3fb288
%ifnarch s390 s390x
3fb288
%global with_openmpi 1
3fb288
%else
3fb288
%global with_openmpi 0
3fb288
%endif
3fb288
6e06a8
Name:		gromacs
692dbc
Version:	4.5.7
692dbc
Release:	1%{?dist}
4fd2f7
Summary:	Fast, Free and Flexible Molecular Dynamics
6e06a8
Group:		Applications/Engineering
6e06a8
License:	GPLv2+
6e06a8
URL:		http://www.gromacs.org
4fd2f7
BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
6e06a8
Source0:	ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
3fb288
# File gotten from 
692dbc
# http://www.gromacs.org/@api/deki/files/190/=manual-4.5.6.pdf
692dbc
Source1:	manual-4.5.6.pdf
6e06a8
Source2:	gromacs-template-makefile-single
6e06a8
Source3:	gromacs-template-makefile-double
6e06a8
Source4:	gromacs-template-makefile-mpi-single
6e06a8
Source5:	gromacs-template-makefile-mpi-double
6e06a8
Source6:	gromacs-README.fedora
6e06a8
6e06a8
# Add shebangs to scripts
6e06a8
Patch0:		gromacs-GMXRC.patch
2d0f49
# Patch gmxdemo for new filenames
2d0f49
Patch1:		gromacs-gmxdemo.patch
6e06a8
3495bd
BuildRequires:	cmake
3495bd
BuildRequires:	atlas-devel
6e06a8
BuildRequires:	fftw-devel
6e06a8
BuildRequires:	gsl-devel
fdbc3c
BuildRequires:	libxml2-devel
6e06a8
BuildRequires:	libX11-devel
3fb288
# To get rid of executable stacks
3fb288
BuildRequires:	prelink
6e06a8
fdbc3c
Requires:	gromacs-common = %{version}-%{release}
3495bd
3495bd
# Libs were branched from gromacs, so there are 64-bit installs that have 32-bit packages installed
3495bd
Obsoletes:	gromacs < 4.5.2-1 
3495bd
6e06a8
6e06a8
%description
4fd2f7
GROMACS is a versatile and extremely well optimized package to perform
4fd2f7
molecular dynamics computer simulations and subsequent trajectory analysis.
4fd2f7
It is developed for biomolecules like proteins, but the extremely high
4fd2f7
performance means it is used also in several other field like polymer chemistry
4fd2f7
and solid state physics.
6e06a8
6e06a8
This package provides single and double precision binaries.
6e06a8
The documentation is in the package gromacs-common.
6e06a8
3495bd
mdrun has been compiled with thread parallellization, so it runs in parallel
3495bd
on shared memory systems. If you want to run on a cluster, you probably want
3495bd
to install one of the MPI parallellized packages.
3495bd
4fd2f7
N.B. All binaries have names starting with g_, for example mdrun has been
4fd2f7
renamed to g_mdrun.
4fd2f7
4fd2f7
6e06a8
%package common
6e06a8
Summary:	GROMACS shared data and documentation
6e06a8
Group:		Applications/Engineering
fdbc3c
BuildArch:	noarch
fdbc3c
# Due to switch to noarch package
3495bd
Obsoletes:	gromacs-common < 4.0.7-1
6e06a8
6e06a8
%description common
4fd2f7
GROMACS is a versatile and extremely well optimized package to perform
4fd2f7
molecular dynamics computer simulations and subsequent trajectory analysis.
4fd2f7
It is developed for biomolecules like proteins, but the extremely high
4fd2f7
performance means it is used also in several other field like polymer chemistry
4fd2f7
and solid state physics.
6e06a8
4fd2f7
This package includes architecture independent data and documentation.
6e06a8
6e06a8
6e06a8
%package devel
6e06a8
Summary:	GROMACS header files and development libraries
6e06a8
Group:		Applications/Engineering
fdbc3c
Requires:	gromacs = %{version}-%{release}
6e06a8
6e06a8
%description devel
4fd2f7
GROMACS is a versatile and extremely well optimized package to perform
4fd2f7
molecular dynamics computer simulations and subsequent trajectory analysis.
4fd2f7
It is developed for biomolecules like proteins, but the extremely high
4fd2f7
performance means it is used also in several other field like polymer chemistry
4fd2f7
and solid state physics.
4fd2f7
4fd2f7
This package contains header files and development libraries for the GROMACS
4fd2f7
molecular dynamics software. You need it if you want to write your own analysis
4fd2f7
programs.
4fd2f7
4fd2f7
3495bd
%package libs
3495bd
Summary:	GROMACS shared libraries
3495bd
Group:		System Environment/Libraries
3495bd
3495bd
%description libs
3495bd
GROMACS is a versatile and extremely well optimized package to perform
3495bd
molecular dynamics computer simulations and subsequent trajectory analysis.
3495bd
It is developed for biomolecules like proteins, but the extremely high
3495bd
performance means it is used also in several other field like polymer chemistry
3495bd
and solid state physics.
3495bd
3495bd
This package contains libraries needed for operation of GROMACS.
3495bd
3495bd
3fb288
%if %{with_openmpi}
fdbc3c
%package openmpi
fdbc3c
Summary:	GROMACS Open MPI binaries and libraries
4fd2f7
Group:		Applications/Engineering
fdbc3c
Obsoletes:	gromacs-mpi < %{version}-%{release}
4fd2f7
Requires:	gromacs-common = %{version}-%{release}
fdbc3c
BuildRequires:	openmpi-devel
fdbc3c
Requires:	openmpi
3fb288
# Libs were branched from gromacs, so there are 64-bit installs that have 32-bit packages installed
3fb288
Obsoletes:	gromacs-openmpi < 4.5.3-2
4fd2f7
fdbc3c
%description openmpi
4fd2f7
GROMACS is a versatile and extremely well optimized package to perform
4fd2f7
molecular dynamics computer simulations and subsequent trajectory analysis.
4fd2f7
It is developed for biomolecules like proteins, but the extremely high
4fd2f7
performance means it is used also in several other field like polymer chemistry
4fd2f7
and solid state physics.
4fd2f7
3495bd
mdrun has been compiled with thread parallellization (for running on
3495bd
a single node) and with Open MPI (for running on multiple nodes).
3495bd
This package single and double precision binaries and libraries.
3495bd
3495bd
3495bd
%package openmpi-libs
3495bd
Summary:	GROMACS Open MPI shared libraries
3495bd
Group:		System Environment/Libraries
3495bd
Obsoletes:	gromacs-mpi-libs < %{version}-%{release}
3495bd
Requires:	openmpi
3495bd
3495bd
%description openmpi-libs
3495bd
GROMACS is a versatile and extremely well optimized package to perform
3495bd
molecular dynamics computer simulations and subsequent trajectory analysis.
3495bd
It is developed for biomolecules like proteins, but the extremely high
3495bd
performance means it is used also in several other field like polymer chemistry
3495bd
and solid state physics.
3495bd
3495bd
This package contains libraries needed for operation of GROMACS Open MPI.
6e06a8
6e06a8
fdbc3c
%package openmpi-devel
fdbc3c
Summary:	GROMACS Open MPI development libraries
6e06a8
Group:		Applications/Engineering
fdbc3c
Obsoletes:	gromacs-mpi-devel < %{version}-%{release}
4fd2f7
Requires:	gromacs-devel = %{version}-%{release}
fdbc3c
Requires:	gromacs-openmpi = %{version}-%{release}
fdbc3c
Requires:	openmpi-devel
6e06a8
4fd2f7
fdbc3c
%description openmpi-devel
4fd2f7
GROMACS is a versatile and extremely well optimized package to perform
4fd2f7
molecular dynamics computer simulations and subsequent trajectory analysis.
4fd2f7
It is developed for biomolecules like proteins, but the extremely high
4fd2f7
performance means it is used also in several other field like polymer chemistry
4fd2f7
and solid state physics.
4fd2f7
fdbc3c
This package contains development libraries for GROMACS Open MPI.
3495bd
You may need it if you want to write your own analysis programs.
3fb288
%endif
3fb288
6e06a8
%package bash
6e06a8
Summary:	GROMACS bash completion
6e06a8
Group:		Applications/Engineering
6e06a8
Requires:	bash-completion
fdbc3c
BuildArch:	noarch
fdbc3c
# Due to switch to noarch package
3495bd
Obsoletes:	gromacs-bash < 4.0.7-1 
fdbc3c
6e06a8
6e06a8
%description bash
4fd2f7
GROMACS is a versatile and extremely well optimized package to perform
4fd2f7
molecular dynamics computer simulations and subsequent trajectory analysis.
4fd2f7
It is developed for biomolecules like proteins, but the extremely high
4fd2f7
performance means it is used also in several other field like polymer chemistry
4fd2f7
and solid state physics.
6e06a8
4fd2f7
This package provides bash completion for GROMACS.
6e06a8
6e06a8
6e06a8
%package zsh
6e06a8
Summary:	GROMACS zsh support
6e06a8
Group:		Applications/Engineering
6e06a8
Requires:	zsh
fdbc3c
BuildArch:	noarch
fdbc3c
# Due to switch to noarch package
3495bd
Obsoletes:	gromacs-zsh < 4.0.7-1
fdbc3c
6e06a8
6e06a8
%description zsh
4fd2f7
GROMACS is a versatile and extremely well optimized package to perform
4fd2f7
molecular dynamics computer simulations and subsequent trajectory analysis.
4fd2f7
It is developed for biomolecules like proteins, but the extremely high
4fd2f7
performance means it is used also in several other field like polymer chemistry
4fd2f7
and solid state physics.
6e06a8
4fd2f7
This package provides scripts needed to run GROMACS with zsh and zsh
4fd2f7
completion.
6e06a8
6e06a8
6e06a8
%package csh
6e06a8
Summary:	GROMACS csh support
6e06a8
Group:		Applications/Engineering
6e06a8
Requires:	csh
fdbc3c
BuildArch:	noarch
fdbc3c
# Due to switch to noarch package
3495bd
Obsoletes:	gromacs-csh < 4.0.7-1 
fdbc3c
6e06a8
6e06a8
%description csh
4fd2f7
GROMACS is a versatile and extremely well optimized package to perform
4fd2f7
molecular dynamics computer simulations and subsequent trajectory analysis.
4fd2f7
It is developed for biomolecules like proteins, but the extremely high
4fd2f7
performance means it is used also in several other field like polymer chemistry
4fd2f7
and solid state physics.
6e06a8
4fd2f7
This package provides scripts needed to run GROMACS with csh and a completion
4fd2f7
script.
6e06a8
6e06a8
%package tutor
6e06a8
Summary:	GROMACS tutorial files
6e06a8
Group:		Applications/Engineering
6e06a8
Requires:	gromacs-common = %{version}-%{release}
fdbc3c
BuildArch:	noarch
fdbc3c
# Due to switch to noarch package
3495bd
Obsoletes:	gromacs-tutor < 4.0.7-1 
6e06a8
6e06a8
%description tutor
4fd2f7
GROMACS is a versatile and extremely well optimized package to perform
4fd2f7
molecular dynamics computer simulations and subsequent trajectory analysis.
4fd2f7
It is developed for biomolecules like proteins, but the extremely high
4fd2f7
performance means it is used also in several other field like polymer chemistry
4fd2f7
and solid state physics.
6e06a8
6e06a8
This package provides tutorials for the use of GROMACS.
6e06a8
6e06a8
%prep
3495bd
%setup -q 
4fd2f7
%patch0 -p1 -b .gmxrc
4fd2f7
%patch1 -p1 -b .gmxdemo
6e06a8
6e06a8
# Fix incorrect permission
4fd2f7
#chmod a-x src/tools/gmx_xpm2ps.c
6e06a8
6e06a8
6e06a8
6e06a8
%build
6e06a8
# Assembly kernels haven't got .note.GNU-stack sections
6e06a8
# because of incompatibilies with Microsoft Assembler.
6e06a8
# Add noexecstack to compiler flags
6e06a8
a90b74
export CFLAGS="%optflags -Wa,--noexecstack -fPIC"
3495bd
export LIBS="-L%{_libdir}/atlas -lblas -llapack"
6e06a8
4fd2f7
# Default options, used for all compilations
ffdf7b
export DEFOPTS="-D BUILD_SHARED_LIBS=ON -DCMAKE_SKIP_RPATH:BOOL=ON -DCMAKE_SKIP_BUILD_RPATH:BOOL=ON -DGMXLIB=%{_lib}"
3495bd
export SINGLE="-D GMX_DOUBLE=OFF" # Single precision
3495bd
export DOUBLE="-D GMX_DOUBLE=ON" # Double precision
3495bd
export MPI="-D GMX_MPI=ON"
fdbc3c
fdbc3c
# Add this to the configure options if you want to build a debug version
3495bd
export NOASM="-D GMX_ACCELERATION=OFF"
4fd2f7
6e06a8
# Single precision
6e06a8
mkdir single
6e06a8
cd single
3495bd
%cmake $DEFOPTS $SINGLE ..
3495bd
make VERBOSE=1 %{?_smp_mflags}
6e06a8
cd ..
6e06a8
6e06a8
# Double precision
6e06a8
mkdir double
6e06a8
cd double
3495bd
%cmake $DEFOPTS $DOUBLE ..
3495bd
make VERBOSE=1 %{?_smp_mflags}
6e06a8
cd ..
6e06a8
6e06a8
fdbc3c
### MPI versions
fdbc3c
export CC=mpicc
fdbc3c
export CXX=mpicxx
fdbc3c
export F77=mpif77
fdbc3c
export F90=mpif90
fdbc3c
export FC=mpif90
6e06a8
fdbc3c
## Open MPI
3fb288
%if %{with_openmpi}
fdbc3c
%{_openmpi_load}
3495bd
# Suffix to be used for single precision is
3495bd
SUFFIXCONF="-D GMX_DEFAULT_SUFFIX=OFF -D GMX_BINARY_SUFFIX=$SUFFIX -D GMX_LIBS_SUFFIX=${MPI_SUFFIX}"
fdbc3c
# single precision
fdbc3c
mkdir openmpi-single
fdbc3c
cd openmpi-single
3495bd
%cmake $DEFOPTS $SINGLE $MPI $SUFFIXCONF ..
3495bd
make VERBOSE=1 %{?_smp_mflags} mdrun
4fd2f7
cd ..
3495bd
fdbc3c
# double precision
3495bd
# Suffix to be used for double precision is
3495bd
SUFFIXCONF="-D GMX_DEFAULT_SUFFIX=OFF -D GMX_BINARY_SUFFIX=$SUFFIX -D GMX_LIBS_SUFFIX=${MPI_SUFFIX}_d"
fdbc3c
mkdir openmpi-double
fdbc3c
cd openmpi-double
3495bd
%cmake $DEFOPTS $DOUBLE $MPI $SUFFIXCONF ..
3495bd
make VERBOSE=1 %{?_smp_mflags} mdrun
6e06a8
cd ..
fdbc3c
# unload
fdbc3c
%{_openmpi_unload}
3fb288
%endif
3fb288
6e06a8
%install
6e06a8
rm -rf %{buildroot}
6e06a8
6e06a8
fdbc3c
## Open MPI
3fb288
%if %{with_openmpi}
fdbc3c
%{_openmpi_load}
3495bd
# Make install-mdrun target is broken, do install manually
3495bd
mkdir -p %{buildroot}%{_libdir}/openmpi/{bin,lib}
fdbc3c
# single precision
fdbc3c
cd openmpi-single
3495bd
install -p -m 755 src/kernel/mdrun %{buildroot}%{_libdir}/openmpi/bin/g_mdrun_openmpi
3495bd
cp -a src/*/*.so* %{buildroot}%{_libdir}/openmpi/lib/
4fd2f7
cd ..
fdbc3c
# double precision
fdbc3c
cd openmpi-double
3495bd
install -p -m 755 src/kernel/mdrun %{buildroot}%{_libdir}/openmpi/bin/g_mdrun_openmpi_d
3495bd
cp -a src/*/*.so* %{buildroot}%{_libdir}/openmpi/lib/
6e06a8
cd ..
fdbc3c
%{_openmpi_unload}
3fb288
%endif
3fb288
fdbc3c
## Serial versions
4fd2f7
fdbc3c
# Single precision
fdbc3c
cd single
fdbc3c
make DESTDIR=%{buildroot} INSTALL="install -p" install
6e06a8
cd ..
fdbc3c
# Double precision
fdbc3c
cd double
fdbc3c
make DESTDIR=%{buildroot} INSTALL="install -p" install
4fd2f7
cd ..
4fd2f7
3495bd
## Now, the rest of the necessary stuff
3495bd
6e06a8
# Install manual & packager's note
6e06a8
install -cpm 644 %{SOURCE1} .
6e06a8
install -cpm 644 %{SOURCE6} README.fedora
6e06a8
6e06a8
# Remove broken makefiles generated by build process
6e06a8
rm -rf %{buildroot}%{_datadir}/%{name}/template/Makefil*
6e06a8
# Install template makefiles
6e06a8
install -cpm 644 %{SOURCE2} %{buildroot}%{_datadir}/%{name}/template/Makefile.single
6e06a8
install -cpm 644 %{SOURCE3} %{buildroot}%{_datadir}/%{name}/template/Makefile.double
6e06a8
install -cpm 644 %{SOURCE4} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.single
6e06a8
install -cpm 644 %{SOURCE5} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.double
6e06a8
6e06a8
# Fix GMXRC file permissions
6e06a8
chmod a+x %{buildroot}%{_bindir}/GMXRC %{buildroot}%{_bindir}/GMXRC.*
6e06a8
6e06a8
# Rename binaries and man pages to prevent clashes
6e06a8
# (This is done here so that we don't need to mess with machine generated makefiles.
3495bd
#for bin in anadock do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp highway luck make_edi make_ndx mdrun mk_angndx ngmx pdb2gmx protonate sigeps tpbconv trjcat trjconv trjorder wheel x2top xpm2ps xrama ; do 
3495bd
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
6e06a8
mv %{buildroot}%{_bindir}/${bin} %{buildroot}%{_bindir}/g_${bin}
6e06a8
mv %{buildroot}%{_bindir}/${bin}_d %{buildroot}%{_bindir}/g_${bin}_d
6e06a8
done
6e06a8
6e06a8
for bin in demux.pl xplor2gmx.pl; do
6e06a8
mv %{buildroot}%{_bindir}/$bin %{buildroot}%{_bindir}/g_${bin}
6e06a8
done
6e06a8
6e06a8
# Man pages
3495bd
#for bin in anadock do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp highway make_edi make_ndx mdrun mk_angndx ngmx pdb2gmx protonate sigeps tpbconv trjcat trjconv trjorder wheel x2top xpm2ps xrama ; do 
3495bd
for bin in do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp make_edi make_ndx mdrun mk_angndx pdb2gmx tpbconv trjcat trjconv trjorder xpm2ps; do
6e06a8
mv %{buildroot}%{_mandir}/man1/${bin}.1 %{buildroot}%{_mandir}/man1/g_${bin}.1
3495bd
#mv %{buildroot}%{_mandir}/man1/${bin}_d.1 %{buildroot}%{_mandir}/man1/g_${bin}_d.1
6e06a8
done
6e06a8
6e06a8
# Move completion files around
6e06a8
chmod a-x %{buildroot}%{_bindir}/completion.*
6e06a8
# Zsh
6e06a8
mkdir -p %{buildroot}%{_datadir}/zsh/site-functions
6e06a8
mv %{buildroot}%{_bindir}/completion.zsh %{buildroot}%{_datadir}/zsh/site-functions/gromacs
6e06a8
# Bash
6e06a8
mkdir -p %{buildroot}%{_sysconfdir}/bash_completion.d
6e06a8
mv %{buildroot}%{_bindir}/completion.bash %{buildroot}/etc/bash_completion.d/gromacs
6e06a8
# Tcsh
6e06a8
mv %{buildroot}%{_bindir}/completion.csh . 
6e06a8
6e06a8
# Remove .la files
fdbc3c
find %{buildroot} -name *.la -exec rm -rf {} \;
4fd2f7
3fb288
# Get rid of executable stacks
3fb288
find %{buildroot} -name *.so.* -exec execstack -c {} \;
3fb288
f78e77
# Remove spurious files
f78e77
find %{buildroot} -name	.cvsignore* -exec rm -rf {} \;
f78e77
f78e77
fdbc3c
# Post install for libs. MPI packages don't need this.
3495bd
%post libs -p /sbin/ldconfig
4fd2f7
3495bd
%postun libs -p /sbin/ldconfig
6e06a8
6e06a8
%clean
6e06a8
rm -rf %{buildroot}
6e06a8
6e06a8
6e06a8
# Files section
6e06a8
6e06a8
%files
6e06a8
%defattr(-,root,root,-)
fdbc3c
%{_bindir}/g_*
6e06a8
6e06a8
%files common
6e06a8
%defattr(-,root,root,-)
692dbc
%doc AUTHORS COPYING README manual-4.5.6.pdf README.fedora
6e06a8
%{_bindir}/GMXRC
6e06a8
%{_bindir}/GMXRC.bash
6e06a8
%{_mandir}/man1/*
3495bd
%{_mandir}/man7/gromacs.*
fdbc3c
%{_datadir}/%{name}/
fdbc3c
%exclude %{_datadir}/%{name}/template/
fdbc3c
%exclude %{_datadir}/%{name}/tutor/
6e06a8
3495bd
%files libs
3495bd
%defattr(-,root,root,-)
3495bd
%{_libdir}/libgmx.so.*
3495bd
%{_libdir}/libgmx_d.so.*
3495bd
%{_libdir}/libgmxana.so.*
3495bd
%{_libdir}/libgmxana_d.so.*
3495bd
%{_libdir}/libgmxpreprocess.so.*
3495bd
%{_libdir}/libgmxpreprocess_d.so.*
3495bd
%{_libdir}/libmd.so.*
3495bd
%{_libdir}/libmd_d.so.*
3495bd
6e06a8
%files devel
6e06a8
%defattr(-,root,root,-)
6e06a8
%{_includedir}/%{name}
6e06a8
%{_libdir}/libgmx.so
6e06a8
%{_libdir}/libgmx_d.so
6e06a8
%{_libdir}/libgmxana.so
6e06a8
%{_libdir}/libgmxana_d.so
3495bd
%{_libdir}/libgmxpreprocess.so
3495bd
%{_libdir}/libgmxpreprocess_d.so
6e06a8
%{_libdir}/libmd.so
6e06a8
%{_libdir}/libmd_d.so
3495bd
%{_libdir}/pkgconfig/*.pc
fdbc3c
%{_datadir}/%{name}/template/
6e06a8
%exclude %{_datadir}/%{name}/template/Makefile.mpi.*
6e06a8
3fb288
%if %{with_openmpi}
fdbc3c
%files openmpi
4fd2f7
%defattr(-,root,root,-)
fdbc3c
%{_libdir}/openmpi/bin/g_mdrun*
3495bd
3495bd
%files openmpi-libs
3495bd
%defattr(-,root,root,-)
fdbc3c
%{_libdir}/openmpi/lib/lib*.so.*
fdbc3c
fdbc3c
%files openmpi-devel
6e06a8
%defattr(-,root,root,-)
fdbc3c
%{_libdir}/openmpi/lib/lib*.so
3fb288
%endif
3fb288
6e06a8
%files zsh
6e06a8
%defattr(-,root,root,-)
6e06a8
%{_datadir}/zsh/site-functions/gromacs
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%{_bindir}/GMXRC.zsh
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%files bash
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%defattr(-,root,root,-)
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%config(noreplace) %{_sysconfdir}/bash_completion.d/gromacs
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%files csh
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%defattr(-,root,root,-)
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%doc completion.csh
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%{_bindir}/GMXRC.csh
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%files tutor
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%defattr(-,root,root,-)
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%{_datadir}/%{name}/tutor/
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%changelog
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* Fri Apr 19 2013 Susi Lehtola <jussilehtola@fedoraproject.org> - 4.5.7-1
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- Update to 4.5.7.
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3a7ee6
* Wed Oct 31 2012 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.5-2
3a7ee6
- Compiled against newer OpenMPI included in RHEL 6.3.
3a7ee6
e35f2b
* Fri Sep 30 2011 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.5-1
e35f2b
- Update to 4.5.5.
e35f2b
41fd7e
* Sat Sep 17 2011 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.4-3
41fd7e
- Build in EL6.
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- Drop MPICH2 since it is not available on ppc64.
41fd7e
3fb288
* Wed Mar 30 2011 Deji Akingunola <dakingun@gmail.com> - 4.5.4-2
3fb288
- Rebuild for mpich2 soname bump
3fb288
3fb288
* Wed Mar 23 2011 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.4-1
3fb288
- Update to 4.5.4.
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3fb288
* Sun Feb 13 2011 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.3-4
3fb288
- Get rid of executable stacks.
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3fb288
* Mon Feb 07 2011 Dan HorĂ¡k <dan[at]danny.cz> - 4.5.3-3
3fb288
- conditionalize OpenMPI support
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- fix build on 64-bit platforms
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3fb288
* Mon Dec 20 2010 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.3-2
3fb288
- Fix rest of BZ #649338.
3fb288
3495bd
* Thu Nov 18 2010 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.3-1
3495bd
- Update to 4.5.3.
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* Fri Nov 05 2010 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.2-3
3495bd
- Rebuild due to libxml2 soname bump.
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* Wed Nov 03 2010 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.2-2
3495bd
- Make gromacs package obsolete older versions of gromacs package due to the
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  branching of libraries.
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3495bd
* Mon Nov 01 2010 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.2-1
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- Update to 4.5.2.
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* Wed Oct 27 2010 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.1-2
3495bd
- Patch around #644950.
3495bd
- Split libraries in own packages to avoid multilib problems.
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* Sat Oct 09 2010 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.5.1-1
3495bd
- Update to 4.5.1.
3495bd
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* Sun Dec 06 2009 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.0.7-1
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- Update to 4.0.7.
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* Sun Dec 06 2009 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.0.6-1
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- Update to 4.0.6.
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* Fri Dec 04 2009 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.0.5-6
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- Fix file conflict.
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* Tue Dec 01 2009 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.0.5-5
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- Put correct MPI devel package requires in place.
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* Tue Dec 01 2009 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.0.5-4
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- Fix obsoletes.
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* Mon Nov 30 2009 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.0.5-3
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- Combine libs with binaries and drop debug packages to avoid explosion of
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  number of packages.
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- Adopt use of MPI guidelines.
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0b7b88
* Fri Jul 24 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 4.0.5-2
0b7b88
- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
0b7b88
4fd2f7
* Fri May 22 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.5-1
4fd2f7
- Update to 4.0.5.
4fd2f7
- Change spec %%defines to %%globals.
4fd2f7
- Add debug subpackages to make debugging of GROMACS possible.
35dce5
ed60a6
* Tue Feb 17 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.4-1
ed60a6
- Update to 4.0.4.
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0ff216
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-4
0ff216
- Retry fixing gmxdemo.
0ff216
2d0f49
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-3
2d0f49
- Fixed gmxdemo.
2d0f49
26363c
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-2
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- Fix EPEL 4 build.
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7b3f14
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-1
7b3f14
- Update to 4.0.3.
7b3f14
ad6f15
* Wed Jan 14 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.2-7
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- Update manual to latest version.
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- Removed Requires: blas and lapack.
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* Mon Nov 10 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.2-6
bb4bd8
- Update to 4.0.2.
bb4bd8
ad6f15
* Sun Nov 09 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.1-5
3f6f44
- Add Requires: blas too.
3f6f44
ad6f15
* Sun Nov 09 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.1-4
a90b74
- Update to 4.0.1.
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- Add Requires: lapack and openmpi to prevent yum from pulling atlas and lam
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instead.
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ad6f15
* Wed Oct 15 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-3
6e06a8
- Rename also man pages.
6e06a8
ad6f15
* Mon Oct 13 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-2
6e06a8
- Added noreplace to bash completion file.
6e06a8
- Changed double precision mpi binary suffix to _mpi_d.
6e06a8
ad6f15
* Sun Oct 12 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-1
6e06a8
- Update to Gromacs 4.0.
6e06a8
- Remove module system and patch file names to begin with g_.
6e06a8
ad6f15
* Wed Oct 08 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.15.rc3
6e06a8
- Changed location of binaries.
6e06a8
- Removed conflict of module file, as the program is binary compatible with older versions.
6e06a8
ad6f15
* Wed Oct 08 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.14.rc3
6e06a8
- The gromacs module is loaded automatically and it conflicts with gromacs3.
6e06a8
ad6f15
* Tue Oct 07 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.13.rc3
6e06a8
- Renamed module files from %%{name}-%%{version} to %%{name}.
6e06a8
ad6f15
* Mon Oct 06 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.12.rc3
6e06a8
- Fix BR to get GROMACS to build in mock for epel-4.
6e06a8
ad6f15
* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.11.rc3
6e06a8
- Fix to get GROMACS to build in mock for epel-5.
6e06a8
ad6f15
* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.10.rc3
6e06a8
- Implement module system & remove binary renaming.
6e06a8
- No need for autoreconf anymore.
6e06a8
- Update to rc3.
6e06a8
ad6f15
* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.9.rc2
6e06a8
- Fall back to autoreconf due to binary renaming.
6e06a8
ad6f15
* Fri Oct 03 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.8.rc2
6e06a8
- Modified install commands to preserve timestamps.
6e06a8
ad6f15
* Fri Oct 03 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.7.rc2
6e06a8
- Even more review fixes.
6e06a8
- Binaries renamed:
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	highway	->	g_highway
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	luck	->	g_luck
6e06a8
	sigeps	->	g_sigeps
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	wheel	->	g_wheel
6e06a8
ad6f15
* Thu Oct 02 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.6.rc2
6e06a8
- Final review fixes.
6e06a8
ad6f15
* Wed Oct 01 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.5.rc2
6e06a8
- Strip down requires by branching tutor to its own package.
6e06a8
ad6f15
* Tue Sep 30 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.4.rc2
6e06a8
- Extensive package review fixes.
6e06a8
- Unclear licenses on some files, filed upstream bug 217.
6e06a8
  http://bugzilla.gromacs.org/show_bug.cgi?id=217
6e06a8
ad6f15
* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.3.rc2
6e06a8
- Move .so files to -devel package.
6e06a8
- Remove .la files.
6e06a8
ad6f15
* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.2.rc2
6e06a8
- Implement out-of-tree-builds.
6e06a8
- Add --noexecstack to CFLAGS.
6e06a8
- Remove execstack procedure and prelink from buildreqs.
6e06a8
- Filed upstream bug 215 to add .note.GNU-stack .
6e06a8
- Fix incorrect file permission on src/tools/gmx_xpm2ps.c .
6e06a8
ad6f15
* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.1.rc2
6e06a8
- Alphabetized buildrequires.
6e06a8
- Changed gromacs-share to gromacs-common.
6e06a8
ad6f15
* Fri Sep 26 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.0.rc2
6e06a8
- Initial build.