Merged changes between repositories by hand

openmmapi/src/ContextImpl.cpp

@@ -39,6 +39,7 @@
 #include "openmm/State.h"
 #include "openmm/VirtualSite.h"
 #include "openmm/Context.h"
+#include <algorithm>
 #include <iostream>
 #include <map>
 #include <utility>
@@ -106,14 +107,40 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
     hasInitializedForces = true;
     vector<string> integratorKernels = integrator.getKernelNames();
     kernelNames.insert(kernelNames.begin(), integratorKernels.begin(), integratorKernels.end());
-    if (platform == 0)
-        this->platform = platform = &Platform::findPlatform(kernelNames);
-    else if (!platform->supportsKernels(kernelNames))
-        throw OpenMMException("Specified a Platform for a Context which does not support all required kernels");
+    
+    // Select a platform to use.
+    
+    vector<pair<double, Platform*> > candidatePlatforms;
+    if (platform == NULL) {
+        for (int i = 0; i < Platform::getNumPlatforms(); i++) {
+            Platform& p = Platform::getPlatform(i);
+            if (p.supportsKernels(kernelNames))
+                candidatePlatforms.push_back(make_pair(p.getSpeed(), &p));
+        }
+        if (candidatePlatforms.size() == 0)
+            throw OpenMMException("No Platform supports all the requested kernels");
+        sort(candidatePlatforms.begin(), candidatePlatforms.end());
+    }
+    else {
+        if (!platform->supportsKernels(kernelNames))
+            throw OpenMMException("Specified a Platform for a Context which does not support all required kernels");
+        candidatePlatforms.push_back(make_pair(platform->getSpeed(), platform));
+    }
+    for (int i = candidatePlatforms.size()-1; i >= 0; i--) {
+        try {
+            this->platform = platform = candidatePlatforms[i].second;
+            platform->contextCreated(*this, properties);
+            break;
+        }
+        catch (...) {
+            if (i > 0)
+                continue;
+            throw;
+        }
+    }
     
     // Create and initialize kernels and other objects.
     
-    platform->contextCreated(*this, properties);
     initializeForcesKernel = platform->createKernel(CalcForcesAndEnergyKernel::Name(), *this);
     initializeForcesKernel.getAs<CalcForcesAndEnergyKernel>().initialize(system);
     updateStateDataKernel = platform->createKernel(UpdateStateDataKernel::Name(), *this);

platforms/cuda/src/CudaContext.cpp

@@ -156,9 +156,6 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
     CHECK_RESULT(cuDeviceGetAttribute(&multiprocessors, CU_DEVICE_ATTRIBUTE_MULTIPROCESSOR_COUNT, device));
     int numThreadBlocksPerComputeUnit = 6;
     numThreadBlocks = numThreadBlocksPerComputeUnit*multiprocessors;
-    bonded = new CudaBondedUtilities(*this);
-    nonbonded = new CudaNonbondedUtilities(*this);
-    int numEnergyBuffers = max(numThreadBlocks*ThreadBlockSize, nonbonded->getNumEnergyBuffers());
     if (useDoublePrecision) {
         posq = CudaArray::create<double4>(*this, paddedNumAtoms, "posq");
         velm = CudaArray::create<double4>(*this, paddedNumAtoms, "velm");
@@ -169,9 +166,6 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
         compilationDefines["make_mixed2"] = "make_double2";
         compilationDefines["make_mixed3"] = "make_double3";
         compilationDefines["make_mixed4"] = "make_double4";
-        energyBuffer = CudaArray::create<double>(*this, numEnergyBuffers, "energyBuffer");
-        int pinnedBufferSize = max(paddedNumAtoms*4, numEnergyBuffers);
-        CHECK_RESULT(cuMemHostAlloc(&pinnedBuffer, pinnedBufferSize*sizeof(double), 0));
     }
     else if (useMixedPrecision) {
         posq = CudaArray::create<float4>(*this, paddedNumAtoms, "posq");
@@ -184,9 +178,6 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
         compilationDefines["make_mixed2"] = "make_double2";
         compilationDefines["make_mixed3"] = "make_double3";
         compilationDefines["make_mixed4"] = "make_double4";
-        energyBuffer = CudaArray::create<float>(*this, numEnergyBuffers, "energyBuffer");
-        int pinnedBufferSize = max(paddedNumAtoms*4, numEnergyBuffers);
-        CHECK_RESULT(cuMemHostAlloc(&pinnedBuffer, pinnedBufferSize*sizeof(double), 0));
     }
     else {
         posq = CudaArray::create<float4>(*this, paddedNumAtoms, "posq");
@@ -197,9 +188,6 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
         compilationDefines["make_mixed2"] = "make_float2";
         compilationDefines["make_mixed3"] = "make_float3";
         compilationDefines["make_mixed4"] = "make_float4";
-        energyBuffer = CudaArray::create<float>(*this, numEnergyBuffers, "energyBuffer");
-        int pinnedBufferSize = max(paddedNumAtoms*6, numEnergyBuffers);
-        CHECK_RESULT(cuMemHostAlloc(&pinnedBuffer, pinnedBufferSize*sizeof(float), 0));
     }
     posCellOffsets.resize(paddedNumAtoms, make_int4(0, 0, 0, 0));
 
@@ -236,6 +224,8 @@ CudaContext::CudaContext(const System& system, int deviceIndex, bool useBlocking
     
     // Create utilities objects.
     
+    bonded = new CudaBondedUtilities(*this);
+    nonbonded = new CudaNonbondedUtilities(*this);
     integration = new CudaIntegrationUtilities(*this, system);
     expression = new CudaExpressionUtilities(*this);
 }
@@ -283,6 +273,22 @@ CudaContext::~CudaContext() {
 void CudaContext::initialize() {
     cuCtxSetCurrent(context);
     string errorMessage = "Error initializing Context";
+    int numEnergyBuffers = max(numThreadBlocks*ThreadBlockSize, nonbonded->getNumEnergyBuffers());
+    if (useDoublePrecision) {
+        energyBuffer = CudaArray::create<double>(*this, numEnergyBuffers, "energyBuffer");
+        int pinnedBufferSize = max(paddedNumAtoms*4, numEnergyBuffers);
+        CHECK_RESULT(cuMemHostAlloc(&pinnedBuffer, pinnedBufferSize*sizeof(double), 0));
+    }
+    else if (useMixedPrecision) {
+        energyBuffer = CudaArray::create<float>(*this, numEnergyBuffers, "energyBuffer");
+        int pinnedBufferSize = max(paddedNumAtoms*4, numEnergyBuffers);
+        CHECK_RESULT(cuMemHostAlloc(&pinnedBuffer, pinnedBufferSize*sizeof(double), 0));
+    }
+    else {
+        energyBuffer = CudaArray::create<float>(*this, numEnergyBuffers, "energyBuffer");
+        int pinnedBufferSize = max(paddedNumAtoms*6, numEnergyBuffers);
+        CHECK_RESULT(cuMemHostAlloc(&pinnedBuffer, pinnedBufferSize*sizeof(float), 0));
+    }
     for (int i = 0; i < numAtoms; i++) {
         double mass = system.getParticleMass(i);
         if (useDoublePrecision || useMixedPrecision)

platforms/cuda/src/CudaKernels.cpp

@@ -1460,8 +1460,9 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
     int numParticles = force.getNumParticles();
     sigmaEpsilon = CudaArray::create<float2>(cu, cu.getPaddedNumAtoms(), "sigmaEpsilon");
     CudaArray& posq = cu.getPosq();
-    float4* posqf = (float4*) cu.getPinnedBuffer();
-    double4* posqd = (double4*) cu.getPinnedBuffer();
+    vector<double4> temp(posq.getSize());
+    float4* posqf = (float4*) &temp[0];
+    double4* posqd = (double4*) &temp[0];
     vector<float2> sigmaEpsilonVector(cu.getPaddedNumAtoms(), make_float2(0, 0));
     vector<vector<int> > exclusionList(numParticles);
     double sumSquaredCharges = 0.0;
@@ -1486,7 +1487,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         exclusionList[exclusions[i].first].push_back(exclusions[i].second);
         exclusionList[exclusions[i].second].push_back(exclusions[i].first);
     }
-    posq.upload(cu.getPinnedBuffer());
+    posq.upload(&temp[0]);
     sigmaEpsilon->upload(sigmaEpsilonVector);
     bool useCutoff = (force.getNonbondedMethod() != NonbondedForce::NoCutoff);
     bool usePeriodic = (force.getNonbondedMethod() != NonbondedForce::NoCutoff && force.getNonbondedMethod() != NonbondedForce::CutoffNonPeriodic);
@@ -2410,8 +2411,9 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF
     cu.addAutoclearBuffer(*bornSum);
     cu.addAutoclearBuffer(*bornForce);
     CudaArray& posq = cu.getPosq();
-    float4* posqf = (float4*) cu.getPinnedBuffer();
-    double4* posqd = (double4*) cu.getPinnedBuffer();
+    vector<double4> temp(posq.getSize());
+    float4* posqf = (float4*) &temp[0];
+    double4* posqd = (double4*) &temp[0];
     vector<float2> paramsVector(cu.getPaddedNumAtoms(), make_float2(1, 1));
     const double dielectricOffset = 0.009;
     for (int i = 0; i < force.getNumParticles(); i++) {
@@ -2424,7 +2426,7 @@ void CudaCalcGBSAOBCForceKernel::initialize(const System& system, const GBSAOBCF
         else
             posqf[i] = make_float4(0, 0, 0, (float) charge);
     }
-    posq.upload(cu.getPinnedBuffer());
+    posq.upload(&temp[0]);
     params->upload(paramsVector);
     prefactor = -ONE_4PI_EPS0*((1.0/force.getSoluteDielectric())-(1.0/force.getSolventDielectric()));
     bool useCutoff = (force.getNonbondedMethod() != GBSAOBCForce::NoCutoff);

platforms/cuda/src/CudaPlatform.cpp

@@ -179,15 +179,24 @@ CudaPlatform::PlatformData::PlatformData(ContextImpl* context, const System& sys
         searchPos = nextPos+1;
     }
     devices.push_back(deviceIndexProperty.substr(searchPos));
-    for (int i = 0; i < (int) devices.size(); i++) {
-        if (devices[i].length() > 0) {
-            unsigned int deviceIndex;
-            stringstream(devices[i]) >> deviceIndex;
-            contexts.push_back(new CudaContext(system, deviceIndex, blocking, precisionProperty, compilerProperty, tempProperty, hostCompilerProperty, *this));
+    try {
+        for (int i = 0; i < (int) devices.size(); i++) {
+            if (devices[i].length() > 0) {
+                unsigned int deviceIndex;
+                stringstream(devices[i]) >> deviceIndex;
+                contexts.push_back(new CudaContext(system, deviceIndex, blocking, precisionProperty, compilerProperty, tempProperty, hostCompilerProperty, *this));
+            }
         }
+        if (contexts.size() == 0)
+            contexts.push_back(new CudaContext(system, -1, blocking, precisionProperty, compilerProperty, tempProperty, hostCompilerProperty, *this));
+    }
+    catch (...) {
+        // If an exception was thrown, do our best to clean up memory.
+        
+        for (int i = 0; i < (int) contexts.size(); i++)
+            delete contexts[i];
+        throw;
     }
-    if (contexts.size() == 0)
-        contexts.push_back(new CudaContext(system, -1, blocking, precisionProperty, compilerProperty, tempProperty, hostCompilerProperty, *this));
     stringstream deviceIndex, deviceName;
     for (int i = 0; i < (int) contexts.size(); i++) {
         if (i > 0) {

platforms/opencl/src/OpenCLContext.cpp

@@ -253,8 +253,6 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
         paddedNumAtoms = TileSize*((numAtoms+TileSize-1)/TileSize);
         numAtomBlocks = (paddedNumAtoms+(TileSize-1))/TileSize;
         numThreadBlocks = numThreadBlocksPerComputeUnit*device.getInfo<CL_DEVICE_MAX_COMPUTE_UNITS>();
-        bonded = new OpenCLBondedUtilities(*this);
-        nonbonded = new OpenCLNonbondedUtilities(*this);
         if (useDoublePrecision) {
             posq = OpenCLArray::create<mm_double4>(*this, paddedNumAtoms, "posq");
             velm = OpenCLArray::create<mm_double4>(*this, paddedNumAtoms, "velm");
@@ -343,6 +341,8 @@ OpenCLContext::OpenCLContext(const System& system, int platformIndex, int device
     
     // Create utilities objects.
     
+    bonded = new OpenCLBondedUtilities(*this);
+    nonbonded = new OpenCLNonbondedUtilities(*this);
     integration = new OpenCLIntegrationUtilities(*this, system);
     expression = new OpenCLExpressionUtilities(*this);
 }

platforms/opencl/src/OpenCLPlatform.cpp

@@ -143,15 +143,24 @@ OpenCLPlatform::PlatformData::PlatformData(const System& system, const string& p
         searchPos = nextPos+1;
     }
     devices.push_back(deviceIndexProperty.substr(searchPos));
-    for (int i = 0; i < (int) devices.size(); i++) {
-        if (devices[i].length() > 0) {
-            unsigned int deviceIndex;
-            stringstream(devices[i]) >> deviceIndex;
-            contexts.push_back(new OpenCLContext(system, platformIndex, deviceIndex, precisionProperty, *this));
+    try {
+        for (int i = 0; i < (int) devices.size(); i++) {
+            if (devices[i].length() > 0) {
+                unsigned int deviceIndex;
+                stringstream(devices[i]) >> deviceIndex;
+                contexts.push_back(new OpenCLContext(system, platformIndex, deviceIndex, precisionProperty, *this));
+            }
         }
+        if (contexts.size() == 0)
+            contexts.push_back(new OpenCLContext(system, platformIndex, -1, precisionProperty, *this));
+    }
+    catch (...) {
+        // If an exception was thrown, do our best to clean up memory.
+        
+        for (int i = 0; i < (int) contexts.size(); i++)
+            delete contexts[i];
+        throw;
     }
-    if (contexts.size() == 0)
-        contexts.push_back(new OpenCLContext(system, platformIndex, -1, precisionProperty, *this));
     stringstream deviceIndex, deviceName;
     for (int i = 0; i < (int) contexts.size(); i++) {
         if (i > 0) {