rpms/hdf5
3
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update to 1.10.6

Browse Source
This commit is contained in:
Orion Poplawski 2020-02-15 15:34:00 -07:00
parent df1a40d7ea
commit 271d4d242d
6 changed files with 11 additions and 194 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
.gitignore vendored
View File

@ -28,3 +28,4 @@ hdf5-1.8.5.tar.bz2
/hdf5-1.10.4.tar.bz2
/hdf5_1.10.4+repack-1.debian.tar.xz
/hdf5-1.10.5.tar.bz2
/hdf5-1.10.6.tar.bz2

150
hdf5-implicit.patch
View File

@ -1,150 +0,0 @@
diff -up hdf5-1.8.18/configure.ac.implicit hdf5-1.8.18/configure.ac
--- hdf5-1.8.18/configure.ac.implicit 2016-12-05 20:44:42.267653275 -0700
+++ hdf5-1.8.18/configure.ac 2016-12-05 20:52:16.666921290 -0700
@@ -1316,9 +1316,9 @@ if test "x$HAVE_SZLIB" = "xyes" -a "x$HA
{
/* SZ_encoder_enabled returns 1 if encoder is present */
if(SZ_encoder_enabled() == 1)
- exit(0);
+ return(0);
else
- exit(1);
+ return(1);
}
], [hdf5_cv_szlib_can_encode=yes], [hdf5_cv_szlib_can_encode=no],)])
@@ -1662,7 +1662,7 @@ for hdf5_cv_printf_ll in l ll L q unknow
char *s = malloc(128);
long long x = (long long)1048576 * (long long)1048576;
sprintf(s,"%${hdf5_cv_printf_ll}d",x);
- exit(strcmp(s,"1099511627776"));
+ return(strcmp(s,"1099511627776"));
}
], [break],,[continue])
done])
@@ -1690,7 +1690,7 @@ AC_CACHE_VAL([hdf5_cv_system_scope_threa
pthread_attr_init(&attribute);
ret=pthread_attr_setscope(&attribute, PTHREAD_SCOPE_SYSTEM);
- exit(ret==0 ? 0 : 1);
+ return(ret==0 ? 0 : 1);
}
], [hdf5_cv_system_scope_threads=yes], [hdf5_cv_system_scope_threads=no],)])
@@ -2308,7 +2308,7 @@ else
ret = 0;
}
}
- exit(ret);
+ return(ret);
]])]
, [hdf5_cv_ldouble_to_long_special=yes], [hdf5_cv_ldouble_to_long_special=no],)])
fi
@@ -2396,7 +2396,7 @@ else
s[12]==0x00 && s[13]==0x00 && s[14]==0x00 && s[15]==0x00)
ret = 0;
}
- exit(ret);
+ return(ret);
]])]
, [hdf5_cv_long_to_ldouble_special=yes], [hdf5_cv_long_to_ldouble_special=no],)])
fi
@@ -2429,6 +2429,7 @@ if test ${ac_cv_sizeof_long_double} = 0;
else
AC_CACHE_VAL([hdf5_cv_ldouble_to_llong_accurate],
[AC_TRY_RUN([
+ #include <string.h>
int main(void)
{
long double ld = 20041683600089727.779961L;
@@ -2463,7 +2464,7 @@ else
}
}
done:
- exit(ret);
+ return(ret);
}
], [hdf5_cv_ldouble_to_llong_accurate=yes], [hdf5_cv_ldouble_to_llong_accurate=no],)])
fi
@@ -2494,6 +2495,7 @@ if test ${ac_cv_sizeof_long_double} = 0;
else
AC_CACHE_VAL([hdf5_cv_llong_to_ldouble_correct],
[AC_TRY_RUN([
+ #include <string.h>
int main(void)
{
long double ld;
@@ -2532,7 +2534,7 @@ else
ret = 1;
}
done:
- exit(ret);
+ return(ret);
}
], [hdf5_cv_llong_to_ldouble_correct=yes], [hdf5_cv_llong_to_ldouble_correct=no],)])
fi
diff -up hdf5-1.8.18/src/H5Dio.c.implicit hdf5-1.8.18/src/H5Dio.c
--- hdf5-1.8.18/src/H5Dio.c.implicit 2016-11-04 12:41:06.000000000 -0600
+++ hdf5-1.8.18/src/H5Dio.c 2016-12-05 20:44:42.259653236 -0700
@@ -30,6 +30,7 @@
#include "H5Iprivate.h" /* IDs */
#include "H5MMprivate.h" /* Memory management */
#include "H5Sprivate.h" /* Dataspace */
+#include "H5Tprivate.h" /* Datatype functions */
#ifdef H5_HAVE_PARALLEL
/* Remove this if H5R_DATASET_REGION is no longer used in this file */
diff -up hdf5-1.8.18/src/H5Tprivate.h.implicit hdf5-1.8.18/src/H5Tprivate.h
--- hdf5-1.8.18/src/H5Tprivate.h.implicit 2016-11-04 12:41:07.000000000 -0600
+++ hdf5-1.8.18/src/H5Tprivate.h 2016-12-05 20:44:42.259653236 -0700
@@ -137,6 +137,7 @@ H5_DLL htri_t H5T_is_sensible(const H5T_
H5_DLL uint32_t H5T_hash(H5F_t * file, const H5T_t *dt);
H5_DLL herr_t H5T_set_latest_version(H5T_t *dt);
H5_DLL herr_t H5T_patch_file(H5T_t *dt, H5F_t *f);
+H5_DLL herr_t H5T_patch_vlen_file(H5T_t *dt, H5F_t *f);
H5_DLL htri_t H5T_is_variable_str(const H5T_t *dt);
/* Reference specific functions */
diff -up hdf5-1.8.18/test/cache_common.h.implicit hdf5-1.8.18/test/cache_common.h
--- hdf5-1.8.18/test/cache_common.h.implicit 2016-11-04 12:41:07.000000000 -0600
+++ hdf5-1.8.18/test/cache_common.h 2016-12-05 20:44:42.259653236 -0700
@@ -684,6 +684,9 @@ void verify_unprotected(void);
/*** H5AC level utility functions ***/
+hbool_t resize_configs_are_equal(const H5C_auto_size_ctl_t *a,
+ const H5C_auto_size_ctl_t *b, hbool_t compare_init);
+
void check_and_validate_cache_hit_rate(hid_t file_id,
double * hit_rate_ptr,
hbool_t dump_data,
diff -up hdf5-1.8.18/testpar/t_span_tree.c.implicit hdf5-1.8.18/testpar/t_span_tree.c
--- hdf5-1.8.18/testpar/t_span_tree.c.implicit 2016-11-04 12:41:07.000000000 -0600
+++ hdf5-1.8.18/testpar/t_span_tree.c 2016-12-05 20:44:42.260653241 -0700
@@ -34,9 +34,15 @@
*/
+#define H5S_PACKAGE /*suppress error about including H5Spkg */
+
+/* Define this macro to indicate that the testing APIs should be available */
+#define H5S_TESTING
+
#include "hdf5.h"
#include "H5private.h"
#include "testphdf5.h"
+#include "H5Spkg.h"
static void coll_write_test(int chunk_factor);
diff -up hdf5-1.8.18/tools/perform/perf.c.implicit hdf5-1.8.18/tools/perform/perf.c
--- hdf5-1.8.18/tools/perform/perf.c.implicit 2016-11-04 12:41:07.000000000 -0600
+++ hdf5-1.8.18/tools/perform/perf.c 2016-12-05 20:44:42.260653241 -0700
@@ -24,6 +24,7 @@
#include "hdf5.h"
#include "H5private.h"
+#include "h5test.h"
#ifdef H5_HAVE_PARALLEL

29
hdf5-mpi.patch
View File

@ -1,29 +0,0 @@
diff -up hdf5-1.8.16/testpar/t_pflush1.c.mpi hdf5-1.8.16/testpar/t_pflush1.c
--- hdf5-1.8.16/testpar/t_pflush1.c.mpi 2015-10-23 23:13:44.000000000 -0600
+++ hdf5-1.8.16/testpar/t_pflush1.c 2016-03-20 21:46:42.089409776 -0600
@@ -171,6 +171,7 @@ main(int argc, char* argv[])
* because MPI_File_close wants to modify the file-handle variable.
*/
+#if 0
/* close file1 */
if(H5Fget_vfd_handle(file1, fapl, (void **)&mpifh_p) < 0) {
printf("H5Fget_vfd_handle for file1 failed\n");
@@ -189,14 +190,17 @@ main(int argc, char* argv[])
printf("MPI_File_close for file2 failed\n");
goto error;
} /* end if */
+#endif
fflush(stdout);
fflush(stderr);
+ MPI_Finalize();
HD_exit(0);
error:
fflush(stdout);
fflush(stderr);
+ MPI_Finalize();
HD_exit(1);
}

6
hdf5-wrappers.patch
View File

@ -71,9 +71,9 @@ diff -up hdf5-1.10.5/fortran/src/h5fc.in.wrappers hdf5-1.10.5/fortran/src/h5fc.i
status=$?
fi
diff -up hdf5-1.10.5/tools/src/misc/h5cc.in.wrappers hdf5-1.10.5/tools/src/misc/h5cc.in
--- hdf5-1.10.5/tools/src/misc/h5cc.in.wrappers 2018-09-03 20:54:44.000000000 -0600
+++ hdf5-1.10.5/tools/src/misc/h5cc.in 2020-01-26 19:13:58.079642156 -0700
diff -up hdf5-1.10.5/bin//h5cc.in.wrappers hdf5-1.10.5/tools/src/misc/h5cc.in
--- hdf5-1.10.5/bin/h5cc.in.wrappers 2018-09-03 20:54:44.000000000 -0600
+++ hdf5-1.10.5/bin/h5cc.in 2020-01-26 19:13:58.079642156 -0700
@@ -89,10 +89,10 @@ CLINKERBASE="@CC@"
# paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in
# from the hdf5 build. The order of the flags is intended to give precedence

17
hdf5.spec
View File

@ -6,8 +6,8 @@
# NOTE: Try not to release new versions to released versions of Fedora
# You need to recompile all users of HDF5 for each version change
Name: hdf5
Version: 1.10.5
Release: 6%{?dist}
Version: 1.10.6
Release: 1%{?dist}
Summary: A general purpose library and file format for storing scientific data
License: BSD
URL: https://portal.hdfgroup.org/display/HDF5/HDF5
@ -17,14 +17,10 @@ Source1: h5comp
# For man pages
Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.10.4+repack-1.debian.tar.xz
Patch0: hdf5-LD_LIBRARY_PATH.patch
# Properly run MPI_Finalize() in t_pflush1
Patch1: hdf5-mpi.patch
# Fix some warnings
Patch2: hdf5-warning.patch
# Fix java build
Patch3: hdf5-build.patch
# Upstream fix for Java tests
Patch4: https://jira.hdfgroup.org/secure/attachment/26110/fix-HDFFV-10745.patch
# Remove Fedora build flags from h5cc/h5c++/h5fc
# https://bugzilla.redhat.com/show_bug.cgi?id=1794625
Patch5: hdf5-wrappers.patch
@ -172,10 +168,8 @@ HDF5 parallel openmpi static libraries
%prep
%setup -q -a 2 -n %{name}-%{version}%{?snaprel}
%patch0 -p1 -b .LD_LIBRARY_PATH
#patch1 -p1 -b .mpi
%patch2 -p1 -b .warning
%patch3 -p1 -b .build
%patch4 -p1 -b .jira
%patch5 -p1 -b .wrappers
# Replace jars with system versions
@ -230,9 +224,6 @@ make LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed"
popd
#MPI builds
export CC=mpicc
export CXX=mpicxx
export F9X=mpif90
export LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed"
for mpi in %{?mpi_list}
do
@ -242,6 +233,7 @@ do
ln -s ../configure .
%configure \
%{configure_opts} \
CC=mpicc CXX=mpicxx F9X=mpif90 \
FCFLAGS="$FCFLAGS -I$MPI_FORTRAN_MOD_DIR" \
--enable-parallel \
--exec-prefix=%{_libdir}/$mpi \
@ -494,6 +486,9 @@ done
%changelog
* Thu Jun 25 2020 Orion Poplawski <orion@nwra.com> - 1.10.6-1
- Update to 1.10.6
* Wed Jan 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.10.5-6
- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild

2
sources
View File

@ -1,2 +1,2 @@
SHA512 (hdf5-1.10.5.tar.bz2) = 769e43b8672e26fe24ed68da0228c010d3d9bc950ca09f0bc60707911a2f26f2f8415c8abc8ec06e07667148d8cdb3b0c7b3e7860d9b19739629c5dfd5ce73d4
SHA512 (hdf5-1.10.6.tar.bz2) = 821392718605e3f7a287d4729d022a55fd7b91ddaa2e9a3f35ab8fce3d3d4871a0cc88215be3052887cbac3615cc8953569c7f131217962103c98151c0ab58d4
SHA512 (hdf5_1.10.4+repack-1.debian.tar.xz) = 7e08a79c8e96b843331e30d027628065ccbe72843a3ac525ad52d506238d328b9ebae57eff772b6215419943fd1804b4879cbdcd612e2f2c160c65a3d44ef965