From cffa5dcb8242d200dc2b01d5827899c3758659ec Mon Sep 17 00:00:00 2001 From: William PC Date: Fri, 9 Dec 2022 00:32:03 +0000 Subject: libraries/PLUMED: Added (PLUgin for MolEcular Dynamics) Signed-off-by: Willy Sudiarto Raharjo --- libraries/PLUMED/PLUMED.SlackBuild | 146 +++++++++++++++++++++++++++++++++++++ libraries/PLUMED/PLUMED.info | 10 +++ libraries/PLUMED/README | 23 ++++++ libraries/PLUMED/slack-desc | 19 +++++ 4 files changed, 198 insertions(+) create mode 100644 libraries/PLUMED/PLUMED.SlackBuild create mode 100644 libraries/PLUMED/PLUMED.info create mode 100644 libraries/PLUMED/README create mode 100644 libraries/PLUMED/slack-desc diff --git a/libraries/PLUMED/PLUMED.SlackBuild b/libraries/PLUMED/PLUMED.SlackBuild new file mode 100644 index 000000000000..d4170e18f69f --- /dev/null +++ b/libraries/PLUMED/PLUMED.SlackBuild @@ -0,0 +1,146 @@ +#!/bin/bash + +# Slackware build script for PLUMED + +# Copyright 2022 William PC - Seattle, USA +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=PLUMED +VERSION=${VERSION:-2.8.0} +BUILD=${BUILD:-1} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +# If the variable PRINT_PACKAGE_NAME is set, then this script will report what +# the name of the created package would be, and then exit. This information +# could be useful to other scripts. +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" + LIBDIRSUFFIX="" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" + LIBDIRSUFFIX="64" +else + SLKCFLAGS="-O2" + LIBDIRSUFFIX="" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf plumed2-$VERSION +tar xvf $CWD/$PRGNAM-$VERSION.tar.gz +cd plumed2-$VERSION + +# remove symlink to avoid error at find +# File system loop detected. +rm src/include/plumed + +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + + +# by default it detects a MPI installation +# the OMP version explicity disable the MPI +# then the else condition forces the default +# slackbuild execution to build the serial PLUMED +if [ "${OMP:-no}" == "yes" ]; then + OPT_BUILD="--enable-openmp --disable-mpi" +elif [ "${MPI:-no}" == "yes" ]; then + OPT_BUILD="--enable-mpi --disable-openmp" +elif [ "${HYBRID:-no}" == "yes" ]; then + OPT_BUILD="--enable-openmp --enable-mpi" +else + OPT_BUILD="--disable-openmp --disable-mpi" +fi + +if [ "${PYTHON:-no}" == "yes" ]; then + OPT_BUILD="$OPT_BUILD --enable-python" + export PYTHON_BIN="python3" +fi + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +./configure \ + --prefix=/usr \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --mandir=/usr/man \ + --htmldir=/usr/doc/$PRGNAM-$VERSION \ + --pdfdir=/usr/doc/$PRGNAM-$VERSION \ + --enable-shared \ + --enable-fftw \ + $OPT_BUILD \ + --build=$ARCH-slackware-linux + +make +make -C vim +make install DESTDIR=$PKG + +if [ "${DOC:-no}" == "yes" ]; then + make doc + cp -av developer-doc $PKG/usr/doc/$PRGNAM-$VERSION + cp -av user-doc $PKG/usr/doc/$PRGNAM-$VERSION +fi + + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + COPYING.LESSER PEOPLE VERSION \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/libraries/PLUMED/PLUMED.info b/libraries/PLUMED/PLUMED.info new file mode 100644 index 000000000000..89a498280e34 --- /dev/null +++ b/libraries/PLUMED/PLUMED.info @@ -0,0 +1,10 @@ +PRGNAM="PLUMED" +VERSION="2.8.0" +HOMEPAGE="https://www.plumed.org" +DOWNLOAD="https://github.com/plumed/plumed2/archive/v2.8.0/PLUMED-2.8.0.tar.gz" +MD5SUM="ad6032b5f2e47726bda1fc855865f26f" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="William PC" +EMAIL="w_calandrini[at]hotmail[dot]com" diff --git a/libraries/PLUMED/README b/libraries/PLUMED/README new file mode 100644 index 000000000000..bb9322ced6f0 --- /dev/null +++ b/libraries/PLUMED/README @@ -0,0 +1,23 @@ + PLUMED is an open-source, community-developed library that provides +a wide range of different methods, which include: + - enhanced-sampling algorithms + - free-energy methods + - tools to analyze the vast amounts of data produced by molecular + dynamics (MD) simulations. + + These techniques can be used in combination with a large toolbox +of collective variables that describe complex processes in physics, +chemistry, material science, and biology. + + + By default PLUMED is compiled in serial mode, if you want to +enable parallel mode set one of the following variables: + - OMP=yes, for enable OpenMP + - MPI=yes, for enable MPI (requires mpich or openmpi) + - HYBRID=yes, OpenMP+MPI (requires mpich or openmpi) + + For building support for python set PYTHON=yes. + +If you want to install the documentation set DOC=yes + + * Optional dependences: blas and lapack (shall improve performance) diff --git a/libraries/PLUMED/slack-desc b/libraries/PLUMED/slack-desc new file mode 100644 index 000000000000..2124395cd733 --- /dev/null +++ b/libraries/PLUMED/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +PLUMED: PLUMED (PLUgin for MolEcular Dynamics) +PLUMED: +PLUMED: +PLUMED: PLUMED is an open-source, community-developed library that provides +PLUMED: a wide range of different methods, which include: +PLUMED: - enhanced-sampling algorithms +PLUMED: - free-energy methods +PLUMED: - tools to analyze the vast amounts of data produced by molecular +PLUMED: dynamics (MD) simulations. +PLUMED: +PLUMED: -- cgit v1.2.3