Add back missing linux packaging scripts

devtools/packaging/scripts/linux/build.sh

+#!/bin/bash
+
+# Build script for Linux distribution, for use in automated packaging.
+# Note that this must be run from outside the checked-out openmm/ directory.
+
+#
+# For Docker build
+#
+
+# Fix hbb issues.
+# If statements needed because multiple Python versions are built in same docker image.
+if [ ! -e /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux ]; then
+    ln -s /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-CentOS-linux/ /opt/rh/devtoolset-2/root/usr/lib/gcc/x86_64-redhat-linux
+fi
+if [ ! -e /opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/x86_64-redhat-linux ]; then
+    ln -s /opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/x86_64-CentOS-linux/ /opt/rh/devtoolset-2/root/usr/include/c++/4.8.2/x86_64-redhat-linux
+fi
+
+# Clang paths
+export CLANG_PREFIX="/opt/clang"
+export PATH=$PATH:$CLANG_PREFIX/bin
+
+# enable devtoolset-2
+# will return an error return code because of python 3.x incompatible code, but this error is inconsequential
+#source /opt/rh/devtoolset-2/enable || true
+export PATH=/opt/rh/devtoolset-2/root/usr/bin${PATH:+:${PATH}}
+export MANPATH=/opt/rh/devtoolset-2/root/usr/share/man:$MANPATH
+export INFOPATH=/opt/rh/devtoolset-2/root/usr/share/info${INFOPATH:+:${INFOPATH}}
+export PCP_DIR=/opt/rh/devtoolset-2/root
+# Some perl Ext::MakeMaker versions install things under /usr/lib/perl5
+# even though the system otherwise would go to /usr/lib64/perl5.
+export PERL5LIB=/opt/rh/devtoolset-2/root//usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi:/opt/rh/devtoolset-2/root/usr/lib/perl5:/opt/rh/devtoolset-2/root//usr/lib/perl5/vendor_perl/5.8.8${PERL5LIB:+:${PERL5LIB}}
+# bz847911 workaround:
+# we need to evaluate rpm's installed run-time % { _libdir }, not rpmbuild time
+# or else /etc/ld.so.conf.d files?
+rpmlibdir=`rpm --eval "%{_libdir}"`
+# bz1017604: On 64-bit hosts, we should include also the 32-bit library path.
+if [ "$rpmlibdir" != "${rpmlibdir/lib64/}" ]; then
+  rpmlibdir32=":/opt/rh/devtoolset-2/root${rpmlibdir/lib64/lib}"
+fi
+export LD_LIBRARY_PATH=/opt/rh/devtoolset-2/root$rpmlibdir$rpmlibdir32${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
+# duplicate python site.py logic for sitepackages
+pythonvers=`python -c 'import sys; print(sys.version[:3])'`
+export PYTHONPATH=/opt/rh/devtoolset-2/root/usr/lib64/python$pythonvers/site-packages:/opt/rh/devtoolset-2/root/usr/lib/python$pythonvers/site-packages${PYTHONPATH:+:${PYTHONPATH}}
+
+# CFLAGS
+export MINIMAL_CFLAGS="-g -O3"
+export CFLAGS="$MINIMAL_CFLAGS"
+export CXXFLAGS="$MINIMAL_CFLAGS"
+export LDFLAGS="$LDPATHFLAGS"
+
+# Set relative workspace path.
+export WORKSPACE=`pwd`
+
+# Add conda binaries to path.
+PATH=$WORKSPACE/miniconda/bin:$PATH
+
+INSTALL=`pwd`/install
+if [ -e $INSTALL ]; then
+    rm -rf $INSTALL
+fi
+
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$INSTALL"
+
+# Don't build tests
+CMAKE_FLAGS+=" -DBUILD_TESTING=OFF"
+
+# Use clang 3.8.1 inside omnia-build-box docker image
+CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=$CLANG_PREFIX/bin/clang -DCMAKE_CXX_COMPILER=$CLANG_PREFIX/bin/clang++"
+
+# Ensure we build a release
+CMAKE_FLAGS+=" -DCMAKE_BUILD_TYPE=Release"
+
+# setting the rpath so that libOpenMMPME.so finds the right libfftw3
+#CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
+# Use NVIDIA CUDA 8.0
+CMAKE_FLAGS+=" -DCUDA_CUDART_LIBRARY=/usr/local/cuda-8.0/lib64/libcudart.so"
+CMAKE_FLAGS+=" -DCUDA_NVCC_EXECUTABLE=/usr/local/cuda-8.0/bin/nvcc"
+CMAKE_FLAGS+=" -DCUDA_SDK_ROOT_DIR=/usr/local/cuda-8.0/"
+CMAKE_FLAGS+=" -DCUDA_TOOLKIT_INCLUDE=/usr/local/cuda-8.0/include"
+CMAKE_FLAGS+=" -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-8.0/"
+# Use AMD APP SDK 3.0
+CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=/opt/AMDAPPSDK-3.0/include/"
+CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so"
+# Generate API docs
+CMAKE_FLAGS+=" -DOPENMM_GENERATE_API_DOCS=ON"
+# Set location for FFTW3
+PREFIX="$WORKSPACE/miniconda"
+CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
+CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
+CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
+# Necessary to find GL headers
+CMAKE_FLAGS+=" -DCMAKE_CXX_FLAGS_RELEASE=-I/usr/include/nvidia/"
+
+# Build in subdirectory.
+if [ -e build ]; then
+    rm -rf build
+fi
+mkdir build
+cd build
+cmake ../openmm $CMAKE_FLAGS
+make -j4 all install
+
+export CFLAGS="$MINIMAL_CFLAGS"
+export CXXFLAGS="$MINIMAL_CFLAGS"
+export LDFLAGS="$LDPATHFLAGS"
+
+make -j4 PythonInstall C++ApiDocs PythonApiDocs sphinxpdf
+
+# Install.
+make install
+
+cd ..

devtools/packaging/scripts/linux/package.sh

+#!/bin/bash
+
+# Packaging script for Linux distribution, for use in automated packaging.
+# Note that this must be run from outside the checked-out openmm/ directory.
+
+# CONFIGURE HERE
+export PACKAGE_DIR="packaging" # directory to stuff packaged source distribution
+export VERSION=$(sed -nr "s/OPENMM_VERSION:STRING=(.*)/\1/p" build/CMakeCache.txt)
+export PACKAGE_SUBDIR="OpenMM-${VERSION}-Linux" # directory where distribution will be unpacked
+export DISTRO_PREFIX="OpenMM-${VERSION}-Linux" # prefix for source distribution (e.g. ${DISTRIBUTION_NAME}.zip)
+
+# Perform all work in a work directory.
+cd work
+
+# Clean up.
+rm -rf $PACKAGE_DIR
+
+# Make a directory to contain packaged source distribution
+mkdir $PACKAGE_DIR
+mkdir $PACKAGE_DIR/$PACKAGE_SUBDIR
+for filename in $( cat openmm/devtools/packaging/manifests/binary/manifest.txt ); do
+   CMD="cp -r install/$filename $PACKAGE_DIR/$PACKAGE_SUBDIR"
+   echo $CMD
+   `$CMD`
+done
+
+# Add the install.sh script
+CMD="cp -r openmm/devtools/packaging/install.sh $PACKAGE_DIR/$PACKAGE_SUBDIR"
+echo $CMD
+`$CMD`
+
+# Make Python source distribution.
+echo "Building Python source distribution..."
+pushd .
+cd build
+make PythonSdist
+cd python/dist
+tar zxf OpenMM-${VERSION}.tar.gz
+mv OpenMM-${VERSION} python
+popd
+cp -r build/python/dist/python $PACKAGE_DIR/$PACKAGE_SUBDIR
+
+# Create archives.
+cd $PACKAGE_DIR
+mkdir compressed
+tar zcf compressed/${DISTRO_PREFIX}.tgz $PACKAGE_SUBDIR
+zip -r compressed/${DISTRO_PREFIX}.zip $PACKAGE_SUBDIR
+cd ..

devtools/packaging/scripts/linux/prepare.sh

+#!/bin/bash
+
+# Prepare for build by ensuring necessary prerequisites are locally installed.
+
+# Set relative workspace path.
+export WORKSPACE=`pwd`
+
+# Install miniconda
+export VERSION="latest"
+export PLATFORM="Linux"
+export ARCH="x86_64"
+export MINICONDA="Miniconda3-$VERSION-$PLATFORM-$ARCH.sh"
+if [ -f miniconda ];
+then
+   echo "miniconda already exists"
+else
+   echo "Downloading miniconda..."
+   rm -rf Miniconda-* miniconda ~/.condarc
+   wget --quiet https://repo.continuum.io/miniconda/${MINICONDA}
+   bash ${MINICONDA} -b -p miniconda
+   PIP_ARGS="-U"
+fi
+
+# Add to path.
+export PATH=$WORKSPACE/miniconda/bin:$PATH
+
+# Workaround for missing libgcrypt
+yum install -y libgcrypt
+
+# Ensure configuration is up to date.
+conda config --add channels omnia
+conda install --yes --quiet swig fftw3f pip doxygen sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen lxml cmake