Merge pull request #1033 from jchodera/openmm-63-beta2

Changes to Jenkins build scripts for OpenMM 6.3

devtools/packaging/manifests/source/manifest.txt

-cmake_modules
-CMakeLists.txt
-docs-source
-examples
-libraries
-olla
-openmmapi
-platforms
-plugins
-serialization
-tests
-wrappers
+openmm/cmake_modules
+openmm/CMakeLists.txt
+openmm/docs-source
+install/docs
+openmm/examples
+openmm/libraries
+openmm/olla
+openmm/openmmapi
+openmm/platforms
+openmm/plugins
+openmm/serialization
+openmm/tests
+openmm/wrappers

devtools/packaging/scripts/linux/build.sh

@@ -24,8 +24,8 @@ CMAKE_FLAGS+=" -DCUDA_NVCC_EXECUTABLE=/usr/local/cuda-7.0/bin/nvcc"
 CMAKE_FLAGS+=" -DCUDA_SDK_ROOT_DIR=/usr/local/cuda-7.0/"
 CMAKE_FLAGS+=" -DCUDA_TOOLKIT_INCLUDE=/usr/local/cuda-7.0/include"
 CMAKE_FLAGS+=" -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-7.0/"
-CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=/usr/local/cuda-7.0/include"
-CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/usr/local/cuda-7.0/lib64/libOpenCL.so"
+CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=/opt/AMDAPPSDK-2.9-1/include/"
+CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPPSDK-2.9-1/lib/x86_64/libOpenCL.so"
 
 # Set location for FFTW3
 PREFIX="$WORKSPACE/miniconda"

devtools/packaging/scripts/linux/prepare.sh

@@ -6,7 +6,7 @@
 export WORKSPACE=`pwd`
 
 # Install miniconda
-export VERSION="3.7.0"
+export VERSION="Latest"
 export PLATFORM="Linux"
 export ARCH="x86_64"
 export MINICONDA="Miniconda-$VERSION-$PLATFORM-$ARCH.sh"

devtools/packaging/scripts/osx/prepare.sh

@@ -6,7 +6,7 @@
 export WORKSPACE=`pwd`
 
 # Install miniconda
-export VERSION="3.7.0"
+export VERSION="Latest"
 export PLATFORM="MacOSX"
 export ARCH="x86_64"
 export MINICONDA="Miniconda-$VERSION-$PLATFORM-$ARCH.sh"

devtools/packaging/scripts/source/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.
+
+# 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"
+
+# setting the rpath so that libOpenMMPME.so finds the right libfftw3
+#CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
+CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_AMOEBA_CUDA_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_CPU_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_CUDA_COMPILER_PLUGIN=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_CUDA_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_DRUDE_CUDA_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_DRUDE_OPENCL_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_OPENCL_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_RPMD_CUDA_LIB=OFF"
+CMAKE_FLAGS+=" -DOPENMM_BUILD_RPMD_OPENCL_LIB=OFF"
+
+# 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"
+
+# Build in subdirectory.
+if [ -e build ]; then
+    rm -rf build
+fi
+mkdir build
+cd build
+cmake ../openmm $CMAKE_FLAGS
+make -j4 all DoxygenApiDocs sphinxpdf
+
+# Install.
+make install

devtools/packaging/scripts/source/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}-Source" # directory where distribution will be unpacked
+export DISTRO_PREFIX="OpenMM-${VERSION}-Source" # 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/source/manifest.txt ); do
+   CMD="cp -r $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/source/prepare.sh

+#!/bin/tcsh
+
+# 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="Miniconda-$VERSION-$PLATFORM-$ARCH.sh"
+if [ -f miniconda ];
+then
+   echo "miniconda already exists"
+else
+   echo "Downloading miniconda..."
+   rm -rf Miniconda-*
+   wget --quiet http://repo.continuum.io/miniconda/${MINICONDA}
+   bash ${MINICONDA} -b -p miniconda
+   PIP_ARGS="-U"
+fi
+
+# Add to path.
+export PATH=$WORKSPACE/miniconda/bin:$PATH
+
+# Ensure configuration is up to date.
+conda config --add channels http://conda.binstar.org/omnia
+conda install --yes --quiet swig fftw3f pip
+pip install sphinxcontrib-bibtex

wrappers/python/setup.py

@@ -3,9 +3,6 @@
 """
 setup.py: Used for building python wrappers for Simbios' OpenMM library.
 """
-__author__ = "Randall J. Radmer"
-__version__ = "1.0"
-
 import ast
 import re
 import os
@@ -18,6 +15,8 @@ MINOR_VERSION_NUM='@OPENMM_MINOR_VERSION@'
 BUILD_INFO='@OPENMM_BUILD_VERSION@'
 IS_RELEASED = False
 
+__author__ = "Randall J. Radmer"
+__version__ = "%s.%s" % (MAJOR_VERSION_NUM, MINOR_VERSION_NUM)
 
 def reportError(message):
     sys.stdout.write("ERROR: ")