Accepting request 390197 from home:michel_mno:branches:science

- add hdf5-mpi.patch same as fedora commit id
  78ddcff82b10fd80eafb7b2dc5e4ce2bb9ecbe3c
  should avoid transient hung of t_pflush1 test

OBS-URL: https://build.opensuse.org/request/show/390197
OBS-URL: https://build.opensuse.org/package/show/science/hdf5?expand=0&rev=25

hdf5-mpi.patch

@@ -0,0 +1,30 @@
+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);
+ }
+ 
+

hdf5.changes

@@ -1,3 +1,10 @@
+-------------------------------------------------------------------
+Fri Apr 15 11:26:40 UTC 2016 - normand@linux.vnet.ibm.com
+
+- add hdf5-mpi.patch same as fedora commit id
+  78ddcff82b10fd80eafb7b2dc5e4ce2bb9ecbe3c
+  should avoid transient hung of t_pflush1 test
+
 -------------------------------------------------------------------
 Fri Mar 18 14:26:42 UTC 2016 - toddrme2178@gmail.com
 

hdf5.spec

@@ -55,6 +55,7 @@ Patch4:         hdf5-1.8.10-tests-arm.patch
 %endif
 Patch5:         hdf5-ldouble-ppc64le.patch
 Patch6:         hdf5-buildcompare.patch
+Patch7:         hdf5-mpi.patch
 BuildRoot:      %{_tmppath}/%{name}-%{version}-build
 BuildRequires:  fdupes
 BuildRequires:  gcc-c++
@@ -69,10 +70,10 @@ BuildRequires:  openmpi-devel
 BuildRequires:  mvapich2-devel
 %endif
 Requires:       libhdf5-%{sonum} = %{version}
-Requires:       libhdf5_hl%{sonum_HL} = %{version}
 Requires:       libhdf5_cpp%{sonum_CXX} = %{version}
-Requires:       libhdf5_hl_cpp%{sonum_HL_CXX} = %{version}
 Requires:       libhdf5_fortran%{sonum_F} = %{version}
+Requires:       libhdf5_hl%{sonum_HL} = %{version}
+Requires:       libhdf5_hl_cpp%{sonum_HL_CXX} = %{version}
 Requires:       libhdf5hl_fortran%{sonum_HL_F} = %{version}
 
 %description
@@ -99,8 +100,8 @@ This package contains utility functions for working with HDF5 files.
 Summary:        Command-line programs for the HDF5 scientific data format
 Group:          Productivity/Scientific/Other
 Requires:       libhdf5-%{sonum}-openmpi = %{version}
-Requires:       libhdf5_hl%{sonum_HL}-openmpi = %{version}
 Requires:       libhdf5_fortran%{sonum_F}-openmpi = %{version}
+Requires:       libhdf5_hl%{sonum_HL}-openmpi = %{version}
 Requires:       libhdf5hl_fortran%{sonum_HL_F}-openmpi = %{version}
 
 %description -n %{name}-openmpi
@@ -128,8 +129,8 @@ with HDF5 files.
 Summary:        Command-line programs for the HDF5 scientific data format
 Group:          Productivity/Scientific/Other
 Requires:       libhdf5-%{sonum}-mvapich2 = %{version}
-Requires:       libhdf5_hl%{sonum_HL}-mvapich2 = %{version}
 Requires:       libhdf5_fortran%{sonum_F}-mvapich2 = %{version}
+Requires:       libhdf5_hl%{sonum_HL}-mvapich2 = %{version}
 Requires:       libhdf5hl_fortran%{sonum_HL_F}-mvapich2 = %{version}
 
 %description -n %{name}-mvapich2
@@ -567,10 +568,10 @@ Requires:       %{name} = %{version}
 Requires:       %{name}-devel-data = %{version}
 # Required by Fortran programs?
 Requires:       libhdf5-%{sonum} = %{version}
-Requires:       libhdf5_hl%{sonum_HL} = %{version}
 Requires:       libhdf5_cpp%{sonum_CXX} = %{version}
-Requires:       libhdf5_hl_cpp%{sonum_HL_CXX} = %{version}
 Requires:       libhdf5_fortran%{sonum_F} = %{version}
+Requires:       libhdf5_hl%{sonum_HL} = %{version}
+Requires:       libhdf5_hl_cpp%{sonum_HL_CXX} = %{version}
 Requires:       libhdf5hl_fortran%{sonum_HL_F} = %{version}
 
 %description devel
@@ -601,8 +602,8 @@ Requires:       %{name}-devel-data = %{version}
 Requires:       %{name}-openmpi = %{version}
 # Required by Fortran programs?
 Requires:       libhdf5-%{sonum}-openmpi = %{version}
-Requires:       libhdf5_hl%{sonum_HL}-openmpi = %{version}
 Requires:       libhdf5_fortran%{sonum_F}-openmpi = %{version}
+Requires:       libhdf5_hl%{sonum_HL}-openmpi = %{version}
 Requires:       libhdf5hl_fortran%{sonum_HL_F}-openmpi = %{version}
 
 %description openmpi-devel
@@ -633,8 +634,8 @@ Requires:       %{name}-devel-data = %{version}
 Requires:       %{name}-mvapich2 = %{version}
 # Required by Fortran programs?
 Requires:       libhdf5-%{sonum}-mvapich2 = %{version}
-Requires:       libhdf5_hl%{sonum_HL}-mvapich2 = %{version}
 Requires:       libhdf5_fortran%{sonum_F}-mvapich2 = %{version}
+Requires:       libhdf5_hl%{sonum_HL}-mvapich2 = %{version}
 Requires:       libhdf5hl_fortran%{sonum_HL_F}-mvapich2 = %{version}
 
 %description mvapich2-devel
@@ -737,10 +738,10 @@ This package provides the static libraries for the mvapich2 version of HDF5.
 Summary:        Examples for %{name}
 Group:          Documentation/Other
 Requires:       libhdf5-%{sonum} = %{version}
-Requires:       libhdf5_hl%{sonum_HL} = %{version}
 Requires:       libhdf5_cpp%{sonum_CXX} = %{version}
-Requires:       libhdf5_hl_cpp%{sonum_HL_CXX} = %{version}
 Requires:       libhdf5_fortran%{sonum_F} = %{version}
+Requires:       libhdf5_hl%{sonum_HL} = %{version}
+Requires:       libhdf5_hl_cpp%{sonum_HL_CXX} = %{version}
 Requires:       libhdf5hl_fortran%{sonum_HL_F} = %{version}
 
 %description examples
@@ -773,6 +774,7 @@ This package provides examples of HDF5 library use.
 %endif
 %patch5 -p1
 %patch6 -p1
+%patch7 -p1
 
 echo "prepare parallel builds: %_mpi"
 for build_dir in build %_mpi; do