Name:		gromacs

Version:	4.0.5

Release:	1%{?dist}

Summary:	Fast, Free and Flexible Molecular Dynamics

Group:		Applications/Engineering

License:	GPLv2+

URL:		http://www.gromacs.org

BuildRoot:	%{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)

Source0:	ftp://ftp.gromacs.org/pub/gromacs/gromacs-%{version}.tar.gz

Source1:	ftp://ftp.gromacs.org/pub/manual/manual-4.0.pdf

Source2:	gromacs-template-makefile-single

Source3:	gromacs-template-makefile-double

Source4:	gromacs-template-makefile-mpi-single

Source5:	gromacs-template-makefile-mpi-double

Source6:	gromacs-README.fedora

# Add shebangs to scripts

Patch0:		gromacs-GMXRC.patch

# Patch gmxdemo for new filenames

Patch1:		gromacs-gmxdemo.patch

# Patch configure for the library suffix

Patch2:		gromacs-configure.patch

Requires:	gromacs-common = %{version}-%{release}

BuildRequires:	fftw-devel

BuildRequires:	gsl-devel

BuildRequires:	libxml2-devel

BuildRequires:	openmpi-devel

%if 0%{?rhel} == 4

BuildRequires:	blas

BuildRequires:	lapack

BuildRequires:	xorg-x11-devel

%else

BuildRequires:	blas-devel

BuildRequires:	lapack-devel

BuildRequires:	libX11-devel

%endif

# Check for mpi-selector or environment-modules

%global selector 0

%global modules 0

%if 0%{?fedora} > 9

%global modules 1

%endif

%if 0%{?rhel} == 4

%global selector 1

%endif

%if 0%{?rhel} == 5

%global selector 1

%endif

%if %modules == 1

BuildRequires:	environment-modules

%endif

%if %selector == 1

BuildRequires:	mpi-selector

%endif

%description

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides single and double precision binaries.

The documentation is in the package gromacs-common.

N.B. All binaries have names starting with g_, for example mdrun has been

renamed to g_mdrun.

%package debug

Summary:	GROMACS debugging binaries without assembly loops

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

%description debug

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides debugging versions of single and

double precision binaries, compiled without assembly loops.

The documentation is in the package gromacs-common.

You do not want this package for production purposes.

N.B. All binaries have names starting with g_, for example mdrun has been

renamed to g_mdrun.

%package libs

Summary:	GROMACS libraries

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

%description libs

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides runtime libraries needed for the single and double

precision binaries.

%package debug-libs

Summary:	GROMACS libraries without assembly loops for debugging

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

%description debug-libs

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides runtime libraries needed for the debugging versions of

the single and double precision binaries.

%package mpi

Summary:	GROMACS MPI binaries

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

%description mpi

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides MPI single precision and double precision binaries.

%package debug-mpi

Summary:	GROMACS debugging MPI binaries without assembly loops

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

%description debug-mpi

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides debugging versions of MPI single precision and double

precision binaries.

%package common

Summary:	GROMACS shared data and documentation

Group:		Applications/Engineering

%description common

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package includes architecture independent data and documentation.

%package devel

Summary:	GROMACS header files and development libraries

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

Requires:	gromacs-libs = %{version}-%{release}

%description devel

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package contains header files and development libraries for the GROMACS

molecular dynamics software. You need it if you want to write your own analysis

programs.

%package debug-devel

Summary:	GROMACS debugging header files and development libraries

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

Requires:	gromacs-devel = %{version}-%{release}

Requires:	gromacs-debug-libs = %{version}-%{release}

%description debug-devel

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package contains header files and development libraries for the debugging

version of the GROMACS molecular dynamics software.

%package mpi-devel

Summary:	GROMACS MPI development libraries

Group:		Applications/Engineering

Requires:	gromacs-mpi-libs = %{version}-%{release}

Requires:	gromacs-devel = %{version}-%{release}

# Need to have this so that yum doesn't install LAM instead

Requires:	openmpi

%description mpi-devel

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package contains development libraries for GROMACS MPI.

You need it if you want to write your own analysis programs.

%package debug-mpi-devel

Summary:	GROMACS debugging MPI development libraries

Group:		Applications/Engineering

Requires:	gromacs-debug-mpi-libs = %{version}-%{release}

Requires:	gromacs-debug-devel = %{version}-%{release}

# Need to have this so that yum doesn't install LAM instead

Requires:	openmpi

%description debug-mpi-devel

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package contains debugging versions of development libraries for the MPI

version of GROMACS.

%package mpi-libs

Summary:	GROMACS MPI libraries

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

# Need to have this so that yum doesn't install LAM instead

Requires:	openmpi

%description mpi-libs

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides runtime libraries needed for the MPI single and double

precision binaries.

%package debug-mpi-libs

Summary:	GROMACS debugging MPI libraries

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

# Need to have this so that yum doesn't install LAM instead

Requires:	openmpi

%description debug-mpi-libs

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides debugging versions of runtime libraries needed for the

debug versions of the MPI single and double precision binaries.

%package bash

Summary:	GROMACS bash completion

Group:		Applications/Engineering

Requires:	bash-completion

%description bash

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides bash completion for GROMACS.

%package zsh

Summary:	GROMACS zsh support

Group:		Applications/Engineering

Requires:	zsh

%description zsh

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides scripts needed to run GROMACS with zsh and zsh

completion.

%package csh

Summary:	GROMACS csh support

Group:		Applications/Engineering

Requires:	csh

%description csh

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides scripts needed to run GROMACS with csh and a completion

script.

%package tutor

Summary:	GROMACS tutorial files

Group:		Applications/Engineering

Requires:	gromacs-common = %{version}-%{release}

%description tutor

GROMACS is a versatile and extremely well optimized package to perform

molecular dynamics computer simulations and subsequent trajectory analysis.

It is developed for biomolecules like proteins, but the extremely high

performance means it is used also in several other field like polymer chemistry

and solid state physics.

This package provides tutorials for the use of GROMACS.

%prep

%setup -q

%patch0 -p1 -b .gmxrc

%patch1 -p1 -b .gmxdemo

%patch2 -p1 -b .libsuffix

# Fix incorrect permission

#chmod a-x src/tools/gmx_xpm2ps.c

%build

# Assembly kernels haven't got .note.GNU-stack sections

# because of incompatibilies with Microsoft Assembler.

# Add noexecstack to compiler flags

export CFLAGS="%optflags -Wa,--noexecstack -fPIC"

export LIBS="-lblas -llapack"

# Default options, used for all compilations

export DEFOPTS="--enable-shared --disable-static --with-external-blas \

	--with-external-lapack --with-gsl --with-x"

export SINGLE="--enable-float" # Single precision

export DOUBLE="--disable-float" # Double precision

export MPI="--enable-mpi"

export NOASM="--disable-ia32-3dnow --disable-ia32-sse --disable-x86-64-sse \

	--disable-ppc-altivec --disable-ia64-asm"

# Single precision

mkdir single

cd single

sed "s|@LIBSUFFIX@||g" < ../configure > configure; chmod 777 configure

%configure $DEFOPTS $SINGLE

sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool

sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool

make %{?_smp_mflags}

cd ..

# Single precision, debug version with no assembly loops

mkdir single-debug

cd single-debug

sed "s|@LIBSUFFIX@|_debug|g" < ../configure > configure; chmod 777 configure

%configure $DEFOPTS $SINGLE $NOASM --program-suffix="_debug"

sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool

sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool

make %{?_smp_mflags}

cd ..

# Double precision

mkdir double

cd double

sed "s|@LIBSUFFIX@|_d|g" < ../configure > configure; chmod 777 configure

%configure $DEFOPTS $DOUBLE --program-suffix="_d"

sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool

sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool

make %{?_smp_mflags}

cd ..

# Double precision, debug version with no assembly loops

mkdir double-debug

cd double-debug

sed "s|@LIBSUFFIX@|_d_debug|g" < ../configure > configure; chmod 777 configure

%configure $DEFOPTS $DOUBLE $NOASM --program-suffix="_d_debug"

sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool

sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool

make %{?_smp_mflags}

cd ..

# Load MPI enviroment

%if %modules == 1

. /etc/profile.d/modules.sh

module load %{_libdir}/openmpi/*/openmpi.module

# The module overrides CFLAGS, need to set them again..

export CFLAGS="%optflags -Wa,--noexecstack -fPIC"

%endif

%if %selector == 1

# Set MPI environment

mpi-selector --set `mpi-selector --list | grep openmpi`

source /etc/profile.d/mpi-selector.sh

%endif

# MPI, single precision

mkdir mpi-single

cd mpi-single

sed "s|@LIBSUFFIX@|_mpi|g" < ../configure > configure; chmod 777 configure

%configure $DEFOPTS $SINGLE $MPI --program-suffix="_mpi"

sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool

sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool

make %{?_smp_mflags} mdrun

#make %{?_smp_mflags}

cd ..

mkdir mpi-single-debug

cd mpi-single-debug

sed "s|@LIBSUFFIX@|_mpi_debug|g" < ../configure > configure; chmod 777 configure

%configure $DEFOPTS $SINGLE $MPI $NOASM --program-suffix="_mpi_debug"

sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool

sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool

make %{?_smp_mflags} mdrun

#make %{?_smp_mflags}

cd ..

# MPI, double precision

mkdir mpi-double

cd mpi-double

sed "s|@LIBSUFFIX@|_mpi_d|g" < ../configure > configure; chmod 777 configure

%configure $DEFOPTS $DOUBLE $MPI --program-suffix="_mpi_d"

sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool

sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool

make %{?_smp_mflags} mdrun

#make %{?_smp_mflags}

cd ..

mkdir mpi-double-debug

cd mpi-double-debug

sed "s|@LIBSUFFIX@|_mpi_d_debug|g" < ../configure > configure; chmod 777 configure

%configure $DEFOPTS $DOUBLE $MPI $NOASM --program-suffix="_mpi_d_debug"

sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool

sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool

make %{?_smp_mflags} mdrun

#make %{?_smp_mflags}

cd ..

%install

rm -rf %{buildroot}

# 4.0.3 needs this to build in EPEL-4

# Load MPI enviroment

%if %modules == 1

. /etc/profile.d/modules.sh

module load %{_libdir}/openmpi/*/openmpi.module

export CFLAGS="%optflags -Wa,--noexecstack -fPIC"

%endif

%if %selector == 1

# Set MPI environment

mpi-selector --set `mpi-selector --list | grep openmpi`

source /etc/profile.d/mpi-selector.sh

%endif

# Single precision

cd single

make DESTDIR=%{buildroot} INSTALL="install -p" install

cd ..

cd single-debug

make DESTDIR=%{buildroot} INSTALL="install -p" install

cd ..

# Double precision

cd double

make DESTDIR=%{buildroot} INSTALL="install -p" install

cd ..

cd double-debug

make DESTDIR=%{buildroot} INSTALL="install -p" install

cd ..

# MPI, single precision

cd mpi-single

make DESTDIR=%{buildroot} INSTALL="install -p" install-mdrun

cd ..

cd mpi-single-debug

make DESTDIR=%{buildroot} INSTALL="install -p" install-mdrun

cd ..

# MPI, double precision

cd mpi-double

make DESTDIR=%{buildroot} INSTALL="install -p" install-mdrun

cd ..

cd mpi-double-debug

make DESTDIR=%{buildroot} INSTALL="install -p" install-mdrun

cd ..

# Install manual & packager's note

install -cpm 644 %{SOURCE1} .

install -cpm 644 %{SOURCE6} README.fedora

# Remove broken makefiles generated by build process

rm -rf %{buildroot}%{_datadir}/%{name}/template/Makefil*

# Install template makefiles

install -cpm 644 %{SOURCE2} %{buildroot}%{_datadir}/%{name}/template/Makefile.single

install -cpm 644 %{SOURCE3} %{buildroot}%{_datadir}/%{name}/template/Makefile.double

install -cpm 644 %{SOURCE4} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.single

install -cpm 644 %{SOURCE5} %{buildroot}%{_datadir}/%{name}/template/Makefile.mpi.double

# Fix GMXRC file permissions

chmod a+x %{buildroot}%{_bindir}/GMXRC %{buildroot}%{_bindir}/GMXRC.*

# Rename binaries and man pages to prevent clashes

# (This is done here so that we don't need to mess with machine generated makefiles.

for bin in anadock do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp highway luck make_edi make_ndx mdrun mk_angndx ngmx pdb2gmx protonate sigeps tpbconv trjcat trjconv trjorder wheel x2top xpm2ps xrama ; do 

mv %{buildroot}%{_bindir}/${bin} %{buildroot}%{_bindir}/g_${bin}

mv %{buildroot}%{_bindir}/${bin}_debug %{buildroot}%{_bindir}/g_${bin}_debug

mv %{buildroot}%{_bindir}/${bin}_d %{buildroot}%{_bindir}/g_${bin}_d

mv %{buildroot}%{_bindir}/${bin}_d_debug %{buildroot}%{_bindir}/g_${bin}_d_debug

done

for bin in demux.pl xplor2gmx.pl; do

mv %{buildroot}%{_bindir}/$bin %{buildroot}%{_bindir}/g_${bin}

done

# MPI-enabled binaries (list will continue when the makefile has

# the possibility to compile all mpi-enabled files

for mpibin in mdrun; do

mv %{buildroot}%{_bindir}/${mpibin}_mpi %{buildroot}%{_bindir}/g_${mpibin}_mpi

mv %{buildroot}%{_bindir}/${mpibin}_mpi_debug %{buildroot}%{_bindir}/g_${mpibin}_mpi_debug

mv %{buildroot}%{_bindir}/${mpibin}_mpi_d %{buildroot}%{_bindir}/g_${mpibin}_mpi_d

mv %{buildroot}%{_bindir}/${mpibin}_mpi_d_debug %{buildroot}%{_bindir}/g_${mpibin}_mpi_d_debug

done

# Man pages

for bin in anadock do_dssp editconf eneconv genbox genconf genion genrestr gmxcheck gmxdump grompp highway make_edi make_ndx mdrun mk_angndx ngmx pdb2gmx protonate sigeps tpbconv trjcat trjconv trjorder wheel x2top xpm2ps xrama ; do 

mv %{buildroot}%{_mandir}/man1/${bin}.1 %{buildroot}%{_mandir}/man1/g_${bin}.1

mv %{buildroot}%{_mandir}/man1/${bin}_d.1 %{buildroot}%{_mandir}/man1/g_${bin}_d.1

done

# Move completion files around

chmod a-x %{buildroot}%{_bindir}/completion.*

# Zsh

mkdir -p %{buildroot}%{_datadir}/zsh/site-functions

mv %{buildroot}%{_bindir}/completion.zsh %{buildroot}%{_datadir}/zsh/site-functions/gromacs

# Bash

mkdir -p %{buildroot}%{_sysconfdir}/bash_completion.d

mv %{buildroot}%{_bindir}/completion.bash %{buildroot}/etc/bash_completion.d/gromacs

# Tcsh

mv %{buildroot}%{_bindir}/completion.csh . 

# Remove .la files

rm -rf %{buildroot}/%{_libdir}/*.la

# Post install for libs

%post libs -p /sbin/ldconfig

%postun libs -p /sbin/ldconfig

%post debug-libs -p /sbin/ldconfig

%postun debug-libs -p /sbin/ldconfig

%post mpi-libs -p /sbin/ldconfig

%postun mpi-libs -p /sbin/ldconfig

%post debug-mpi-libs -p /sbin/ldconfig

%postun debug-mpi-libs -p /sbin/ldconfig

%clean

rm -rf %{buildroot}

# Files section

%files

%defattr(-,root,root,-)

%{_bindir}/*

%exclude %{_bindir}/*_debug

%exclude %{_bindir}/g_mdrun_mpi*

%exclude %{_bindir}/GMXRC*

%files debug

%defattr(-,root,root,-)

%{_bindir}/*_debug

%exclude %{_bindir}/g_mdrun_mpi_debug

%exclude %{_bindir}/g_mdrun_mpi_d_debug

%files libs

%defattr(-,root,root,-)

%{_libdir}/libgmx.so.*

%{_libdir}/libgmx_d.so.*

%{_libdir}/libgmxana.so.*

%{_libdir}/libgmxana_d.so.*

%{_libdir}/libmd.so.*

%{_libdir}/libmd_d.so.*

%files debug-libs

%defattr(-,root,root,-)

%{_libdir}/libgmx_debug.so.*

%{_libdir}/libgmx_d_debug.so.*

%{_libdir}/libgmxana_debug.so.*

%{_libdir}/libgmxana_d_debug.so.*

%{_libdir}/libmd_debug.so.*

%{_libdir}/libmd_d_debug.so.*

%files mpi

%defattr(-,root,root,-)

%{_bindir}/g_mdrun_mpi

%{_bindir}/g_mdrun_mpi_d

%files debug-mpi

%defattr(-,root,root,-)

%{_bindir}/g_mdrun_mpi_debug

%{_bindir}/g_mdrun_mpi_d_debug

%files mpi-libs

%defattr(-,root,root,-)

%{_libdir}/libgmx_mpi.so.*

%{_libdir}/libgmx_mpi_d.so.*

%{_libdir}/libmd_mpi.so.*

%{_libdir}/libmd_mpi_d.so.*

%files debug-mpi-libs

%defattr(-,root,root,-)

%{_libdir}/libgmx_mpi_debug.so.*

%{_libdir}/libgmx_mpi_d_debug.so.*

%{_libdir}/libmd_mpi_debug.so.*

%{_libdir}/libmd_mpi_d_debug.so.*

%files common

%defattr(-,root,root,-)

%doc AUTHORS COPYING README manual-4.0.pdf README.fedora

%{_bindir}/GMXRC

%{_bindir}/GMXRC.bash

%{_mandir}/man1/*

%{_datadir}/%{name}

%exclude %{_datadir}/%{name}/template

%exclude %{_datadir}/%{name}/tutor

%files devel

%defattr(-,root,root,-)

%{_includedir}/%{name}

%{_libdir}/libgmx.so

%{_libdir}/libgmx_d.so

%{_libdir}/libgmxana.so

%{_libdir}/libgmxana_d.so

%{_libdir}/libmd.so

%{_libdir}/libmd_d.so

%{_datadir}/%{name}/template