Merge pull request #151 from michellab/devel

Merging in devel to create the 2017.1.0 release

.gitignore

@@ -45,3 +45,6 @@ wrapper/Py++/pyplusplus
 
 # Python autogenerated backup wrappers
 *~
+
+#Atom
+.idea

.travis.yml

@@ -1,37 +1,135 @@
+language: c++
 sudo: false
 
-language: cpp
+dummy: true
 
-compiler:
- - gcc
+env:
+  global:
+    # variables used to control build of Sire - limit to 4 core build,
+    # don't have Sire phone home (as would create false stats) and 
+    # install into the home directory, sire.app
+    - NCORES=4
+    - SIRE_DONT_PHONEHOME=1
+    - INSTALL_SIRE_DIR=$HOME/sire.app
+
+cache:
+  directories:
+    - ${TRAVIS_BUILD_DIR}/deps/llvm-3.9.0
 
-# Travis CI is powered with Ubuntu 12.04, whose toolchain is outdated.
 addons:
   apt:
-    # Travis white list of ppa.
-    # https://github.com/travis-ci/apt-source-whitelist/blob/master/ubuntu.json
-    sources:
-      - ubuntu-toolchain-r-test     # For gcc 5.2
-      - george-edison55-precise-backports # cmake 3.2.3 / doxygen 1.8.3
-    # Travis whitelist of packages.
-    # https://github.com/travis-ci/apt-package-whitelist/blob/master/ubuntu-precise
+    sources: &sources
+      - ubuntu-toolchain-r-test # for gcc 5.2 and gcc 6
     packages:
-      - cmake
-      - cmake-data
+      - g++-6
       - g++-5
+      #- g++-4.9 # commented out as this takes more than 90 minutes to compile!
+
+matrix:
+  exclude:
+    # exclude the default dummy build
+    - dummy: true
+
+  include:
+    # OS X, clang 3.7.2 (Apple LLVM 8.0.0) - disabling for now as takes
+    # more than our allocation to compile and install
+    #- os: osx
+    #  env: CXX_COMPILER=clang++ C_COMPILER=clang
+    #  osx_image: xcode8
+
+    # Linux, GCC 6.2.0
+    - os: linux
+      env: CXX_COMPILER=g++-6 C_COMPILER=gcc-6
+      compiler: gcc
+
+    # Linux, GCC 5.4.1
+    - os: linux
+      env: CXX_COMPILER=g++-5 C_COMPILER=gcc-5
+      compiler: gcc
+
+    # Linux, GCC 4.9 (any earlier doesn't have C++ 11, and 4.8 is broken - ice fault)
+    # (possibly because ran out of memory when compiling wrappers - now use 2 cores for this)
+    #- os: linux
+    #  env: CXX_COMPILER=g++-4.9 C_COMPILER=gcc-4.9 NPYCORES=2
+    #  compiler: gcc
+
+    # dependencies of Sire fail to compile on linux with clang
+    #- os: linux
+    #  env: LLVM_VERSION=3.9.0
+    #  compiler: clang
+
+install:
+  ############################################################################
+  # All the dependencies are installed in ${TRAVIS_BUILD_DIR}/deps/
+  ############################################################################
+  - DEPS_DIR="${TRAVIS_BUILD_DIR}/deps"
+  - mkdir -p ${DEPS_DIR} && cd ${DEPS_DIR}
+
+  ############################################################################
+  # Setup default versions and override compiler if needed
+  ############################################################################
+  - if [[ "${LLVM_VERSION}" == "default" ]]; then LLVM_VERSION=3.9.0; fi
+
+  - |
+    if [[ "${CXX_COMPILER}" != "" ]]; then 
+      echo "Using compiler ${CXX_COMPILER} | ${C_COMPILER}"
+      export CXX=${CXX_COMPILER}
+      export CC=${C_COMPILER}
+    fi
+
+  ############################################################################
+  # Install a recent CMake
+  ############################################################################
+  - |
+    if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
+      CMAKE_URL="https://cmake.org/files/v3.7/cmake-3.7.2-Linux-x86_64.tar.gz"
+      mkdir cmake && travis_retry wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C cmake
+      export PATH=${DEPS_DIR}/cmake/bin:${PATH}
+    else
+      brew install cmake
+      brew upgrade cmake
+    fi
+  - cmake --version
+
+  ############################################################################
+  # Install Clang, libc++ and libc++abi
+  ############################################################################
+  - |
+    if [[ "${LLVM_VERSION}" != "" ]]; then
+      LLVM_DIR=${DEPS_DIR}/llvm-${LLVM_VERSION}
+      if [[ -z "$(ls -A ${LLVM_DIR})" ]]; then
+        LLVM_URL="http://llvm.org/releases/${LLVM_VERSION}/llvm-${LLVM_VERSION}.src.tar.xz"
+        LIBCXX_URL="http://llvm.org/releases/${LLVM_VERSION}/libcxx-${LLVM_VERSION}.src.tar.xz"
+        LIBCXXABI_URL="http://llvm.org/releases/${LLVM_VERSION}/libcxxabi-${LLVM_VERSION}.src.tar.xz"
+        CLANG_URL="http://llvm.org/releases/${LLVM_VERSION}/clang+llvm-${LLVM_VERSION}-x86_64-linux-gnu-ubuntu-14.04.tar.xz"
+        mkdir -p ${LLVM_DIR} ${LLVM_DIR}/build ${LLVM_DIR}/projects/libcxx ${LLVM_DIR}/projects/libcxxabi ${LLVM_DIR}/clang
+        travis_retry wget --quiet -O - ${LLVM_URL}      | tar --strip-components=1 -xJ -C ${LLVM_DIR}
+        travis_retry wget --quiet -O - ${LIBCXX_URL}    | tar --strip-components=1 -xJ -C ${LLVM_DIR}/projects/libcxx
+        travis_retry wget --quiet -O - ${LIBCXXABI_URL} | tar --strip-components=1 -xJ -C ${LLVM_DIR}/projects/libcxxabi
+        travis_retry wget --quiet -O - ${CLANG_URL}     | tar --strip-components=1 -xJ -C ${LLVM_DIR}/clang
+        (cd ${LLVM_DIR}/build && cmake .. -DCMAKE_INSTALL_PREFIX=${LLVM_DIR}/install -DCMAKE_CXX_COMPILER=clang++)
+        (cd ${LLVM_DIR}/build/projects/libcxx && make install -j2)
+        (cd ${LLVM_DIR}/build/projects/libcxxabi && make install -j2)
+      fi
+      export CXXFLAGS="-nostdinc++ -isystem ${LLVM_DIR}/install/include/c++/v1"
+      export LDFLAGS="-L ${LLVM_DIR}/install/lib -l c++ -l c++abi"
+      export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${LLVM_DIR}/install/lib"
+      export PATH="${LLVM_DIR}/clang/bin:${PATH}"
+    fi
+  - ${CXX} --version
 
-before_install:
-  - export NCORES=4
-  - export SIRE_DONT_PHONEHOME=1
-  - export INSTALL_SIRE_DIR=$HOME/sire.app
-  - if [ "$CC" = "gcc"   ]; then export CC=gcc-5 CXX=g++-5; fi
-  - if [ "$CC" = "clang" ]; then export CC=clang-3.6 CXX=clang++-3.6; fi
+before_script:
+  ############################################################################
+  # Go back to the root of the project and setup the build directory
+  ############################################################################
+  - cd ${TRAVIS_BUILD_DIR}
 
 script:
   - cmake --version
   - $CXX --version
+  - which $CXX
   - bash compile_sire.sh
-  - $HOME/sire.app/bin/sire_test
+  - $HOME/sire.app/bin/sire_test -OpenMM
 
 after_success:
-  - echo "Time to go home and have a cup of tea! :)"
+  - echo "Congratulations - everything worked :-)"

build/build_sire.py

@@ -36,8 +36,18 @@ def print_progress():
         import multiprocessing
         NCORES = multiprocessing.cpu_count()
 
+    # Get the number of cores to use for compiling the python wrappers - this 
+    # defaults to NCORES
+    if "NPYCORES" in os.environ:
+        NPYCORES = int(os.environ["NPYCORES"])
+    else:
+        NPYCORES = NCORES
+
     print("Number of cores used for compilation = %d" % NCORES)
 
+    if NPYCORES != NCORES:
+        print("Number of cores used for wrapper compilation = %d" % NPYCORES)
+
     python_exe = None
     conda_exe = None
 
@@ -90,16 +100,27 @@ def print_progress():
     except:
         print("Installing openmm from the omnia repository...")
         os.system("%s config --add channels http://conda.binstar.org/omnia" % conda_exe)
-        os.system("%s install --yes openmm" % conda_exe)
+        os.system("%s install --yes openmm=7.0" % conda_exe)
 
     # Now that the miniconda distribution is ok, the next step
     # is to use cmake to build the corelib and wrapper in the build/corelib
     # and build/wrapper directories
 
+    # first, get the value of the CXX environment variable
+    cxx = os.getenv("CXX")
+    compiler_ext = None
+
+    if cxx:
+        if cxx.find("icpc") != -1:
+            compiler_ext = "intel"
+
     # change into the build/corelib directory
     OLDPWD = os.path.abspath(os.curdir)
 
-    coredir = "%s/corelib" % build_dir
+    if compiler_ext:
+        coredir = "%s/corelib_%s" % (build_dir,compiler_ext)
+    else:
+        coredir = "%s/corelib" % build_dir
 
     if not os.path.exists(coredir):
         os.makedirs(coredir)
@@ -146,7 +167,10 @@ def print_progress():
     # python wrappers
     os.chdir(OLDPWD)
 
-    wrapperdir = "%s/wrapper" % build_dir
+    if compiler_ext:
+        wrapperdir = "%s/wrapper_%s" % (build_dir,compiler_ext)
+    else:
+        wrapperdir = "%s/wrapper" % build_dir
 
     if not os.path.exists(wrapperdir):
         os.makedirs(wrapperdir)
@@ -176,14 +200,14 @@ def print_progress():
         sys.exit(-1)
 
     # Now that cmake has run, we can compile wrapper
-    status = os.system("make -j %s" % NCORES)
+    status = os.system("make -j %s" % NPYCORES)
 
     if status != 0:
         print("SOMETHING WENT WRONG WHEN COMPILING WRAPPER!")
         sys.exit(-1)
 
     # Now the compilation has finished, install wrapper
-    status = os.system("make -j %s install" % NCORES)
+    status = os.system("make -j %s install" % NPYCORES)
 
     if status != 0:
         print("SOMETHING WENT WRONG WHEN INSTALLING WRAPPER!")

compile_sire.sh

@@ -21,7 +21,6 @@ case $key in
     --install)
     INSTALL_SIRE_DIR="$2"
     echo "Installing Sire into ${INSTALL_SIRE_DIR}"
-    exit 0
     ;;
     --clean)
     echo "Completely cleaning the build directories..."
@@ -34,8 +33,8 @@ esac
 
 # Set the version of miniconda to use. Choose "latest" for the latest
 # miniconda, or set a specific version here
-#MINICONDA_VERSION="3.9.1"
-MINICONDA_VERSION="latest"
+MINICONDA_VERSION="4.2.12"
+#MINICONDA_VERSION="latest"
 
 if [ -z "$INSTALL_SIRE_DIR" ]; then
     # Ask the user where they would like to install sire. By default