diff --git a/.gitignore b/.gitignore index 6633521..46e5004 100644 --- a/.gitignore +++ b/.gitignore @@ -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 diff --git a/hdf5-implicit.patch b/hdf5-implicit.patch deleted file mode 100644 index 286b9f8..0000000 --- a/hdf5-implicit.patch +++ /dev/null @@ -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 - 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 - 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 - diff --git a/hdf5-mpi.patch b/hdf5-mpi.patch deleted file mode 100644 index e2e9386..0000000 --- a/hdf5-mpi.patch +++ /dev/null @@ -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); - } - diff --git a/hdf5-wrappers.patch b/hdf5-wrappers.patch index b822b9d..34f903e 100644 --- a/hdf5-wrappers.patch +++ b/hdf5-wrappers.patch @@ -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 diff --git a/hdf5.spec b/hdf5.spec index cb7b9ac..c73dba3 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -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 - 1.10.6-1 +- Update to 1.10.6 + * Wed Jan 29 2020 Fedora Release Engineering - 1.10.5-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild diff --git a/sources b/sources index 54ddbfb..9a4d6c9 100644 --- a/sources +++ b/sources @@ -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