First release

4 files changed, 149 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..fa147b392a20
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,37 @@
+pkgbase = pmemd
+	pkgdesc = PMEMD module of AMBER software package
+	pkgver = 18
+	pkgrel = 1
+	url = http://ambermd.org/
+	arch = x86_64
+	license = custom
+	makedepends = make
+	makedepends = gcc7
+	makedepends = gcc7-fortran
+	makedepends = tcsh
+	makedepends = imake
+	makedepends = patch
+	depends = openmpi3-gcc7
+	depends = fakeroot
+	depends = zlib
+	depends = bzip2
+	depends = gcc7-libs
+	depends = flex
+	depends = python2
+	optdepends = plumed-patches: PLUMED support
+	optdepends = plumed: metadynamics support
+	optdepends = plumed-mpi: metadynamics support with MPI
+	options = staticlibs
+	options = !buildflags
+	options = !makeflags
+	source = local://AmberTools19.tar.bz2
+	source = local://Amber18.tar.bz2
+	source = pmemd
+	source = pmemd.MPI
+	md5sums = afffe8a5473a0bd143b98f0396f52f0f
+	md5sums = 6b38d9cfb6e33b719bdf7fe73b26e841
+	md5sums = 3fcea0f27a2b47ac98a1725e48a80136
+	md5sums = 16a34c0e34f31e3f5eeaa5d0723b154a
+
+pkgname = pmemd
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..375f86b430e8
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,98 @@
+# Maintainer: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
+
+pkgname=pmemd
+pkgver=18
+_toolsver=19
+_gccver=7.4.1
+pkgrel=1
+pkgdesc="PMEMD module of AMBER software package"
+url="http://ambermd.org/"
+license=('custom')
+arch=('x86_64')
+depends=('openmpi3-gcc7' 'fakeroot' 'zlib' 'bzip2' 'gcc7-libs' 'flex' 'python2')
+makedepends=('make' 'gcc7' 'gcc7-fortran' 'tcsh' 'imake' 'patch')
+optdepends=('plumed-patches: PLUMED support'
+            'plumed: metadynamics support'
+            'plumed-mpi: metadynamics support with MPI')
+md5sums=('afffe8a5473a0bd143b98f0396f52f0f'
+         '6b38d9cfb6e33b719bdf7fe73b26e841'
+         '3fcea0f27a2b47ac98a1725e48a80136'
+         '16a34c0e34f31e3f5eeaa5d0723b154a')
+options=(staticlibs !buildflags !makeflags)
+
+# Due to licensing issues you must register and download AmberTools package from AmberMD url and put it in directory with PKGBUILD.
+# Moreover, you MUST purchase Amber package from AmberMD group and also place it in directory with PKGBUILD.
+source=("local://AmberTools${_toolsver}.tar.bz2"
+        "local://Amber${pkgver}.tar.bz2"
+        "pmemd"
+        "pmemd.MPI")
+
+prepare() {
+  cd ${srcdir}/amber${pkgver}
+
+  export AMBERHOME="${srcdir}/amber${pkgver}"
+  ./update_amber --update
+}
+
+build() {
+  # set necessary variables
+  export LD_PRELOAD=/usr/lib/libstdc++.so
+  export AMBER_PREFIX="${srcdir}/amber${pkgver}"
+  export AMBERHOME="${srcdir}/amber${pkgver}"
+
+  if [ -z "${LD_LIBRARY_PATH}" ]; then
+     export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib"
+  else
+     export LD_LIBRARY_PATH="${AMBER_PREFIX}/lib:${LD_LIBRARY_PATH}"
+  fi
+
+  export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:${LD_LIBRARY_PATH}"
+
+  # build serial version
+  cd ${srcdir}/amber${pkgver}
+  LANG=en_US.UTF-8 CC=gcc-7 CXX=g++-7 FC=gfortran-7 ./configure --with-python /usr/bin/python2 --no-updates gnu
+
+  # add support for PLUMED
+  if [ -e "/usr/bin/plumed-mpi-patch" -a -e "/usr/lib/plumed-mpi/patches/amber${pkgver}.diff" ]; then
+    msg2 "Adding support for PLUMED (with MPI)"
+    plumed-mpi-patch -p -e amber${pkgver}
+  elif [ -e "/usr/bin/plumed-patch" -a -e "/usr/lib/plumed/patches/amber${pkgver}.diff" ]; then
+    msg2 "Adding support for PLUMED"
+    plumed-patch -p -e amber${pkgver}
+  fi
+
+  # build internal libraries
+  cd ${srcdir}/amber${pkgver}/AmberTools/src/xblas
+  make lib-amb
+  mv libxblas-amb.a ../../../lib
+
+  cd ${srcdir}/amber${pkgver}/AmberTools/src/blas
+  make install
+
+  cd ${srcdir}/amber${pkgver}/AmberTools/src/lapack
+  make install
+
+  cd ${srcdir}/amber${pkgver}/AmberTools/src/arpack
+  make install
+
+  cd ${srcdir}/amber${pkgver}/src
+  make install
+
+  # build parallel version
+  cd ${srcdir}/amber${pkgver}
+  LANG=en_US.UTF-8 CC=gcc-7 CXX=g++-7 FC=gfortran-7 ./configure --with-python /usr/bin/python2 --no-updates -mpi gnu
+  cd ${srcdir}/amber${pkgver}/src
+  make install
+}
+
+package() {
+  cd ${srcdir}/amber${pkgver}/bin
+
+  # install binaries
+  install -Dm755 pmemd ${pkgdir}/usr/lib/${pkgname}/bin/pmemd
+  install -Dm755 pmemd.MPI ${pkgdir}/usr/lib/${pkgname}/bin/pmemd.MPI
+
+  # install wrappers
+  install -Dm755 ${srcdir}/pmemd ${pkgdir}/usr/bin/pmemd
+  install -Dm755 ${srcdir}/pmemd.MPI ${pkgdir}/usr/bin/pmemd.MPI
+}
diff --git a/pmemd b/pmemd
new file mode 100644
index 000000000000..752fe936a652
--- /dev/null
+++ b/pmemd
@@ -0,0 +1,7 @@
+#!/usr/bin/bash
+
+export _gccver=7.4.1
+export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
+/usr/lib/pmemd/bin/pmemd "$@"
+
+exit 0
diff --git a/pmemd.MPI b/pmemd.MPI
new file mode 100644
index 000000000000..90e7e7e78aca
--- /dev/null
+++ b/pmemd.MPI
@@ -0,0 +1,7 @@
+#!/usr/bin/bash
+
+export _gccver=7.4.1
+export LD_LIBRARY_PATH="/usr/lib/gcc/x86_64-pc-linux-gnu/${_gccver}:$LD_LIBRARY_PATH"
+/usr/lib/pmemd/bin/pmemd.MPI "$@"
+
+exit 0