Created a property for setting the number of CPU cores to use

docs/usersguide/library.rst

@@ -1878,6 +1878,24 @@ values.  For example,
 
 This tells it to use both devices 0 and 1, splitting the work between them.
 
+CPU Platform
+************
+
+The CPU Platform recognizes the following Platform-specific properties:
+
+* CpuThreads: This specifies the number of CPU threads to use.  If you do not
+  specify this, OpenMM will select a default number of threads as follows:
+
+  * If an environment variable called OPENMM_CPU_THREADS is set, its value is
+    used as the number of threads.
+  * Otherwise, the number of threads is set to the number of logical CPU cores
+    in the computer it is running on.
+
+  Usually the default value works well.  This is mainly useful when you are
+  running something else on the computer at the same time, and you want to
+  prevent OpenMM from monopolizing all available cores.
+
+
 .. _using-openmm-with-software-written-in-languages-other-than-c++:
 
 Using OpenMM with Software Written in Languages Other than C++

openmmapi/include/openmm/internal/ThreadPool.h

@@ -53,7 +53,13 @@ class OPENMM_EXPORT ThreadPool {
 public:
     class Task;
     class ThreadData;
-    ThreadPool();
+    /**
+     * Create a ThreadPool.
+     *
+     * @param numThreads  the number of worker threads to create.  If this is 0 (the default), the
+     *                    number of threads is set equal to the number of logical CPU cores available
+     */
+    ThreadPool(int numThreads=0);
     ~ThreadPool();
     /**
      * Get the number of worker threads in the pool.

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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -60,8 +60,10 @@ static void* threadBody(void* args) {
     return 0;
 }
 
-ThreadPool::ThreadPool() {
+ThreadPool::ThreadPool(int numThreads) {
+    if (numThreads <= 0)
         numThreads = getNumProcessors();
+    this->numThreads = numThreads;
     pthread_cond_init(&startCondition, NULL);
     pthread_cond_init(&endCondition, NULL);
     pthread_mutex_init(&lock, NULL);

platforms/cpu/include/CpuPlatform.h

@@ -55,27 +55,37 @@ public:
         return name;
     }
     double getSpeed() const;
+    const std::string& getPropertyValue(const Context& context, const std::string& property) const;
     bool supportsDoublePrecision() const;
     static bool isProcessorSupported();
     void contextCreated(ContextImpl& context, const std::map<std::string, std::string>& properties) const;
     void contextDestroyed(ContextImpl& context) const;
+    /**
+     * This is the name of the parameter for selecting the number of threads to use.
+     */
+    static const std::string& CpuThreads() {
+        static const std::string key = "CpuThreads";
+        return key;
+    }
     /**
      * We cannot use the standard mechanism for platform data, because that is already used by the superclass.
      * Instead, we maintain a table of ContextImpls to PlatformDatas.
      */
     static PlatformData& getPlatformData(ContextImpl& context);
+    static const PlatformData& getPlatformData(const ContextImpl& context);
 private:
-    static std::map<ContextImpl*, PlatformData*> contextData;
+    static std::map<const ContextImpl*, PlatformData*> contextData;
 };
 
 class CpuPlatform::PlatformData {
 public:
-    PlatformData(int numParticles);
+    PlatformData(int numParticles, int numThreads);
     AlignedArray<float> posq;
     std::vector<AlignedArray<float> > threadForce;
     ThreadPool threads;
     bool isPeriodic;
     CpuRandom random;
+    std::map<std::string, std::string> propertyValues;
 };
 
 } // namespace OpenMM

platforms/cpu/src/CpuPlatform.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2014 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -35,6 +35,7 @@
 #include "CpuSETTLE.h"
 #include "ReferenceConstraints.h"
 #include "openmm/internal/hardware.h"
+#include <sstream>
 
 using namespace OpenMM;
 using namespace std;
@@ -53,7 +54,7 @@ extern "C" OPENMM_EXPORT_CPU void registerPlatforms() {
 }
 #endif
 
-map<ContextImpl*, CpuPlatform::PlatformData*> CpuPlatform::contextData;
+map<const ContextImpl*, CpuPlatform::PlatformData*> CpuPlatform::contextData;
 
 CpuPlatform::CpuPlatform() {
     CpuKernelFactory* factory = new CpuKernelFactory();
@@ -63,6 +64,23 @@ CpuPlatform::CpuPlatform() {
     registerKernelFactory(CalcNonbondedForceKernel::Name(), factory);
     registerKernelFactory(CalcGBSAOBCForceKernel::Name(), factory);
     registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
+    platformProperties.push_back(CpuThreads());
+    int threads = getNumProcessors();
+    char* threadsEnv = getenv("OPENMM_CPU_THREADS");
+    if (threadsEnv != NULL)
+        stringstream(threadsEnv) >> threads;
+    stringstream defaultThreads;
+    defaultThreads << threads;
+    setPropertyDefaultValue(CpuThreads(), defaultThreads.str());
+}
+
+const string& CpuPlatform::getPropertyValue(const Context& context, const string& property) const {
+    const ContextImpl& impl = getContextImpl(context);
+    const PlatformData& data = getPlatformData(impl);
+    map<string, string>::const_iterator value = data.propertyValues.find(property);
+    if (value != data.propertyValues.end())
+        return value->second;
+    return ReferencePlatform::getPropertyValue(context, property);
 }
 
 double CpuPlatform::getSpeed() const {
@@ -87,7 +105,11 @@ bool CpuPlatform::isProcessorSupported() {
 
 void CpuPlatform::contextCreated(ContextImpl& context, const map<string, string>& properties) const {
     ReferencePlatform::contextCreated(context, properties);
-    PlatformData* data = new PlatformData(context.getSystem().getNumParticles());
+    const string& threadsPropValue = (properties.find(CpuThreads()) == properties.end() ?
+            getPropertyDefaultValue(CpuThreads()) : properties.find(CpuThreads())->second);
+    int numThreads;
+    stringstream(threadsPropValue) >> numThreads;
+    PlatformData* data = new PlatformData(context.getSystem().getNumParticles(), numThreads);
     contextData[&context] = data;
     ReferenceConstraints& constraints = *(ReferenceConstraints*) reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData())->constraints;
     if (constraints.settle != NULL) {
@@ -107,10 +129,17 @@ CpuPlatform::PlatformData& CpuPlatform::getPlatformData(ContextImpl& context) {
     return *contextData[&context];
 }
 
-CpuPlatform::PlatformData::PlatformData(int numParticles) : posq(4*numParticles) {
-    int numThreads = threads.getNumThreads();
+const CpuPlatform::PlatformData& CpuPlatform::getPlatformData(const ContextImpl& context) {
+    return *contextData[&context];
+}
+
+CpuPlatform::PlatformData::PlatformData(int numParticles, int numThreads) : posq(4*numParticles), threads(numThreads) {
+    numThreads = threads.getNumThreads();
     threadForce.resize(numThreads);
     for (int i = 0; i < numThreads; i++)
         threadForce[i].resize(4*numParticles);
     isPeriodic = false;
+    stringstream threadsProperty;
+    threadsProperty << numThreads;
+    propertyValues[CpuThreads()] = threadsProperty.str();
 }