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Name:		gromacs
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Version:	4.0.3
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Release:	2%{?dist}
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Summary:	GROMACS binaries
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Group:		Applications/Engineering
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License:	GPLv2+
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URL:		http://www.gromacs.org
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Source0:	ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
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Source1:	ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf
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Source2:	gromacs-template-makefile-single
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Source3:	gromacs-template-makefile-double
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Source4:	gromacs-template-makefile-mpi-single
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Source5:	gromacs-template-makefile-mpi-double
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Source6:	gromacs-README.fedora
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# Add shebangs to scripts
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Patch0:		gromacs-GMXRC.patch
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BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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Requires:	gromacs-common  = %{version}-%{release}
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BuildRequires:	fftw-devel
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BuildRequires:	gsl-devel
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BuildRequires:	libxml2-devel
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BuildRequires:	openmpi-devel
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%if 0%{?rhel} == 4
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BuildRequires:	blas
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BuildRequires:	lapack
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BuildRequires:	xorg-x11-devel
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%else
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BuildRequires:	blas-devel
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BuildRequires:	lapack-devel
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BuildRequires:	libX11-devel
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%endif
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# Check for mpi-selector or environment-modules
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%define selector 0
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%define modules 0
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%if 0%{?fedora} > 9
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%define modules 1
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%endif
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%if 0%{?rhel} == 4
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%define selector 1
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%endif
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%if 0%{?rhel} == 5
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%define selector 1
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%endif
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%if %modules == 1
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BuildRequires:	environment-modules
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%endif
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%if %selector == 1
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BuildRequires:	mpi-selector
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%endif
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%description
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package provides single and double precision binaries.
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The documentation is in the package gromacs-common.
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N.B. All binaries have names starting with g_, for example
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mdrun has been renamed to g_mdrun.
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%package libs
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Summary:	GROMACS libraries
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Group:		Applications/Engineering
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Requires:	gromacs-common = %{version}-%{release}
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# Need to have this so that yum doesn't pull atlas instead
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Requires:	blas
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Requires:	lapack
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%description libs
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package provides runtime libraries needed for the
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single and double precision binaries.
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%package mpi
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Summary:	GROMACS MPI binaries
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Group:		Applications/Engineering
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Requires:	gromacs-common = %{version}-%{release}
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# Need to have this so that yum doesn't pull atlas instead
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Requires:	blas
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Requires:	lapack
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%description mpi
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package provides MPI single precision and double
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precision binaries.
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%package common
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Summary:	GROMACS shared data and documentation
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Group:		Applications/Engineering
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%description common
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package includes architecture independent data and
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documentation.
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%package devel
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Summary:	GROMACS header files and development libraries
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Group:		Applications/Engineering
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Requires:	gromacs-common = %{version}-%{release}
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Requires:	gromacs-libs = %{version}-%{release}
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%description devel
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package contains header files, development libraries,
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and a program example for the GROMACS molecular
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dynamics software. You need it if you want to write your
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own analysis programs.
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%package mpi-devel
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Summary:	GROMACS MPI development libraries
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Group:		Applications/Engineering
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Requires:	gromacs-mpi-libs = %{version}-%{release}
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Requires:	gromacs-devel =  %{version}-%{release}
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# Need to have this so that yum doesn't install LAM instead
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Requires:	openmpi
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%description mpi-devel
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package contains development libraries for GROMACS MPI.
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You need it if you want to write your own analysis programs.
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%package mpi-libs
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Summary:	GROMACS libraries
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Group:		Applications/Engineering
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Requires:	gromacs-common = %{version}-%{release}
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# Need to have this so that yum doesn't install LAM instead
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Requires:	openmpi
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# Need to have this so that yum doesn't pull atlas instead
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Requires:	blas
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Requires:	lapack
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%description mpi-libs
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package provides runtime libraries needed for the
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MPI single and double precision binaries.
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%package bash
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Summary:	GROMACS bash completion
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Group:		Applications/Engineering
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Requires:	bash-completion
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%description bash
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package provides the needed 
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bash completion for GROMACS
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%package zsh
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Summary:	GROMACS zsh support
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Group:		Applications/Engineering
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Requires:	zsh
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%description zsh
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package provides scripts needed to run GROMACS with
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zsh, also it provides zsh completion.
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%package csh
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Summary:	GROMACS csh support
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Group:		Applications/Engineering
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Requires:	csh
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%description csh
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package provides scripts needed to run GROMACS with
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csh and a completion script.
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%package tutor
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Summary:	GROMACS tutorial files
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Group:		Applications/Engineering
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Requires:	gromacs-common = %{version}-%{release}
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%description tutor
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GROMACS is a versatile and extremely well optimized package
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to perform molecular dynamics computer simulations and
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subsequent trajectory analysis. It is developed for
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biomolecules like proteins, but the extremely high
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performance means it is used also in several other field
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like polymer chemistry and solid state physics.
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This package provides tutorials for the use of GROMACS.
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%prep
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%setup -q
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%patch0 -p1
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# Fix incorrect permission
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chmod a-x src/tools/gmx_xpm2ps.c
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%build
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# Assembly kernels haven't got .note.GNU-stack sections
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# because of incompatibilies with Microsoft Assembler.
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# Add noexecstack to compiler flags
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export CFLAGS="%optflags -Wa,--noexecstack -fPIC"
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export LIBS="-lblas -llapack"
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# Single precision
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mkdir single
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cd single
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ln -s ../configure .
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%configure --enable-shared \
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	--disable-static --enable-float \
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	--with-external-blas --with-external-lapack \
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	--with-gsl --with-x
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sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
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sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
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make %{?_smp_mflags}
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cd ..
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# Double precision
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mkdir double
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cd double
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ln -s ../configure .
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%configure --disable-rpath --enable-shared \
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	--disable-static --disable-float \
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	--with-external-blas --with-external-lapack \
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	--with-gsl --with-x \
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	--program-suffix=_d
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sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
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sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
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make %{?_smp_mflags}
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cd ..
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# Load MPI enviroment
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%if %modules == 1
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. /etc/profile.d/modules.sh
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module load %{_libdir}/openmpi/*/openmpi.module
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%endif
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%if %selector == 1
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# Set MPI environment
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mpi-selector --set `mpi-selector --list | grep openmpi`
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source /etc/profile.d/mpi-selector.sh
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%endif
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# MPI, single precision
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mkdir mpi-single
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cd mpi-single
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ln -s ../configure .
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%configure --enable-shared \
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	--disable-static --enable-float \
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	--with-external-blas --with-external-lapack \
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	--with-gsl --with-x --enable-mpi \
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	--program-suffix=_mpi
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sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
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sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
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make %{?_smp_mflags} mdrun
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#make %{?_smp_mflags}
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cd ..
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# MPI, double precision
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mkdir mpi-double
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cd mpi-double
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ln -s ../configure .
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%configure --enable-shared \
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	--disable-static --disable-float \
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	--with-external-blas --with-external-lapack \
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	--with-gsl --with-x --enable-mpi \
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	--program-suffix=_mpi_d
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sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
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sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
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make %{?_smp_mflags} mdrun
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#make %{?_smp_mflags}
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cd ..
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%install
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rm -rf %{buildroot}
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# 4.0.3 needs this to build in EPEL-4
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# Load MPI enviroment
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%if %modules == 1
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. /etc/profile.d/modules.sh
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module load %{_libdir}/openmpi/*/openmpi.module
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%endif
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%if %selector == 1
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# Set MPI environment
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mpi-selector --set `mpi-selector --list | grep openmpi`
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source /etc/profile.d/mpi-selector.sh
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%endif
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# Single precision
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cd single
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make DESTDIR=%{buildroot} INSTALL="install -p" install
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cd ..
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# Double precision
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cd double
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make DESTDIR=%{buildroot} INSTALL="install -p" install
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cd ..
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# MPI, single precision
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cd mpi-single
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make DESTDIR=%{buildroot} INSTALL="install -p" install-mdrun
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cd ..
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# MPI, double precision
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cd mpi-double
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make DESTDIR=%{buildroot} INSTALL="install -p" install-mdrun
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cd ..
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# Install manual & packager's note
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install -cpm 644 %{SOURCE1} .
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install -cpm 644 %{SOURCE6} README.fedora
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# Remove broken makefiles generated by build process
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rm -rf %{buildroot}%{_datadir}/%{name}/template/Makefil*
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# Install template makefiles
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install -cpm 644 %{SOURCE2} %{buildroot}%{_datadir}/%{name}/template/Makefile.single
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install -cpm 644 %{SOURCE3} %{buildroot}%{_datadir}/%{name}/template/Makefile.double
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install -cpm 644 %{SOURCE4} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.single
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install -cpm 644 %{SOURCE5} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.double
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# Fix GMXRC file permissions
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chmod a+x %{buildroot}%{_bindir}/GMXRC %{buildroot}%{_bindir}/GMXRC.*
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# Rename binaries and man pages to prevent clashes
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# (This is done here so that we don't need to mess with machine generated makefiles.
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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 
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mv %{buildroot}%{_bindir}/${bin} %{buildroot}%{_bindir}/g_${bin}
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mv %{buildroot}%{_bindir}/${bin}_d %{buildroot}%{_bindir}/g_${bin}_d
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done
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for bin in demux.pl xplor2gmx.pl; do
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mv %{buildroot}%{_bindir}/$bin %{buildroot}%{_bindir}/g_${bin}
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done
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# MPI-enabled binaries (list will continue when the makefile has
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# the possibility to compile all mpi-enabled files
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for mpibin in mdrun; do
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mv %{buildroot}%{_bindir}/${mpibin}_mpi %{buildroot}%{_bindir}/g_${mpibin}_mpi
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mv %{buildroot}%{_bindir}/${mpibin}_mpi_d %{buildroot}%{_bindir}/g_${mpibin}_mpi_d
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done
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# Man pages
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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 
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mv %{buildroot}%{_mandir}/man1/${bin}.1 %{buildroot}%{_mandir}/man1/g_${bin}.1
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mv %{buildroot}%{_mandir}/man1/${bin}_d.1 %{buildroot}%{_mandir}/man1/g_${bin}_d.1
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done
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# Move completion files around
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chmod a-x %{buildroot}%{_bindir}/completion.*
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# Zsh
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mkdir -p %{buildroot}%{_datadir}/zsh/site-functions
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mv %{buildroot}%{_bindir}/completion.zsh %{buildroot}%{_datadir}/zsh/site-functions/gromacs
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# Bash
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mkdir -p %{buildroot}%{_sysconfdir}/bash_completion.d
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mv %{buildroot}%{_bindir}/completion.bash %{buildroot}/etc/bash_completion.d/gromacs
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# Tcsh
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mv %{buildroot}%{_bindir}/completion.csh . 
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# Remove .la files
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rm -rf %{buildroot}/%{_libdir}/*.la
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# Post install for libs
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%post libs -p /sbin/ldconfig
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%postun libs -p /sbin/ldconfig
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%post mpi-libs -p /sbin/ldconfig
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%postun mpi-libs -p /sbin/ldconfig
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%clean
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rm -rf %{buildroot}
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# Files section
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%files
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%defattr(-,root,root,-)
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%{_bindir}/*
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%exclude %{_bindir}/g_mdrun_mpi
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%exclude %{_bindir}/g_mdrun_mpi_d
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%exclude %{_bindir}/GMXRC*
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%files libs
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%defattr(-,root,root,-)
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%{_libdir}/libgmx.so.*
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%{_libdir}/libgmx_d.so.*
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%{_libdir}/libgmxana.so.*
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%{_libdir}/libgmxana_d.so.*
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%{_libdir}/libmd.so.*
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%{_libdir}/libmd_d.so.*
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%files mpi
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%defattr(-,root,root,-)
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%{_bindir}/g_mdrun_mpi
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%{_bindir}/g_mdrun_mpi_d
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%files mpi-libs
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%defattr(-,root,root,-)
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%{_libdir}/libgmx_mpi.so.*
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%{_libdir}/libgmx_mpi_d.so.*
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%{_libdir}/libmd_mpi.so.*
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%{_libdir}/libmd_mpi_d.so.*
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%files common
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%defattr(-,root,root,-)
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%doc AUTHORS COPYING README manual-4.0.pdf README.fedora
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%{_bindir}/GMXRC
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%{_bindir}/GMXRC.bash
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%{_mandir}/man1/*
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%{_datadir}/%{name}
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%exclude %{_datadir}/%{name}/template
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%exclude %{_datadir}/%{name}/tutor
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%files devel
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%defattr(-,root,root,-)
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%{_includedir}/%{name}
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%{_libdir}/libgmx.so
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%{_libdir}/libgmx_d.so
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%{_libdir}/libgmxana.so
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%{_libdir}/libgmxana_d.so
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%{_libdir}/libmd.so
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%{_libdir}/libmd_d.so
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%{_datadir}/%{name}/template
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%exclude %{_datadir}/%{name}/template/Makefile.mpi.*
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%files mpi-devel
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%defattr(-,root,root,-)
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%{_libdir}/libgmx_mpi.so
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%{_libdir}/libgmx_mpi_d.so
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%{_libdir}/libmd_mpi.so
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%{_libdir}/libmd_mpi_d.so
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%{_datadir}/%{name}/template/Makefile.mpi.*
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%files zsh
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%defattr(-,root,root,-)
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%{_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
26363c
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-2
26363c
- Fix EPEL 4 build.
26363c
7b3f14
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-1
7b3f14
- Update to 4.0.3.
7b3f14
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* 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
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* Sun Nov 09 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.1-5
3f6f44
- Add Requires: blas too.
3f6f44
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* Sun Nov 09 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.1-4
a90b74
- Update to 4.0.1.
a90b74
- Add Requires: lapack and openmpi to prevent yum from pulling atlas and lam
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instead.
a90b74
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* Wed Oct 15 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-3
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- Rename also man pages.
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* 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
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* 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
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* 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
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* 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
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* 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
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* 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
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* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.10.rc3
6e06a8
- Implement module system & remove binary renaming.
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- No need for autoreconf anymore.
6e06a8
- Update to rc3.
6e06a8
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* 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
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* Fri Oct 03 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.8.rc2
6e06a8
- Modified install commands to preserve timestamps.
6e06a8
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* 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
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	sigeps	->	g_sigeps
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	wheel	->	g_wheel
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* Thu Oct 02 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.6.rc2
6e06a8
- Final review fixes.
6e06a8
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* 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
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* Tue Sep 30 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.4.rc2
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- Extensive package review fixes.
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- Unclear licenses on some files, filed upstream bug 217.
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  http://bugzilla.gromacs.org/show_bug.cgi?id=217
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* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.3.rc2
6e06a8
- Move .so files to -devel package.
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- Remove .la files.
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* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.2.rc2
6e06a8
- Implement out-of-tree-builds.
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- Add --noexecstack to CFLAGS.
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- Remove execstack procedure and prelink from buildreqs.
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- Filed upstream bug 215 to add .note.GNU-stack .
6e06a8
- Fix incorrect file permission on src/tools/gmx_xpm2ps.c .
6e06a8
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* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.1.rc2
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- Alphabetized buildrequires.
6e06a8
- Changed gromacs-share to gromacs-common.
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* Fri Sep 26 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.0.rc2
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- Initial build.