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[svn-r5690] Purpose:

Browse Source 
Bug Fix

Description:
    When parallel I/O is used, the MPI-I/O VFL driver uses a "lazy" model to
    call MPI_File_set_view() in order to reduce the number of calls to this
    function.  However, this is unsafe, because if a collective I/O which uses
    MPI derived types (and thus uses MPI_File_set_view()) is immediately
    followed by an independent I/O, the code will attempt to call
    MPI_File_set_view() in order to switch back to the default view of the
    file.  MPI_File_set_view() is a collective call however, and this causes
    the application to hang.

Solution:
    Removed "lazy" MPI_File_set_view() code, instead set the file view when it
    is needed (with MPI derived types) and immediately set the file view back to
    the default view before leaving the I/O routine.

Platforms tested:
    IRIX64 6.5 (modi4) w/parallel.  Also, tested with the latest development
    and release code for the SAF library, which now works correctly with this
    change.  (Although the release branch of the SAF library seems to have a
    bug, this 1.4.4 release candidate code gets as far as the version the SAF
    library is released on top of (1.4.2-patch1, I believe)).
This commit is contained in:
Quincey Koziol 2002-06-24 08:47:14 -05:00
parent 4e184b81a2
commit ace1f474b7
2 changed files with 45 additions and 29 deletions
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3
release_docs/RELEASE.txt
View File

@ -35,6 +35,9 @@ Bug Fixes since HDF5-1.4.0
Library
-------
* Fixed bug in parallel I/O routines where a collective I/O which used
MPI derived types, followed by an independent I/O would cause the library
to hang. QAK 2002/06/24
* Fixed bug in chunking routines where they were using internal allocation
free routines, instead of malloc/free, preventing user filters from
working correctly. Chunks are now allocated/freed with malloc/free and

71
src/H5FDmpio.c
View File

@ -56,7 +56,6 @@ typedef struct H5FD_mpio_t {
haddr_t eof; /*end-of-file marker */
haddr_t eoa; /*end-of-address marker */
haddr_t last_eoa; /* Last known end-of-address marker */
unsigned old_use_view; /*remember value of use_view */
} H5FD_mpio_t;
/* Prototypes */
@ -1178,6 +1177,11 @@ H5FD_mpio_get_eof(H5FD_t *_file)
* the address of the dataset in MPI_File_set_view() calls, as
* necessary.
*
* Quincey Koziol - 2002/06/24
* Removed "lazy" MPI_File_set_view() calls, since they would fail
* if the first I/O was a collective I/O using MPI derived types
* and the next I/O was an independent I/O.
*
*-------------------------------------------------------------------------
*/
static herr_t
@ -1191,7 +1195,7 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t dxpl_id, haddr_t add
MPI_Status mpi_stat;
MPI_Datatype buf_type, file_type;
int size_i, bytes_read, n;
unsigned use_view_this_time=0, used_view_last_time;
unsigned use_view_this_time=0;
H5P_genplist_t *plist; /* Property list pointer */
herr_t ret_value=SUCCEED;
@ -1256,7 +1260,8 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t dxpl_id, haddr_t add
*/
mpi_disp=mpi_off;
mpi_off=0;
} else {
} /* end if */
else {
/*
* Prepare for a simple xfer of a contiguous block of bytes. The
* btype, ftype, and disp fields are not used.
@ -1264,23 +1269,17 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t dxpl_id, haddr_t add
buf_type = MPI_BYTE;
file_type = MPI_BYTE;
mpi_disp = 0; /* mpi_off is alread set */
}
} /* end else */
/*
* Don't bother to reset the view if we're not using the types this time,
* and did we didn't use them last time either.
* Set the file view when we are using MPI derived types
*/
used_view_last_time = file->old_use_view;
if (used_view_last_time || /* change to new ftype or MPI_BYTE */
use_view_this_time) { /* almost certainly a different ftype */
if (use_view_this_time) {
/*OKAY: CAST DISCARDS CONST QUALIFIER*/
if (MPI_SUCCESS != MPI_File_set_view(file->f, mpi_disp, MPI_BYTE, file_type, (char*)"native", file->info))
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "MPI_File_set_view failed");
}
} /* end if */
/* Keep the 'use view' flag around for the next I/O */
file->old_use_view = use_view_this_time;
/* Read the data. */
assert(H5FD_MPIO_INDEPENDENT==dx->xfer_mode || H5FD_MPIO_COLLECTIVE==dx->xfer_mode);
if (H5FD_MPIO_INDEPENDENT==dx->xfer_mode) {
@ -1341,6 +1340,15 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t dxpl_id, haddr_t add
if (bytes_read<0 || bytes_read>size_i)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed");
/*
* Reset the file view when we used MPI derived types
*/
if (use_view_this_time) {
/*OKAY: CAST DISCARDS CONST QUALIFIER*/
if (MPI_SUCCESS != MPI_File_set_view(file->f, 0, MPI_BYTE, MPI_BYTE, (char*)"native", file->info))
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "MPI_File_set_view failed");
} /* end if */
/*
* This gives us zeroes beyond end of physical MPI file. What about
* reading past logical end of HDF5 file???
@ -1471,6 +1479,11 @@ done:
* the address of the dataset in MPI_File_set_view() calls, as
* necessary.
*
* Quincey Koziol - 2002/06/24
* Removed "lazy" MPI_File_set_view() calls, since they would fail
* if the first I/O was a collective I/O using MPI derived types
* and the next I/O was an independent I/O.
*
*-------------------------------------------------------------------------
*/
static herr_t
@ -1484,7 +1497,7 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr,
MPI_Status mpi_stat;
MPI_Datatype buf_type, file_type;
int size_i, bytes_written;
unsigned use_view_this_time=0, used_view_last_time;
unsigned use_view_this_time=0;
H5P_genplist_t *plist; /* Property list pointer */
herr_t ret_value=SUCCEED;
@ -1549,7 +1562,8 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr,
*/
mpi_disp=mpi_off;
mpi_off=0;
} else {
} /* end if */
else {
/*
* Prepare for a simple xfer of a contiguous block of bytes.
* The btype, ftype, and disp fields are not used.
@ -1557,27 +1571,17 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr,
buf_type = MPI_BYTE;
file_type = MPI_BYTE;
mpi_disp = 0; /* mpi_off is already set */
}
} /* end else */
/*
* Don't bother to reset the view if we're not using the types this time,
* and did we didn't use them last time either.
* Set the file view when we are using MPI derived types
*/
used_view_last_time = file->old_use_view;
if (used_view_last_time || /* change to new ftype or MPI_BYTE */
use_view_this_time) { /* almost certainly a different ftype */
if (use_view_this_time) {
/*OKAY: CAST DISCARDS CONST QUALIFIER*/
if (MPI_SUCCESS != MPI_File_set_view(file->f, mpi_disp, MPI_BYTE, file_type, (char*)"native", file->info))
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "MPI_File_set_view failed");
}
} /* end if */
/*
* We always set the use_view flag to 0 because the default is not to
* use types next time, unless someone explicitly requests it by setting
* this flag to !=0.
*/
file->old_use_view = use_view_this_time;
/* Only p<round> will do the actual write if all procs in comm write same data */
if ((type!=H5FD_MEM_DRAW) && H5_mpi_1_metawrite_g) {
if (file->mpi_rank != file->mpi_round) {
@ -1654,6 +1658,15 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr,
if (bytes_written<0 || bytes_written>size_i)
HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file write failed");
/*
* Reset the file view when we used MPI derived types
*/
if (use_view_this_time) {
/*OKAY: CAST DISCARDS CONST QUALIFIER*/
if (MPI_SUCCESS != MPI_File_set_view(file->f, 0, MPI_BYTE, MPI_BYTE, (char*)"native", file->info))
HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "MPI_File_set_view failed");
} /* end if */
/* Forget the EOF value (see H5FD_mpio_get_eof()) --rpm 1999-08-06 */
file->eof = HADDR_UNDEF;