academic/OpenMM: Added (high-perf toolkit for molecular simulation)

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

4 files changed, 204 insertions, 0 deletions

diff --git a/academic/OpenMM/OpenMM.SlackBuild b/academic/OpenMM/OpenMM.SlackBuild
new file mode 100644
index 0000000000000..2d2a060830a43
--- /dev/null
+++ b/academic/OpenMM/OpenMM.SlackBuild
@@ -0,0 +1,165 @@
+#!/bin/bash
+
+# Slackware build script for OpenMM
+
+# 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=OpenMM
+VERSION=${VERSION:-7.7.0}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+PKGTYPE=${PKGTYPE:-tgz}
+
+SRCNAM=${PRGNAM,,}
+
+if [ -z "$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 $SRCNAM-$VERSION
+tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
+cd $SRCNAM-$VERSION
+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 {} \;
+
+# fix library installation path
+# note: the other solution requires less lines,
+# but it was after cmake
+sed -i \
+  -e 's#/lib RUNTIME_DIRECTORY /lib#/lib'${LIBDIRSUFFIX}' RUNTIME_DIRECTORY /lib'${LIBDIRSUFFIX}'#' \
+  -e 's#/lib/plugins RUNTIME_DIRECTORY /lib/plugins#/lib'${LIBDIRSUFFIX}'/plugins RUNTIME_DIRECTORY /lib'${LIBDIRSUFFIX}'/plugins#' \
+	platforms/*/*/CMakeLists.txt \
+	plugins/*/CMakeLists.txt \
+	plugins/*/platforms/*/CMakeLists.txt
+
+sed -i 's#${CMAKE_INSTALL_PREFIX}/lib#&'${LIBDIRSUFFIX}'#' \
+	plugins/*/CMakeLists.txt \
+	plugins/*/platforms/*/CMakeLists.txt \
+	platforms/*/CMakeLists.txt \
+	platforms/*/*/CMakeLists.txt
+
+# fix installation path for examples and licenses
+sed -i 's#\(DESTINATION\) \(examples\)#\1 share/'$PRGNAM'/\2#' \
+	examples/CMakeLists.txt
+sed -i 's#\(DESTINATION\) \(licenses\)#\1 doc/'$PRGNAM-$VERSION'/\2#' \
+	docs-source/CMakeLists.txt
+
+mkdir -p build
+cd build
+  cmake \
+    -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DBUILD_SHARED_LIBS=ON \
+    -DPYTHON_EXECUTABLE=/usr/bin/python3 \
+    $OPT_BUILD \
+    -DCMAKE_BUILD_TYPE=Release ..
+ 
+  # fix installation path of library "libOpenMM.so"
+  sed -i 's#${CMAKE_INSTALL_PREFIX}/lib#&'${LIBDIRSUFFIX}'#' \
+	  cmake_install.cmake
+
+  make
+  make install/strip DESTDIR=$PKG
+
+  if [ ${PYTHON:-no} == yes ]; then
+    cd python
+      # require the CFLAGS for linking with the OpenMM libraries
+      CFLAGS="-L$PKG/usr/lib${LIBDIRSUFFIX}" \
+      OPENMM_INCLUDE_PATH="/usr/include;$PKG/usr/include" \
+      OPENMM_LIB_PATH="/usr/lib${LIBDIRSUFFIX};$PKG/usr/lib${LIBDIRSUFFIX}" \
+      python3 setup.py install --root=$PKG
+      # remove temporary folder from python module library path
+      PYVER=$( python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])' )
+      sed -i 's#;'$PKG'/usr/lib'${LIBDIRSUFFIX}'##' $PKG/usr/lib${LIBDIRSUFFIX}/python$PYVER/site-packages/openmm/version.py
+    cd ..
+  fi
+cd ..
+
+# update example's makefile
+sed -i \
+  -e '21s#/usr/local/openmm#/usr#' \
+  -e '31s#/lib#&'${LIBDIRSUFFIX}'#' \
+  $PKG/usr/share/$PRGNAM/examples/Makefile
+
+# prune empty dirc "usr/docs"
+rm -fr $PKG/usr/docs
+
+
+# Don't ship .la files:
+rm -f $PKG/{,usr/}lib${LIBDIRSUFFIX}/*.la
+
+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 \
+  {CODE_OF_CONDUCT,CONTRIBUTING,SUPPORT}.md \
+  $PKG/usr/doc/$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/academic/OpenMM/OpenMM.info b/academic/OpenMM/OpenMM.info
new file mode 100644
index 0000000000000..7368a298ed823
--- /dev/null
+++ b/academic/OpenMM/OpenMM.info
@@ -0,0 +1,10 @@
+PRGNAM="OpenMM"
+VERSION="7.7.0"
+HOMEPAGE="https://openmm.org"
+DOWNLOAD="https://github.com/openmm/openmm/archive/7.7.0/OpenMM-7.7.0.tar.gz"
+MD5SUM="659712580bffde569f0c1663f7df7e68"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="William PC"
+EMAIL="w_calandrini[at]hotmail[dot]com"
diff --git a/academic/OpenMM/README b/academic/OpenMM/README
new file mode 100644
index 0000000000000..3bd6b80eb9e86
--- /dev/null
+++ b/academic/OpenMM/README
@@ -0,0 +1,10 @@
+  A high-performance toolkit for molecular simulation. Use it as an
+application, a library, or a flexible programming environment. We
+include extensive language bindings for Python, C, C++, and even 
+Fortran.
+
+  If you want to build the Python package set the environment 
+variable PYTHON=yes (this requires numpy3).
+
+NOTE: if you want to use the python module with OpenCL you shall,
+install a OpenCL runtime, such as pocl, or other vendor specific.
diff --git a/academic/OpenMM/slack-desc b/academic/OpenMM/slack-desc
new file mode 100644
index 0000000000000..70197f20a309b
--- /dev/null
+++ b/academic/OpenMM/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------------------------------------------------------|
+OpenMM: OpenMM (high-performance toolkit for molecular simulation)
+OpenMM:
+OpenMM:
+OpenMM:
+OpenMM:   A high-performance toolkit for molecular simulation. Use it as an 
+OpenMM: application, a library, or a flexible programming environment. We
+OpenMM: include extensive language bindings for Python, C, C++, and even
+OpenMM: Fortran. 
+OpenMM:
+OpenMM:
+OpenMM: