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Commit 9963e51a authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #1741 from peastman/lamda 

Use lambdas for thread pool tasks
parents 2c559596 50054664
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Showing with 63 additions and 104 deletions
.travis.yml
View file @ 9963e51a
......@@ -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
View file @ 9963e51a
......@@ -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)
......@@ -117,6 +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
......
appveyor.yml
View file @ 9963e51a
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
View file @ 9963e51a
......@@ -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
......
openmmapi/include/openmm/internal/ThreadPool.h
View file @ 9963e51a
......@@ -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/ThreadPool.cpp
View file @ 9963e51a
......@@ -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
View file @ 9963e51a
......@@ -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
View file @ 9963e51a
/* 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
View file @ 9963e51a
/* 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
View file @ 9963e51a
/* 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
View file @ 9963e51a
/* 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
View file @ 9963e51a
......@@ -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
View file @ 9963e51a
......@@ -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
View file @ 9963e51a
/* 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
View file @ 9963e51a
......@@ -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
View file @ 9963e51a
/* 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
View file @ 9963e51a
......@@ -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
View file @ 9963e51a
......@@ -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.
......
platforms/cpu/src/CpuCustomGBForce.cpp
View file @ 9963e51a
/* 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
......@@ -33,16 +33,6 @@
using namespace OpenMM;
using namespace std;
class CpuCustomGBForce::ComputeForceTask : public ThreadPool::Task {
public:
ComputeForceTask(CpuCustomGBForce& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeForce(threads, threadIndex);
}
CpuCustomGBForce& owner;
};
CpuCustomGBForce::ThreadData::ThreadData(int numAtoms, int numThreads, int threadIndex,
const vector<Lepton::CompiledExpression>& valueExpressions,
const vector<vector<Lepton::CompiledExpression> >& valueDerivExpressions,
......@@ -206,7 +196,7 @@ void CpuCustomGBForce::calculateIxn(int numberOfAtoms, float* posq, RealOpenMM**
// Calculate the first computed value.
ComputeForceTask task(*this);
auto task = [&] (ThreadPool& threads, int threadIndex) { threadComputeForce(threads, threadIndex); };
gmx_atomic_set(&counter, 0);
threads.execute(task);
threads.waitForThreads();
......
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @ 9963e51a
/* 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
......@@ -37,16 +37,6 @@
using namespace OpenMM;
using namespace std;
class CpuCustomManyParticleForce::ComputeForceTask : public ThreadPool::Task {
public:
ComputeForceTask(CpuCustomManyParticleForce& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeForce(threads, threadIndex);
}
CpuCustomManyParticleForce& owner;
};
CpuCustomManyParticleForce::CpuCustomManyParticleForce(const CustomManyParticleForce& force, ThreadPool& threads) :
threads(threads), useCutoff(false), usePeriodic(false), neighborList(NULL) {
numParticles = force.getNumParticles();
......@@ -141,8 +131,7 @@ void CpuCustomManyParticleForce::calculateIxn(AlignedArray<float>& posq, RealOpe
// Signal the threads to start running and wait for them to finish.
ComputeForceTask task(*this);
threads.execute(task);
threads.execute([&] (ThreadPool& threads, int threadIndex) { threadComputeForce(threads, threadIndex); });
threads.waitForThreads();
// Combine the energies from all the threads.
......
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