Merge branch 'master' of github.com:pandegroup/openmm into dpme

.travis.yml

@@ -108,6 +108,11 @@ before_install:
       brew install doxygen fftw;
       sudo easy_install pytest;
     fi
+  - if [[ "${TRAVIS_OS_NAME}" == "linux" ]]; then
+      CMAKE_URL="https://cmake.org/files/v3.7/cmake-3.7.2-Linux-x86_64.tar.gz";
+      mkdir $HOME/cmake && travis_retry wget --no-check-certificate --quiet -O - ${CMAKE_URL} | tar --strip-components=1 -xz -C $HOME/cmake;
+      export PATH=${HOME}/cmake/bin:${PATH};
+    fi
   - if [[ "$OPENCL" == "true" ]]; then
       wget http://s3.amazonaws.com/omnia-ci/AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2;
       tar -xjf AMD-APP-SDK*.tar.bz2;

CMakeLists.txt

@@ -21,10 +21,11 @@ IF( NOT PROJECT_NAME )
     PROJECT (OpenMM)
 ENDIF( NOT PROJECT_NAME )
 
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
-if("${CMAKE_VERSION}" VERSION_GREATER "3.0" OR "${CMAKE_VERSION}" VERSION_EQUAL "3.0")
-    CMAKE_POLICY(SET CMP0042 OLD)
-endif()
+CMAKE_MINIMUM_REQUIRED(VERSION 3.1)
+CMAKE_POLICY(SET CMP0042 OLD)
+CMAKE_POLICY(SET CMP0003 NEW)
+CMAKE_POLICY(SET CMP0005 NEW)
+CMAKE_POLICY(SET CMP0011 NEW)
 
 #SET(CMAKE_VERBOSE_MAKEFILE 1)
 
@@ -39,21 +40,6 @@ IF(NOT cmv EQUAL "2.4") # This whole file...
 # We have custom cmake modules for FindOpenMM and running python tests
 SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake_modules")
 
-# Older cmake versions do not have cmake_policy command
-# Cmake 2.4.5, the default cmake on red hat linux, has the
-# cmake_policy command, but it does not work
-# "if(POLICY ..." does not work with cmake 2.4.[56] on red hat
-# (cmake 2.4.7 is OK)
-if(COMMAND cmake_policy)
-    if(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5)
-        cmake_policy(SET CMP0003 NEW)
-        cmake_policy(SET CMP0005 NEW)
-    endif(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 5)
-    if(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2)
-        cmake_policy(SET CMP0011 NEW)
-    endif(CMAKE_MAJOR_VERSION GREATER 2 OR CMAKE_MINOR_VERSION GREATER 6 OR CMAKE_PATCH_VERSION GREATER 2)
-endif(COMMAND cmake_policy)
-
 # Where to install
 IF(WIN32)
     IF(NOT OPENMM_INSTALL_PREFIX)
@@ -69,6 +55,9 @@ IF(WIN32)
     ADD_DEFINITIONS(-DWIN32)
 ENDIF(WIN32)
 
+# What type of libraries to build
+SET(OPENMM_BUILD_SHARED_LIB ON CACHE BOOL "Whether to build shared OpenMM libraries")
+SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
 
 # Include CPU-Features for Android
 IF (ANDROID)
@@ -114,6 +103,7 @@ ELSE( CMAKE_SIZEOF_VOID_P EQUAL 8 )
   SET( LIB64  )
 ENDIF( CMAKE_SIZEOF_VOID_P EQUAL 8 )
 
+SET (CMAKE_CXX_STANDARD 11)
 
 IF (APPLE AND (NOT PNACL))
     # Build 64 bit binaries compatible with OS X 10.7
@@ -283,7 +273,7 @@ IF (ANDROID OR PNACL)
 ELSE (ANDROID OR PNACL)
     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))
+IF (NOT (ANDROID OR PNACL OR (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})
@@ -302,8 +292,6 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
 
 INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
-SET(OPENMM_BUILD_SHARED_LIB ON CACHE BOOL "Whether to build shared OpenMM libraries")
-
 SET(EXTRA_LINK_FLAGS ${EXTRA_COMPILE_FLAGS})
 IF (CMAKE_SYSTEM_NAME MATCHES "Linux")
     IF (NOT ANDROID)
@@ -319,7 +307,6 @@ IF(OPENMM_BUILD_SHARED_LIB)
     SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DPTHREAD_BUILDING_SHARED_LIBRARY")
 ENDIF(OPENMM_BUILD_SHARED_LIB)
 
-SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
 IF(OPENMM_BUILD_STATIC_LIB)
     ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
     SET(EXTRA_COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DLEPTON_USE_STATIC_LIBRARIES -DPTW32_STATIC_LIB")

appveyor.yml

-os: Windows Server 2012 R2
+os: Visual Studio 2015
+platform: x64
+configuration: Release
 shallow_clone: true
 install:
 
-# Setup shell for VS2010, x64, release mode
-  - >
-    "%ProgramFiles%\Microsoft SDKs\Windows\v7.1\Bin\SetEnv.cmd" /x64 /release
+# Setup shell for VS2015, x64
+  - call "c:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat" amd64
 # Set path to python, git-bash tools.
-  - "set PATH=C:\\Python34-x64;C:\\Python34-x64\\Scripts;%PATH%"
+  - "set PATH=C:\\Python35-x64;C:\\Python35-x64\\Scripts;%PATH%"
   - "set PATH=C:\\Program Files (x86)\\Git\\bin;%PATH%"
   - pip install pytest
 

docs-source/usersguide/library.rst

@@ -404,7 +404,7 @@ version of Visual Studio.
 Install CMake
 =============
 
-CMake is the build system used for OpenMM.  You must install CMake version 2.8
+CMake is the build system used for OpenMM.  You must install CMake version 3.1
 or higher before attempting to build OpenMM from source.  You can get CMake from
 http://www.cmake.org/.  If you choose to build CMake from source on Linux, make
 sure you have the curses library installed beforehand, so that you will be able
@@ -509,7 +509,7 @@ Windows
 
 On Windows, perform the following steps:
 
-#. Click Start->All Programs->CMake 2.8->CMake
+#. Click Start->All Programs->CMake 3.1->CMake
 #. In the box labeled "Where is the source code:" browse to OpenMM src directory
    (containing top CMakeLists.txt)
 #. In the box labeled "Where to build the binaries" browse to your build_openmm

libraries/lbfgs/src/lbfgs.cpp

@@ -408,6 +408,7 @@ int lbfgs(
         pf = (lbfgsfloatval_t*)vecalloc(param.past * sizeof(lbfgsfloatval_t));
     }
 
+    try {
         /* Evaluate the function value and its gradient. */
         fx = cd.proc_evaluate(cd.instance, x, g, cd.n, 0);
         if (0. != param.orthantwise_c) {
@@ -613,6 +614,26 @@ int lbfgs(
              */
             step = 1.0;
         }
+    }
+    catch (...) {
+        vecfree(pf);
+
+        /* Free memory blocks used by this function. */
+        if (lm != NULL) {
+            for (i = 0;i < m;++i) {
+                vecfree(lm[i].s);
+                vecfree(lm[i].y);
+            }
+            vecfree(lm);
+        }
+        vecfree(pg);
+        vecfree(w);
+        vecfree(d);
+        vecfree(gp);
+        vecfree(g);
+        vecfree(xp);
+        throw;
+    }
 
 lbfgs_exit:
     /* Return the final value of the objective function. */

openmmapi/include/openmm/internal/ThreadPool.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -34,6 +34,7 @@
 
 #define NOMINMAX
 #include "windowsExport.h"
+#include <functional>
 #include <pthread.h>
 #include <vector>
 
@@ -69,6 +70,10 @@ public:
      * Execute a Task in parallel on the worker threads.
      */
     void execute(Task& task);
+    /**
+     * Execute a function in parallel on the worker threads.
+     */
+    void execute(std::function<void (ThreadPool&, int)> task);
     /**
      * This is called by the worker threads to block until all threads have reached the same point
      * and the master thread instructs them to continue by calling resumeThreads().
@@ -90,6 +95,8 @@ private:
     std::vector<ThreadData*> threadData;
     pthread_cond_t startCondition, endCondition;
     pthread_mutex_t lock;
+    Task* currentTask;
+    std::function<void (ThreadPool& pool, int)> currentFunction;
 };
 
 /**

openmmapi/src/LocalEnergyMinimizer.cpp

@@ -105,12 +105,13 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
 void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxIterations) {
     const System& system = context.getSystem();
     int numParticles = system.getNumParticles();
-    lbfgsfloatval_t *x = lbfgs_malloc(numParticles*3);
-    if (x == NULL)
-        throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory");
     double constraintTol = context.getIntegrator().getConstraintTolerance();
     double workingConstraintTol = std::max(1e-4, constraintTol);
     double k = tolerance/workingConstraintTol;
+    lbfgsfloatval_t *x = lbfgs_malloc(numParticles*3);
+    if (x == NULL)
+        throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory");
+    try {
 
         // Initialize the minimizer.
 
@@ -182,6 +183,11 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
                 }
             }
         }
+    }
+    catch (...) {
+        lbfgs_free(x);
+        throw;
+    }
     lbfgs_free(x);
     
     // If necessary, do a final constraint projection to make sure they are satisfied

openmmapi/src/ThreadPool.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -40,10 +40,17 @@ class ThreadPool::ThreadData {
 public:
     ThreadData(ThreadPool& owner, int index) : owner(owner), index(index), isDeleted(false) {
     }
+    void executeTask() {
+        if (owner.currentTask != NULL)
+            owner.currentTask->execute(owner, index);
+        else
+            owner.currentFunction(owner, index);
+    }
     ThreadPool& owner;
     int index;
     bool isDeleted;
     Task* currentTask;
+    function<void (ThreadPool& pool, int)> currentFunction;
 };
 
 static void* threadBody(void* args) {
@@ -54,13 +61,13 @@ static void* threadBody(void* args) {
         data.owner.syncThreads();
         if (data.isDeleted)
             break;
-        data.currentTask->execute(data.owner, data.index);
+        data.executeTask();
     }
     delete &data;
     return 0;
 }
 
-ThreadPool::ThreadPool(int numThreads) {
+ThreadPool::ThreadPool(int numThreads) : currentTask(NULL) {
     if (numThreads <= 0)
         numThreads = getNumProcessors();
     this->numThreads = numThreads;
@@ -99,8 +106,13 @@ int ThreadPool::getNumThreads() const {
 }
 
 void ThreadPool::execute(Task& task) {
-    for (int i = 0; i < (int) threadData.size(); i++)
-        threadData[i]->currentTask = &task;
+    currentTask = &task;
+    resumeThreads();
+}
+
+void ThreadPool::execute(function<void (ThreadPool&, int)> task) {
+    currentTask = NULL;
+    currentFunction = task;
     resumeThreads();
 }
 

platforms/cpu/include/CpuBondForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2014 Stanford University and the Authors.           *
+ * Portions copyright (c) 2014-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -46,7 +46,6 @@ namespace OpenMM {
  */
 class OPENMM_EXPORT_CPU CpuBondForce {
 public:
-    class ComputeForceTask;
     CpuBondForce();
     /**
      * Analyze the set of bonds and decide which to compute with each thread.

platforms/cpu/include/CpuCustomGBForce.h

 
-/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -39,7 +39,6 @@ namespace OpenMM {
 
 class CpuCustomGBForce {
 private:
-    class ComputeForceTask;
     class ThreadData;
 
     bool cutoff;

platforms/cpu/include/CpuCustomManyParticleForce.h

 
-/* Portions copyright (c) 2009-2014 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -48,7 +48,6 @@ private:
     class DistanceTermInfo;
     class AngleTermInfo;
     class DihedralTermInfo;
-    class ComputeForceTask;
     class ThreadData;
     int numParticles, numParticlesPerSet, numPerParticleParameters, numTypes;
     bool useCutoff, usePeriodic, triclinic, centralParticleMode;

platforms/cpu/include/CpuCustomNonbondedForce.h

 
-/* Portions copyright (c) 2009-2016 Stanford University and Simbios.
+/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -122,7 +122,6 @@ class CpuCustomNonbondedForce {
                           RealOpenMM* fixedParameters, const std::map<std::string, double>& globalParameters,
                           std::vector<AlignedArray<float> >& threadForce, bool includeForce, bool includeEnergy, double& totalEnergy, double* energyParamDerivs);
 private:
-    class ComputeForceTask;
     class ThreadData;
 
     bool cutoff;

platforms/cpu/include/CpuGBSAOBCForce.h

 
-/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2017 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -36,7 +36,6 @@ namespace OpenMM {
 
 class CpuGBSAOBCForce {
 public:
-    class ComputeTask;
     CpuGBSAOBCForce();
 
     /**

platforms/cpu/include/CpuGayBerneForce.h

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2016 Stanford University and the Authors.           *
+ * Portions copyright (c) 2016-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,7 +45,6 @@ namespace OpenMM {
 class CpuGayBerneForce {
 public:
     struct Matrix;
-    class ComputeTask;
 
     /**
      * Constructor.

platforms/cpu/include/CpuKernels.h

@@ -54,8 +54,6 @@ namespace OpenMM {
  */
 class CpuCalcForcesAndEnergyKernel : public CalcForcesAndEnergyKernel {
 public:
-    class InitForceTask;
-    class SumForceTask;
     CpuCalcForcesAndEnergyKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data, ContextImpl& context);
     /**
      * Initialize the kernel.

platforms/cpu/include/CpuLangevinDynamics.h

 
-/* Portions copyright (c) 2013-2016 Stanford University and Simbios.
+/* Portions copyright (c) 2013-2017 Stanford University and Simbios.
  * Authors: Peter Eastman
  * Contributors: 
  *
@@ -35,9 +35,6 @@ namespace OpenMM {
 
 class CpuLangevinDynamics : public ReferenceStochasticDynamics {
 public:
-    class Update1Task;
-    class Update2Task;
-    class Update3Task;
     /**
      * Constructor.
      *

platforms/cpu/include/CpuNeighborList.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,7 +45,6 @@ namespace OpenMM {
 
 class OPENMM_EXPORT_CPU CpuNeighborList {
 public:
-    class ThreadTask;
     class Voxels;
     CpuNeighborList(int blockSize);
     void computeNeighborList(int numAtoms, const AlignedArray<float>& atomLocations, const std::vector<std::set<int> >& exclusions,

platforms/cpu/include/CpuNonbondedForce.h

 
-/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2017 Stanford University and Simbios.
  * Contributors: Pande Group
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -39,7 +39,6 @@ namespace OpenMM {
 
 class CpuNonbondedForce {
     public:
-        class ComputeDirectTask;
 
       /**---------------------------------------------------------------------------------------
       

platforms/cpu/include/CpuSETTLE.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,8 +45,6 @@ namespace OpenMM {
  */
 class OPENMM_EXPORT_CPU CpuSETTLE : public ReferenceConstraintAlgorithm {
 public:
-    class ApplyToPositionsTask;
-    class ApplyToVelocitiesTask;
     CpuSETTLE(const System& system, const ReferenceSETTLEAlgorithm& settle, ThreadPool& threads);
     ~CpuSETTLE();
 

platforms/cpu/src/CpuBondForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2014-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2014-2017 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -35,25 +35,6 @@
 using namespace OpenMM;
 using namespace std;
 
-class CpuBondForce::ComputeForceTask : public ThreadPool::Task {
-public:
-    ComputeForceTask(CpuBondForce& owner, vector<RealVec>& atomCoordinates, RealOpenMM** parameters, vector<RealVec>& forces, 
-        vector<RealOpenMM>& threadEnergy, RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn) : owner(owner), atomCoordinates(atomCoordinates),
-        parameters(parameters), forces(forces), threadEnergy(threadEnergy), totalEnergy(totalEnergy), referenceBondIxn(referenceBondIxn) {
-    }
-    void execute(ThreadPool& threads, int threadIndex) {
-        RealOpenMM* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
-        owner.threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
-    }
-    CpuBondForce& owner;
-    vector<RealVec>& atomCoordinates;
-    RealOpenMM** parameters;
-    vector<RealVec>& forces;
-    vector<RealOpenMM>& threadEnergy;
-    RealOpenMM* totalEnergy;
-    ReferenceBondIxn& referenceBondIxn;
-};
-
 CpuBondForce::CpuBondForce() {
 }
 
@@ -188,8 +169,10 @@ void CpuBondForce::calculateForce(vector<RealVec>& atomCoordinates, RealOpenMM**
     // Have the worker threads compute their forces.
     
     vector<RealOpenMM> threadEnergy(threads->getNumThreads(), 0);
-    ComputeForceTask task(*this, atomCoordinates, parameters, forces, threadEnergy, totalEnergy, referenceBondIxn);
-    threads->execute(task);
+    threads->execute([&] (ThreadPool& threads, int threadIndex) {
+        RealOpenMM* energy = (totalEnergy == NULL ? NULL : &threadEnergy[threadIndex]);
+        threadComputeForce(threads, threadIndex, atomCoordinates, parameters, forces, energy, referenceBondIxn);
+    });
     threads->waitForThreads();
     
     // Compute any "extra" bonds.