Merge pull request #848 from peastman/pinned

Fixed a performance regression in multi-GPU on CUDA

examples/benchmark.py

@@ -6,9 +6,9 @@ import sys
 from datetime import datetime
 from optparse import OptionParser
 
-def timeIntegration(context, steps):
+def timeIntegration(context, steps, initialSteps):
     """Integrate a Context for a specified number of steps, then return how many seconds it took."""
-    context.getIntegrator().step(5) # Make sure everything is fully initialized
+    context.getIntegrator().step(initialSteps) # Make sure everything is fully initialized
     context.getState(getEnergy=True)
     start = datetime.now()
     context.getIntegrator().step(steps)
@@ -79,11 +79,14 @@ def runOneTest(testName, options):
         system = ff.createSystem(pdb.topology, nonbondedMethod=method, nonbondedCutoff=cutoff, constraints=constraints, hydrogenMass=hydrogenMass)
     print('Step Size: %g fs' % dt.value_in_unit(unit.femtoseconds))
     properties = {}
+    initialSteps = 5
     if options.device is not None:
         if platform.getName() == 'CUDA':
             properties['CudaDeviceIndex'] = options.device
         elif platform.getName() == 'OpenCL':
             properties['OpenCLDeviceIndex'] = options.device
+        if ',' in options.device or ' ' in options.device:
+            initialSteps = 250
     if options.precision is not None:
         if platform.getName() == 'CUDA':
             properties['CudaPrecision'] = options.precision
@@ -102,7 +105,7 @@ def runOneTest(testName, options):
     context.setVelocitiesToTemperature(300*unit.kelvin)
     steps = 20
     while True:
-        time = timeIntegration(context, steps)
+        time = timeIntegration(context, steps, initialSteps)
         if time >= 0.5*options.seconds:
             break
         if time < 0.5:

platforms/cuda/include/CudaParallelKernels.h

@@ -83,7 +83,7 @@ private:
     std::vector<Kernel> kernels;
     std::vector<long long> completionTimes;
     std::vector<double> contextNonbondedFractions;
-    std::vector<int> tileCounts;
+    int* tileCounts;
     CudaArray* contextForces;
     void* pinnedPositionBuffer;
     long long* pinnedForceBuffer;

platforms/cuda/src/CudaParallelKernels.cpp

@@ -141,7 +141,7 @@ private:
 
 CudaParallelCalcForcesAndEnergyKernel::CudaParallelCalcForcesAndEnergyKernel(string name, const Platform& platform, CudaPlatform::PlatformData& data) :
         CalcForcesAndEnergyKernel(name, platform), data(data), completionTimes(data.contexts.size()), contextNonbondedFractions(data.contexts.size()),
-        tileCounts(data.contexts.size()), contextForces(NULL), pinnedPositionBuffer(NULL), pinnedForceBuffer(NULL) {
+        tileCounts(NULL), contextForces(NULL), pinnedPositionBuffer(NULL), pinnedForceBuffer(NULL) {
     for (int i = 0; i < (int) data.contexts.size(); i++)
         kernels.push_back(Kernel(new CudaCalcForcesAndEnergyKernel(name, platform, *data.contexts[i])));
 }
@@ -156,6 +156,8 @@ CudaParallelCalcForcesAndEnergyKernel::~CudaParallelCalcForcesAndEnergyKernel()
         cuMemFreeHost(pinnedForceBuffer);
     cuEventDestroy(event);
     cuStreamDestroy(peerCopyStream);
+    if (tileCounts != NULL)
+        cuMemFreeHost(tileCounts);
 }
 
 void CudaParallelCalcForcesAndEnergyKernel::initialize(const System& system) {
@@ -163,12 +165,14 @@ void CudaParallelCalcForcesAndEnergyKernel::initialize(const System& system) {
     cu.setAsCurrent();
     CUmodule module = cu.createModule(CudaKernelSources::parallel);
     sumKernel = cu.getKernel(module, "sumForces");
-    for (int i = 0; i < (int) kernels.size(); i++)
+    int numContexts = data.contexts.size();
+    for (int i = 0; i < numContexts; i++)
         getKernel(i).initialize(system);
-    for (int i = 0; i < (int) contextNonbondedFractions.size(); i++)
-        contextNonbondedFractions[i] = 1/(double) contextNonbondedFractions.size();
+    for (int i = 0; i < numContexts; i++)
+        contextNonbondedFractions[i] = 1/(double) numContexts;
     CHECK_RESULT(cuEventCreate(&event, 0), "Error creating event");
     CHECK_RESULT(cuStreamCreate(&peerCopyStream, CU_STREAM_NON_BLOCKING), "Error creating stream");
+    CHECK_RESULT(cuMemHostAlloc((void**) &tileCounts, numContexts*sizeof(int), 0), "Error creating tile count buffer");
 }
 
 void CudaParallelCalcForcesAndEnergyKernel::beginComputation(ContextImpl& context, bool includeForce, bool includeEnergy, int groups) {