From d61d4b303650778acfe52d412c8ab1d0f7242459 Mon Sep 17 00:00:00 2001 From: Dominik 'Rathann' Mierzejewski Date: Aug 15 2015 23:20:10 +0000 Subject: update to 5.1 - drop ancient Obsoletes:/Provides: - drop Group: tags - build mdrun-only MPI binaries again - use Reference instead of None for non-SSE2 builds (should be faster) --- diff --git a/.gitignore b/.gitignore index e054a76..b7ff55e 100644 --- a/.gitignore +++ b/.gitignore @@ -26,3 +26,5 @@ manual-4.0.pdf /manual-5.0.5.pdf /gromacs-5.0.6.tar.gz /manual-5.0.6.pdf +/gromacs-5.1.tar.gz +/manual-5.1.pdf diff --git a/gromacs.spec b/gromacs.spec index 36409d8..0825490 100644 --- a/gromacs.spec +++ b/gromacs.spec @@ -5,10 +5,9 @@ %endif Name: gromacs -Version: 5.0.6 -Release: 6%{?dist} +Version: 5.1 +Release: 1%{?dist} Summary: Fast, Free and Flexible Molecular Dynamics -Group: Applications/Engineering License: GPLv2+ URL: http://www.gromacs.org @@ -55,7 +54,6 @@ renamed to g_mdrun. %package common Summary: GROMACS shared data and documentation -Group: Applications/Engineering BuildArch: noarch Provides: gromacs-bash = %{version}-%{release} Obsoletes: gromacs-bash < 5.0.4-1 @@ -87,8 +85,8 @@ This package the manual in PDF format. %package devel Summary: GROMACS header files and development libraries -Group: Applications/Engineering Requires: gromacs-libs = %{version}-%{release} +Requires: cmake %description devel GROMACS is a versatile and extremely well optimized package to perform @@ -104,7 +102,6 @@ programs. %package libs Summary: GROMACS shared libraries -Group: System Environment/Libraries %description libs GROMACS is a versatile and extremely well optimized package to perform @@ -119,8 +116,6 @@ This package contains libraries needed for operation of GROMACS. %if %{with_openmpi} %package openmpi Summary: GROMACS Open MPI binaries and libraries -Group: Applications/Engineering -Obsoletes: gromacs-mpi < %{version}-%{release} Requires: gromacs-common = %{version}-%{release} Requires: gromacs-openmpi-libs = %{version}-%{release} BuildRequires: openmpi-devel @@ -139,8 +134,6 @@ This package single and double precision binaries and libraries. %package openmpi-libs Summary: GROMACS Open MPI shared libraries -Group: System Environment/Libraries -Obsoletes: gromacs-mpi-libs < %{version}-%{release} %description openmpi-libs GROMACS is a versatile and extremely well optimized package to perform @@ -154,10 +147,9 @@ This package contains libraries needed for operation of GROMACS Open MPI. %package openmpi-devel Summary: GROMACS Open MPI development libraries -Group: Applications/Engineering -Obsoletes: gromacs-mpi-devel < %{version}-%{release} Requires: gromacs-devel = %{version}-%{release} Requires: gromacs-openmpi = %{version}-%{release} +BuildRequires: openmpi-devel Requires: openmpi-devel @@ -175,11 +167,8 @@ You may need it if you want to write your own analysis programs. %package mpich Summary: GROMACS MPICH binaries and libraries -Group: Applications/Engineering Requires: gromacs-common = %{version}-%{release} Requires: gromacs-mpich-libs = %{version}-%{release} -Provides: %{name}-mpich2 = %{version}-%{release} -Obsoletes: gromacs-mpich2 < 4.6.3-2 %description mpich GROMACS is a versatile and extremely well optimized package to perform @@ -194,9 +183,6 @@ This package single and double precision binaries and libraries. %package mpich-libs Summary: GROMACS MPICH shared libraries -Group: System Environment/Libraries -Provides: %{name}-mpich2-libs = %{version}-%{release} -Obsoletes: %{name}-mpich2-libs < 4.6.3-2 %description mpich-libs GROMACS is a versatile and extremely well optimized package to perform @@ -210,13 +196,10 @@ This package contains libraries needed for operation of GROMACS MPICH. %package mpich-devel Summary: GROMACS MPICH development libraries -Group: Applications/Engineering Requires: gromacs-devel = %{version}-%{release} Requires: gromacs-mpich = %{version}-%{release} BuildRequires: mpich-devel Requires: mpich-devel -Provides: %{name}-mpich2-devel = %{version}-%{release} -Obsoletes: %{name}-mpich2-devel < 4.6.3-2 %description mpich-devel GROMACS is a versatile and extremely well optimized package to perform @@ -231,7 +214,6 @@ You may need it if you want to write your own analysis programs. %package zsh Summary: GROMACS zsh support -Group: Applications/Engineering Requires: zsh BuildArch: noarch @@ -249,7 +231,6 @@ completion. %package csh Summary: GROMACS csh support -Group: Applications/Engineering Requires: csh BuildArch: noarch @@ -291,10 +272,10 @@ export DEFOPTS="\ -DGMX_X11=ON \ " export DOUBLE="-D GMX_DOUBLE=ON" # Double precision -export MPI="-DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DGMX_DEFAULT_SUFFIX=OFF" +export MPI="-DGMX_BUILD_MDRUN_ONLY=ON -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DGMX_DEFAULT_SUFFIX=OFF" # Acceleration flag -export CPUACC="None" +export CPUACC="Reference" # .. but on x86_64 we know that SSE2 is available always, so %ifarch x86_64 export CPUACC="SSE2" @@ -338,8 +319,8 @@ done mkdir -p %{buildroot}{$MPI_BIN,$MPI_LIB} for p in '' _d ; do cd openmpi${p} -install -p -m 755 bin/gmx* %{buildroot}$MPI_BIN/ -cp -a lib/libgromacs${MPI_SUFFIX}${p}.so* %{buildroot}$MPI_LIB/ +install -p -m 755 bin/mdrun${MPI_SUFFIX}${p} %{buildroot}$MPI_BIN/ +cp -a lib/libgromacs_mdrun${MPI_SUFFIX}${p}.so* %{buildroot}$MPI_LIB/ cd .. done %{_openmpi_unload} @@ -350,8 +331,8 @@ done mkdir -p %{buildroot}{$MPI_BIN,$MPI_LIB} for p in '' _d ; do cd mpich${p} -install -p -m 755 bin/gmx* %{buildroot}$MPI_BIN/ -cp -a lib/libgromacs${MPI_SUFFIX}${p}.so* %{buildroot}$MPI_LIB/ +install -p -m 755 bin/mdrun${MPI_SUFFIX}${p} %{buildroot}$MPI_BIN/ +cp -a lib/libgromacs_mdrun${MPI_SUFFIX}${p}.so* %{buildroot}$MPI_LIB/ cd .. done %{_mpich_unload} @@ -372,14 +353,6 @@ pushd %{buildroot} # Fix GMXRC file permissions chmod a+x ./%{_bindir}/GMXRC ./%{_bindir}/GMXRC.* -# Rename binaries to prevent clashes -# (This is done here so that we don't need to mess with machine generated makefiles. -for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps; do -for p in '' _d ; do -mv ./%{_bindir}/${bin}${p} ./%{_bindir}/g_${bin}${p} -done -done - for bin in demux.pl xplor2gmx.pl; do mv ./%{_bindir}/$bin ./%{_bindir}/g_${bin} done @@ -444,7 +417,6 @@ done %{_bindir}/GMXRC %{_bindir}/GMXRC.bash %{_mandir}/man1/gmx*.1* -%{_mandir}/man7/gromacs.7* %{_datadir}/%{name} %exclude %{_datadir}/%{name}/template @@ -459,26 +431,27 @@ done %{_libdir}/libgromacs*.so %{_libdir}/pkgconfig/libgromacs*.pc %{_datadir}/%{name}/template +%{_datadir}/cmake/gromacs* %if %{with_openmpi} %files openmpi -%{_libdir}/openmpi/bin/gmx* +%{_libdir}/openmpi/bin/mdrun_openmpi* %files openmpi-libs -%{_libdir}/openmpi/lib/libgromacs_openmpi*.so.* +%{_libdir}/openmpi/lib/libgromacs_mdrun_openmpi*.so.* %files openmpi-devel -%{_libdir}/openmpi/lib/libgromacs_openmpi*.so +%{_libdir}/openmpi/lib/libgromacs_mdrun_openmpi*.so %endif %files mpich -%{_libdir}/mpich/bin/gmx* +%{_libdir}/mpich/bin/mdrun_mpich* %files mpich-libs -%{_libdir}/mpich/lib/libgromacs_mpich*.so.* +%{_libdir}/mpich/lib/libgromacs_mdrun_mpich*.so.* %files mpich-devel -%{_libdir}/mpich/lib/libgromacs_mpich*.so +%{_libdir}/mpich/lib/libgromacs_mdrun_mpich*.so %files zsh %{_bindir}/GMXRC.zsh @@ -487,6 +460,13 @@ done %{_bindir}/GMXRC.csh %changelog +* Sat Aug 15 2015 Dominik 'Rathann' Mierzejewski - 5.1-1 +- update to 5.1 +- drop ancient Obsoletes:/Provides: +- drop Group: tags +- build mdrun-only MPI binaries again +- use Reference instead of None for non-SSE2 builds (should be faster) + * Sat Aug 15 2015 Zbigniew Jędrzejewski-Szmek - 5.0.6-6 - Rebuild for MPI provides diff --git a/sources b/sources index ba034ee..2227154 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -b0bb547227143e15b3715c0115a2f4af gromacs-5.0.6.tar.gz -044b65a24c810884616d61cdd121fd67 manual-5.0.6.pdf +e5ba00d47c4c6dec107951a7d4605f31 gromacs-5.1.tar.gz +4e14934c5a323510012f3ac1ed303118 manual-5.1.pdf