Hello community, here is the log from the commit of package gromacs for openSUSE:Factory checked in at 2014-02-11 11:19:37 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/gromacs (Old) and /work/SRC/openSUSE:Factory/.gromacs.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "gromacs" Changes: -------- --- /work/SRC/openSUSE:Factory/gromacs/gromacs.changes 2013-03-06 09:36:01.000000000 +0100 +++ /work/SRC/openSUSE:Factory/.gromacs.new/gromacs.changes 2014-02-11 11:19:38.000000000 +0100 @@ -1,0 +2,13 @@ +Mon Feb 10 16:47:31 UTC 2014 - [email protected] + +- added %check + +------------------------------------------------------------------- +Sun Feb 9 16:23:45 UTC 2014 - [email protected] + +- version bumped to 4.5.6 +- fix GMX_CPU_ACCELERATION to SSE2 for older i386 machines +- added openmpi package +- split doc, bash-completion into separate packages + +------------------------------------------------------------------- Old: ---- gromacs-4.6.1.tar.bz2 New: ---- gromacs-4.6.5.tar.gz manual-4.6.5.pdf regressiontests-4.6.5.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ gromacs.spec ++++++ --- /var/tmp/diff_new_pack.WJpow6/_old 2014-02-11 11:19:41.000000000 +0100 +++ /var/tmp/diff_new_pack.WJpow6/_new 2014-02-11 11:19:41.000000000 +0100 @@ -1,7 +1,7 @@ # # spec file for package gromacs # -# Copyright (c) 2013 SUSE LINUX Products GmbH, Nuernberg, Germany. +# Copyright (c) 2013,2014 SUSE LINUX Products GmbH, Nuernberg, Germany. # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -15,106 +15,197 @@ # Please submit bugfixes or comments via http://bugs.opensuse.org/ # - Name: gromacs -Version: 4.6.1 +Version: 4.6.5 Release: 0 -%define srcversion 4.6.1 Summary: Molecular Dynamics Package License: GPL-2.0+ Group: Productivity/Scientific/Chemistry Url: http://www.gromacs.org -Source0: gromacs-%{srcversion}.tar.bz2 +Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz +Source1: ftp://ftp.gromacs.org/pub/manual/manual-%{version}.pdf +Source2: https://gromacs.googlecode.com/files/regressiontests-%{version}.tar.gz BuildRequires: cmake BuildRequires: fdupes -BuildRequires: fftw3-devel -BuildRequires: gcc-c++ -BuildRequires: libstdc++-devel -BuildRequires: libxml2-devel -BuildRequires: xorg-x11-devel +BuildRequires: openmpi-devel +%if %{defined fedora} +BuildRequires: pkgconfig +%else +BuildRequires: pkg-config +%endif +BuildRequires: pkgconfig(fftw3) BuildRoot: %{_tmppath}/%{name}-%{version}-build %description GROMACS is a versatile and extremely well optimized package to perform -molecular dynamics computer simulations and subsequent trajectory -analysis. It is developed for biomolecules like proteins, but the -extremely high performance means it is used also in several other field -like polymer chemistry and solid state physics. This version has the -dynamic libs and executables; to hack new utility programs you also -need the headers and static libs in gromacs-dev. Linux kernel 2.4 or -later is STRONGLY recommended on Pentium III and later processors since -GROMACS then can use assembly loops with SSE instructions. - +molecular dynamics computer simulations and subsequent trajectory analysis. +It is developed for biomolecules like proteins, but the extremely high +performance means it is used also in several other field like polymer chemistry +and solid state physics. %package devel Summary: Molecular dynamics package -Group: Productivity/Scientific/Chemistry +Group: Development/Libraries/C and C++ Requires: %{name} = %{version} -Requires: fftw3-devel -Requires: glibc-devel -Requires: xorg-x11-devel %description devel GROMACS is a versatile and extremely well optimized package to perform -molecular dynamics computer simulations and subsequent trajectory -analysis. It is developed for biomolecules like proteins, but the -extremely high performance means it is used also in several other field -like polymer chemistry and solid state physics. This version has the -dynamic libs and executables; to hack new utility programs you also -need the headers and static libs in gromacs-dev. Linux kernel 2.4 or -later is STRONGLY recommended on Pentium III and later processors since -GROMACS then can use assembly loops with SSE instructions. +molecular dynamics computer simulations and subsequent trajectory analysis. +It is developed for biomolecules like proteins, but the extremely high +performance means it is used also in several other field like polymer chemistry +and solid state physics. + +This package contains development libraries and header for GROMACS + +%package bash +Summary: Bash completion for Gromacs +Group: Productivity/Other +Requires: %{name} = %{version}-%{release} +Requires: bash-completion +BuildArch: noarch + +%description bash +GROMACS is a versatile and extremely well optimized package to perform +molecular dynamics computer simulations and subsequent trajectory analysis. +It is developed for biomolecules like proteins, but the extremely high +performance means it is used also in several other field like polymer chemistry +and solid state physics. + +This package contains bash completion support for gromacs. + +%package doc +Summary: Documentation for Gromacs +Group: Productivity/Scientific/Chemistry +Requires: %{name} = %{version}-%{release} +BuildArch: noarch + +%description doc +GROMACS is a versatile and extremely well optimized package to perform +molecular dynamics computer simulations and subsequent trajectory analysis. +It is developed for biomolecules like proteins, but the extremely high +performance means it is used also in several other field like polymer chemistry +and solid state physics. + +This package contains documentation for gromacs. + +%package openmpi +Summary: Molecular dynamics package +Group: Productivity/Scientific/Chemistry +Requires: %{name} = %{version} + +%description openmpi +GROMACS is a versatile and extremely well optimized package to perform +molecular dynamics computer simulations and subsequent trajectory analysis. +It is developed for biomolecules like proteins, but the extremely high +performance means it is used also in several other field like polymer chemistry +and solid state physics. + +This package contains the openmpi version of GROMACS. %prep -%setup -q -n %{name}-%{srcversion} +%setup -q +tar -xzf %{S:2} %build -%if 0%{?fedora} -export RPM_OPT_FLAGS="%{optflags} -DFEDORA" +%ifarch i386 x86_64 +#increse to SSE4.1, AVX_128_FMA, AVX_256 when possible +%define acce SSE2 +%else +%define acce None %endif -mkdir build -cd build +mkdir nompi openmpi +cd nompi cmake \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_VERBOSE_MAKEFILE=TRUE \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_C_FLAGS_RELEASE:STRING="%{optflags} -fno-strict-aliasing" \ -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags}" \ - -DCMAKE_SKIP_RPATH=1 \ - -DPACKAGE_ARCHITECTURE=uname -m \ - -DLIB=%{_lib} \ + -DCMAKE_SKIP_INSTALL_RPATH=ON \ + -DGMX_CPU_ACCELERATION=%{acce} \ + -DGMX_MPI=OFF \ + -DGMX_THREAD_MPI=ON \ + -DGMX_OPENMP=ON \ + -DREGRESSIONTEST_PATH="$PWD/../regressiontests-%{version}" \ -DGMXLIB=%{_lib} \ .. +make %{?_smp_mflags} +cd ../openmpi -make +%if %{defined fedora} +%{_openmpi_load} +%endif +cmake \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_VERBOSE_MAKEFILE=TRUE \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_C_FLAGS_RELEASE:STRING="%{optflags} -fno-strict-aliasing" \ + -DCMAKE_CXX_FLAGS_RELEASE:STRING="%{optflags}" \ + -DCMAKE_SKIP_RPATH=1 \ + -DGMX_CPU_ACCELERATION=%{acce} \ + -DGMX_MPI=ON \ + -DGMX_OPENMP=ON \ + -DGMXLIB=%{_lib} \ + .. +#only mdrun uses mpi, change for gromacs>=5.0 +make %{?_smp_mflags} mdrun %install -cd build -%makeinstall -rm -f %{buildroot}%{_libdir}/*.la -%fdupes %{buildroot}/usr/share/gromacs +make -C nompi install DESTDIR=%{buildroot} +make -C openmpi install-mdrun DESTDIR=%{buildroot} +%fdupes %{buildroot}%{_prefix} + +#not need when installed in /usr +rm -f %{buildroot}%{_bindir}/GMXRC* +# Move bash completion file to correct location +mkdir -p %{buildroot}%{_sysconfdir}/bash_completion.d +cp %{buildroot}%{_bindir}/completion.bash %{buildroot}%{_sysconfdir}/bash_completion.d/gromacs +#TODO make a csh and zsh completion in the future maybe +rm -f %{buildroot}%{_bindir}/completion.* + +cp %{S:1} %{buildroot}%{_datadir}/gromacs + +%check +%if %{defined fedora} +%{_openmpi_unload} +%endif +make -C nompi check %post -p /sbin/ldconfig %postun -p /sbin/ldconfig +%post openmpi -p /sbin/ldconfig +%postun openmpi -p /sbin/ldconfig %files -%defattr(-,root,root) +%defattr(-,root,root,-) %{_bindir}/* -%{_datadir}/gromacs/ +%exclude %{_bindir}/*_mpi +%{_datadir}/gromacs +%exclude %{_datadir}/gromacs/html %exclude %{_datadir}/gromacs/template -%doc %{_datadir}/gromacs/html/ -%{_libdir}/libgmx.so.* -%{_libdir}/libgmxana.so.* -%{_libdir}/libmd.so.* -%{_libdir}/libgmxpreprocess.so.* +%exclude %{_datadir}/gromacs/*.pdf +%{_libdir}/lib*.so.* +%exclude %{_libdir}/lib*_mpi.so.* %{_mandir}/man1/* %{_mandir}/man7/* +%files doc +%defattr(-,root,root,-) +%doc %{_datadir}/gromacs/html +%doc %{_datadir}/gromacs/*.pdf + +%files openmpi +%defattr(-,root,root,-) +%{_bindir}/*_mpi +%{_libdir}/lib*_mpi.so.* + %files devel -%defattr(644,root,root,755) +%defattr(-,root,root) %{_datadir}/gromacs/template %{_includedir}/gromacs/ %{_libdir}/*.so %{_libdir}/pkgconfig/* -%changelog +%files bash +%defattr(-,root,root,-) +%config %{_sysconfdir}/bash_completion.d/gromacs -- To unsubscribe, e-mail: [email protected] For additional commands, e-mail: [email protected]
