+++ /dev/null
-Name: gromacs
-Version: 4.5
-Release: 7%{?dist}
-Summary: GROMACS binaries
-Group: Applications/Engineering
-License: LGPLv2.1
-URL: http://www.gromacs.org
-Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
-Source1: ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf
-Source2: gromacs-template-makefile-single
-Source3: gromacs-template-makefile-double
-Source4: gromacs-template-makefile-mpi-single
-Source5: gromacs-template-makefile-mpi-double
-Source6: gromacs-README.fedora
-
-# Add shebangs to scripts
-Patch0: gromacs-GMXRC.patch
-
-BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
-Requires: gromacs-common = %{version}-%{release}
-
-BuildRequires: fftw-devel
-BuildRequires: gsl-devel
-BuildRequires: libxml2-devel
-BuildRequires: openmpi-devel
-
-%if 0%{?rhel} == 4
-BuildRequires: blas
-BuildRequires: lapack
-BuildRequires: xorg-x11-devel
-%else
-BuildRequires: blas-devel
-BuildRequires: lapack-devel
-BuildRequires: libX11-devel
-%endif
-
-# Check for mpi-selector or environment-modules
-
-%define selector 0
-%define modules 0
-
-%if 0%{?fedora} > 9
-%define modules 1
-%endif
-
-%if 0%{?rhel} == 4
-%define selector 1
-%endif
-
-%if 0%{?rhel} == 5
-%define selector 1
-%endif
-
-%if %modules == 1
-BuildRequires: environment-modules
-%endif
-
-%if %selector == 1
-BuildRequires: mpi-selector
-%endif
-
-
-%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 package provides single and double precision binaries.
-The documentation is in the package gromacs-common.
-
-N.B. All binaries have names starting with g_, for example
-mdrun has been renamed to g_mdrun.
-
-%package libs
-Summary: GROMACS libraries
-Group: Applications/Engineering
-Requires: gromacs-common = %{version}-%{release}
-# Need to have this so that yum doesn't pull atlas instead
-Requires: blas
-Requires: lapack
-
-%description libs
-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 provides runtime libraries needed for the
-single and double precision binaries.
-
-
-%package mpi
-Summary: GROMACS MPI binaries
-Group: Applications/Engineering
-Requires: gromacs-common = %{version}-%{release}
-# Need to have this so that yum doesn't pull atlas instead
-Requires: blas
-Requires: lapack
-
-%description mpi
-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 provides MPI single precision and double
-precision binaries.
-
-
-%package common
-Summary: GROMACS shared data and documentation
-Group: Applications/Engineering
-
-%description common
-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 includes architecture independent data and
-documentation.
-
-
-%package devel
-Summary: GROMACS header files and development libraries
-Group: Applications/Engineering
-Requires: gromacs-common = %{version}-%{release}
-Requires: gromacs-libs = %{version}-%{release}
-
-%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 package contains header files, development libraries,
-and a program example for the GROMACS molecular
-dynamics software. You need it if you want to write your
-own analysis programs.
-
-
-%package mpi-devel
-Summary: GROMACS MPI development libraries
-Group: Applications/Engineering
-Requires: gromacs-mpi-libs = %{version}-%{release}
-Requires: gromacs-devel = %{version}-%{release}
-# Need to have this so that yum doesn't install LAM instead
-Requires: openmpi
-
-%description mpi-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 package contains development libraries for GROMACS MPI.
-You need it if you want to write your own analysis programs.
-
-
-%package mpi-libs
-Summary: GROMACS libraries
-Group: Applications/Engineering
-Requires: gromacs-common = %{version}-%{release}
-# Need to have this so that yum doesn't install LAM instead
-Requires: openmpi
-# Need to have this so that yum doesn't pull atlas instead
-Requires: blas
-Requires: lapack
-
-%description mpi-libs
-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 provides runtime libraries needed for the
-MPI single and double precision binaries.
-
-
-%package bash
-Summary: GROMACS bash completion
-Group: Applications/Engineering
-Requires: bash-completion
-
-%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 provides the needed
-bash completion for GROMACS
-
-
-%package zsh
-Summary: GROMACS zsh support
-Group: Applications/Engineering
-Requires: zsh
-
-%description zsh
-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 provides scripts needed to run GROMACS with
-zsh, also it provides zsh completion.
-
-
-%package csh
-Summary: GROMACS csh support
-Group: Applications/Engineering
-Requires: csh
-
-%description csh
-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 provides scripts needed to run GROMACS with
-csh and a completion script.
-
-%package tutor
-Summary: GROMACS tutorial files
-Group: Applications/Engineering
-Requires: gromacs-common = %{version}-%{release}
-
-%description tutor
-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 provides tutorials for the use of GROMACS.
-
-%prep
-%setup -q
-%patch0 -p1
-
-# Fix incorrect permission
-chmod a-x src/tools/gmx_xpm2ps.c
-
-
-
-%build
-# Assembly kernels haven't got .note.GNU-stack sections
-# because of incompatibilies with Microsoft Assembler.
-# Add noexecstack to compiler flags
-
-export CFLAGS="%optflags -Wa,--noexecstack -fPIC"
-export LIBS="-lblas -llapack"
-
-# Single precision
-mkdir single
-cd single
-ln -s ../configure .
-%configure --enable-shared \
- --disable-static --enable-float \
- --with-external-blas --with-external-lapack \
- --with-gsl --with-x
-sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
-sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
-
-make %{?_smp_mflags}
-cd ..
-
-# Double precision
-mkdir double
-cd double
-ln -s ../configure .
-%configure --disable-rpath --enable-shared \
- --disable-static --disable-float \
- --with-external-blas --with-external-lapack \
- --with-gsl --with-x \
- --program-suffix=_d
-sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
-sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
-
-make %{?_smp_mflags}
-cd ..
-
-# Load MPI enviroment
-
-%if %modules == 1
-. /etc/profile.d/modules.sh
-module load %{_libdir}/openmpi/*/openmpi.module
-%endif
-
-%if %selector == 1
-# Set MPI environment
-mpi-selector --set `mpi-selector --list | grep openmpi`
-source /etc/profile.d/mpi-selector.sh
-%endif
-
-
-# MPI, single precision
-
-mkdir mpi-single
-cd mpi-single
-ln -s ../configure .
-%configure --enable-shared \
- --disable-static --enable-float \
- --with-external-blas --with-external-lapack \
- --with-gsl --with-x --enable-mpi \
- --program-suffix=_mpi
-sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
-sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
-
-make %{?_smp_mflags} mdrun
-#make %{?_smp_mflags}
-cd ..
-
-# MPI, double precision
-mkdir mpi-double
-cd mpi-double
-ln -s ../configure .
-%configure --enable-shared \
- --disable-static --disable-float \
- --with-external-blas --with-external-lapack \
- --with-gsl --with-x --enable-mpi \
- --program-suffix=_mpi_d
-sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
-sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
-
-make %{?_smp_mflags} mdrun
-#make %{?_smp_mflags}
-cd ..
-
-
-%install
-rm -rf %{buildroot}
-
-# Single precision
-cd single
-make DESTDIR=%{buildroot} INSTALL="install -p" install
-cd ..
-
-# Double precision
-cd double
-make DESTDIR=%{buildroot} INSTALL="install -p" install
-cd ..
-
-
-
-# MPI, single precision
-cd mpi-single
-make DESTDIR=%{buildroot} INSTALL="install -p" install-mdrun
-cd ..
-
-# MPI, double precision
-cd mpi-double
-make DESTDIR=%{buildroot} INSTALL="install -p" install-mdrun
-cd ..
-
-# Install manual & packager's note
-install -cpm 644 %{SOURCE1} .
-install -cpm 644 %{SOURCE6} README.fedora
-
-# Remove broken makefiles generated by build process
-rm -rf %{buildroot}%{_datadir}/%{name}/template/Makefil*
-# Install template makefiles
-install -cpm 644 %{SOURCE2} %{buildroot}%{_datadir}/%{name}/template/Makefile.single
-install -cpm 644 %{SOURCE3} %{buildroot}%{_datadir}/%{name}/template/Makefile.double
-install -cpm 644 %{SOURCE4} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.single
-install -cpm 644 %{SOURCE5} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.double
-
-
-# Fix GMXRC file permissions
-chmod a+x %{buildroot}%{_bindir}/GMXRC %{buildroot}%{_bindir}/GMXRC.*
-
-# Rename binaries and man pages to prevent clashes
-# (This is done here so that we don't need to mess with machine generated makefiles.
-for bin in anadock do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp highway make_edi make_ndx mdrun mk_angndx ngmx pdb2gmx protonate sigeps tpbconv trjcat trjconv trjorder wheel x2top xpm2ps xrama ; do
-mv %{buildroot}%{_bindir}/${bin} %{buildroot}%{_bindir}/g_${bin}
-mv %{buildroot}%{_bindir}/${bin}_d %{buildroot}%{_bindir}/g_${bin}_d
-done
-
-for bin in demux.pl xplor2gmx.pl; do
-mv %{buildroot}%{_bindir}/$bin %{buildroot}%{_bindir}/g_${bin}
-done
-
-# MPI-enabled binaries (list will continue when the makefile has
-# the possibility to compile all mpi-enabled files
-for mpibin in mdrun; do
-mv %{buildroot}%{_bindir}/${mpibin}_mpi %{buildroot}%{_bindir}/g_${mpibin}_mpi
-mv %{buildroot}%{_bindir}/${mpibin}_mpi_d %{buildroot}%{_bindir}/g_${mpibin}_mpi_d
-done
-
-# Man pages
-for bin in anadock do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp highway make_edi make_ndx mdrun mk_angndx ngmx pdb2gmx protonate sigeps tpbconv trjcat trjconv trjorder wheel x2top xpm2ps xrama ; do
-mv %{buildroot}%{_mandir}/man1/${bin}.1 %{buildroot}%{_mandir}/man1/g_${bin}.1
-mv %{buildroot}%{_mandir}/man1/${bin}_d.1 %{buildroot}%{_mandir}/man1/g_${bin}_d.1
-done
-
-# Move completion files around
-chmod a-x %{buildroot}%{_bindir}/completion.*
-# Zsh
-mkdir -p %{buildroot}%{_datadir}/zsh/site-functions
-mv %{buildroot}%{_bindir}/completion.zsh %{buildroot}%{_datadir}/zsh/site-functions/gromacs
-# Bash
-mkdir -p %{buildroot}%{_sysconfdir}/bash_completion.d
-mv %{buildroot}%{_bindir}/completion.bash %{buildroot}/etc/bash_completion.d/gromacs
-# Tcsh
-mv %{buildroot}%{_bindir}/completion.csh .
-
-# Remove .la files
-rm -rf %{buildroot}/%{_libdir}/*.la
-
-# Post install for libs
-
-%post libs -p /sbin/ldconfig
-
-%postun libs -p /sbin/ldconfig
-
-%post mpi-libs -p /sbin/ldconfig
-
-%postun mpi-libs -p /sbin/ldconfig
-
-
-%clean
-rm -rf %{buildroot}
-
-
-
-
-# Files section
-
-%files
-%defattr(-,root,root,-)
-%{_bindir}/*
-%exclude %{_bindir}/g_mdrun_mpi
-%exclude %{_bindir}/g_mdrun_mpi_d
-%exclude %{_bindir}/GMXRC*
-
-%files libs
-%defattr(-,root,root,-)
-%{_libdir}/libgmx.so.*
-%{_libdir}/libgmx_d.so.*
-%{_libdir}/libgmxana.so.*
-%{_libdir}/libgmxana_d.so.*
-%{_libdir}/libmd.so.*
-%{_libdir}/libmd_d.so.*
-
-%files mpi
-%defattr(-,root,root,-)
-%{_bindir}/g_mdrun_mpi
-%{_bindir}/g_mdrun_mpi_d
-
-
-%files mpi-libs
-%defattr(-,root,root,-)
-%{_libdir}/libgmx_mpi.so.*
-%{_libdir}/libgmx_mpi_d.so.*
-%{_libdir}/libmd_mpi.so.*
-%{_libdir}/libmd_mpi_d.so.*
-
-
-
-%files common
-%defattr(-,root,root,-)
-%doc AUTHORS COPYING README manual-4.0.pdf README.fedora
-%{_bindir}/GMXRC
-%{_bindir}/GMXRC.bash
-%{_mandir}/man1/*
-%{_datadir}/%{name}
-%exclude %{_datadir}/%{name}/template
-%exclude %{_datadir}/%{name}/tutor
-
-%files devel
-%defattr(-,root,root,-)
-%{_includedir}/%{name}
-%{_libdir}/libgmx.so
-%{_libdir}/libgmx_d.so
-%{_libdir}/libgmxana.so
-%{_libdir}/libgmxana_d.so
-%{_libdir}/libmd.so
-%{_libdir}/libmd_d.so
-%{_datadir}/%{name}/template
-%exclude %{_datadir}/%{name}/template/Makefile.mpi.*
-
-%files mpi-devel
-%defattr(-,root,root,-)
-%{_libdir}/libgmx_mpi.so
-%{_libdir}/libgmx_mpi_d.so
-%{_libdir}/libmd_mpi.so
-%{_libdir}/libmd_mpi_d.so
-%{_datadir}/%{name}/template/Makefile.mpi.*
-
-
-%files zsh
-%defattr(-,root,root,-)
-%{_datadir}/zsh/site-functions/gromacs
-%{_bindir}/GMXRC.zsh
-
-%files bash
-%defattr(-,root,root,-)
-%config(noreplace) %{_sysconfdir}/bash_completion.d/gromacs
-
-
-%files csh
-%defattr(-,root,root,-)
-%doc completion.csh
-%{_bindir}/GMXRC.csh
-
-%files tutor
-%defattr(-,root,root,-)
-%{_datadir}/%{name}/tutor
-
-
-%changelog
-* Wed Jan 14 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.2-7
-- Update manual to latest version.
-- Removed Requires: blas and lapack.
-
-* Mon Nov 10 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.2-6
-- Update to 4.0.2.
-
-* Sun Nov 09 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.1-5
-- Add Requires: blas too.
-
-* Sun Nov 09 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.1-4
-- Update to 4.0.1.
-- Add Requires: lapack and openmpi to prevent yum from pulling atlas and lam
-instead.
-
-* Wed Oct 15 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-3
-- Rename also man pages.
-
-* Mon Oct 13 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-2
-- Added noreplace to bash completion file.
-- Changed double precision mpi binary suffix to _mpi_d.
-
-* Sun Oct 12 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-1
-- Update to Gromacs 4.0.
-- Remove module system and patch file names to begin with g_.
-
-* Wed Oct 08 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.15.rc3
-- Changed location of binaries.
-- Removed conflict of module file, as the program is binary compatible with older versions.
-
-* Wed Oct 08 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.14.rc3
-- The gromacs module is loaded automatically and it conflicts with gromacs3.
-
-* Tue Oct 07 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.13.rc3
-- Renamed module files from %%{name}-%%{version} to %%{name}.
-
-* Mon Oct 06 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.12.rc3
-- Fix BR to get GROMACS to build in mock for epel-4.
-
-* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.11.rc3
-- Fix to get GROMACS to build in mock for epel-5.
-
-* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.10.rc3
-- Implement module system & remove binary renaming.
-- No need for autoreconf anymore.
-- Update to rc3.
-
-* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.9.rc2
-- Fall back to autoreconf due to binary renaming.
-
-* Fri Oct 03 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.8.rc2
-- Modified install commands to preserve timestamps.
-
-* Fri Oct 03 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.7.rc2
-- Even more review fixes.
-- Binaries renamed:
- highway -> g_highway
- luck -> g_luck
- sigeps -> g_sigeps
- wheel -> g_wheel
-
-* Thu Oct 02 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.6.rc2
-- Final review fixes.
-
-* Wed Oct 01 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.5.rc2
-- Strip down requires by branching tutor to its own package.
-
-* Tue Sep 30 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.4.rc2
-- Extensive package review fixes.
-- Unclear licenses on some files, filed upstream bug 217.
- http://bugzilla.gromacs.org/show_bug.cgi?id=217
-
-* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.3.rc2
-- Move .so files to -devel package.
-- Remove .la files.
-
-* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.2.rc2
-- Implement out-of-tree-builds.
-- Add --noexecstack to CFLAGS.
-- Remove execstack procedure and prelink from buildreqs.
-- Filed upstream bug 215 to add .note.GNU-stack .
-- Fix incorrect file permission on src/tools/gmx_xpm2ps.c .
-
-* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.1.rc2
-- Alphabetized buildrequires.
-- Changed gromacs-share to gromacs-common.
-
-* Fri Sep 26 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.0.rc2
-- Initial build.
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff