chunk dimensions */ + hssize_t startf[H5S_MAX_RANK], /* Selection start bounds */ + endf[H5S_MAX_RANK]; /* Selection end bounds */ + unsigned dim_rankf; /* Number of dimensions of file dataspace */ + int pcheck_hyper,check_hyper, /* Flags for checking if selection is in one chunk */ + tnum_chunkf, /* Number of chunks selection overlaps */ + max_chunkf, /* Maximum number of chunks selection overlaps */ + min_chunkf, /* Minimum number of chunks selection overlaps */ + num_chunks_same; /* Flag indicating whether all processes have the same # of chunks to operate on */ + unsigned dim_chunks; /* Temporary number of chunks in a dimension */ + MPI_Comm comm; /* MPI communicator for file */ + int mpi_rank; /* Rank in MPI communicator */ + int mpi_code; /* MPI return code */ + unsigned u; /* Local index variable */ + + /* Getting MPI communicator and rank */ + if((comm = H5F_mpi_get_comm(file))==MPI_COMM_NULL) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve MPI communicator") + if((mpi_rank = H5F_mpi_get_rank(file))<0) + HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve MPI rank") + + /* Currently collective chunking storage + inside HDF5 is supported for either one of the following two cases: + 1. All the hyperslabs for one process is inside one chunk. + 2. For single hyperslab selection, the number of chunks that covered + the single selection for all processes should be equal. + KY, 2004/7/14 + */ + + /* Quincey, please read. + This is maybe redundant, I think only when both memory and file space be SCALAR + space, the collective IO can work. Otherwise, SELECT_POINT will be reached,collective + IO shouldn't work. + Please clarify and correct the code on the following, + Quincey said that it was probably okay if only one data space is SCALAR, + Still keep the code here until we added more tests later. + Kent */ + if(H5S_SCALAR==mem_space->extent.type || H5S_SCALAR ==file_space->extent.type) { + if(!(H5S_SCALAR==mem_space->extent.type && H5S_SCALAR ==file_space->extent.type)) + HGOTO_DONE(FALSE) + else + HGOTO_DONE(TRUE) + } /* end if */ + + dim_rankf = file_space->extent.rank; + + if(H5S_SELECT_BOUNDS(file_space,startf,endf)==FAIL) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE,FAIL, "invalid check for single selection blocks"); + + for(u=0; u < layout->u.chunk.ndims; u++) + chunk_dim[u] = layout->u.chunk.dim[u]; + + /* Case 1: check whether all hyperslab in this process is inside one chunk. + Note: we don't handle when starting point is less than zero since that may cover + two chunks. */ + + /*for file space checking*/ + pcheck_hyper = 1; + for (u=0; u<dim_rankf; u++) + if(endf[u]/chunk_dim[u]!=startf[u]/chunk_dim[u]) { + pcheck_hyper = 0; + break; + } + + if (MPI_SUCCESS != (mpi_code= MPI_Reduce(&pcheck_hyper,&check_hyper,1,MPI_INT,MPI_LAND,0,comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Reduce failed", mpi_code) + if (MPI_SUCCESS != (mpi_code= MPI_Bcast(&check_hyper,1,MPI_INT,0,comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code) + + /*if check_hyper is true, condition for collective IO case is fulfilled, no + need to do further test. */ + if(check_hyper) + HGOTO_DONE(TRUE); + + /* Case 2:Check whether the number of chunks that covered the single hyperslab is the same. + If not,no collective chunk IO. + KY, 2004/7/14 + */ + + c1 = H5S_SELECT_IS_SINGLE(file_space); + c2 = H5S_SELECT_IS_SINGLE(mem_space); + + if(c1==FAIL || c2 ==FAIL) + HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "invalid check for single selection blocks"); + if(c1==FALSE || c2 ==FALSE) + HGOTO_DONE(FALSE); + + /* Compute the number of chunks covered by the selection on this process */ + tnum_chunkf = 1; + for (u=0; u<dim_rankf; u++) { + dim_chunks = (endf[u]/chunk_dim[u]-startf[u]/chunk_dim[u])+1; + tnum_chunkf = dim_chunks*tnum_chunkf; + } + + /* Determine the minimum and maximum # of chunks for all processes */ + if (MPI_SUCCESS != (mpi_code= MPI_Reduce(&tnum_chunkf,&max_chunkf,1,MPI_INT,MPI_MAX,0,comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Reduce failed", mpi_code) + if (MPI_SUCCESS != (mpi_code= MPI_Reduce(&tnum_chunkf,&min_chunkf,1,MPI_INT,MPI_MIN,0,comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Reduce failed", mpi_code) + + /* Let the rank==0 process determine if the same number of chunks will be operated on by all processes */ + if(mpi_rank == 0) + num_chunks_same = (max_chunkf==min_chunkf); + + /* Broadcast the flag indicating the number of chunks are the same */ + if (MPI_SUCCESS != (mpi_code= MPI_Bcast(&num_chunks_same,1,MPI_INT,0,comm))) + HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code) + + /* Can't handle case when number of chunks is different (yet) */ + if(!num_chunks_same) + HGOTO_DONE(FALSE); + } + done: FUNC_LEAVE_NOAPI(ret_value); } /* H5S_mpio_opt_possible() */ - #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Spkg.h b/src/H5Spkg.h index 82bfec2..ce93770 100644 --- a/src/H5Spkg.h +++ b/src/H5Spkg.h @@ -224,24 +224,10 @@ H5_DLL herr_t H5S_extent_copy(H5S_extent_t *dst, const H5S_extent_t *src); /* Operations on selections */ #ifdef H5_HAVE_PARALLEL -/* MPI-IO function to read directly from app buffer to file rky980813 */ -H5_DLL herr_t H5S_mpio_spaces_read(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, - H5D_t *dset, const H5D_storage_t *store, - size_t nelmts, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - void *buf/*out*/); - -/* MPI-IO function to write directly from app buffer to file rky980813 */ -H5_DLL herr_t H5S_mpio_spaces_write(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, - H5D_t *dset, const H5D_storage_t *store, - size_t nelmts, size_t elmt_size, - const H5S_t *file_space, const H5S_t *mem_space, - const void *buf); - /* MPI-IO function to check if a direct I/O transfer is possible between * memory and the file */ -H5_DLL htri_t H5S_mpio_opt_possible(const H5S_t *mem_space, - const H5S_t *file_space, const unsigned flags); +H5_DLL htri_t H5S_mpio_opt_possible(const H5F_t *file, const H5S_t *mem_space, + const H5S_t *file_space, const unsigned flags, const H5O_layout_t *layout); #endif /* H5_HAVE_PARALLEL */ diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h index 7de895a..efa9b30 100644 --- a/src/H5Sprivate.h +++ b/src/H5Sprivate.h @@ -206,8 +206,8 @@ typedef struct H5S_conv_t { /* Operations on dataspaces */ H5_DLL H5S_t *H5S_copy(const H5S_t *src, hbool_t share_selection); H5_DLL herr_t H5S_close(H5S_t *ds); -H5_DLL H5S_conv_t *H5S_find(const H5S_t *mem_space, const H5S_t *file_space, - unsigned flags, hbool_t *use_par_opt_io); +H5_DLL H5S_conv_t *H5S_find(const H5F_t *file,const H5S_t *mem_space, const H5S_t *file_space, + unsigned flags, hbool_t *use_par_opt_io,const H5O_layout_t *layout ); H5_DLL H5S_class_t H5S_get_simple_extent_type(const H5S_t *ds); H5_DLL hssize_t H5S_get_simple_extent_npoints(const H5S_t *ds); H5_DLL hsize_t H5S_get_npoints_max(const H5S_t *ds); @@ -287,8 +287,6 @@ H5_DLL herr_t H5S_select_elements (H5S_t *space, H5S_seloper_t op, /* Operations on hyperslab selections */ H5_DLL herr_t H5S_select_hyperslab (H5S_t *space, H5S_seloper_t op, const hssize_t start[], const hsize_t *stride, const hsize_t count[], const hsize_t *block); -H5_DLL herr_t H5S_get_select_hyper_blocklist(H5S_t *space, hbool_t internal, - hsize_t startblock, hsize_t numblocks, hsize_t *buf); H5_DLL herr_t H5S_hyper_add_span_element(H5S_t *space, unsigned rank, hssize_t *coords); H5_DLL herr_t H5S_hyper_reset_scratch(H5S_t *space); @@ -314,6 +312,14 @@ H5_DLL herr_t H5S_select_iter_release(H5S_sel_iter_t *sel_iter); /* (Defined in H5S.c) */ H5_DLLVAR hbool_t H5S_mpi_opt_types_g; #endif /* _H5S_IN_H5S_C */ + +H5_DLL herr_t +H5S_mpio_space_type( const H5S_t *space, size_t elmt_size, + /* out: */ + MPI_Datatype *new_type, + size_t *count, + hsize_t *extra_offset, + hbool_t *is_derived_type ); #endif /* H5_HAVE_PARALLEL */ #endif /* _H5Sprivate_H */ diff --git a/src/H5config.h.in b/src/H5config.h.in index f91986b..365122d 100644 --- a/src/H5config.h.in +++ b/src/H5config.h.in @@ -7,6 +7,9 @@ /* Define if `dev_t' is a scalar */ #undef DEV_T_IS_SCALAR +/* Define if gettimeofday() populates the tz pointer passed in */ +#undef GETTIMEOFDAY_GIVES_TZ + /* Define if the __attribute__(()) extension is present */ #undef HAVE_ATTRIBUTE @@ -88,6 +91,10 @@ /* Define to 1 if you have the <gpfs.h> header file. */ #undef HAVE_GPFS_H +/* Define if library will contain instrumentation to detect correct + optimization operation */ +#undef HAVE_INSTRUMENTED_LIBRARY + /* Define to 1 if you have the <inttypes.h> header file. */ #undef HAVE_INTTYPES_H @@ -356,9 +363,6 @@ /* Define if `__tm_gmtoff' is a member of `struct tm' */ #undef HAVE___TM_GMTOFF -/* Define if gettimeofday() populates the tz pointer passed in */ -#undef GETTIMEOFDAY_GIVES_TZ - /* Define if your system's `MPI_File_set_size' function works for files over 2GB. */ #undef MPI_FILE_SET_SIZE_BIG diff --git a/src/Makefile.in b/src/Makefile.in index 96fe515..0458936 100644 --- a/src/Makefile.in +++ b/src/Makefile.in @@ -31,19 +31,19 @@ DISTCLEAN=libhdf5.settings ## Source and object files for the library (lexicographically)... LIB_SRC=H5.c H5A.c H5AC.c H5B.c H5D.c H5Dcontig.c H5Dcompact.c H5Dio.c \ - H5Distore.c H5Dseq.c H5Dtest.c H5E.c H5F.c H5FD.c H5FDcore.c \ - H5FDfamily.c H5FDgass.c H5FDlog.c H5FDmpi.c H5FDmpio.c H5FDmpiposix.c \ - H5FDmulti.c H5FDsec2.c H5FDsrb.c H5FDstdio.c H5FDstream.c H5FL.c \ - H5FO.c H5FS.c H5G.c H5Gent.c H5Gnode.c H5Gstab.c H5HG.c H5HL.c H5HP.c \ - H5I.c H5MF.c H5MM.c H5O.c H5Oattr.c H5Obogus.c H5Ocont.c H5Odtype.c \ - H5Oefl.c H5Ofill.c H5Olayout.c H5Omtime.c H5Oname.c H5Onull.c \ - H5Opline.c H5Osdspace.c H5Oshared.c H5Ostab.c H5P.c H5Pdcpl.c \ - H5Pdxpl.c H5Pfapl.c H5Pfcpl.c H5Ptest.c H5R.c H5RC.c H5RS.c H5S.c \ - H5Sall.c H5Shyper.c H5Smpio.c H5Snone.c H5Spoint.c H5Sselect.c \ - H5Stest.c H5ST.c H5T.c H5Tarray.c H5Tbit.c H5Tcommit.c H5Tcompound.c \ - H5Tconv.c H5Tcset.c H5Tenum.c H5Tfields.c H5Tfixed.c H5Tfloat.c \ - H5Tinit.c H5Tnative.c H5Toffset.c H5Topaque.c H5Torder.c H5Tpad.c \ - H5Tprecis.c H5Tstrpad.c H5Tvlen.c H5TB.c H5TS.c H5V.c H5Z.c \ + H5Distore.c H5Dmpio.c H5Dseq.c H5Dtest.c H5E.c H5F.c H5FD.c \ + H5FDcore.c H5FDfamily.c H5FDgass.c H5FDlog.c H5FDmpi.c H5FDmpio.c \ + H5FDmpiposix.c H5FDmulti.c H5FDsec2.c H5FDsrb.c H5FDstdio.c \ + H5FDstream.c H5FL.c H5FO.c H5FS.c H5G.c H5Gent.c H5Gnode.c H5Gstab.c \ + H5HG.c H5HL.c H5HP.c H5I.c H5MF.c H5MM.c H5O.c H5Oattr.c H5Obogus.c \ + H5Ocont.c H5Odtype.c H5Oefl.c H5Ofill.c H5Olayout.c H5Omtime.c \ + H5Oname.c H5Onull.c H5Opline.c H5Osdspace.c H5Oshared.c H5Ostab.c \ + H5P.c H5Pdcpl.c H5Pdxpl.c H5Pfapl.c H5Pfcpl.c H5Ptest.c H5R.c H5RC.c \ + H5RS.c H5S.c H5Sall.c H5Shyper.c H5Smpio.c H5Snone.c H5Spoint.c \ + H5Sselect.c H5Stest.c H5ST.c H5T.c H5Tarray.c H5Tbit.c H5Tcommit.c \ + H5Tcompound.c H5Tconv.c H5Tcset.c H5Tenum.c H5Tfields.c H5Tfixed.c \ + H5Tfloat.c H5Tinit.c H5Tnative.c H5Toffset.c H5Topaque.c H5Torder.c \ + H5Tpad.c H5Tprecis.c H5Tstrpad.c H5Tvlen.c H5TB.c H5TS.c H5V.c H5Z.c \ H5Zdeflate.c H5Zfletcher32.c H5Zshuffle.c H5Zszip.c LIB_OBJ=$(LIB_SRC:.c=.lo) |