Rework .travis.yml to increase speed, especially for OpenCL

New advanced options OPENMM_BUILD_CPU_TESTS, OPENMM_BUILD_SERIALIZATION_TESTS,
OPENMM_BUILD_REFERENCE_TESTS were added to the cmake configuration and disabled
in the OpenCL test matrix element to increase speed. Redundant or unnecessary
apt packages removed from the travis installation.

.travis.yml

@@ -2,11 +2,7 @@ language: python
 
 addons:
   apt:
-    sources:
-      - ubuntu-toolchain-r-test
     packages:
-      - libpcre3
-      - libpcre3-dev
       - gromacs
       - doxygen
       - python-numpy
@@ -15,47 +11,73 @@ addons:
 matrix:
   include:
     - sudo: required
-      python: 3.4
-      env: SUDO=true OPENMM_BUILD_STATIC_LIB=OFF CC=gcc CXX=g++
+      env: OPENCL=true
+           CC=gcc
+           CXX=g++
+           CMAKE_FLAGS="
+           -OPENMM_BUILD_OPENCL_LIB=ON
+           -DOPENMM_BUILD_OPENCL_TESTS=ON
+           -DOPENMM_BUILD_STATIC_LIB=OFF
+           -DOPENMM_BUILD_CPU_LIB=OFF
+           -DOPENMM_BUILD_REFERENCE_TESTS=OFF
+           -DOPENMM_BUILD_SERIALIZATION_TESTS=OFF
+           -DOPENMM_BUILD_PME_PLUGIN=OFF
+           -DOPENMM_BUILD_AMOEBA_PLUGIN=OFF
+           -DOPENMM_BUILD_PYTHON_WRAPPERS=OFF
+           -DOPENMM_BUILD_C_AND_FORTRAN_WRAPPERS=OFF
+           -DOPENMM_BUILD_EXAMPLES=OFF"
+      addons: {apt: {packages: []}}
+
     - sudo: false
       python: 2.7_with_system_site_packages
-      env: SUDO=false OPENMM_BUILD_STATIC_LIB=ON CC=clang CXX=clang++
+      env: OPENCL=false
+           CC=clang
+           CXX=clang++
+           CMAKE_FLAGS="-DOPENMM_BUILD_STATIC_LIB=ON"
+
     - sudo: false
       python: 2.7_with_system_site_packages
-      env: SUDO=false OPENMM_BUILD_STATIC_LIB=OFF CC=clang CXX=clang++
+      env: OPENCL=false
+           CC=clang
+           CXX=clang++
+           CMAKE_FLAGS="-DOPENMM_BUILD_STATIC_LIB=OFF"
+
     - sudo: false
       python: 3.4
-      env: SUDO=false OPENMM_BUILD_STATIC_LIB=OFF CC=gcc CXX=g++
-  allow_failures:
-   - sudo: required
+      env: OPENCL=false
+           CC=gcc
+           CXX=g++
+           CMAKE_FLAGS="-DOPENMM_BUILD_STATIC_LIB=OFF"
 
 before_install:
-  - echo $SUDO
-  - if [[ "$SUDO" == "true" ]]; then sudo apt-get install -qq fglrx=2:8.960-0ubuntu1 opencl-headers; fi
-
-  - wget https://anaconda.org/anaconda/swig/3.0.2/download/linux-64/swig-3.0.2-0.tar.bz2
-  - mkdir $HOME/swig
-  - tar -xjvf swig-3.0.2-0.tar.bz2 -C $HOME/swig
-  - export PATH=$HOME/swig/bin:$PATH
-  - export SWIG_LIB=$HOME/swig/share/swig/3.0.2
+  - if [[ "$OPENCL" == "true" ]]; then
+      sudo apt-get -yq update &>> ~/apt-get-update.log;
+      sudo apt-get install -qq fglrx=2:8.960-0ubuntu1 opencl-headers;
+    fi
+  - if [[ "$OPENCL" == "false" ]]; then
+      wget https://anaconda.org/anaconda/swig/3.0.2/download/linux-64/swig-3.0.2-0.tar.bz2;
+      mkdir $HOME/swig;
+      tar -xjvf swig-3.0.2-0.tar.bz2 -C $HOME/swig;
+      export PATH=$HOME/swig/bin:$PATH;
+      export SWIG_LIB=$HOME/swig/share/swig/3.0.2;
+    fi
 
 script:
-  - CTEST_STOP_TIME=$(python -c "from datetime import datetime, timedelta; import sys; sys.stdout.write((datetime.now() + timedelta(minutes=30)).strftime('%H:%M:%S'))")
-  - cmake -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM -DOPENMM_BUILD_STATIC_LIB=$OPENMM_BUILD_STATIC_LIB .
+  - CTEST_STOP_TIME=$(python -c "from datetime import datetime, timedelta; import sys; sys.stdout.write((datetime.now() + timedelta(minutes=25)).strftime('%H:%M:%S'))")
+  - cmake . $CMAKE_FLAGS -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM
+
   - make -j2 install
-  - if [[ "$SUDO" == "true" ]]; then ./TestOpenCLDeviceQuery; fi
-  - make PythonInstall
-  - # Run the testInstallation script
-  - python -m simtk.testInstallation
+  - if [[ "$OPENCL" == "true" ]]; then ./TestOpenCLDeviceQuery; fi
+  - if [[ "$OPENCL" == "false" ]]; then
+      make PythonInstall;
+      python -m simtk.testInstallation;
+      (cd python/tests && py.test -v *);
+    fi
+
   - # run all of the tests, making sure failures at this stage don't cause travis failures
   - ctest -j2 --output-on-failure --schedule-random --stop-time $CTEST_STOP_TIME || true
   - # get a list of all of the failed tests into this stupid ctest format
   - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
-  - # rerun all of the failed tests
-  - if [ -s Testing/Temporary/LastTestsFailed.log ]; then ctest -I FailedTests.log; fi;
-  - # run the python tests too
-  - cd python/tests
-  - # nosetests -vv --processes=-1 --process-timeout=200
-  - # nosetests -vv
-  - py.test -v *
-  - cd -
+  - if [ -s Testing/Temporary/LastTestsFailed.log ]; then
+      ctest -I FailedTests.log;
+    fi

CMakeLists.txt

@@ -341,9 +341,14 @@ ENDIF(DL_LIBRARY)
 
 IF(BUILD_TESTING)
     INCLUDE_DIRECTORIES(${CMAKE_SOURCE_DIR}/tests)
-    ADD_SUBDIRECTORY(platforms/reference/tests)
 ENDIF(BUILD_TESTING)
 
+set(OPENMM_BUILD_REFERENCE_TESTS TRUE CACHE BOOL "Whether to build Reference platform test cases")
+MARK_AS_ADVANCED(OPENMM_BUILD_REFERENCE_TESTS)
+IF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
+    ADD_SUBDIRECTORY(platforms/reference/tests)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
+
 # Which hardware platforms to build
 
 # A bit of tedium because we are using custom FindCUDA files that happen to work...

platforms/cpu/CMakeLists.txt

@@ -12,9 +12,11 @@
 #   libOpenMMCPU_static.a
 #----------------------------------------------------
 
-IF(BUILD_TESTING)
+SET(OPENMM_BUILD_CPU_TESTS TRUE CACHE BOOL "Whether to build CPU platform test cases")
+MARK_AS_ADVANCED(OPENMM_BUILD_CPU_TESTS)
+IF(BUILD_TESTING AND OPENMM_BUILD_CPU_TESTS)
     SUBDIRS(tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_CPU_TESTS)
 
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.

plugins/amoeba/CMakeLists.txt

@@ -40,7 +40,7 @@ SET(API_AMOEBA_INCLUDE_DIRS) # start empty
 FOREACH(subdir ${OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS})
     # append
     SET(API_AMOEBA_INCLUDE_DIRS ${API_AMOEBA_INCLUDE_DIRS}
-                                     ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include 
+                                     ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include
                                      ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/internal)
 ENDFOREACH(subdir)
 
@@ -162,6 +162,6 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
   SET (TEST_PATH .)
 ENDIF (EXECUTABLE_OUTPUT_PATH)
 
-IF(BUILD_TESTING)
+IF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)
     ADD_SUBDIRECTORY(serialization/tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)

plugins/amoeba/platforms/reference/CMakeLists.txt

@@ -75,6 +75,6 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 
-IF(BUILD_TESTING)
+IF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
     SUBDIRS (tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)

plugins/drude/CMakeLists.txt

@@ -145,6 +145,6 @@ ENDIF (EXECUTABLE_OUTPUT_PATH)
 
 #INCLUDE(ApiDoxygen.cmake)
 
-IF(BUILD_TESTING)
+IF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)
     ADD_SUBDIRECTORY(serialization/tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)

plugins/drude/platforms/reference/CMakeLists.txt

@@ -75,6 +75,6 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 
-IF(BUILD_TESTING)
+IF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
     SUBDIRS (tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)

plugins/rpmd/platforms/reference/CMakeLists.txt

@@ -75,6 +75,6 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS
 
 INSTALL(TARGETS ${SHARED_TARGET} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib/plugins)
 
-IF(BUILD_TESTING)
+IF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)
     SUBDIRS (tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_REFERENCE_TESTS)

serialization/CMakeLists.txt

@@ -6,6 +6,8 @@ INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/in
 INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/openmm/serialization/SerializationProxy.h)
 INSTALL_FILES(/include/openmm/serialization FILES ${CMAKE_CURRENT_SOURCE_DIR}/include/openmm/serialization/XmlSerializer.h)
 
-IF(BUILD_TESTING)
+SET(OPENMM_BUILD_SERIALIZATION_TESTS TRUE CACHE BOOL "Whether to build serialization test cases")
+MARK_AS_ADVANCED(OPENMM_BUILD_SERIALIZATION_TESTS)
+IF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)
     ADD_SUBDIRECTORY(tests)
-ENDIF(BUILD_TESTING)
+ENDIF(BUILD_TESTING AND OPENMM_BUILD_SERIALIZATION_TESTS)