Initial commit for the 2016 version

3 files changed, 126 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..5ce923827e33
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,28 @@
+pkgbase = gromacs-2016-complete
+	pkgdesc = A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
+	pkgver = 2016.4
+	pkgrel = 1
+	url = http://www.gromacs.org/
+	arch = i686
+	arch = x86_64
+	license = LGPL
+	makedepends = cmake
+	makedepends = libxml2
+	makedepends = hwloc
+	makedepends = gcc6
+	depends = lapack
+	depends = zlib
+	depends = libx11
+	optdepends = cuda: Nvidia GPU support
+	optdepends = openmotif: needed for gmx view
+	optdepends = perl: needed for demux.pl and xplor2gmx.pl
+	optdepends = opencl-mesa: OpenCL support for AMD GPU
+	optdepends = opencl-nvidia: OpenCL support for Nvidia GPU
+	options = !libtool
+	source = http://ftp.gromacs.org/pub/gromacs/gromacs-2016.4.tar.gz
+	source = GMXRC.bash.cmakein.patch
+	sha1sums = b142c9c77e793fa8def24aeacebaf8b8f1dd55fc
+	sha1sums = 014b2cbfa13db9b495c88f653805c330747117dc
+
+pkgname = gromacs-2016-complete
+
diff --git a/GMXRC.bash.cmakein.patch b/GMXRC.bash.cmakein.patch
new file mode 100644
index 000000000000..f0408d787a2e
--- /dev/null
+++ b/GMXRC.bash.cmakein.patch
@@ -0,0 +1,14 @@
+--- GMXRC.bash.cmakein	2013-11-08 13:09:33.000000000 +0200
++++ GMXRC.bash.cmakein.patch	2015-02-20 12:48:10.770670309 +0200
+@@ -4,6 +4,11 @@
+ # This is not 100% necessary, but very useful when we
+ # repeatedly switch between gmx versions in a shell.
+ 
++#Patch to avoid problems when gromacs is installed using /usr/ as root
++if [ "$GMXLDLIB" == "/usr/lib" ]; then export GMXLDLIB=""; fi
++if [ "$GMXBIN" == "/usr/bin" ]; then export GMXBIN=""; fi
++if [ "$GMXMAN" == "/usr/share/man" ]; then export GMXMAN=""; fi
++
+ # First remove gromacs part of ld_library_path
+ tmppath=""
+ for i in `echo $LD_LIBRARY_PATH | sed "s/:/ /g"`; do
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..c58d8919eb35
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,84 @@
+# $Id: PKGBUILD 57440 2011-10-27 20:16:15Z lcarlier $
+# Maintainer: Hector <hsearaDOTatDOTgmailDOTcom>
+
+pkgname=gromacs-2016-complete
+pkgver=2016.4
+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=("LGPL")
+arch=('i686' 'x86_64')
+depends=('lapack' 'zlib' 'libx11')
+optdepends=('cuda: Nvidia GPU support'
+            'openmotif:  needed for gmx view'
+            'perl: needed for demux.pl and xplor2gmx.pl'
+	    'opencl-mesa: OpenCL support for AMD GPU'
+	    'opencl-nvidia: OpenCL support for Nvidia GPU')
+makedepends=('cmake' 'libxml2' 'hwloc' 'gcc6')
+options=('!libtool')
+source=(http://ftp.gromacs.org/pub/gromacs/gromacs-${pkgver}.tar.gz
+        GMXRC.bash.cmakein.patch)
+sha1sums=('b142c9c77e793fa8def24aeacebaf8b8f1dd55fc'
+          '014b2cbfa13db9b495c88f653805c330747117dc')
+
+#With gcc6 currently there are less errors in the tests
+# also the compilation is possible in CUDA capable machines
+export CC=gcc-6
+export CXX=g++-6
+export CFLAGS="-march=native -O2 -pipe -fstack-protector-strong"
+export CXXFLAGS="${CFLAGS}"
+
+export VMDDIR=/usr/lib/vmd/ #If vmd is available at compilation time
+                            #Gromacs will have the ability to read any
+                            #trajectory file format that can be read by
+                            #VMD installation (e.g. AMBER's DCD format). 
+prepare() {
+cd ${srcdir}/gromacs-${pkgver}/scripts/
+ls
+patch -p0 -i ${srcdir}/GMXRC.bash.cmakein.patch
+}
+
+build() {
+  mkdir -p ${srcdir}/{single,double}
+
+  msg2 "Building the double precision files"
+  cd ${srcdir}/double	
+  cmake ../gromacs-${pkgver}/ \
+        -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs-${pkgver}/ \
+        -DCMAKE_INSTALL_LIBDIR=lib \
+        -DBUILD_SHARED_LIBS=ON \
+        -DGMX_DOUBLE=ON \
+        -DGMX_BUILD_OWN_FFTW=ON \
+        -DREGRESSIONTEST_DOWNLOAD=ON
+  #      -DGMX_LIBS_SUFFIX=_d
+  make
+
+  msg2 "Building the single precision files"
+  cd ${srcdir}/single
+  cmake ../gromacs-${pkgver}/ \
+        -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromacs-${pkgver}/ \
+        -DCMAKE_INSTALL_LIBDIR=lib \
+        -DBUILD_SHARED_LIBS=ON \
+        -DGMX_BUILD_OWN_FFTW=ON \
+        -DREGRESSIONTEST_DOWNLOAD=ON
+  make
+}
+
+check () {
+  msg2 "Testing double precision compilation"
+  cd ${srcdir}/double
+  make check
+  msg2 "Testing single precision compilation"
+  cd ${srcdir}/single
+  make check
+}
+
+package() {
+  msg2 "Making the single precision executables"
+  cd ${srcdir}/single
+  make  DESTDIR=${pkgdir} install
+
+  msg2 "Making the double precision executables"
+  cd ${srcdir}/double
+  make DESTDIR=${pkgdir} install
+}