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merge ejh_par_leak

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This commit is contained in:
Ed Hartnett 2018-05-30 05:03:42 -06:00
commit 3949bd61bc
3 changed files with 9 additions and 128 deletions
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42
libhdf5/hdf5file.c
View File

@ -695,48 +695,6 @@ dumpopenobjects(NC_HDF5_FILE_INFO_T* h5)
return;
}
#ifdef NC4NOTUSED
/**
* @internal Define the names of attributes to ignore added by the
* HDF5 dimension scale; these attached to variables. They cannot be
* modified thru the netcdf-4 API.
*/
static const char* NC_RESERVED_VARATT_LIST[] = {
NC_ATT_REFERENCE_LIST,
NC_ATT_CLASS,
NC_ATT_DIMENSION_LIST,
NC_ATT_NAME,
NC_ATT_COORDINATES,
NC_DIMID_ATT_NAME,
NULL
};
/**
* @internal Define the names of attributes to ignore because they are
* "hidden" global attributes. They can be read, but not modified thru
* the netcdf-4 API.
*/
static const char* NC_RESERVED_ATT_LIST[] = {
NC_ATT_FORMAT,
NC3_STRICT_ATT_NAME,
NCPROPS,
ISNETCDF4ATT,
SUPERBLOCKATT,
NULL
};
/**
* @internal Define the subset of the reserved list that is readable
* by name only
*/
static const char* NC_RESERVED_SPECIAL_LIST[] = {
ISNETCDF4ATT,
SUPERBLOCKATT,
NCPROPS,
NULL
};
#endif
size_t nc4_chunk_cache_size = CHUNK_CACHE_SIZE; /**< Default chunk cache size. */
size_t nc4_chunk_cache_nelems = CHUNK_CACHE_NELEMS; /**< Default chunk cache number of elements. */
float nc4_chunk_cache_preemption = CHUNK_CACHE_PREEMPTION; /**< Default chunk cache preemption. */

66
libhdf5/nc4hdf.c
View File

@ -684,13 +684,8 @@ nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
#endif
int retval = NC_NOERR, range_error = 0, i, d2;
void *bufr = NULL;
#ifndef HDF5_CONVERT
int need_to_convert = 0;
size_t len = 1;
#endif
#ifdef HDF5_CONVERT
hid_t mem_typeid = 0;
#endif
/* Find our metadata for this file, group, and var. */
assert(nc);
@ -782,7 +777,6 @@ nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
BAIL(NC_EHDFERR);
}
#ifndef HDF5_CONVERT
/* Are we going to convert any data? (No converting of compound or
* opaque types.) */
if ((mem_nc_type != var->type_info->hdr.id || (var->type_info->hdr.id == NC_INT && is_long)) &&
@ -811,28 +805,12 @@ nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
BAIL(NC_ENOMEM);
}
else
#endif /* ifndef HDF5_CONVERT */
bufr = data;
#ifdef HDF5_CONVERT
/* Get the HDF type of the data in memory. */
if ((retval = nc4_get_hdf_typeid(h5, mem_nc_type, &mem_typeid,
var->type_info->endianness)))
BAIL(retval);
#endif
/* Create the data transfer property list. */
if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0)
BAIL(NC_EHDFERR);
/* Apply the callback function which will detect range
* errors. Which one to call depends on the length of the
* destination buffer type. */
#ifdef HDF5_CONVERT
if (H5Pset_type_conv_cb(xfer_plistid, except_func, &range_error) < 0)
BAIL(NC_EHDFERR);
#endif
#ifdef USE_PARALLEL4
/* Set up parallel I/O, if needed. */
if ((retval = set_par_access(h5, var, xfer_plistid)))
@ -918,7 +896,6 @@ nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
}
}
#ifndef HDF5_CONVERT
/* Do we need to convert the data? */
if (need_to_convert)
{
@ -927,7 +904,6 @@ nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
(h5->cmode & NC_CLASSIC_MODEL), is_long, 0)))
BAIL(retval);
}
#endif
/* Write the data. At last! */
LOG((4, "about to H5Dwrite datasetid 0x%x mem_spaceid 0x%x "
@ -950,19 +926,13 @@ nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
range_error = 0;
exit:
#ifdef HDF5_CONVERT
if (mem_typeid > 0 && H5Tclose(mem_typeid) < 0)
BAIL2(NC_EHDFERR);
#endif
if (file_spaceid > 0 && H5Sclose(file_spaceid) < 0)
BAIL2(NC_EHDFERR);
if (mem_spaceid > 0 && H5Sclose(mem_spaceid) < 0)
BAIL2(NC_EHDFERR);
if (xfer_plistid && (H5Pclose(xfer_plistid) < 0))
BAIL2(NC_EPARINIT);
#ifndef HDF5_CONVERT
if (need_to_convert && bufr) free(bufr);
#endif
/* If there was an error return it, otherwise return any potential
range error value. If none, return NC_NOERR as usual.*/
@ -1018,13 +988,8 @@ nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp,
int fill_value_size[NC_MAX_VAR_DIMS];
int scalar = 0, retval = NC_NOERR, range_error = 0, i, d2;
void *bufr = NULL;
#ifdef HDF5_CONVERT
hid_t mem_typeid = 0;
#endif
#ifndef HDF5_CONVERT
int need_to_convert = 0;
size_t len = 1;
#endif
/* Find our metadata for this file, group, and var. */
assert(nc);
@ -1184,7 +1149,6 @@ nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp,
bufr = *(char **)data;
}
#ifndef HDF5_CONVERT
/* Are we going to convert any data? (No converting of compound or
* opaque types.) */
if ((mem_nc_type != var->type_info->hdr.id || (var->type_info->hdr.id == NC_INT && is_long)) &&
@ -1206,29 +1170,13 @@ nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp,
BAIL(NC_ENOMEM);
}
else
#endif /* ifndef HDF5_CONVERT */
if(!bufr)
bufr = data;
/* Get the HDF type of the data in memory. */
#ifdef HDF5_CONVERT
if ((retval = nc4_get_hdf_typeid(h5, mem_nc_type, &mem_typeid,
var->type_info->endianness)))
BAIL(retval);
#endif
/* Create the data transfer property list. */
if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0)
BAIL(NC_EHDFERR);
#ifdef HDF5_CONVERT
/* Apply the callback function which will detect range
* errors. Which one to call depends on the length of the
* destination buffer type. */
if (H5Pset_type_conv_cb(xfer_plistid, except_func, &range_error) < 0)
BAIL(NC_EHDFERR);
#endif
#ifdef USE_PARALLEL4
/* Set up parallel I/O, if needed. */
if ((retval = set_par_access(h5, var, xfer_plistid)))
@ -1241,12 +1189,7 @@ nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp,
mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0)
BAIL(NC_EHDFERR);
#ifndef HDF5_CONVERT
/* Eventually the block below will go away. Right now it's
needed to support conversions between int/float, and range
checking converted data in the netcdf way. These features are
being added to HDF5 at the HDF5 World Hall of Coding right
now, by a staff of thousands of programming gnomes. */
/* Convert data if needed. */
if (need_to_convert)
{
if ((retval = nc4_convert_type(bufr, data, var->type_info->hdr.id, mem_nc_type,
@ -1262,7 +1205,6 @@ nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp,
range_error)
range_error = 0;
}
#endif
/* For strict netcdf-3 rules, ignore erange errors between UBYTE
* and BYTE types. */
@ -1357,10 +1299,6 @@ nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp,
}
exit:
#ifdef HDF5_CONVERT
if (mem_typeid > 0 && H5Tclose(mem_typeid) < 0)
BAIL2(NC_EHDFERR);
#endif
if (file_spaceid > 0)
{
if (H5Sclose(file_spaceid) < 0)
@ -1376,10 +1314,8 @@ exit:
if (H5Pclose(xfer_plistid) < 0)
BAIL2(NC_EHDFERR);
}
#ifndef HDF5_CONVERT
if (need_to_convert && bufr != NULL)
free(bufr);
#endif
if (xtend_size)
free(xtend_size);
if (fillvalue)

29
nc_test4/tst_parallel3.c
View File

@ -1,22 +1,9 @@
/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
* Copyright by the Board of Trustees of the University of Illinois. *
* All rights reserved. *
* *
* This file is part of HDF5. The full HDF5 copyright notice, including *
* terms governing use, modification, and redistribution, is contained in *
* the files COPYING and Copyright.html. COPYING can be found at the root *
* of the source code distribution tree; Copyright.html can be found at the *
* root level of an installed copy of the electronic HDF5 document set and *
* is linked from the top-level documents page. It can also be found at *
* http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have *
* access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. *
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
/*
* Main driver of the Parallel NetCDF4 tests
*
*/
/* This test of netCDF-4 parallel I/O was contributed by the HDF5
* team. */
#include <nc_tests.h>
#include "err_macros.h"
@ -45,9 +32,9 @@
dimension to be divided evenly, the best set of number of processor
should be 2 power n. However, for NetCDF4 tests, the following numbers
are generally treated as good numbers:
1,2,3,4,6,8,12,16,24,32,48,64,96,128,192,256
1,2,3,4,6,8,12,16
The maximum number of processor is 256.*/
The maximum number of processor is 16.*/
int test_pio(int);
int test_pio_attr(int);
@ -64,7 +51,7 @@ int main(int argc, char **argv)
{
int mpi_size, mpi_rank; /* mpi variables */
int i;
int NUMP[16] ={1,2,3,4,6,8,12,16,24,32,48,64,96,128,192,256};
int NUMP[8] ={1,2,3,4,6,8,12,16};
int size_flag = 0;
/* Un-buffer the stdout and stderr */
@ -78,7 +65,7 @@ int main(int argc, char **argv)
if (mpi_rank == 0)
printf("\n*** Testing more advanced parallel access.\n");
for (i = 0; i < 16; i++){
for (i = 0; i < 8; i++){
if(mpi_size == NUMP[i])
{
size_flag = 1;
@ -88,7 +75,7 @@ int main(int argc, char **argv)
if(!size_flag){
printf("mpi_size is wrong\n");
printf(" The number of processor must be chosen from\n");
printf(" 1,2,3,4,6,8,12,16,24,32,48,64,96,128,192,256 \n");
printf(" 1,2,3,4,6,8,12,16 \n");
return -1;
}
@ -711,7 +698,7 @@ int test_pio_extend(int flag){
int dimsVrtx[2];
size_t start[2];
size_t count[2];
int vertices[] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10};
int vertices[] = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15};
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &procs);