Add documentation and remove gcc build scripts

devtools/packaging/README.md

+# Packaging OpenMM into ZIP installers
+
+## Source
+
+Start the docker container:
+```bash
+docker run -i -t --rm -v `pwd`:/io jchodera/omnia-build-box:cuda80-amd30-clang38 bash
+```
+Inside the docker container:
+```bash
+# Clone the OpenMM beta or release candidate tag $TAG
+git clone https://github.com/pandegroup/openmm.git
+cd openmm; git checkout $TAG; cd ..
+# Build and package
+source openmm/devtools/packaging/scripts/source/prepare.sh       
+source openmm/devtools/packaging/scripts/source/build.sh
+source openmm/devtools/packaging/scripts/source/package.sh
+# Recover the packages to host directory
+cp packaging/compressed/* /io
+```
+
+## Linux
+
+Start the docker container:
+```bash
+docker run -i -t --rm -v `pwd`:/io jchodera/omnia-build-box:cuda80-amd30-clang38 bash
+```
+Inside the docker container:
+```bash
+# Clone the OpenMM beta or release candidate tag $TAG
+git clone https://github.com/pandegroup/openmm.git
+cd openmm; git checkout $TAG; cd ..
+# Build and package
+source openmm/devtools/packaging/scripts/linux/prepare.sh
+source openmm/devtools/packaging/scripts/linux/build.sh
+source openmm/devtools/packaging/scripts/linux/package.sh
+# Recover the packages to host directory
+cp packaging/compressed/* /io
+```
+
+## OS X
+
+On an `osx` machine with XCode and the OS X 10.9 frameworks installed:
+```bash
+# Clone the OpenMM beta or release candidate tag $TAG
+git clone https://github.com/pandegroup/openmm.git
+cd openmm; git checkout $TAG; cd ..
+# Build and package
+source openmm/devtools/packaging/scripts/osx/prepare.sh
+source openmm/devtools/packaging/scripts/osx/build.sh
+source openmm/devtools/packaging/scripts/osx/package.sh
+```
+

devtools/packaging/scripts/linux/build-gcc.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.
-
-# 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"
-
-# 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
-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

devtools/packaging/scripts/source/build-clang.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 ..