Update/Rebuild for MUMPS-5.3.5 on EPEL7

petsc-3.14-hypre_2.11.2_reverting.patch

@@ -3,7 +3,7 @@ From: Satish Balay <balay@mcs.anl.gov>
 Date: Fri, 30 Mar 2018 09:53:12 -0500
 Subject: [PATCH] hypre: update to version 2.14.0
 
-Reported-by: Antonio Trande <anto.trande@gmail.com>
+Reported-by: Antonio Trande <sagitter@fedoraproject.org>
 ---
  config/BuildSystem/config/packages/hypre.py | 2 +-
  src/mat/impls/hypre/mhypre.c                | 2 +-
@@ -13,26 +13,22 @@ diff --git a/config/BuildSystem/config/packages/hypre.py b/config/BuildSystem/co
 index 1249b39..620e516 100644
 --- a/config/BuildSystem/config/packages/hypre.py
 +++ b/config/BuildSystem/config/packages/hypre.py
-@@ -4,7 +4,7 @@ import os
+@@ -5,7 +5,7 @@
- class Configure(config.package.GNUPackage):
    def __init__(self, framework):
      config.package.GNUPackage.__init__(self, framework)
--    self.gitcommit = 'v2.12.0'
+     self.version         = '2.19.0'
-+    self.gitcommit = 'v2.15.1'
+-    self.minversion      = '2.14'
-     self.download  = ['git://https://github.com/LLNL/hypre','https://github.com/LLNL/hypre/archive/'+self.gitcommit+'.tar.gz']
++    self.minversion      = '2.11.2'
-     self.functions = ['HYPRE_IJMatrixCreate']
+     self.versionname     = 'HYPRE_RELEASE_VERSION'
-     self.includes  = ['HYPRE.h']
+     self.versioninclude  = 'HYPRE_config.h'
-diff --git a/src/mat/impls/hypre/mhypre.c b/src/mat/impls/hypre/mhypre.c
+     self.requiresversion = 1
-index 8a51581..65595f2 100644
+--- a/src/mat/impls/hypre/mhypre.c	
---- a/src/mat/impls/hypre/mhypre.c
 +++ b/src/mat/impls/hypre/mhypre.c
-@@ -1450,6 +1450,6 @@ PETSC_EXTERN PetscErrorCode MatCreate_HYPRE(Mat B)
+@@ -2131,6 +2131,6 @@
  static PetscErrorCode hypre_array_destroy(void *ptr)
  {
     PetscFunctionBegin;
--   hypre_TFree(ptr);
+-   hypre_TFree(ptr,HYPRE_MEMORY_HOST);
-+   hypre_TFree(ptr,HYPRE_MEMORY_HOST);
++   hypre_TFree(ptr);
     PetscFunctionReturn(0);
  }
--- 
-2.10.5

petsc.spec

@@ -9,10 +9,8 @@
 %{?el7:%global _pkgdocdir %{_docdir}/%{name}}
 #
 
-%if 0%{?fedora}
 %bcond_without mpich
 %bcond_without openmpi
-%endif
 
 %if %{?__isa_bits:%{__isa_bits}}%{!?__isa_bits:32} == 64
 %bcond_without arch64
@@ -33,15 +31,6 @@
 %global blasvar p
 %endif
 
-%if 0%{?rhel} && 0%{?rhel} >= 7
-%bcond_without mpich
-%bcond_without openmpi
-%endif
-
-%if 0%{?rhel} == 7
-%global dts devtoolset-8-
-%endif
-
 #
 ## PETSC looks incompatible with serial MUMPS
 %bcond_without mumps_serial
@@ -53,7 +42,7 @@
 #
 
 ## Suitesparse
-## Currently, suitesparse-5.4.0 is available on Fedora 32+, but this version of PETSc needs at least 5.6.0
+## Currently, suitesparse-5.4.0 is available on Fedora 32+, but this version of PETSc needs the 5.6.0 at least
 %bcond_with suitesparse
 %if 0%{?fedora} && 0%{?fedora} >= 32
 %bcond_with suitesparse64
@@ -61,7 +50,19 @@
 #
 
 ## SuperLUDIST needs parmetis
+%if 0%{?fedora} || 0%{?rhel} > 7
 %bcond_without superludist
+%bcond_without cgns
+%bcond_without hdf5
+%else
+# Needed superludist >= 6.1.1
+%bcond_with superludist
+
+# hdf5 is required by cgns
+# and see rhbz#1904164
+%bcond_with cgns
+%bcond_with hdf5
+%endif
 %bcond_with superlumt
 #
 
@@ -72,10 +73,6 @@
 %endif
 #
 
-# hdf5' is required by 'cgns'
-%bcond_without cgns
-%bcond_without hdf5
-
 # 'scalapack' is required by 'mumps'
 %if %{with openmpi}
 %bcond_without mpi
@@ -184,9 +181,10 @@
   --with-shared-libraries=1 \\\
   --with-fortran-interfaces=1 \\\
   --with-windows-graphics=0 \\\
-  --with-cc=mpicc \\\
+  --with-cc=${MPI_BIN}/mpicc \\\
-  --with-cxx=mpicxx \\\
+  --with-cxx=${MPI_BIN}/mpicxx \\\
-  --with-fc=mpif77 \\\
+  --with-fc=${MPI_BIN}/mpif90 \\\
+  --with-mpiexec="${MPI_BIN}/mpiexec -n `getconf _NPROCESSORS_ONLN` -env MPIEXEC_TIMEOUT 3000 --mca btl_base_warn_component_unused 0" \\\
   --with-shared-ld=ld \\\
   --with-pic=1 \\\
   --with-clib-autodetect=0 \\\
@@ -262,7 +260,7 @@
 Name:    petsc
 Summary: Portable Extensible Toolkit for Scientific Computation
 Version: %{releasever}.1
-Release: 2%{?dist}
+Release: 3%{?dist}
 License: BSD
 URL:     https://www.mcs.anl.gov/petsc
 Source0: https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-%{version}.tar.gz
@@ -274,7 +272,7 @@ Patch0:  %{name}-3.11-no-rpath.patch
 Patch1:  %{name}-lib64.patch
 
 # Reverting patch for Hypre-2.11.2
-Patch2:  %{name}-3.11-hypre_2.11.2_reverting.patch
+Patch2:  %{name}-3.14-hypre_2.11.2_reverting.patch
 
 Patch3:  %{name}-3.13-fix_mumps_includes.patch
 Patch4:  %{name}-3.13.0-fix_metis64.patch
@@ -301,15 +299,12 @@ BuildRequires: suitesparse-devel >= 5.6.0
 %if %{with blas}
 BuildRequires: %{blaslib}-devel
 %endif
-BuildRequires: %{?dts}gcc, %{?dts}gcc-c++, cmake3
+BuildRequires: gcc, gcc-c++, cmake3
-BuildRequires: %{?dts}gcc-gfortran
+BuildRequires: gcc-gfortran
+BuildRequires: make
 BuildRequires: libX11-devel
-%if 0%{?el7}
-BuildRequires: python2-devel
-%else
 BuildRequires: python3-devel
 BuildRequires: python3-setuptools
-%endif
 BuildRequires: pcre-devel
 %if 0%{?el7}
 BuildRequires: pkgconfig
@@ -346,11 +341,7 @@ Portable Extensible Toolkit for Scientific Computation (developer files).
 
 %package doc
 Summary:    Portable Extensible Toolkit for Scientific Computation (documentation files)
-%if 0%{?el7}
-BuildRequires: python2-sphinx
-%else
 BuildRequires: python3-sphinx
-%endif
 BuildArch:  noarch
 %description doc
 Portable Extensible Toolkit for Scientific Computation.
@@ -507,15 +498,13 @@ pushd %{name}-%{version}
 
 %patch7 -p1
 
-%if 0%{?fedora} || 0%{?rhel} >= 8
 find . -name 'setup.py' | xargs pathfix.py -pn -i "%{__python3}"
 find . -name 'configure' | xargs pathfix.py -pn -i "%{__python3}"
 find config -name '*.py' | xargs pathfix.py -pn -i "%{__python3}"
 find src/benchmarks/streams -name '*.py' | xargs pathfix.py -pn -i "%{__python3}"
-%endif
 
 %if 0%{?el7}
-%patch2 -R -p1
+%patch2 -p1
 %endif
 popd
 
@@ -549,12 +538,7 @@ popd
 
 %build
 pushd %{name}-%{version}
-%if 0%{?el7}
-%{?dts:source /opt/rh/devtoolset-8/enable}
-%configure --with-cc=/opt/rh/devtoolset-8/root/usr/bin/gcc --with-cxx=/opt/rh/devtoolset-8/root/usr/bin/g++ --with-fc=/opt/rh/devtoolset-8/root/usr/bin/gfortran \
-%else
 %configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran \
-%endif
  %{petsc_build_options} \
  --with-64-bit-indices=0 \
 %if %{with blas}
@@ -587,12 +571,7 @@ popd
 
 %if %{with arch64}
 pushd build64
-%if 0%{?el7}
-%{?dts:source /opt/rh/devtoolset-8/enable}
-%configure --with-cc=/opt/rh/devtoolset-8/root/usr/bin/gcc --with-cxx=/opt/rh/devtoolset-8/root/usr/bin/g++ --with-fc=/opt/rh/devtoolset-8/root/usr/bin/gfortran \
-%else
 %configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran \
-%endif
  %{petsc_build_options} \
  --with-64-bit-indices=1 \
 %if %{with metis64}
@@ -621,14 +600,10 @@ popd
 %if %{with openmpi}
 pushd buildopenmpi_dir
 
-%if 0%{?el7}
-%{?dts:source /opt/rh/devtoolset-8/enable}
-%endif
-
 %{_openmpi_load}
 %configure \
  --FC_LINKER_FLAGS="$LDFLAGS -lgfortran -lmpi_mpifh" \
- --LIBS=" -lmpi_mpifh" \
+ --LIBS=" -lmpi -lmpi_mpifh" \
  %{petsc_mpibuild_options} \
 %if %{with metis}
  --with-metis=1 \
@@ -654,14 +629,10 @@ popd
 %if %{with mpich}
 pushd buildmpich_dir
 
-%if 0%{?el7}
-%{?dts:source /opt/rh/devtoolset-8/enable}
-%endif
-
 %{_mpich_load}
 %configure \
- --FC_LINKER_FLAGS="$LDFLAGS -lgfortran -lmpifort" \
+ --FC_LINKER_FLAGS="$LDFLAGS -lgfortran -lfmpich -lmpichf90" \
- --LIBS=" -lmpifort" \
+ --LIBS=" -lmpich -lfmpich -lmpichf90" \
  %{petsc_mpibuild_options} \
 %if %{with metis}
  --with-metis=1 \
@@ -836,17 +807,19 @@ cp -a %{name}-%{version}/docs/* $RPM_BUILD_ROOT%{_pkgdocdir}
 
 %if %{with check}
 %check
+
 %if %{with openmpi}
 %{_openmpi_load}
 export LD_LIBRARY_PATH=%{_builddir}/%{name}-%{version}/buildopenmpi_dir/%{_arch}/lib
 export PETSC_DIR=%{_builddir}/%{name}-%{version}/buildopenmpi_dir
 export PETSC_ARCH=%{_arch}
 export MPI_INTERFACE_HOSTNAME=localhost
+export OMPI_MCA_btl_base_warn_component_unused=0
 %if %{with debug}
 export PETSCVALGRIND_OPTIONS=" --tool=memcheck --leak-check=yes --track-origins=yes"
 export CFLAGS="-O0 -g -Wl,-z,now -fPIC"
 export CXXFLAGS="-O0 -g -Wl,-z,now -fPIC"
-export FFLAGS="-O0 -g -Wl,-z,now -fPIC -I%{_libdir}/gfortran/modules"
+export FFLAGS="-O0 -g -Wl,-z,now -fPIC -I${MPI_FORTRAN_MOD_DIR}"
 xvfb-run -a make all test -C buildopenmpi_dir V=1 MPIEXEC='%{_builddir}/%{name}-%{version}/buildopenmpi_dir/lib/petsc/bin/petscmpiexec -valgrind'
 %else
 xvfb-run -a make all test -C buildopenmpi_dir V=1
@@ -854,25 +827,24 @@ xvfb-run -a make all test -C buildopenmpi_dir V=1
 %{_openmpi_unload}
 %endif
 
-%if 0%{?fedora} || 0%{?rhel} >= 7
 %if %{with mpich}
 %{_mpich_load}
 export LD_LIBRARY_PATH=%{_builddir}/%{name}-%{version}/buildmpich_dir/%{_arch}/lib
 export PETSC_DIR=%{_builddir}/%{name}-%{version}/buildmpich_dir
 export PETSC_ARCH=%{_arch}
 export MPI_INTERFACE_HOSTNAME=localhost
+export OMPI_MCA_btl_base_warn_component_unused=0
 %if %{with debug}
 export PETSCVALGRIND_OPTIONS=" --tool=memcheck --leak-check=yes --track-origins=yes"
 export CFLAGS="-O0 -g -Wl,-z,now -fPIC"
 export CXXFLAGS="-O0 -g -Wl,-z,now -fPIC"
-export FFLAGS="-O0 -g -Wl,-z,now -fPIC -I%{_libdir}/gfortran/modules"
+export FFLAGS="-O0 -g -Wl,-z,now -fPIC -I${MPI_FORTRAN_MOD_DIR}"
 xvfb-run -a make all test -C buildmpich_dir V=1 MPIEXEC='%{_builddir}/%{name}-%{version}/buildmpich_dir/lib/petsc/bin/petscmpiexec -valgrind'
 %else
 xvfb-run -a make all test -C buildmpich_dir V=1
 %endif
 %{_mpich_unload}
 %endif
-%endif
 
 export LD_LIBRARY_PATH=%{_libdir}:%{_builddir}/%{name}-%{version}/%{name}-%{version}/%{_arch}/lib
 export PETSC_DIR=%{_builddir}/%{name}-%{version}/%{name}-%{version}
@@ -883,9 +855,9 @@ export PETSCVALGRIND_OPTIONS=" --tool=memcheck --leak-check=yes --track-origins=
 export CFLAGS="-O0 -g -Wl,-z,now -fPIC"
 export CXXFLAGS="-O0 -g -Wl,-z,now -fPIC"
 export FFLAGS="-O0 -g -Wl,-z,now -fPIC -I%{_libdir}/gfortran/modules"
-xvfb-run -a make all test -C %{name}-%{version} V=1 MPIEXEC='%{_builddir}/%{name}-%{version}/%{name}-%{version}/lib/petsc/bin/petscmpiexec -valgrind'
+xvfb-run -a make all test -C %{name}-%{version} V=1 MPIEXEC='%{_builddir}/%{name}-%{version}/%{name}-%{version}/lib/petsc/bin/petscmpiexec -n `getconf _NPROCESSORS_ONLN` -valgrind'
 %else
-xvfb-run -a make all test -C %{name}-%{version} V=1
+xvfb-run -a make all test -C %{name}-%{version} V=1 MPIEXEC='%{_builddir}/%{name}-%{version}/%{name}-%{version}/lib/petsc/bin/petscmpiexec -n `getconf _NPROCESSORS_ONLN`'
 %endif
 
 %if %{with arch64}
@@ -902,9 +874,9 @@ export PETSCVALGRIND_OPTIONS=" --tool=memcheck --leak-check=yes --track-origins=
 export CFLAGS="-O0 -g -Wl,-z,now -fPIC"
 export CXXFLAGS="-O0 -g -Wl,-z,now -fPIC"
 export FFLAGS="-O0 -g -Wl,-z,now -fPIC -I%{_libdir}/gfortran/modules"
-xvfb-run -a make all test -C build64 V=1 MPIEXEC='%{_builddir}/%{name}-%{version}/build64/lib/petsc/bin/petscmpiexec -valgrind'
+xvfb-run -a make all test -C build64 V=1 MPIEXEC='%{_builddir}/%{name}-%{version}/build64/lib/petsc/bin/petscmpiexec -n `getconf _NPROCESSORS_ONLN` -valgrind'
 %else
-xvfb-run -a make all test -C build64 V=1
+xvfb-run -a make all test -C build64 V=1 MPIEXEC='%{_builddir}/%{name}-%{version}/build64/lib/petsc/bin/petscmpiexec -n `getconf _NPROCESSORS_ONLN`'
 %endif
 %endif
 %endif
@@ -976,6 +948,11 @@ xvfb-run -a make all test -C build64 V=1
 %endif
 
 %changelog
+* Sat Dec 05 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.14.1-3
+- Update/Rebuild for MUMPS-5.3.5 on EPEL7
+- Exclude superludist support on EPEL7
+- Add Make BR
+
 * Fri Nov 20 2020 Antonio Trande <sagitter@fedoraproject.org> - 3.14.1-2
 - Fix pkg-config files