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Commit 04042076 authored by Andreas Krämer's avatar Andreas Krämer
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Merge branch 'master' into charmmfixes

parents d59f19e4 2ff59259
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Showing with 351 additions and 96 deletions
.travis.yml
View file @ 04042076
......@@ -65,6 +65,7 @@ matrix:
- language: objective-c
os: osx
osx_image: xcode9.3
env: ==OSX==
OPENCL=false
CUDA=false
......@@ -108,9 +109,10 @@ before_install:
- wget http://anaconda.org/omnia/ccache/3.2.4/download/${TRAVIS_OS_NAME}-64/ccache-3.2.4-0.tar.bz2
- mkdir -p $HOME/ccache && tar xf ccache-3.2.4-0.tar.bz2 -C $HOME/ccache
- if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
brew cask uninstall oclint;
brew install fftw;
brew install -y https://raw.githubusercontent.com/Homebrew/homebrew-core/5b680fb58fedfb00cd07a7f69f5a621bb9240f3b/Formula/doxygen.rb;
sudo easy_install pytest;
sudo pip install -U pytest --ignore-installed six;
fi
- if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
CMAKE_URL="http://cmake.org/files/v3.7/cmake-3.7.2-Linux-x86_64.tar.gz";
......@@ -130,9 +132,9 @@ before_install:
${AMDAPPSDK}/bin/x86_64/clinfo;
sudo apt-get install -y libgl1-mesa-dev;
fi
# Install swig for Python wrappers. However, testing CUDA and OpenCL, we
# skip the Python wrapper for speed. We're not using anaconda python,
# but this is a fast way to get an apparently functional precompiled
# Install SWIG and Cython for Python wrappers. However, testing CUDA and
# OpenCL, we skip the Python wrapper for speed. We're not using anaconda
# python, but this is a fast way to get an apparently functional precompiled
# build of swig that's more modern than what's in apt.
- if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "linux" ]]; then
wget http://anaconda.org/omnia/swig/3.0.7/download/linux-64/swig-3.0.7-0.tar.bz2;
......@@ -140,6 +142,7 @@ before_install:
tar -xjvf swig-3.0.7-0.tar.bz2 -C $HOME/swig;
export PATH=$HOME/swig/bin:$PATH;
export SWIG_LIB=$HOME/swig/share/swig/3.0.7;
pip install cython;
fi
- if [[ "$OPENCL" == "false" && "$CUDA" == "false" && "$TRAVIS_OS_NAME" == "osx" ]]; then
wget http://anaconda.org/omnia/swig/3.0.7/download/osx-64/swig-3.0.7-0.tar.bz2;
......@@ -147,6 +150,7 @@ before_install:
tar -xjvf swig-3.0.7-0.tar.bz2 -C $HOME/swig;
export PATH=$HOME/swig/bin:$PATH;
export SWIG_LIB=$HOME/swig/share/swig/3.0.7;
sudo pip install cython;
fi
- if [[ "$CUDA" == "true" ]]; then
......@@ -181,8 +185,9 @@ script:
- python devtools/run-ctest.py --start-time $START_TIME
- if [[ ! -z "${DOCS_DEPLOY}" && "${DOCS_DEPLOY}" = "true" ]]; then
pip install sphinx==1.5.6 sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen;
pip install sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen;
make sphinxhtml;
make sphinxpdf;
make C++ApiDocs PythonApiDocs;
mkdir -p api-docs;
mv sphinx-docs/userguide/html api-docs/userguide;
......
CMakeLists.txt
View file @ 04042076
......@@ -33,6 +33,21 @@ MARK_AS_ADVANCED(DART_ROOT)
# We have custom cmake modules for FindOpenMM and running python tests
SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake_modules")
# Determine what architecture we are compiling for.
INCLUDE(TargetArch)
target_architecture(TARGET_ARCH)
if ("${TARGET_ARCH}" MATCHES "x86_64|i386")
set(X86 ON)
endif()
if ("${TARGET_ARCH}" MATCHES "arm")
set(ARM ON)
add_compile_definitions(__ARM__=1)
endif()
if ("${TARGET_ARCH}" MATCHES "ppc")
set(PPC ON)
add_compile_definitions(__PPC__=1)
endif()
# Where to install
IF(WIN32)
IF(NOT OPENMM_INSTALL_PREFIX)
......@@ -69,7 +84,10 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
# The source is organized into subdirectories, but we handle them all from
# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/irrxml libraries/vecmath)
SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/irrxml)
IF(X86 OR ARM)
SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/vecmath)
ENDIF()
IF(WIN32)
SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/pthreads)
ELSE(WIN32)
......@@ -82,7 +100,7 @@ ENDIF(WIN32)
SET (CMAKE_CXX_STANDARD 11)
IF (APPLE AND (NOT PNACL))
IF(APPLE)
# Build 64 bit binaries compatible with OS X 10.7
IF (NOT CMAKE_OSX_DEPLOYMENT_TARGET)
SET (CMAKE_OSX_DEPLOYMENT_TARGET "10.7" CACHE STRING "The minimum version of OS X to support" FORCE)
......@@ -102,19 +120,17 @@ IF (APPLE AND (NOT PNACL))
# Improve the linking behavior of Mac libraries
SET (CMAKE_INSTALL_NAME_DIR "@rpath")
SET(EXTRA_COMPILE_FLAGS "-msse2 -stdlib=libc++")
ELSE (APPLE AND (NOT PNACL))
IF (MSVC OR ANDROID OR PNACL)
SET(EXTRA_COMPILE_FLAGS)
IF (MSVC)
# Use warning level 2, not whatever warning level CMake picked.
STRING(REGEX REPLACE "/W[0-4]" "/W2" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
# Explicitly suppress warnings 4305 and 4244.
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4305 /wd4244")
ENDIF (MSVC)
ELSE (MSVC OR ANDROID OR PNACL)
SET(EXTRA_COMPILE_FLAGS "-msse2")
ENDIF (MSVC OR ANDROID OR PNACL)
ENDIF (APPLE AND (NOT PNACL))
ELSEIF(MSVC)
SET(EXTRA_COMPILE_FLAGS)
# Use warning level 2, not whatever warning level CMake picked.
STRING(REGEX REPLACE "/W[0-4]" "/W2" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
# Explicitly suppress warnings 4305 and 4244.
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4305 /wd4244")
ELSEIF(X86)
SET(EXTRA_COMPILE_FLAGS "-msse2")
ELSE()
SET(EXTRA_COMPILE_FLAGS)
ENDIF()
IF(UNIX AND NOT CMAKE_BUILD_TYPE)
SET(CMAKE_BUILD_TYPE Release CACHE STRING "Debug or Release build" FORCE)
......@@ -141,7 +157,7 @@ ENDIF (NOT CMAKE_CXX_FLAGS_RELEASE)
SET(OPENMM_LIBRARY_NAME OpenMM)
SET(OPENMM_MAJOR_VERSION 7)
SET(OPENMM_MINOR_VERSION 2)
SET(OPENMM_MINOR_VERSION 4)
SET(OPENMM_BUILD_VERSION 0)
ADD_DEFINITIONS(-DOPENMM_LIBRARY_NAME=${OPENMM_LIBRARY_NAME}
......@@ -219,19 +235,19 @@ FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
## OpenMM was previously installed there.
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
ENDFOREACH(subdir)
IF (ANDROID OR PNACL)
SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/libraries/sfmt/src/SFMT.cpp PROPERTIES COMPILE_FLAGS "-UHAVE_SSE2")
ELSE (ANDROID OR PNACL)
IF(X86)
SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/libraries/sfmt/src/SFMT.cpp PROPERTIES COMPILE_FLAGS "-DHAVE_SSE2=1")
ENDIF(ANDROID OR PNACL)
IF (NOT (ANDROID OR PNACL OR (WIN32 AND OPENMM_BUILD_STATIC_LIB)))
ELSE()
SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/libraries/sfmt/src/SFMT.cpp PROPERTIES COMPILE_FLAGS "-UHAVE_SSE2")
ENDIF()
IF(X86 AND NOT (WIN32 AND OPENMM_BUILD_STATIC_LIB))
FILE(GLOB src_files ${CMAKE_CURRENT_SOURCE_DIR}/libraries/asmjit/*/*.cpp)
FILE(GLOB incl_files ${CMAKE_CURRENT_SOURCE_DIR}/libraries/asmjit/*.h)
SET(SOURCE_FILES ${SOURCE_FILES} ${src_files})
SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
INCLUDE_DIRECTORIES(BEFORE "${CMAKE_CURRENT_SOURCE_DIR}/libraries/asmjit")
SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DLEPTON_USE_JIT")
ENDIF (NOT (ANDROID OR PNACL OR (WIN32 AND OPENMM_BUILD_STATIC_LIB)))
ENDIF()
# If API wrappers are being generated, and add them to the build.
SET(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS ON CACHE BOOL "Build wrappers for C and Fortran")
......
appveyor.yml
View file @ 04042076
......@@ -11,6 +11,7 @@ install:
- "set PATH=C:\\Program Files (x86)\\Git\\bin;%PATH%"
- pip install pytest
- pip install numpy
- pip install cython
# Use cclash for compiler caching (experimental)
- ps: wget https://github.com/inorton/cclash/releases/download/0.3.14/cclash-0.3.14.zip -OutFile cclash-0.3.14.zip
......@@ -27,9 +28,10 @@ install:
- "set PATH=C:\\fftw;%PATH%"
# Download and install some OpenMM build dependencies (doxygen, swig)
- choco install -y doxygen.portable swig > null
- choco install -y doxygen.install swig > null
# Download OpenCL Headers and build the ICD loader
- ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12;"
- ps: $opencl_registry = "https://www.khronos.org/registry/cl"
- ps: $opencl_github = "KhronosGroup/OpenCL-Headers"
- ps: mkdir C:/opencl > $null
......@@ -39,7 +41,7 @@ install:
- ps: 7z x opencl-icd-1.2.11.0.tar > $null
- ps: mv .\icd\* .
- ps: mkdir inc/CL > $null
- ps: wget https://github.com/$opencl_github/tree/master/opencl20/CL | select -ExpandProperty links | where {$_.href -like "*.h*"} | select -ExpandProperty outerText | foreach{ wget https://raw.githubusercontent.com/$opencl_github/master/opencl20/CL/$_ -OutFile inc/CL/$_ }
- ps: wget https://github.com/$opencl_github/tree/master/CL -UseBasicParsing | select -ExpandProperty links | where {$_.href -like "*.h*"} | select -ExpandProperty title | foreach{ wget https://raw.githubusercontent.com/$opencl_github/master/CL/$_ -OutFile inc/CL/$_ -UseBasicParsing}
- ps: mkdir lib > $null
- ps: cd lib
- cmake -G "NMake Makefiles" ..
......
cmake_modules/TargetArch.cmake 0 → 100644
View file @ 04042076
# This is from Solar CMake (https://github.com/axr/solar-cmake).
#
# Copyright (c) 2012 Petroules Corporation. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
#
# Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
# IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
# INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
# OF THE POSSIBILITY OF SUCH DAMAGE.
# Based on the Qt 5 processor detection code, so should be very accurate
# https://qt.gitorious.org/qt/qtbase/blobs/master/src/corelib/global/qprocessordetection.h
# Currently handles arm (v5, v6, v7), x86 (32/64), ia64, and ppc (32/64)
# Regarding POWER/PowerPC, just as is noted in the Qt source,
# "There are many more known variants/revisions that we do not handle/detect."
set(archdetect_c_code "
#if defined(__arm__) || defined(__TARGET_ARCH_ARM)
#if defined(__ARM_ARCH_7__) \\
|| defined(__ARM_ARCH_7A__) \\
|| defined(__ARM_ARCH_7R__) \\
|| defined(__ARM_ARCH_7M__) \\
|| (defined(__TARGET_ARCH_ARM) && __TARGET_ARCH_ARM-0 >= 7)
#error cmake_ARCH armv7
#elif defined(__ARM_ARCH_6__) \\
|| defined(__ARM_ARCH_6J__) \\
|| defined(__ARM_ARCH_6T2__) \\
|| defined(__ARM_ARCH_6Z__) \\
|| defined(__ARM_ARCH_6K__) \\
|| defined(__ARM_ARCH_6ZK__) \\
|| defined(__ARM_ARCH_6M__) \\
|| (defined(__TARGET_ARCH_ARM) && __TARGET_ARCH_ARM-0 >= 6)
#error cmake_ARCH armv6
#elif defined(__ARM_ARCH_5TEJ__) \\
|| (defined(__TARGET_ARCH_ARM) && __TARGET_ARCH_ARM-0 >= 5)
#error cmake_ARCH armv5
#else
#error cmake_ARCH arm
#endif
#elif defined(__i386) || defined(__i386__) || defined(_M_IX86)
#error cmake_ARCH i386
#elif defined(__x86_64) || defined(__x86_64__) || defined(__amd64) || defined(_M_X64)
#error cmake_ARCH x86_64
#elif defined(__ia64) || defined(__ia64__) || defined(_M_IA64)
#error cmake_ARCH ia64
#elif defined(__ppc__) || defined(__ppc) || defined(__powerpc__) \\
|| defined(_ARCH_COM) || defined(_ARCH_PWR) || defined(_ARCH_PPC) \\
|| defined(_M_MPPC) || defined(_M_PPC)
#if defined(__ppc64__) || defined(__powerpc64__) || defined(__64BIT__)
#error cmake_ARCH ppc64
#else
#error cmake_ARCH ppc
#endif
#endif
#error cmake_ARCH unknown
")
# Set ppc_support to TRUE before including this file or ppc and ppc64
# will be treated as invalid architectures since they are no longer supported by Apple
function(target_architecture output_var)
if(APPLE AND CMAKE_OSX_ARCHITECTURES)
# On OS X we use CMAKE_OSX_ARCHITECTURES *if* it was set
# First let's normalize the order of the values
# Note that it's not possible to compile PowerPC applications if you are using
# the OS X SDK version 10.6 or later - you'll need 10.4/10.5 for that, so we
# disable it by default
# See this page for more information:
# http://stackoverflow.com/questions/5333490/how-can-we-restore-ppc-ppc64-as-well-as-full-10-4-10-5-sdk-support-to-xcode-4
# Architecture defaults to i386 or ppc on OS X 10.5 and earlier, depending on the CPU type detected at runtime.
# On OS X 10.6+ the default is x86_64 if the CPU supports it, i386 otherwise.
foreach(osx_arch ${CMAKE_OSX_ARCHITECTURES})
if("${osx_arch}" STREQUAL "ppc" AND ppc_support)
set(osx_arch_ppc TRUE)
elseif("${osx_arch}" STREQUAL "i386")
set(osx_arch_i386 TRUE)
elseif("${osx_arch}" STREQUAL "x86_64")
set(osx_arch_x86_64 TRUE)
elseif("${osx_arch}" STREQUAL "ppc64" AND ppc_support)
set(osx_arch_ppc64 TRUE)
else()
message(FATAL_ERROR "Invalid OS X arch name: ${osx_arch}")
endif()
endforeach()
# Now add all the architectures in our normalized order
if(osx_arch_ppc)
list(APPEND ARCH ppc)
endif()
if(osx_arch_i386)
list(APPEND ARCH i386)
endif()
if(osx_arch_x86_64)
list(APPEND ARCH x86_64)
endif()
if(osx_arch_ppc64)
list(APPEND ARCH ppc64)
endif()
else()
file(WRITE "${CMAKE_BINARY_DIR}/arch.c" "${archdetect_c_code}")
enable_language(C)
# Detect the architecture in a rather creative way...
# This compiles a small C program which is a series of ifdefs that selects a
# particular #error preprocessor directive whose message string contains the
# target architecture. The program will always fail to compile (both because
# file is not a valid C program, and obviously because of the presence of the
# #error preprocessor directives... but by exploiting the preprocessor in this
# way, we can detect the correct target architecture even when cross-compiling,
# since the program itself never needs to be run (only the compiler/preprocessor)
try_run(
run_result_unused
compile_result_unused
"${CMAKE_BINARY_DIR}"
"${CMAKE_BINARY_DIR}/arch.c"
COMPILE_OUTPUT_VARIABLE ARCH
CMAKE_FLAGS CMAKE_OSX_ARCHITECTURES=${CMAKE_OSX_ARCHITECTURES}
)
# Parse the architecture name from the compiler output
string(REGEX MATCH "cmake_ARCH ([a-zA-Z0-9_]+)" ARCH "${ARCH}")
# Get rid of the value marker leaving just the architecture name
string(REPLACE "cmake_ARCH " "" ARCH "${ARCH}")
# If we are compiling with an unknown architecture this variable should
# already be set to "unknown" but in the case that it's empty (i.e. due
# to a typo in the code), then set it to unknown
if (NOT ARCH)
set(ARCH unknown)
endif()
endif()
set(${output_var} "${ARCH}" PARENT_SCOPE)
endfunction()
devtools/Jenkinsfile 0 → 100644
View file @ 04042076
pipeline {
agent any
stages {
stage("Build and test") {
parallel {
stage("Build and test CUDA platform") {
agent { label "cuda" }
steps {
sh '''#!/bin/bash -lex
git clean -fxd && git checkout .
env
module load cuda conda
export OPENMM_CUDA_COMPILER=`which nvcc`
bash -e devtools/ci/jenkins/install.sh
bash -e devtools/ci/jenkins/test.sh -R 'TestCuda' --parallel 2
'''
}
}
stage("Build and test OpenCL platform") {
agent { label "cuda" }
steps {
sh '''#!/bin/bash -lex
git clean -fxd && git checkout .
env
module load cuda conda
export OPENMM_CUDA_COMPILER=`which nvcc`
bash -e devtools/ci/jenkins/install.sh
bash -e devtools/ci/jenkins/test.sh -R 'TestOpenCL' --parallel 2
'''
}
}
stage("Build/test CPU platforms") {
agent {
dockerfile {
dir "devtools/ci/jenkins"
label "docker"
}
}
steps {
sh '''#!/bin/bash -lex
git clean -fxd && git checkout .
bash -e devtools/ci/jenkins/install_and_test_cpu.sh
'''
}
}
} // parallel
}
}
}
devtools/ci/jenkins/Dockerfile 0 → 100644
View file @ 04042076
FROM ubuntu:xenial
ENV PATH="/opt/miniconda/bin:${PATH}"
RUN apt-get update && \
apt-get install -y wget git gromacs doxygen gfortran libfftw3-dev gcc g++ bzip2 automake make lsb-core && \
wget https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh -O miniconda.sh && \
bash miniconda.sh -b -p "/opt/miniconda" && \
rm -f miniconda.sh && \
mkdir /.conda && chmod -R 777 /.conda && chmod -R 777 /opt/miniconda && \
conda install -y cmake numpy scipy pytest swig cython
devtools/ci/jenkins/install.sh
View file @ 04042076
......@@ -8,36 +8,15 @@ swig -version
echo "Using cmake (`which cmake`) version":
cmake --version
echo "Using clang (`which clang`) version:"
clang --version
module load cuda conda/jenkins
# Constants
CONDAENV=openmm-test-3.5
INSTALL_DIRECTORY="${WORKSPACE}/openmm-install"
SRC_DIRECTORY="${WORKSPACE}/openmm-src" # set in the Jenkins configuration
export OPENMM_CUDA_COMPILER=`which nvcc`
# Create a conda environment, but clean up after one first. If it doesn't exist, don't complain.
# But since we are invoking this shell with -e (exit on all errors), we need || true to prevent this
# command from crashing the whole shell
conda remove -yn ${CONDAENV} --all --quiet || true
conda create -yn ${CONDAENV} python=3.5 --no-default-packages --quiet
conda install -yn ${CONDAENV} numpy scipy pytest --quiet
source activate ${CONDAENV} # enter our new environment
# Build OpenMM
cd "${SRC_DIRECTORY}"
cmake -DCMAKE_INSTALL_PREFIX="${INSTALL_DIRECTORY}" -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang .
make -j4 install
make PythonInstall
# Now run the tests
python -m simtk.testInstallation
cd python/tests && py.test -v && cd ../..
python devtools/run-ctest.py --job-duration=120 --timeout 300
# Now remove the conda environment
source deactivate
conda remove -yn ${CONDAENV} --all --quiet
\ No newline at end of file
echo "Using g++ (`which g++`) version:"
g++ --version
if [ ! -z "$OPENMM_CUDA_COMPILER" ]; then
echo "Using nvcc ($OPENMM_CUDA_COMPILER) version:"
$OPENMM_CUDA_COMPILER --version
CUDA_ARGS="-DCUDA_TOOLKIT_ROOT_DIR=${CUDA_HOME}"
fi
cmake -DCMAKE_INSTALL_PREFIX="`pwd`/install" -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc \
-DSWIG_EXECUTABLE=`which swig` $CUDA_ARGS $EXTRA_CMAKE_ARGS .
make -j6 install
devtools/ci/jenkins/install_and_test_cpu.sh 0 → 100644
View file @ 04042076
#!/bin/bash
EXTRA_CMAKE_ARGS="-DOPENMM_BUILD_CUDA_LIB=false -DOPENMM_BUILD_OPENCL_LIB=false"
. devtools/ci/jenkins/install.sh
python devtools/run-ctest.py --job-duration=120 --timeout 300 --in-order -R 'Test(Cpu|Reference)' --parallel 4
# Build & test Python
make PythonInstall
python -m simtk.testInstallation
cd python/tests && py.test -v
devtools/ci/jenkins/test.sh 0 → 100644
View file @ 04042076
#!/bin/sh
python devtools/run-ctest.py --job-duration=120 --timeout 300 --in-order $*
\ No newline at end of file
devtools/packaging/install.sh
View file @ 04042076
......@@ -26,10 +26,10 @@ fi
# Make sure it's a supported Python version.
pythonOk=$(${pythonBin} -c "import sys; v=sys.version_info; print((v[0]==2 and v[1]>5) or v[0]>2)")
pythonOk=$(${pythonBin} -c "import sys; v=sys.version_info; print((v[0]==2 and v[1]>6) or v[0]>2)")
if [ ${pythonOk} != "True" ]
then
echo "Unsupported Python version. Only versions 2.6 and higher are supported."
echo "Unsupported Python version. Only versions 2.7 and higher are supported."
exit
fi
......
devtools/packaging/scripts/windows/Vagrantfile
View file @ 04042076
Vagrant.configure("2") do |config|
config.vm.box = "gusztavvargadr/windows10ee"
config.vm.box = "gusztavvargadr/windows-10"
config.vm.provision :shell, path: "prepare.ps1"
config.vm.provider :virtualbox do |vb|
......
devtools/packaging/scripts/windows/prepare.ps1
View file @ 04042076
......@@ -2,8 +2,8 @@ cd C:\Users\vagrant
# Install CUDA.
wget https://developer.nvidia.com/compute/cuda/8.0/prod/network_installers/cuda_8.0.44_win10_network-exe -UseBasicParsing -OutFile cuda_8.0.44_win10_network.exe
.\cuda_8.0.44_win10_network.exe -s compiler_8.0 cudart_8.0 cufft_8.0 cufft_dev_8.0 nvrtc_8.0 nvrtc_dev_8.0 | Out-Null
wget https://developer.nvidia.com/compute/cuda/10.1/Prod/network_installers/cuda_10.1.168_win10_network.exe -UseBasicParsing -OutFile cuda_10.1.168_win10_network.exe
.\cuda_10.1.168_win10_network.exe -s nvcc_10.1 cudart_10.1 cufft_10.1 cufft_dev_10.1 nvrtc_10.1 nvrtc_dev_10.1 | Out-Null
# Install AMD APP SDK.
......@@ -14,12 +14,14 @@ wget https://s3.amazonaws.com/omnia-ci/AMD-APP-SDK-v2.9-1.599.381-GA-Full-window
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Windows-x86_64.exe -UseBasicParsing -OutFile Miniconda3-latest-Windows-x86_64.exe
.\Miniconda3-latest-Windows-x86_64.exe /S /D=C:\Miniconda3 | Out-Null
[Environment]::SetEnvironmentVariable("Path", $env:Path + ";C:\Miniconda3;C:\Miniconda3\Scripts;C:\Miniconda3\Library\bin", [EnvironmentVariableTarget]::User)
# Install software with conda.
& "C:\Miniconda3\Scripts\conda.exe" install -y -c omnia fftw3f jinja2 lxml sphinx sphinxcontrib-autodoc_doxygen sphinxcontrib-lunrsearch conda-build anaconda-client
& "C:\Miniconda3\Scripts\conda.exe" config --add channels omnia --add channels conda-forge
& "C:\Miniconda3\Scripts\conda.exe" install -y fftw3f==3.3.4=vc14_2 jinja2 lxml sphinx sphinxcontrib-autodoc_doxygen sphinxcontrib-lunrsearch conda-build anaconda-client
& "C:\Miniconda3\Scripts\pip.exe" install sphinxcontrib.bibtex
# Install software with choco.
choco install -y doxygen.portable swig cmake doxygen.install vcbuildtools git jom
choco install -y doxygen.portable swig cmake doxygen.install vcbuildtools git jom patch
devtools/run-ctest.py
View file @ 04042076
......@@ -43,16 +43,26 @@ def main():
help="Timeout for individual tests (seconds). Default=180",
type=str,
default='180')
parser.add_argument(
'--in-order',
help='Run the tests in order',
default=False,
action='store_true')
parser.add_argument(
'--parallel',
help='Number of processors to use',
type=int,
default=1)
args = parser.parse_args()
args, raw_args = parser.parse_known_args()
status = execute_tests(args)
status = execute_tests(args, raw_args)
if status != 0:
status = execute_failed_tests(args)
status = execute_failed_tests(args, raw_args)
return status
def execute_tests(options):
def execute_tests(options, raw_options):
start_time = datetime.fromtimestamp(options.start_time)
stop_time = start_time + timedelta(minutes=options.job_duration)
......@@ -68,13 +78,14 @@ def execute_tests(options):
shutil.rmtree('Testing')
return call(['ctest',
'--output-on-failure',
'--schedule-random',
'--parallel', str(options.parallel),
'-T', 'Test',
'--timeout', options.timeout,
'--stop-time', stop_time.strftime('%H:%M:%S')])
'--stop-time', stop_time.strftime('%H:%M:%S')] + raw_options +
(['--schedule-random'] if options.in_order else []))
def execute_failed_tests(options):
def execute_failed_tests(options, raw_options):
matches = glob('Testing/*/Test.xml')
assert len(matches) == 1
root = ElementTree.parse(matches[0])
......@@ -93,12 +104,13 @@ def execute_failed_tests(options):
start_time = datetime.fromtimestamp(options.start_time)
stop_time = start_time + timedelta(minutes=options.job_duration)
return call(['ctest',
return call(['ctest'] + raw_options + [
'--output-on-failure',
'--schedule-random',
'--parallel', str(options.parallel),
'-R', '|'.join(failed_tests),
'--timeout', options.timeout,
'--stop-time', stop_time.strftime('%H:%M:%S')])
'--stop-time', stop_time.strftime('%H:%M:%S')] +
(['--schedule-random'] if options.in_order else []))
if __name__ == '__main__':
......
docs-source/api-python/process-docstring.py
View file @ 04042076
......@@ -14,8 +14,11 @@ def process_docstring(app, what, name, obj, options, lines):
s = m.group(1)
if not s.startswith(linesep):
s = linesep + s
newline = '|LINEBREAK|.. admonition:: Deprecated' + linesep
newline = '|LINEBREAK|.. admonition::|LINEBREAK| Deprecated' + linesep
return newline + ' ' + s.replace(linesep, linesep + ' ')
def repl3(m):
s = m.group(1)
return '*' + s + '*'
linesep = '|LINEBREAK|'
joined = linesep.join(lines)
......@@ -23,6 +26,7 @@ def process_docstring(app, what, name, obj, options, lines):
joined = re.sub(r'<tt><pre>((|LINEBREAK|)?.*?)</pre></tt>', repl, joined)
joined = re.sub(r'<tt>(.*?)</tt>', repl, joined)
joined = re.sub(r'@deprecated(.*?\|LINEBREAK\|)', repl2, joined, flags=re.IGNORECASE)
joined = re.sub(r'<i>(.*?)</i>', repl3, joined)
lines[:] = [(l if not l.isspace() else '') for l in joined.split(linesep)]
......
docs-source/developerguide/conf.py
View file @ 04042076
......@@ -42,7 +42,7 @@ master_doc = 'index'
# General information about the project.
project = u'OpenMM Developer Guide'
copyright = u'2011-2014, Stanford University'
copyright = u'2011-2017, Stanford University'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
......
docs-source/developerguide/developer.rst
View file @ 04042076
......@@ -325,10 +325,10 @@ look in ReferenceKernels.cpp, you will find code for extracting the correct
values of these fields. For example:
::
static vector<RealVec>& extractPositions(ContextImpl& context) {
static vector<Vec3>& extractPositions(ContextImpl& context) {
ReferencePlatform::PlatformData* data =
reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *((vector<RealVec>*) data->positions);
return *((vector<Vec3>*) data->positions);
}
The PlatformData’s vector of forces contains one element for each particle. At
......
docs-source/developerguide/license.rst
View file @ 04042076
Portions copyright (c) 2011-2016 Stanford University and the Authors
Portions copyright (c) 2011-2017 Stanford University and the Authors
Contributors: Peter Eastman
......
docs-source/sphinx/autonumber.py
View file @ 04042076
from docutils.parsers.rst import roles
from docutils.nodes import Text, reference, section
from docutils.nodes import Text, reference, section, label
from sphinx.roles import XRefRole
class autonumber(Text):
class autonumber(label):
pass
class autonumber_ref(reference):
pass
def autonumber_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
return ([autonumber(text)], [])
return ([autonumber(text=text)], [])
def doctree_resolved(app, doctree, docname):
index = {};
refTable = {}
if app.config.autonumber_by_chapter:
# Record the number of each chapter
env = app.builder.env
sectionNumbers = {}
for doc in env.toc_secnumbers:
......@@ -24,9 +24,9 @@ def doctree_resolved(app, doctree, docname):
for sectionId in sections:
sectionNumbers[sectionId[1:]] = sections[sectionId]
lastChapter = -1
# Assign numbers to all the autonumbered objects.
for node in doctree.traverse(autonumber):
category = node.astext().split(',')[0]
if category in index:
......@@ -47,13 +47,13 @@ def doctree_resolved(app, doctree, docname):
newNode = Text('%s %d-%d' % (category, chapter, nextNumber))
lastChapter = chapter
else:
newNode = Text('%s %d' % (category, nextNumber))
newNode = Text('%s %d' % (category, nextNumber))
index[category] = nextNumber
refTable[node.astext()] = newNode
node.parent.replace(node, newNode)
# Replace references with the name of the referenced object
for ref_info in doctree.traverse(autonumber_ref):
target = ref_info['reftarget']
if target not in refTable:
......@@ -68,4 +68,3 @@ def setup(app):
app.add_role('autonumref', XRefRole(nodeclass=autonumber_ref))
app.connect('doctree-resolved', doctree_resolved)
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