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[svn-r2646] Purpose:

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Bug fix (done by Kim Yates)
Description:
    The optimized mpio code was broken and when read was done, it hanged.
Solution:
H5FDmpio.c:
    In H5FD_mpio_write, moved the 16-line block of code in which
    all procs other than p0 skip the actual write
    to be just before the call to MPI_File_write_at.
    Previously, the values of the local vars that controlled
    "allsame" were not always set correctly when the moved block
    was reached.
H5S.c:
    Changed default value of H5_mpi_opt_types_g to TRUE, so that
    the MPI-IO hyperslab code is executed by default in parallel HDF5,
    rather than executing the serial hyperslab code.
H5Smpio.c:
    In function H5S_mpio_hyper_type, added a call to free
    an intermediate type. Cures a small memory leak.
    Added code for cases of empty hyperslab
    Changed displacements to be MPI_Aint
Platforms tested:
    modi4 -64: worked fine with mpich 1.2.0 but failed with the messages
    saying it ran out of entries for MPI_Types during the collective_read
    test.  After tracing the code all the way to the collective read, all
    MPI Types have been freed properly.  It aborted with the above message
    when it executed the line
if (MPI_SUCCESS!= MPI_File_read_at_all(file->f, mpi_off, buf, size_i, buf_type, &mpi_stat ))
    Could not see any problem with this line.  It could be a bug in the
    SGI version of MPI.
This commit is contained in:
Albert Cheng 2000-10-09 21:32:45 -05:00
parent d68bdee92f
commit 884b83d606
2 changed files with 28 additions and 6 deletions
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2
src/H5S.c
View File

@ -42,7 +42,7 @@ static size_t H5S_nconv_g = 0; /*entries used*/
#ifdef H5_HAVE_PARALLEL
/* Global var whose value comes from environment variable */
hbool_t H5_mpi_opt_types_g = FALSE;
hbool_t H5_mpi_opt_types_g = TRUE;
#endif
/* Declare a free list to manage the H5S_simple_t struct */

32
src/H5Smpio.c
View File

@ -126,6 +126,9 @@ H5S_mpio_all_type( const H5S_t *space, const size_t elmt_size,
* Programmer: rky 980813
*
* Modifications: ppw 990401
* rky, ppw 2000-09-26 Freed old type after creating struct type.
* rky 2000-10-05 Changed displacements to be MPI_Aint.
* rky 2000-10-06 Added code for cases of empty hyperslab.
*
*-------------------------------------------------------------------------
*/
@ -145,20 +148,23 @@ H5S_mpio_hyper_type( const H5S_t *space, const size_t elmt_size,
} d[32];
int i, err, new_rank, num_to_collapse;
int offset[32], max_xtent[32], block_length[2], displacement[2];
int offset[32], max_xtent[32], block_length[2];
H5S_hyper_dim_t *diminfo; /* [rank] */
intn rank;
MPI_Datatype inner_type, outer_type, old_type[32];
MPI_Aint extent_len;
MPI_Aint extent_len, displacement[2];
FUNC_ENTER (H5S_mpio_hyper_type, FAIL);
/* Check and abbreviate args */
assert (space);
assert(sizeof(MPI_Aint) >= sizeof(elmt_size));
diminfo = space->select.sel_info.hslab.diminfo;
assert (diminfo);
rank = space->extent.u.simple.rank;
assert (rank >= 0);
if (0==rank) goto empty;
if (0==elmt_size) goto empty;
/* make a local copy of the dimension info so we can transform them */
assert(rank<=32); /* within array bounds */
@ -175,6 +181,9 @@ H5S_mpio_hyper_type( const H5S_t *space, const size_t elmt_size,
if (i==0) fprintf(stdout, " rank=%d\n", rank );
else fprintf(stdout, "\n" );
#endif
if (0==d[i].block) goto empty;
if (0==d[i].count) goto empty;
if (0==d[i].xtent) goto empty;
}
/**********************************************************************
@ -232,11 +241,11 @@ H5S_mpio_hyper_type( const H5S_t *space, const size_t elmt_size,
} /* end for */
num_to_collapse = i;
if (num_to_collapse == rank) num_to_collapse--;
printf ("num_to_collapse=%d\n", num_to_collapse);
assert(0<=num_to_collapse && num_to_collapse<rank);
new_rank = rank - num_to_collapse;
#ifdef H5Smpi_DEBUG
fprintf(stdout, "num_to_collapse=%d\n", num_to_collapse);
fprintf(stdout, "hyper_type: new_rank=%d\n", new_rank );
#endif
@ -389,6 +398,10 @@ H5S_mpio_hyper_type( const H5S_t *space, const size_t elmt_size,
if (err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't create MPI struct type");
}
MPI_Type_free (&old_type[0]);
if (err) {
HRETURN_ERROR(H5E_DATASPACE, H5E_MPI, FAIL,"couldn't resize MPI vector type");
}
}
else {
*new_type = inner_type;
@ -402,9 +415,18 @@ H5S_mpio_hyper_type( const H5S_t *space, const size_t elmt_size,
/* fill in the remaining return values */
*count = 1; /* only have to move one of these suckers! */
*is_derived_type = 1;
goto done;
empty:
/* special case: empty hyperslab */
*new_type = MPI_BYTE;
*count = 0;
*is_derived_type = 0;
done:
#ifdef H5Smpi_DEBUG
fprintf(stdout, "Leave %s\n", FUNC );
HDfprintf(stdout, "Leave %s, count=%Hu is_derived_type=%d\n",
FUNC, *count, *is_derived_type );
#endif
FUNC_LEAVE (SUCCEED);
}
@ -574,7 +596,7 @@ H5S_mpio_spaces_xfer(H5F_t *f, const struct H5O_layout_t *layout,
/* calculate the absolute base addr (i.e., the file view disp) */
disp = f->shared->base_addr + layout->addr;
#ifdef H5Smpi_DEBUG
fprintf(stdout, "spaces_xfer: disp=%Hu\n", disp.offset );
HDfprintf(stdout, "spaces_xfer: disp=%Hu\n", disp );
#endif
/* Effective address determined by base addr and the MPI file type */