Merge branch 'master' into ELPA_GPU

INSTALL.md

@@ -103,11 +103,11 @@ It this is not desired, it is possible to build *ELPA* with only one (not necess
 real and complex valued case, respectively. This can be done with the "--with-real-..-kernel-only" and
 "--with-complex-..-kernel-only" configure options. For details please do a "configure --help"
 
-### Non MPI one node shared-memory version of ELPA ###
+### No MPI, one node shared-memory version of ELPA ###
 
 Since release 2016.05.001 it is possible to build *ELPA* without any MPI support. This version can be used
 by applications, which do not have any MPI parallelisation. To set this version, use the
-"--enable-shared-memory-only" configure flag. It is strongly recommmended to also set the "--enable-openmp"
+"--with-mpi=0" configure flag. It is strongly recommmended to also set the "--enable-openmp"
 option, otherwise no parallelisation whatsoever will be present.
 
 ### Doxygen documentation ###

README.md

@@ -2,7 +2,7 @@
 
 ## Current Release ##
 
-The current release is ELPA 2015.11.001
+The current release is ELPA 2016.05.001
 
 ## About *ELPA*
 

USERS_GUIDE.md

@@ -85,7 +85,7 @@ please have a look at the man pages and/or the online documentation (see above)
 
 #### Shared-memory version of *ELPA* ####
 
-If the *ELPA* library has been compiled with the configure option "--enable-shared-memory-only",
+If the *ELPA* library has been compiled with the configure option "--with-mpi=0",
 no MPI will be used.
 
 Still the **same** call sequence as in the MPI case can be used (see above).

configure.ac

 AC_PREREQ([2.69])
 
+# Remember to change the version also in elpa.spec
 AC_INIT([elpa],[2016.05.001], [elpa-library@mpcdf.mpg.de])
+
 AC_SUBST([PACKAGE_VERSION])
 
 AC_CONFIG_SRCDIR([src/elpa1.F90])
@@ -19,8 +21,6 @@ AC_CONFIG_MACRO_DIR([m4])
 AC_CONFIG_HEADERS([config.h])
 AM_SILENT_RULES([yes])
 
-rm -rf config.h config-f90.h
-
 # Set the libtool library version, see LIBRARY_INTERFACE
 #
 # See http://www.gnu.org/software/libtool/manual/html_node/Updating-version-info.html
@@ -68,25 +68,21 @@ if test x"${enable_openmp}" = x"yes"; then
 	AC_DEFINE([WITH_OPENMP], [1], [use OpenMP threading])
 fi
 
-AC_MSG_CHECKING(whether --enable-shared-memory-only is specified)
-AC_ARG_ENABLE([shared-memory-only],
-		AS_HELP_STRING([--enable-shared-memory-only],
-			       [do not use MPI; ELPA will be build for one node shared-memory runs only]),
-	      [],
-	      [enable_shared_memory_only=no])
-AC_MSG_RESULT([${enable_shared_memory_only}])
-AM_CONDITIONAL([WITH_MPI],[test x"$enable_shared_memory_only" = x"no"])
-if test x"${enable_shared_memory_only}" = x"no"; then
-	AC_DEFINE([WITH_MPI], [1], [use MPI])
+dnl mpi
+AC_ARG_WITH(mpi, [AS_HELP_STRING([--with-mpi=[[yes|no]]], [compile with MPI. Default: yes])],,[with_mpi=yes])
+AM_CONDITIONAL([WITH_MPI],[test x"with_mpi" = x"yes"])
+if test x"${with_mpi}" = x"yes"; then
+       AC_DEFINE([WITH_MPI], [1], [use MPI])
 fi
 
-dnl check whether mpi compilers are available;
-dnl if not abort since it is mandatory
-
-
 # C
 AC_LANG([C])
-AX_PROG_CC_MPI([test x"$enable_shared_memory_only" = xno],[use_mpi=yes],[use_mpi=no])
+AX_PROG_CC_MPI([test x"$with_mpi" = x"yes"],[found_mpi_c=yes],[found_mpi_c=no])
+if test x"$with_mpi" = x"yes"; then
+  if test x"$found_mpi_c" = x"no"; then
+    AC_MSG_ERROR([Could not compile an MPI C program])
+  fi
+fi
 
 if test x"${enable_openmp}" = x"yes"; then
   AX_ELPA_OPENMP
@@ -111,7 +107,12 @@ AC_MSG_RESULT([${want_single_precision}])
 
 AC_LANG([Fortran])
 m4_include([m4/ax_prog_fc_mpi.m4])
-AX_PROG_FC_MPI([test x"$enable_shared_memory_only" = xno],[use_mpi=yes],[use_mpi=no])
+AX_PROG_FC_MPI([test x"$with_mpi" = x"yes"],[found_mpi_f=yes],[found_mpi_f=no])
+if test x"$with_mpi" = x"yes"; then
+  if test x"$found_mpi_f" = x"no"; then
+    AC_MSG_ERROR([Could not compile an MPI Fortran program])
+  fi
+fi
 if test x"${enable_openmp}" = x"yes"; then
   AX_ELPA_OPENMP
   if test "$ac_cv_prog_fc_openmp" = unsupported; then
@@ -495,9 +496,9 @@ else
     AC_MSG_ERROR([could not link with lapack: specify path])
   fi
 
-  if test x"${enable_shared_memory_only}" = x"no"; then
+  if test x"${with_mpi}" = x"yes"; then
     dnl test whether scalapack already contains blacs
-    scalapack_libs="mpiscalapack scalapack"
+    scalapack_libs="mpiscalapack scalapack scalapack-openmpi"
     old_LIBS="$LIBS"
     for lib in ${scalapack_libs}; do
       LIBS="-l${lib} ${old_LIBS}"
@@ -514,6 +515,12 @@ else
 
       dnl Test for stand-alone blacs
       AC_SEARCH_LIBS([bi_f77_init],[mpiblacsF77init],[],[],[-lmpiblacs])
+
+      dnl for debian
+      AC_SEARCH_LIBS([blacs_gridinit],[blacs-openmpi],[have_blacs=yes],[have_blacs=no],[-lblacsCinit-openmpi -lscalapack-openmpi])
+      if test x"${have_blacs}" = x"no"; then
+        unset ac_cv_search_blacs_gridinit
+      fi
       AC_SEARCH_LIBS([blacs_gridinit],[mpiblacs blacs],[have_blacs=yes],[have_blacs=no])
 
       if test x"${have_blacs}" = x"no"; then
@@ -961,26 +968,6 @@ AC_CONFIG_FILES([
 
 AC_OUTPUT
 
-
-if test -e config.h ; then
-  grep "^#define" config.h > config-f90.h
-else
-  echo "Warning! No config.h was generated, check for errors and re-run configure!"
-  exit 1
-fi
-
-echo "Generating elpa/elpa_generated.h..."
-mkdir -p elpa
-grep -h "^ *!c>" $srcdir/src/elpa_c_interface.F90 | sed 's/^ *!c>//;' > elpa/elpa_generated.h || exit 1
-
-echo "Generating Fortran interfaces for C kernels"
-grep -h "^ *!f>" $srcdir/src/elpa2_kernels/*.c | sed 's/^ *!f>//;' > elpa/elpa_generated_fortran_interfaces.h || exit 1
-#grep -h "^ *!f>" $srcdir/src/elpa2_kernels/*.cpp | sed 's/^ *!f>//;' >> elpa/elpa_generated_fortran_interfaces.h || exit 1
-
-echo "Generating test/shared_sources/generated.h..."
-mkdir -p test/shared_sources
-grep -h "^ *!c>" $srcdir/test/shared_sources/*.F90 | sed 's/^ *!c>//;' > test/shared_sources/generated.h || exit 1
-
 if test "${can_compile_avx}" = "no" ; then
 #  if test x"${want_avx}" = x"yes" ; then
     AC_MSG_WARN([Could not compile AVX instructions])
@@ -995,3 +982,5 @@ fi
 if test "${can_compile_sse}" = "no" ; then
   AC_MSG_WARN([Could not compile SSE instructions])
 fi
+
+make -f $srcdir/generated_headers.am generated-headers top_srcdir="$srcdir"

elpa.spec

+#
+# spec file for package elpa
+#
+# Copyright (c) 2015 Lorenz Hüdepohl
+#
+# All modifications and additions to the file contributed by third parties
+# remain the property of their copyright owners, unless otherwise agreed
+# upon. The license for this file, and modifications and additions to the
+# file, is the same license as for the pristine package itself (unless the
+# license for the pristine package is not an Open Source License, in which
+# case the license is the MIT License). An "Open Source License" is a
+# license that conforms to the Open Source Definition (Version 1.9)
+# published by the Open Source Initiative.
+
+%define so_version 4
+
+# OpenMP support requires an MPI implementation with MPI_THREAD_MULTIPLE support,
+# which is only available for a sufficiently configured openmpi >= 1.8
+# Set to 0 to disable
+%define with_openmp 1
+
+Name:           elpa
+Version:        2016.05.001
+Release:        2
+Summary:        A massively parallel eigenvector solver
+License:        LGPL-3.0
+Group:          System/Libraries
+Url:            https://elpa.rzg.mpg.de/
+Source0:        https://elpa.mpcdf.mpg.de/html/Releases/%{version}/%{name}-%{version}.tar.gz
+Requires:       openmpi
+BuildRequires:  gcc-c++
+BuildRequires:  gcc-fortran
+BuildRequires:  openmpi-devel
+BuildRequires:  blas
+BuildRequires:  blas-devel
+BuildRequires:  lapack
+BuildRequires:  lapack-devel
+BuildRequires:  pkg-config
+
+%if %{defined fedora}
+BuildRequires:  scalapack-openmpi
+BuildRequires:  scalapack-openmpi-devel
+BuildRequires:  blacs-openmpi
+BuildRequires:  blacs-openmpi-devel
+BuildRequires:  environment-modules
+%endif
+
+%if %{defined suse_version}
+BuildRequires:  libscalapack2-openmpi-devel
+%endif
+
+# For make check, mpirun of openmpi needs an installed openssh
+BuildRequires:  openssh
+
+%description
+A new efficient distributed parallel direct eigenvalue solver for
+symmetric matrices. It contains both an improved one-step ScaLAPACK type solver
+(ELPA1) and the two-step solver ELPA2.
+
+ELPA uses the same matrix layout as ScaLAPACK. The actual parallel linear
+algebra routines are completely rewritten. ELPA1 implements the same linear
+algebra as traditional solutions (reduction to tridiagonal form by Householder
+transforms, divide & conquer solution, eigenvector backtransform). In ELPA2,
+the reduction to tridiagonal form and the corresponding backtransform are
+replaced by a two-step version, giving an additional significant performance
+improvement.
+
+ELPA has demonstrated good scalability for large matrices on up to 294.000
+cores of a BlueGene/P system.
+
+%package     -n lib%{name}%{so_version}
+Summary:        A massively parallel eigenvector solver
+Group:          System/Libraries
+Provides:       %{name} = %{version}
+Requires:       %{name}-tools >= %{version}
+
+%description -n lib%{name}%{so_version}
+A new efficient distributed parallel direct eigenvalue solver for
+symmetric matrices. It contains both an improved one-step ScaLAPACK type solver
+(ELPA1) and the two-step solver ELPA2.
+
+ELPA uses the same matrix layout as ScaLAPACK. The actual parallel linear
+algebra routines are completely rewritten. ELPA1 implements the same linear
+algebra as traditional solutions (reduction to tridiagonal form by Householder
+transforms, divide & conquer solution, eigenvector backtransform). In ELPA2,
+the reduction to tridiagonal form and the corresponding backtransform are
+replaced by a two-step version, giving an additional significant performance
+improvement.
+
+ELPA has demonstrated good scalability for large matrices on up to 294.000
+cores of a BlueGene/P system.
+
+%package        tools
+Summary:        Utility program for %{name}
+Group:          Development/Libraries
+Requires:       %{name} = %{version}
+
+%description    tools
+A small tool program for %{name}, elpa2_print_kernels, which prints the available and
+currently selected numerical kernel for ELPA2.
+
+%package        devel
+Summary:        Development files for %{name}
+Group:          Development/Libraries
+Requires:       %{name} = %{version}
+Requires:       openmpi
+Requires:       libstdc++-devel
+Requires:       lapack-devel
+Requires:       blas-devel
+Requires:       libscalapack2-openmpi-devel
+
+%description    devel
+The %{name}-devel package contains libraries and header files for
+developing applications that use %{name}.
+
+%package        devel-static
+Summary:        Development files for %{name} - static libraries
+Group:          Development/Libraries
+Requires:       %{name}-devel
+
+%description    devel-static
+This package provides the static libraries for developing applications
+that use %{name}.
+
+%if %{defined with_openmp}
+
+%package     -n lib%{name}_openmp%{so_version}
+Requires:       openmpi >= 1.8
+BuildRequires:  openmpi-devel >= 1.8
+Summary:        A massively parallel eigenvector solver
+Group:          System/Libraries
+Provides:       %{name}_openmp = %{version}
+Requires:       %{name}_openmp-tools >= %{version}
+
+%description -n lib%{name}_openmp%{so_version}
+OpenMP parallelized version of %{name}, use with an Open MPI implementation
+that was configured and tested with MPI_THREAD_MULTIPLE support.
+
+%package     -n %{name}_openmp-tools
+Summary:        Utility program for %{name}_openmp
+Group:          Development/Libraries
+Provides:       %{name}_openmp = %{version}
+
+%description -n %{name}_openmp-tools
+A small tool program for %{name}_openmp, elpa2_print_kernels_openmp, which
+prints the available and currently selected numerical kernel for ELPA2.
+
+%package     -n %{name}_openmp-devel
+Summary:        Development files for %{name}_openmp
+Group:          Development/Libraries
+Requires:       %{name}_openmp = %{version}
+Requires:       openmpi
+Requires:       libstdc++-devel
+Requires:       lapack-devel
+Requires:       blas-devel
+Requires:       libscalapack2-openmpi-devel
+
+%description -n %{name}_openmp-devel
+The %{name}_openmp-devel package contains libraries and header files for
+developing applications that use %{name}_openmp.
+
+%package     -n %{name}_openmp-devel-static
+Summary:        Development files for %{name} - static libraries
+Group:          Development/Libraries
+Requires:       %{name}-devel
+
+%description -n %{name}_openmp-devel-static
+This package provides the static libraries for developing applications
+that use %{name}_openmp.
+%endif
+
+%prep
+%setup
+
+%build
+%if %{defined fedora}
+module load mpi/openmpi-%{_arch}
+%endif
+mkdir build
+pushd build
+%define _configure ../configure
+%configure --docdir=%{_docdir}/%{name}-%{version}
+make %{?_smp_mflags} V=1
+popd
+
+%if %{defined with_openmp}
+mkdir build_openmp
+pushd build_openmp
+%configure --docdir=%{_docdir}/%{name}_openmp-%{version} --enable-openmp
+make %{?_smp_mflags} V=1
+popd
+%endif
+
+
+%check
+%if %{defined fedora}
+module load mpi/openmpi-%{_arch}
+%endif
+
+pushd build
+make check TEST_FLAGS="1500 50 16" || { echo "Tests failed: Content of ./test-suite.log:"; cat ./test-suite.log; echo; exit 1; }
+popd
+
+%if %{defined with_openmp}
+pushd build_openmp
+make check TEST_FLAGS="1500 50 16" || { echo "Tests failed: Content of ./test-suite.log:"; cat ./test-suite.log; echo; exit 1; }
+popd
+%endif
+
+
+%install
+%if %{defined with_openmp}
+pushd build_openmp
+make V=1 install DESTDIR=%{buildroot}
+popd
+%endif
+pushd build
+make V=1 install DESTDIR=%{buildroot}
+popd
+
+%post   -n lib%{name}%{so_version} -p /sbin/ldconfig
+%postun -n lib%{name}%{so_version} -p /sbin/ldconfig
+
+%if %{defined with_openmp}
+%post   -n lib%{name}_openmp%{so_version} -p /sbin/ldconfig
+%postun -n lib%{name}_openmp%{so_version} -p /sbin/ldconfig
+%endif
+
+%files -n lib%{name}%{so_version}
+# See http://en.opensuse.org/openSUSE:Shared_library_packaging_policy
+# to explain this package's name
+%defattr(0755,root,root)
+%{_libdir}/lib%{name}.so.*
+%doc
+%defattr(0644,root,root)
+%{_docdir}/%{name}-%{version}/*
+%dir %{_docdir}/%{name}-%{version}
+
+%files tools
+%attr(0755,root,root) %{_bindir}/elpa2_print_kernels
+%attr(0644,root,root) %_mandir/man1/elpa2_print_kernels.1.gz
+
+%files devel
+%defattr(0644,root,root)
+%{_libdir}/pkgconfig/%{name}-%{version}.pc
+%{_includedir}/%{name}-%{version}
+%{_libdir}/lib%{name}.so
+%{_libdir}/lib%{name}.la
+%_mandir/man3/*
+
+%files devel-static
+%defattr(0644,root,root)
+%{_libdir}/lib%{name}.a
+
+%if %{defined with_openmp}
+
+%files -n lib%{name}_openmp%{so_version}
+%defattr(0755,root,root)
+%{_libdir}/lib%{name}_openmp.so.*
+%doc
+%defattr(0644,root,root)
+%{_docdir}/%{name}_openmp-%{version}/*
+%dir %{_docdir}/%{name}_openmp-%{version}
+
+%files -n %{name}_openmp-tools
+%defattr(0755,root,root)
+%{_bindir}/elpa2_print_kernels_openmp
+
+%files -n %{name}_openmp-devel
+%defattr(0644,root,root)
+%{_libdir}/pkgconfig/%{name}_openmp-%{version}.pc
+%{_includedir}/%{name}_openmp-%{version}
+%{_libdir}/lib%{name}_openmp.so
+%{_libdir}/lib%{name}_openmp.la
+
+%files -n %{name}_openmp-devel-static
+%defattr(0644,root,root)
+%{_libdir}/lib%{name}_openmp.a
+
+%endif
+
+%changelog

generated_headers.am

+define extract_interface
+	@echo "Generating $@...";
+	@grep -h "^ *$1" $^ | sed 's/^ *$1//;' > $@ || { rm $@; exit 1; }
+endef
+
+elpa test:
+	mkdir $@
+
+test/shared_sources: | test
+	mkdir $@
+
+config-f90.h: config.h
+	@echo "Generating $@...";
+	@grep "^#define" $^ > $@ || { rm $@; exit 1; }
+
+elpa/elpa_generated.h: $(top_srcdir)/src/elpa_c_interface.F90 | elpa
+	$(call extract_interface,!c>)
+
+test/shared_sources/generated.h: $(wildcard $(top_srcdir)/test/shared_sources/*.F90) | test/shared_sources
+	$(call extract_interface,!c>)
+
+elpa/elpa_generated_fortran_interfaces.h: $(wildcard $(top_srcdir)/src/elpa2_kernels/*.c) | elpa
+	$(call extract_interface,!f>)
+
+generated_headers= config-f90.h elpa/elpa_generated.h test/shared_sources/generated.h elpa/elpa_generated_fortran_interfaces.h
+generated-headers: $(generated_headers)