Package Details: gromacs-mpi 2016-7

Git Clone URL: https://aur.archlinux.org/gromacs-mpi.git (read-only)
Package Base: gromacs-mpi
Description: molecular dynamics simulation suite
Upstream URL: http://www.gromacs.org/
Licenses: LGPL2
Conflicts: gromacs
Submitter: duca
Maintainer: jbarnett
Last Packager: jbarnett
Votes: 3
Popularity: 0.000050
First Submitted: 2009-03-19 15:02
Last Updated: 2016-08-30 13:07

Dependencies (14)

Required by (0)

Sources (1)

Latest Comments

eomarjee commented on 2014-12-05 14:48

47c47
< install -D -m755 ${srcdir}/${_pkgname}-${pkgver}/scripts/completion.bash "${pkgdir}/usr/share/bash-completion/completions/gromacs"
---
> install -D -m755 ${srcdir}/${_pkgname}-${pkgver}/src/programs/completion/gmx-completion.bash "${pkgdir}/usr/share/bash-completion/completions/gromacs"

duca commented on 2014-10-28 03:17

Thanks Familia, i will merge it asap

familia commented on 2014-05-06 15:00

Duca, two new updates. This ones are optional and just to meet someones specific needs.

Here goes a modification of the PKGBUILD of gromacs-mpi in case you'r interested in having the non-mpi version of gromacs installed in your computer along with it's mpi version:


#d $Id: PKGBUILD 57440 2011-10-27 20:16:15Z lcarlier $
# Maintainer: Eduardo Martins Lopes "duca" <edumlopes@gmail.com>
# Maintainer: Abhishek Dasgupta <abhidg@gmail.com>
# Contributor: Ricardo <rikardo.horo@gmail.com>

pkgname=gromacs-mpi
_pkgname=gromacs
pkgver=4.6.5
pkgrel=2
pkgdesc='A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.'
url='http://www.gromacs.org/'
license=("GPL")
arch=('i686' 'x86_64')
depends=('fftw' 'lesstif' 'perl' 'libxml2' 'libsm' 'libx11' 'openmpi')
makedepends=('cmake')
options=('!libtool')
source=(ftp://ftp.gromacs.org/pub/gromacs/${_pkgname}-${pkgver}.tar.gz)
md5sums=('184a537ea52429dbc2a681f98b46ed84')

build() {
mkdir -p ${srcdir}/{single,singlempi}

msg2 "Building the single precision files"
cd ${srcdir}/single
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr/ -DGMX_THREADS=ON -DGMX_SHARED_LIBS=ON -DGMX_X11=ON ../${_pkgname}-${pkgver}/
make

msg2 "Building the single precision files for MPI"
cd ${srcdir}/singlempi
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr/ -DGMX_THREADS=OFF -DGMX_MPI=ON -DGMX_SHARED_LIBS=ON -DGMX_X11=ON ../${_pkgname}-${pkgver}/
make


mkdir -p ${srcdir}/{double,doublempi}

msg2 "Building the double precision files"
cd ${srcdir}/double
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr -DGMX_THREADS=ON -DGMX_SHARED_LIBS=ON -DGMX_DOUBLE=ON -DGMX_X11=ON -DGMX_LIBS_SUFFIX=_d ../${_pkgname}-${pkgver}/
make

msg2 "Building the double precision files for MPI"
cd ${srcdir}/doublempi
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr -DGMX_THREADS=OFF -DGMX_MPI=ON -DGMX_SHARED_LIBS=ON -DGMX_DOUBLE=ON -DGMX_X11=ON -DGMX_LIBS_SUFFIX=_d ../${_pkgname}-${pkgver}/
make

}

package() {

mkdir -p ${pkgdir}/etc/profile.d/
mkdir -p ${pkgdir}/usr/share/bash-completion/completions

msg2 "Making the single precision executables"
cd ${srcdir}/single
make DESTDIR=${pkgdir} install

msg2 "Making the single mpi precision executables"
cd ${srcdir}/singlempi
make DESTDIR=${pkgdir} install

msg2 "Making the double precision executables"
cd ${srcdir}/double
make DESTDIR=${pkgdir} install

msg2 "Making the double precision executables"
cd ${srcdir}/doublempi
make DESTDIR=${pkgdir} install

# installing completions in correct location and environment setup script
install -D -m755 ${srcdir}/${_pkgname}-${pkgver}/scripts/completion.bash "${pkgdir}/usr/share/bash-completion/completions/gromacs"
mv ${pkgdir}/usr/bin/GMXRC.* ${pkgdir}/etc/profile.d/
sed "s:/usr/bin:/etc/profile.d:" ${pkgdir}/usr/bin/GMXRC > ${pkgdir}/etc/profile.d/GMXRC
chmod 755 ${pkgdir}/etc/profile.d/GMXRC
rm -f ${pkgdir}/usr/bin/completion.*
rm -f ${pkgdir}/usr/bin/GMXRC
}


And if you'r interested in having the non-mpi version of gromacs installed along with the mpi version of mdrun (just the mdrun):


#d $Id: PKGBUILD 57440 2011-10-27 20:16:15Z lcarlier $
# Maintainer: Eduardo Martins Lopes "duca" <edumlopes@gmail.com>
# Maintainer: Abhishek Dasgupta <abhidg@gmail.com>
# Contributor: Ricardo <rikardo.horo@gmail.com>

pkgname=gromacs-mpi
_pkgname=gromacs
pkgver=4.6.5
pkgrel=2
pkgdesc='A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.'
url='http://www.gromacs.org/'
license=("GPL")
arch=('i686' 'x86_64')
depends=('fftw' 'lesstif' 'perl' 'libxml2' 'libsm' 'libx11' 'openmpi')
makedepends=('cmake')
options=('!libtool')
source=(ftp://ftp.gromacs.org/pub/gromacs/${_pkgname}-${pkgver}.tar.gz)
md5sums=('184a537ea52429dbc2a681f98b46ed84')

build() {
mkdir -p ${srcdir}/{single,singlempi}

msg2 "Building the single precision files"
cd ${srcdir}/single
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr/ -DGMX_THREADS=ON -DGMX_SHARED_LIBS=ON -DGMX_X11=ON ../${_pkgname}-${pkgver}/
make

msg2 "Building the single precision files for MPI"
cd ${srcdir}/singlempi
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr/ -DGMX_THREADS=OFF -DGMX_MPI=ON -DGMX_SHARED_LIBS=ON -DGMX_X11=ON ../${_pkgname}-${pkgver}/
make


mkdir -p ${srcdir}/{double,doublempi}

msg2 "Building the double precision files"
cd ${srcdir}/double
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr -DGMX_THREADS=ON -DGMX_SHARED_LIBS=ON -DGMX_DOUBLE=ON -DGMX_X11=ON -DGMX_LIBS_SUFFIX=_d ../${_pkgname}-${pkgver}/
make

msg2 "Building the double precision files for MPI"
cd ${srcdir}/doublempi
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr -DGMX_THREADS=OFF -DGMX_MPI=ON -DGMX_SHARED_LIBS=ON -DGMX_DOUBLE=ON -DGMX_X11=ON -DGMX_LIBS_SUFFIX=_d ../${_pkgname}-${pkgver}/
make

}

package() {

mkdir -p ${pkgdir}/etc/profile.d/
mkdir -p ${pkgdir}/usr/share/bash-completion/completions

msg2 "Making the single precision executables"
cd ${srcdir}/single
make DESTDIR=${pkgdir} install

msg2 "Making the single mpi precision executables"
cd ${srcdir}/singlempi
make DESTDIR=${pkgdir} install-mdrun

msg2 "Making the double precision executables"
cd ${srcdir}/double
make DESTDIR=${pkgdir} install

msg2 "Making the double precision executables"
cd ${srcdir}/doublempi
make DESTDIR=${pkgdir} install-mdrun

# installing completions in correct location and environment setup script
install -D -m755 ${srcdir}/${_pkgname}-${pkgver}/scripts/completion.bash "${pkgdir}/usr/share/bash-completion/completions/gromacs"
mv ${pkgdir}/usr/bin/GMXRC.* ${pkgdir}/etc/profile.d/
sed "s:/usr/bin:/etc/profile.d:" ${pkgdir}/usr/bin/GMXRC > ${pkgdir}/etc/profile.d/GMXRC
chmod 755 ${pkgdir}/etc/profile.d/GMXRC
rm -f ${pkgdir}/usr/bin/completion.*
rm -f ${pkgdir}/usr/bin/GMXRC
}


Hope this can help anyone who needs it!

familia commented on 2014-04-23 19:01

No problem duca. Glad i could help!

duca commented on 2014-03-07 00:39

Thank you familia, it's nice to see this package getting some atention.

duca commented on 2014-03-06 11:21

thank you, i'll update as soon as possible

familia commented on 2014-03-03 14:54

If anybody runs into the same problem the solution is this new PKBUILD file:

#d $Id: PKGBUILD 57440 2011-10-27 20:16:15Z lcarlier $
# Maintainer: Eduardo Martins Lopes "duca" <edumlopes@gmail.com>
# Maintainer: Abhishek Dasgupta <abhidg@gmail.com>
# Contributor: Ricardo <rikardo.horo@gmail.com>

pkgname=gromacs-mpi
_pkgname=gromacs
pkgver=4.6.5
pkgrel=1
pkgdesc='A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.'
url='http://www.gromacs.org/'
license=("GPL")
arch=('i686' 'x86_64')
depends=('fftw' 'lesstif' 'perl' 'libxml2' 'libsm' 'libx11' 'openmpi')
makedepends=('cmake')
options=('!libtool')
source=(ftp://ftp.gromacs.org/pub/gromacs/${_pkgname}-${pkgver}.tar.gz)
md5sums=('184a537ea52429dbc2a681f98b46ed84')

build() {
mkdir -p ${srcdir}/{single,double}
msg2 "Building the doulbe precision files"
cd ${srcdir}/double
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr -DGMX_THREADS=OFF -DGMX_MPI=ON -DGMX_SHARED_LIBS=ON -DGMX_DOUBLE=ON -DGMX_X11=ON -DGMX_LIBS_SUFFIX=_d ../${_pkgname}-${pkgver}/
make

msg2 "Building the single precision files"
cd ${srcdir}/single
cmake -DCMAKE_PREFIX=/usr/ -DCMAKE_INSTALL_PREFIX=/usr/ -DGMX_THREADS=OFF -DGMX_MPI=ON -DGMX_SHARED_LIBS=ON -DGMX_X11=ON ../${_pkgname}-${pkgver}/
make
}

package() {

mkdir -p ${pkgdir}/etc/profile.d/
mkdir -p ${pkgdir}/usr/share/bash-completion/completions
msg2 "Making the single precision executables"
cd ${srcdir}/single
make DESTDIR=${pkgdir} install

# Cleaning up, kept the csh completion at default location
msg2 "Making the double precision executables"
cd ${srcdir}/double
make DESTDIR=${pkgdir} install

# installing completions in correct location and environment setup script
install -D -m755 ${srcdir}/${_pkgname}-${pkgver}/scripts/completion.bash "${pkgdir}/usr/share/bash-completion/completions/gromacs"
mv ${pkgdir}/usr/bin/GMXRC.* ${pkgdir}/etc/profile.d/
sed "s:/usr/bin:/etc/profile.d:" ${pkgdir}/usr/bin/GMXRC > ${pkgdir}/etc/profile.d/GMXRC
chmod 755 ${pkgdir}/etc/profile.d/GMXRC
rm -f ${pkgdir}/usr/bin/completion.*
rm -f ${pkgdir}/usr/bin/GMXRC
}

familia commented on 2014-02-26 23:18

Hello,


I am having some problems installing this version of gromacs:

==> Building and installing package
==> Making package: gromacs-mpi 4.6.5-1 (Wed Feb 26 23:17:12 WET 2014)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Retrieving sources...
-> Downloading gromacs-4.6.5.tar.gz...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 10.4M 100 10.4M 0 0 896k 0 0:00:11 0:00:11 --:--:-- 1078k
==> Validating source files with md5sums...
gromacs-4.6.5.tar.gz ... Passed
==> Extracting sources...
-> Extracting gromacs-4.6.5.tar.gz with bsdtar
==> Starting build()...
mkdir: cannot create directory ‘/tmp/yaourt-tmp-myuser/aur-gromacs-mpi/pkg’: Permission denied
==> ERROR: A failure occurred in build().
Aborting...
==> ERROR: Makepkg was unable to build gromacs-mpi.


Any idea?
Thanks.