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6e06a80 |
Name: gromacs
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4fd2f7f |
Version: 4.0.5
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1b055a1 |
Release: 3%{?dist}
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4fd2f7f |
Summary: Fast, Free and Flexible Molecular Dynamics
|
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6e06a80 |
Group: Applications/Engineering
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6e06a80 |
License: GPLv2+
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6e06a80 |
URL: http://www.gromacs.org
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4fd2f7f |
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
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6e06a80 |
Source0: ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz
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ad6f154 |
Source1: ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf
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6e06a80 |
Source2: gromacs-template-makefile-single
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6e06a80 |
Source3: gromacs-template-makefile-double
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6e06a80 |
Source4: gromacs-template-makefile-mpi-single
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6e06a80 |
Source5: gromacs-template-makefile-mpi-double
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6e06a80 |
Source6: gromacs-README.fedora
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6e06a80 |
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6e06a80 |
# Add shebangs to scripts
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|
6e06a80 |
Patch0: gromacs-GMXRC.patch
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|
2d0f49e |
# Patch gmxdemo for new filenames
|
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2d0f49e |
Patch1: gromacs-gmxdemo.patch
|
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|
4fd2f7f |
# Patch configure for the library suffix
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|
4fd2f7f |
Patch2: gromacs-configure.patch
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6e06a80 |
|
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|
1b055a1 |
BuildRequires: blas-devel
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6e06a80 |
BuildRequires: fftw-devel
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|
6e06a80 |
BuildRequires: gsl-devel
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|
6e06a80 |
BuildRequires: lapack-devel
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|
1b055a1 |
BuildRequires: libxml2-devel
|
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|
6e06a80 |
BuildRequires: libX11-devel
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6e06a80 |
|
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6e06a80 |
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1b055a1 |
Requires: gromacs-common = %{version}-%{release}
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6e06a80 |
|
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6e06a80 |
|
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6e06a80 |
%description
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|
4fd2f7f |
GROMACS is a versatile and extremely well optimized package to perform
|
|
|
4fd2f7f |
molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
4fd2f7f |
It is developed for biomolecules like proteins, but the extremely high
|
|
|
4fd2f7f |
performance means it is used also in several other field like polymer chemistry
|
|
|
4fd2f7f |
and solid state physics.
|
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|
6e06a80 |
|
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|
6e06a80 |
This package provides single and double precision binaries.
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6e06a80 |
The documentation is in the package gromacs-common.
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6e06a80 |
|
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|
4fd2f7f |
N.B. All binaries have names starting with g_, for example mdrun has been
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|
4fd2f7f |
renamed to g_mdrun.
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4fd2f7f |
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4fd2f7f |
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6e06a80 |
%package common
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6e06a80 |
Summary: GROMACS shared data and documentation
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6e06a80 |
Group: Applications/Engineering
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1b055a1 |
BuildArch: noarch
|
|
|
1b055a1 |
# Due to switch to noarch package
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|
|
1b055a1 |
Obsoletes: gromacs-common < %{version}-%{release}
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|
|
6e06a80 |
|
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|
6e06a80 |
%description common
|
|
|
4fd2f7f |
GROMACS is a versatile and extremely well optimized package to perform
|
|
|
4fd2f7f |
molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
4fd2f7f |
It is developed for biomolecules like proteins, but the extremely high
|
|
|
4fd2f7f |
performance means it is used also in several other field like polymer chemistry
|
|
|
4fd2f7f |
and solid state physics.
|
|
|
6e06a80 |
|
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|
4fd2f7f |
This package includes architecture independent data and documentation.
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6e06a80 |
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|
6e06a80 |
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|
6e06a80 |
%package devel
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|
6e06a80 |
Summary: GROMACS header files and development libraries
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6e06a80 |
Group: Applications/Engineering
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|
1b055a1 |
Requires: gromacs = %{version}-%{release}
|
|
|
6e06a80 |
|
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|
6e06a80 |
%description devel
|
|
|
4fd2f7f |
GROMACS is a versatile and extremely well optimized package to perform
|
|
|
4fd2f7f |
molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
4fd2f7f |
It is developed for biomolecules like proteins, but the extremely high
|
|
|
4fd2f7f |
performance means it is used also in several other field like polymer chemistry
|
|
|
4fd2f7f |
and solid state physics.
|
|
|
4fd2f7f |
|
|
|
4fd2f7f |
This package contains header files and development libraries for the GROMACS
|
|
|
4fd2f7f |
molecular dynamics software. You need it if you want to write your own analysis
|
|
|
4fd2f7f |
programs.
|
|
|
4fd2f7f |
|
|
|
4fd2f7f |
|
|
|
1b055a1 |
%package openmpi
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|
|
1b055a1 |
Summary: GROMACS Open MPI binaries and libraries
|
|
|
4fd2f7f |
Group: Applications/Engineering
|
|
|
1b055a1 |
Obsoletes: gromacs-mpi < %{version}-%{release}
|
|
|
4fd2f7f |
Requires: gromacs-common = %{version}-%{release}
|
|
|
1b055a1 |
BuildRequires: openmpi-devel
|
|
|
a90b748 |
Requires: openmpi
|
|
|
6e06a80 |
|
|
|
1b055a1 |
%description openmpi
|
|
|
4fd2f7f |
GROMACS is a versatile and extremely well optimized package to perform
|
|
|
4fd2f7f |
molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
4fd2f7f |
It is developed for biomolecules like proteins, but the extremely high
|
|
|
4fd2f7f |
performance means it is used also in several other field like polymer chemistry
|
|
|
4fd2f7f |
and solid state physics.
|
|
|
6e06a80 |
|
|
|
1b055a1 |
This package provides Open MPI single precision and double precision binaries
|
|
|
1b055a1 |
and libraries.
|
|
|
6e06a80 |
|
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|
6e06a80 |
|
|
|
1b055a1 |
%package openmpi-devel
|
|
|
1b055a1 |
Summary: GROMACS Open MPI development libraries
|
|
|
4fd2f7f |
Group: Applications/Engineering
|
|
|
1b055a1 |
Obsoletes: gromacs-mpi-devel < %{version}-%{release}
|
|
|
1b055a1 |
Requires: gromacs-devel = %{version}-%{release}
|
|
|
1b055a1 |
Requires: openmpi-devel
|
|
|
4fd2f7f |
|
|
|
6e06a80 |
|
|
|
1b055a1 |
%description openmpi-devel
|
|
|
4fd2f7f |
GROMACS is a versatile and extremely well optimized package to perform
|
|
|
4fd2f7f |
molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
4fd2f7f |
It is developed for biomolecules like proteins, but the extremely high
|
|
|
4fd2f7f |
performance means it is used also in several other field like polymer chemistry
|
|
|
4fd2f7f |
and solid state physics.
|
|
|
4fd2f7f |
|
|
|
1b055a1 |
This package contains development libraries for GROMACS Open MPI.
|
|
|
1b055a1 |
You need it if you want to write your own analysis programs.
|
|
|
4fd2f7f |
|
|
|
4fd2f7f |
|
|
|
1b055a1 |
#%package mpich2
|
|
|
1b055a1 |
#Summary: GROMACS MPICH2 binaries and libraries
|
|
|
1b055a1 |
#Group: Applications/Engineering
|
|
|
1b055a1 |
#Requires: gromacs-common = %{version}-%{release}
|
|
|
1b055a1 |
#Requires: mpich2
|
|
|
1b055a1 |
#
|
|
|
1b055a1 |
#%description mpich2
|
|
|
1b055a1 |
#GROMACS is a versatile and extremely well optimized package to perform
|
|
|
1b055a1 |
#molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
1b055a1 |
#It is developed for biomolecules like proteins, but the extremely high
|
|
|
1b055a1 |
#performance means it is used also in several other field like polymer chemistry
|
|
|
1b055a1 |
#and solid state physics.
|
|
|
1b055a1 |
#
|
|
|
1b055a1 |
#This package provides MPICH2 single precision and double precision binaries
|
|
|
1b055a1 |
#and libraries.
|
|
|
1b055a1 |
|
|
|
1b055a1 |
|
|
|
1b055a1 |
#%package mpich2-devel
|
|
|
1b055a1 |
#Summary: GROMACS MPICH2 development libraries
|
|
|
1b055a1 |
#Group: Applications/Engineering
|
|
|
1b055a1 |
#Requires: gromacs-devel = %{version}-%{release}
|
|
|
1b055a1 |
#BuildRequires: mpich2-devel
|
|
|
1b055a1 |
#Requires: mpich2-devel
|
|
|
1b055a1 |
#
|
|
|
1b055a1 |
#%description mpich2-devel
|
|
|
1b055a1 |
#GROMACS is a versatile and extremely well optimized package to perform
|
|
|
1b055a1 |
#molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
1b055a1 |
#It is developed for biomolecules like proteins, but the extremely high
|
|
|
1b055a1 |
#performance means it is used also in several other field like polymer chemistry
|
|
|
1b055a1 |
#and solid state physics.
|
|
|
1b055a1 |
#
|
|
|
1b055a1 |
#This package contains development libraries for GROMACS MPICH2.
|
|
|
1b055a1 |
#You need it if you want to write your own analysis programs.
|
|
|
4fd2f7f |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%package bash
|
|
|
6e06a80 |
Summary: GROMACS bash completion
|
|
|
6e06a80 |
Group: Applications/Engineering
|
|
|
6e06a80 |
Requires: bash-completion
|
|
|
1b055a1 |
BuildArch: noarch
|
|
|
1b055a1 |
# Due to switch to noarch package
|
|
|
1b055a1 |
Obsoletes: gromacs-common < %{version}-%{release}
|
|
|
1b055a1 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%description bash
|
|
|
4fd2f7f |
GROMACS is a versatile and extremely well optimized package to perform
|
|
|
4fd2f7f |
molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
4fd2f7f |
It is developed for biomolecules like proteins, but the extremely high
|
|
|
4fd2f7f |
performance means it is used also in several other field like polymer chemistry
|
|
|
4fd2f7f |
and solid state physics.
|
|
|
6e06a80 |
|
|
|
4fd2f7f |
This package provides bash completion for GROMACS.
|
|
|
6e06a80 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%package zsh
|
|
|
6e06a80 |
Summary: GROMACS zsh support
|
|
|
6e06a80 |
Group: Applications/Engineering
|
|
|
6e06a80 |
Requires: zsh
|
|
|
1b055a1 |
BuildArch: noarch
|
|
|
1b055a1 |
# Due to switch to noarch package
|
|
|
1b055a1 |
Obsoletes: gromacs-common < %{version}-%{release}
|
|
|
1b055a1 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%description zsh
|
|
|
4fd2f7f |
GROMACS is a versatile and extremely well optimized package to perform
|
|
|
4fd2f7f |
molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
4fd2f7f |
It is developed for biomolecules like proteins, but the extremely high
|
|
|
4fd2f7f |
performance means it is used also in several other field like polymer chemistry
|
|
|
4fd2f7f |
and solid state physics.
|
|
|
6e06a80 |
|
|
|
4fd2f7f |
This package provides scripts needed to run GROMACS with zsh and zsh
|
|
|
4fd2f7f |
completion.
|
|
|
6e06a80 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%package csh
|
|
|
6e06a80 |
Summary: GROMACS csh support
|
|
|
6e06a80 |
Group: Applications/Engineering
|
|
|
6e06a80 |
Requires: csh
|
|
|
1b055a1 |
BuildArch: noarch
|
|
|
1b055a1 |
# Due to switch to noarch package
|
|
|
1b055a1 |
Obsoletes: gromacs-common < %{version}-%{release}
|
|
|
1b055a1 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%description csh
|
|
|
4fd2f7f |
GROMACS is a versatile and extremely well optimized package to perform
|
|
|
4fd2f7f |
molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
4fd2f7f |
It is developed for biomolecules like proteins, but the extremely high
|
|
|
4fd2f7f |
performance means it is used also in several other field like polymer chemistry
|
|
|
4fd2f7f |
and solid state physics.
|
|
|
6e06a80 |
|
|
|
4fd2f7f |
This package provides scripts needed to run GROMACS with csh and a completion
|
|
|
4fd2f7f |
script.
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%package tutor
|
|
|
6e06a80 |
Summary: GROMACS tutorial files
|
|
|
6e06a80 |
Group: Applications/Engineering
|
|
|
6e06a80 |
Requires: gromacs-common = %{version}-%{release}
|
|
|
1b055a1 |
BuildArch: noarch
|
|
|
1b055a1 |
# Due to switch to noarch package
|
|
|
1b055a1 |
Obsoletes: gromacs-common < %{version}-%{release}
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%description tutor
|
|
|
4fd2f7f |
GROMACS is a versatile and extremely well optimized package to perform
|
|
|
4fd2f7f |
molecular dynamics computer simulations and subsequent trajectory analysis.
|
|
|
4fd2f7f |
It is developed for biomolecules like proteins, but the extremely high
|
|
|
4fd2f7f |
performance means it is used also in several other field like polymer chemistry
|
|
|
4fd2f7f |
and solid state physics.
|
|
|
6e06a80 |
|
|
|
6e06a80 |
This package provides tutorials for the use of GROMACS.
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%prep
|
|
|
6e06a80 |
%setup -q
|
|
|
4fd2f7f |
%patch0 -p1 -b .gmxrc
|
|
|
4fd2f7f |
%patch1 -p1 -b .gmxdemo
|
|
|
4fd2f7f |
%patch2 -p1 -b .libsuffix
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# Fix incorrect permission
|
|
|
4fd2f7f |
#chmod a-x src/tools/gmx_xpm2ps.c
|
|
|
6e06a80 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%build
|
|
|
6e06a80 |
# Assembly kernels haven't got .note.GNU-stack sections
|
|
|
6e06a80 |
# because of incompatibilies with Microsoft Assembler.
|
|
|
6e06a80 |
# Add noexecstack to compiler flags
|
|
|
6e06a80 |
|
|
|
a90b748 |
export CFLAGS="%optflags -Wa,--noexecstack -fPIC"
|
|
|
6e06a80 |
export LIBS="-lblas -llapack"
|
|
|
6e06a80 |
|
|
|
4fd2f7f |
# Default options, used for all compilations
|
|
|
4fd2f7f |
export DEFOPTS="--enable-shared --disable-static --with-external-blas \
|
|
|
4fd2f7f |
--with-external-lapack --with-gsl --with-x"
|
|
|
4fd2f7f |
export SINGLE="--enable-float" # Single precision
|
|
|
4fd2f7f |
export DOUBLE="--disable-float" # Double precision
|
|
|
4fd2f7f |
export MPI="--enable-mpi"
|
|
|
1b055a1 |
|
|
|
1b055a1 |
# Add this to the configure options if you want to build a debug version
|
|
|
4fd2f7f |
export NOASM="--disable-ia32-3dnow --disable-ia32-sse --disable-x86-64-sse \
|
|
|
4fd2f7f |
--disable-ppc-altivec --disable-ia64-asm"
|
|
|
4fd2f7f |
|
|
|
4fd2f7f |
|
|
|
6e06a80 |
# Single precision
|
|
|
6e06a80 |
mkdir single
|
|
|
6e06a80 |
cd single
|
|
|
4fd2f7f |
sed "s|@LIBSUFFIX@||g" < ../configure > configure; chmod 777 configure
|
|
|
4fd2f7f |
%configure $DEFOPTS $SINGLE
|
|
|
6e06a80 |
sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
|
|
|
6e06a80 |
sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
|
|
|
6e06a80 |
|
|
|
6e06a80 |
make %{?_smp_mflags}
|
|
|
6e06a80 |
cd ..
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# Double precision
|
|
|
6e06a80 |
mkdir double
|
|
|
6e06a80 |
cd double
|
|
|
4fd2f7f |
sed "s|@LIBSUFFIX@|_d|g" < ../configure > configure; chmod 777 configure
|
|
|
4fd2f7f |
%configure $DEFOPTS $DOUBLE --program-suffix="_d"
|
|
|
6e06a80 |
sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
|
|
|
6e06a80 |
sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
|
|
|
6e06a80 |
|
|
|
6e06a80 |
make %{?_smp_mflags}
|
|
|
6e06a80 |
cd ..
|
|
|
6e06a80 |
|
|
|
6e06a80 |
|
|
|
1b055a1 |
### MPI versions
|
|
|
1b055a1 |
export CC=mpicc
|
|
|
1b055a1 |
export CXX=mpicxx
|
|
|
1b055a1 |
export F77=mpif77
|
|
|
1b055a1 |
export F90=mpif90
|
|
|
1b055a1 |
export FC=mpif90
|
|
|
6e06a80 |
|
|
|
1b055a1 |
## Open MPI
|
|
|
1b055a1 |
%{_openmpi_load}
|
|
|
1b055a1 |
# single precision
|
|
|
1b055a1 |
mkdir openmpi-single
|
|
|
1b055a1 |
cd openmpi-single
|
|
|
4fd2f7f |
sed "s|@LIBSUFFIX@|_mpi|g" < ../configure > configure; chmod 777 configure
|
|
|
1b055a1 |
%configure $DEFOPTS $SINGLE $MPI --program-suffix=${MPI_SUFFIX} --bindir=${MPI_BIN} --libdir=${MPI_LIB}
|
|
|
4fd2f7f |
sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
|
|
|
4fd2f7f |
sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
|
|
|
4fd2f7f |
make %{?_smp_mflags} mdrun
|
|
|
4fd2f7f |
cd ..
|
|
|
1b055a1 |
# double precision
|
|
|
1b055a1 |
mkdir openmpi-double
|
|
|
1b055a1 |
cd openmpi-double
|
|
|
1b055a1 |
sed "s|@LIBSUFFIX@|_mpi_d|g" < ../configure > configure; chmod 777 configure
|
|
|
1b055a1 |
%configure $DEFOPTS $DOUBLE $MPI --program-suffix=${MPI_SUFFIX}_d --bindir=${MPI_BIN} --libdir=${MPI_LIB}
|
|
|
6e06a80 |
sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
|
|
|
6e06a80 |
sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
|
|
|
6e06a80 |
make %{?_smp_mflags} mdrun
|
|
|
6e06a80 |
cd ..
|
|
|
1b055a1 |
# unload
|
|
|
1b055a1 |
%{_openmpi_unload}
|
|
|
1b055a1 |
|
|
|
1b055a1 |
## MPICH2
|
|
|
1b055a1 |
#{_mpich2_load}
|
|
|
1b055a1 |
# single precision
|
|
|
1b055a1 |
#mkdir mpich2-single
|
|
|
1b055a1 |
#cd mpich2-single
|
|
|
1b055a1 |
#sed "s|@LIBSUFFIX@|_mpi|g" < ../configure > configure; chmod 777 configure
|
|
|
1b055a1 |
#configure $DEFOPTS $SINGLE $MPI --program-suffix=${MPI_SUFFIX} --bindir=${MPI_BIN} --libdir=${MPI_LIB}
|
|
|
1b055a1 |
#sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
|
|
|
1b055a1 |
#sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
|
|
|
1b055a1 |
#make %{?_smp_mflags} mdrun
|
|
|
1b055a1 |
#cd ..
|
|
|
1b055a1 |
# double precision
|
|
|
1b055a1 |
#mkdir mpich2-double
|
|
|
1b055a1 |
#cd mpich2-double
|
|
|
1b055a1 |
#sed "s|@LIBSUFFIX@|_mpi_d|g" < ../configure > configure; chmod 777 configure
|
|
|
1b055a1 |
#configure $DEFOPTS $DOUBLE $MPI --program-suffix=${MPI_SUFFIX}_d --bindir=${MPI_BIN} --libdir=${MPI_LIB}
|
|
|
1b055a1 |
#sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
|
|
|
1b055a1 |
#sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
|
|
|
1b055a1 |
#make %{?_smp_mflags} mdrun
|
|
|
1b055a1 |
#cd ..
|
|
|
1b055a1 |
#{_mpich2_unload}
|
|
|
6e06a80 |
|
|
|
4fd2f7f |
|
|
|
1b055a1 |
%install
|
|
|
1b055a1 |
rm -rf %{buildroot}
|
|
|
4fd2f7f |
|
|
|
4fd2f7f |
|
|
|
1b055a1 |
## Open MPI
|
|
|
1b055a1 |
%{_openmpi_load}
|
|
|
1b055a1 |
# single precision
|
|
|
1b055a1 |
cd openmpi-single
|
|
|
1b055a1 |
make DESTDIR=%{buildroot} INSTALL="install -p" BINDIR=${MPI_BIN} LIBDIR=${MPI_LIB} install-mdrun
|
|
|
4fd2f7f |
cd ..
|
|
|
1b055a1 |
# double precision
|
|
|
1b055a1 |
cd openmpi-double
|
|
|
1b055a1 |
make DESTDIR=%{buildroot} INSTALL="install -p" BINDIR=${MPI_BIN} LIBDIR=${MPI_LIB} install-mdrun
|
|
|
6e06a80 |
cd ..
|
|
|
1b055a1 |
%{_openmpi_unload}
|
|
|
6e06a80 |
|
|
|
1b055a1 |
## MPICH 2
|
|
|
1b055a1 |
#{_mpich2_load}
|
|
|
1b055a1 |
# single precision
|
|
|
1b055a1 |
#cd mpich2-single
|
|
|
1b055a1 |
#make DESTDIR=%{buildroot} INSTALL="install -p" BINDIR=${MPI_BIN} LIBDIR=${MPI_LIB} install-mdrun
|
|
|
1b055a1 |
#cd ..
|
|
|
1b055a1 |
# double precision
|
|
|
1b055a1 |
#cd mpich2-double
|
|
|
1b055a1 |
#make DESTDIR=%{buildroot} INSTALL="install -p" BINDIR=${MPI_BIN} LIBDIR=${MPI_LIB} install-mdrun
|
|
|
1b055a1 |
#cd ..
|
|
|
1b055a1 |
#{_mpich2_unload}
|
|
|
6e06a80 |
|
|
|
26363c1 |
|
|
|
1b055a1 |
## Serial versions
|
|
|
26363c1 |
|
|
|
6e06a80 |
# Single precision
|
|
|
6e06a80 |
cd single
|
|
|
6e06a80 |
make DESTDIR=%{buildroot} INSTALL="install -p" install
|
|
|
6e06a80 |
cd ..
|
|
|
6e06a80 |
# Double precision
|
|
|
6e06a80 |
cd double
|
|
|
6e06a80 |
make DESTDIR=%{buildroot} INSTALL="install -p" install
|
|
|
6e06a80 |
cd ..
|
|
|
6e06a80 |
|
|
|
4fd2f7f |
|
|
|
6e06a80 |
# Install manual & packager's note
|
|
|
6e06a80 |
install -cpm 644 %{SOURCE1} .
|
|
|
6e06a80 |
install -cpm 644 %{SOURCE6} README.fedora
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# Remove broken makefiles generated by build process
|
|
|
6e06a80 |
rm -rf %{buildroot}%{_datadir}/%{name}/template/Makefil*
|
|
|
6e06a80 |
# Install template makefiles
|
|
|
6e06a80 |
install -cpm 644 %{SOURCE2} %{buildroot}%{_datadir}/%{name}/template/Makefile.single
|
|
|
6e06a80 |
install -cpm 644 %{SOURCE3} %{buildroot}%{_datadir}/%{name}/template/Makefile.double
|
|
|
6e06a80 |
install -cpm 644 %{SOURCE4} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.single
|
|
|
6e06a80 |
install -cpm 644 %{SOURCE5} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.double
|
|
|
6e06a80 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# Fix GMXRC file permissions
|
|
|
6e06a80 |
chmod a+x %{buildroot}%{_bindir}/GMXRC %{buildroot}%{_bindir}/GMXRC.*
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# Rename binaries and man pages to prevent clashes
|
|
|
6e06a80 |
# (This is done here so that we don't need to mess with machine generated makefiles.
|
|
|
6e06a80 |
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
|
|
|
6e06a80 |
mv %{buildroot}%{_bindir}/${bin} %{buildroot}%{_bindir}/g_${bin}
|
|
|
6e06a80 |
mv %{buildroot}%{_bindir}/${bin}_d %{buildroot}%{_bindir}/g_${bin}_d
|
|
|
6e06a80 |
done
|
|
|
6e06a80 |
|
|
|
6e06a80 |
for bin in demux.pl xplor2gmx.pl; do
|
|
|
6e06a80 |
mv %{buildroot}%{_bindir}/$bin %{buildroot}%{_bindir}/g_${bin}
|
|
|
6e06a80 |
done
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# MPI-enabled binaries (list will continue when the makefile has
|
|
|
6e06a80 |
# the possibility to compile all mpi-enabled files
|
|
|
1b055a1 |
for mpi in openmpi mpich2; do
|
|
|
1b055a1 |
for mpibin in mdrun; do
|
|
|
1b055a1 |
mv %{buildroot}%{_libdir}/$mpi/bin/${mpibin}_${mpi} %{buildroot}%{_libdir}/$mpi/bin/g_${mpibin}_${mpi}
|
|
|
1b055a1 |
mv %{buildroot}%{_libdir}/$mpi/bin/${mpibin}_${mpi}_d %{buildroot}%{_libdir}/$mpi/bin/g_${mpibin}_${mpi}_d
|
|
|
1b055a1 |
done
|
|
|
6e06a80 |
done
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# Man pages
|
|
|
6e06a80 |
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
|
|
|
6e06a80 |
mv %{buildroot}%{_mandir}/man1/${bin}.1 %{buildroot}%{_mandir}/man1/g_${bin}.1
|
|
|
6e06a80 |
mv %{buildroot}%{_mandir}/man1/${bin}_d.1 %{buildroot}%{_mandir}/man1/g_${bin}_d.1
|
|
|
6e06a80 |
done
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# Move completion files around
|
|
|
6e06a80 |
chmod a-x %{buildroot}%{_bindir}/completion.*
|
|
|
6e06a80 |
# Zsh
|
|
|
6e06a80 |
mkdir -p %{buildroot}%{_datadir}/zsh/site-functions
|
|
|
6e06a80 |
mv %{buildroot}%{_bindir}/completion.zsh %{buildroot}%{_datadir}/zsh/site-functions/gromacs
|
|
|
6e06a80 |
# Bash
|
|
|
6e06a80 |
mkdir -p %{buildroot}%{_sysconfdir}/bash_completion.d
|
|
|
6e06a80 |
mv %{buildroot}%{_bindir}/completion.bash %{buildroot}/etc/bash_completion.d/gromacs
|
|
|
6e06a80 |
# Tcsh
|
|
|
6e06a80 |
mv %{buildroot}%{_bindir}/completion.csh .
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# Remove .la files
|
|
|
1b055a1 |
find %{buildroot} -name *.la -exec rm -rf {} \;
|
|
|
4fd2f7f |
|
|
|
1b055a1 |
# Post install for libs. MPI packages don't need this.
|
|
|
1b055a1 |
%post -p /sbin/ldconfig
|
|
|
4fd2f7f |
|
|
|
1b055a1 |
%postun -p /sbin/ldconfig
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%clean
|
|
|
6e06a80 |
rm -rf %{buildroot}
|
|
|
6e06a80 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
# Files section
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%files
|
|
|
6e06a80 |
%defattr(-,root,root,-)
|
|
|
6e06a80 |
%{_bindir}/*
|
|
|
6e06a80 |
%{_libdir}/libgmx.so.*
|
|
|
6e06a80 |
%{_libdir}/libgmx_d.so.*
|
|
|
6e06a80 |
%{_libdir}/libgmxana.so.*
|
|
|
6e06a80 |
%{_libdir}/libgmxana_d.so.*
|
|
|
6e06a80 |
%{_libdir}/libmd.so.*
|
|
|
6e06a80 |
%{_libdir}/libmd_d.so.*
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%files common
|
|
|
6e06a80 |
%defattr(-,root,root,-)
|
|
|
ad6f154 |
%doc AUTHORS COPYING README manual-4.0.pdf README.fedora
|
|
|
6e06a80 |
%{_bindir}/GMXRC
|
|
|
6e06a80 |
%{_bindir}/GMXRC.bash
|
|
|
6e06a80 |
%{_mandir}/man1/*
|
|
|
6e06a80 |
%{_datadir}/%{name}
|
|
|
6e06a80 |
%exclude %{_datadir}/%{name}/template
|
|
|
6e06a80 |
%exclude %{_datadir}/%{name}/tutor
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%files devel
|
|
|
6e06a80 |
%defattr(-,root,root,-)
|
|
|
6e06a80 |
%{_includedir}/%{name}
|
|
|
6e06a80 |
%{_libdir}/libgmx.so
|
|
|
6e06a80 |
%{_libdir}/libgmx_d.so
|
|
|
6e06a80 |
%{_libdir}/libgmxana.so
|
|
|
6e06a80 |
%{_libdir}/libgmxana_d.so
|
|
|
6e06a80 |
%{_libdir}/libmd.so
|
|
|
6e06a80 |
%{_libdir}/libmd_d.so
|
|
|
6e06a80 |
%{_datadir}/%{name}/template
|
|
|
6e06a80 |
%exclude %{_datadir}/%{name}/template/Makefile.mpi.*
|
|
|
6e06a80 |
|
|
|
1b055a1 |
%files openmpi
|
|
|
6e06a80 |
%defattr(-,root,root,-)
|
|
|
1b055a1 |
%{_libdir}/openmpi/bin/g_mdrun*
|
|
|
1b055a1 |
%{_libdir}/openmpi/lib/lib*.so.*
|
|
|
6e06a80 |
|
|
|
1b055a1 |
%files openmpi-devel
|
|
|
4fd2f7f |
%defattr(-,root,root,-)
|
|
|
1b055a1 |
%{_libdir}/openmpi/lib/lib*.so
|
|
|
4fd2f7f |
|
|
|
1b055a1 |
#%files mpich2
|
|
|
1b055a1 |
#%defattr(-,root,root,-)
|
|
|
1b055a1 |
#%{_libdir}/mpich2/bin/g_mdrun*
|
|
|
1b055a1 |
#%{_libdir}/mpich2/lib/lib*.so.*
|
|
|
1b055a1 |
|
|
|
1b055a1 |
#%files mpich2-devel
|
|
|
1b055a1 |
#%defattr(-,root,root,-)
|
|
|
1b055a1 |
#%{_libdir}/mpich2/lib/lib*.so
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%files zsh
|
|
|
6e06a80 |
%defattr(-,root,root,-)
|
|
|
6e06a80 |
%{_datadir}/zsh/site-functions/gromacs
|
|
|
6e06a80 |
%{_bindir}/GMXRC.zsh
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%files bash
|
|
|
6e06a80 |
%defattr(-,root,root,-)
|
|
|
6e06a80 |
%config(noreplace) %{_sysconfdir}/bash_completion.d/gromacs
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%files csh
|
|
|
6e06a80 |
%defattr(-,root,root,-)
|
|
|
6e06a80 |
%doc completion.csh
|
|
|
6e06a80 |
%{_bindir}/GMXRC.csh
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%files tutor
|
|
|
6e06a80 |
%defattr(-,root,root,-)
|
|
|
6e06a80 |
%{_datadir}/%{name}/tutor
|
|
|
6e06a80 |
|
|
|
6e06a80 |
|
|
|
6e06a80 |
%changelog
|
|
|
1b055a1 |
* Mon Nov 30 2009 Jussi Lehtola <jussilehtola@fedoraproject.org> - 4.0.5-3
|
|
|
1b055a1 |
- Combine libs with binaries and drop debug packages to avoid explosion of
|
|
|
1b055a1 |
number of packages.
|
|
|
1b055a1 |
- Adopt use of MPI guidelines. MPICH2 support still missing due to broken
|
|
|
1b055a1 |
mpich2 package.
|
|
|
1b055a1 |
|
|
|
0b7b88a |
* Fri Jul 24 2009 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 4.0.5-2
|
|
|
0b7b88a |
- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
|
|
|
0b7b88a |
|
|
|
4fd2f7f |
* Fri May 22 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.5-1
|
|
|
4fd2f7f |
- Update to 4.0.5.
|
|
|
4fd2f7f |
- Change spec %%defines to %%globals.
|
|
|
4fd2f7f |
- Add debug subpackages to make debugging of GROMACS possible.
|
|
|
35dce57 |
|
|
|
ed60a6b |
* Tue Feb 17 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.4-1
|
|
|
ed60a6b |
- Update to 4.0.4.
|
|
|
ed60a6b |
|
|
|
0ff216d |
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-4
|
|
|
0ff216d |
- Retry fixing gmxdemo.
|
|
|
0ff216d |
|
|
|
2d0f49e |
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-3
|
|
|
2d0f49e |
- Fixed gmxdemo.
|
|
|
2d0f49e |
|
|
|
26363c1 |
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-2
|
|
|
26363c1 |
- Fix EPEL 4 build.
|
|
|
26363c1 |
|
|
|
7b3f14a |
* Mon Jan 19 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.3-1
|
|
|
7b3f14a |
- Update to 4.0.3.
|
|
|
7b3f14a |
|
|
|
ad6f154 |
* Wed Jan 14 2009 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.2-7
|
|
|
ad6f154 |
- Update manual to latest version.
|
|
|
ad6f154 |
- Removed Requires: blas and lapack.
|
|
|
ad6f154 |
|
|
|
ad6f154 |
* Mon Nov 10 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.2-6
|
|
|
bb4bd8c |
- Update to 4.0.2.
|
|
|
bb4bd8c |
|
|
|
ad6f154 |
* Sun Nov 09 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.1-5
|
|
|
3f6f449 |
- Add Requires: blas too.
|
|
|
3f6f449 |
|
|
|
ad6f154 |
* Sun Nov 09 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0.1-4
|
|
|
a90b748 |
- Update to 4.0.1.
|
|
|
a90b748 |
- Add Requires: lapack and openmpi to prevent yum from pulling atlas and lam
|
|
|
a90b748 |
instead.
|
|
|
a90b748 |
|
|
|
ad6f154 |
* Wed Oct 15 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-3
|
|
|
6e06a80 |
- Rename also man pages.
|
|
|
6e06a80 |
|
|
|
ad6f154 |
* Mon Oct 13 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-2
|
|
|
6e06a80 |
- Added noreplace to bash completion file.
|
|
|
6e06a80 |
- Changed double precision mpi binary suffix to _mpi_d.
|
|
|
6e06a80 |
|
|
|
ad6f154 |
* Sun Oct 12 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-1
|
|
|
6e06a80 |
- Update to Gromacs 4.0.
|
|
|
6e06a80 |
- Remove module system and patch file names to begin with g_.
|
|
|
6e06a80 |
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ad6f154 |
* Wed Oct 08 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.15.rc3
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6e06a80 |
- Changed location of binaries.
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6e06a80 |
- Removed conflict of module file, as the program is binary compatible with older versions.
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6e06a80 |
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ad6f154 |
* Wed Oct 08 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.14.rc3
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6e06a80 |
- The gromacs module is loaded automatically and it conflicts with gromacs3.
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6e06a80 |
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ad6f154 |
* Tue Oct 07 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.13.rc3
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6e06a80 |
- Renamed module files from %%{name}-%%{version} to %%{name}.
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6e06a80 |
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ad6f154 |
* Mon Oct 06 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.12.rc3
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6e06a80 |
- Fix BR to get GROMACS to build in mock for epel-4.
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6e06a80 |
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ad6f154 |
* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.11.rc3
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6e06a80 |
- Fix to get GROMACS to build in mock for epel-5.
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6e06a80 |
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ad6f154 |
* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.10.rc3
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6e06a80 |
- Implement module system & remove binary renaming.
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6e06a80 |
- No need for autoreconf anymore.
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6e06a80 |
- Update to rc3.
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6e06a80 |
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ad6f154 |
* Sat Oct 04 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.9.rc2
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6e06a80 |
- Fall back to autoreconf due to binary renaming.
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6e06a80 |
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ad6f154 |
* Fri Oct 03 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.8.rc2
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6e06a80 |
- Modified install commands to preserve timestamps.
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6e06a80 |
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ad6f154 |
* Fri Oct 03 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.7.rc2
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6e06a80 |
- Even more review fixes.
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6e06a80 |
- Binaries renamed:
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6e06a80 |
highway -> g_highway
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6e06a80 |
luck -> g_luck
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6e06a80 |
sigeps -> g_sigeps
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6e06a80 |
wheel -> g_wheel
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6e06a80 |
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ad6f154 |
* Thu Oct 02 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.6.rc2
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6e06a80 |
- Final review fixes.
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6e06a80 |
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ad6f154 |
* Wed Oct 01 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.5.rc2
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6e06a80 |
- Strip down requires by branching tutor to its own package.
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6e06a80 |
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ad6f154 |
* Tue Sep 30 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.4.rc2
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6e06a80 |
- Extensive package review fixes.
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6e06a80 |
- Unclear licenses on some files, filed upstream bug 217.
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6e06a80 |
http://bugzilla.gromacs.org/show_bug.cgi?id=217
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6e06a80 |
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ad6f154 |
* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.3.rc2
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6e06a80 |
- Move .so files to -devel package.
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6e06a80 |
- Remove .la files.
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6e06a80 |
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ad6f154 |
* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.2.rc2
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6e06a80 |
- Implement out-of-tree-builds.
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6e06a80 |
- Add --noexecstack to CFLAGS.
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6e06a80 |
- Remove execstack procedure and prelink from buildreqs.
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6e06a80 |
- Filed upstream bug 215 to add .note.GNU-stack .
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6e06a80 |
- Fix incorrect file permission on src/tools/gmx_xpm2ps.c .
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6e06a80 |
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ad6f154 |
* Mon Sep 29 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.1.rc2
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6e06a80 |
- Alphabetized buildrequires.
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6e06a80 |
- Changed gromacs-share to gromacs-common.
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6e06a80 |
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ad6f154 |
* Fri Sep 26 2008 Jussi Lehtola <jussi.lehtola@iki.fi> - 4.0-0.0.rc2
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6e06a80 |
- Initial build.
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