Merge branch 'master' into nucleic

platforms/cpu/tests/TestCpuGBSAOBCForce.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) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,244 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CPU implementation of GBSAOBCForce.
- */
+#include "CpuTests.h"
+#include "TestGBSAOBCForce.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CpuPlatform.h"
-#include "openmm/GBSAOBCForce.h"
-#include "openmm/System.h"
-#include "openmm/LangevinIntegrator.h"
-#include "openmm/NonbondedForce.h"
-#include "SimTKOpenMMRealType.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-void testSingleParticle() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(2.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForce* forceField = new GBSAOBCForce();
-    forceField->addParticle(0.5, 0.15, 1);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, 0, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-    double bornRadius = 0.15-0.009; // dielectric offset
-    double eps0 = EPSILON0;
-    double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
-    double extendedRadius = 0.15+0.14; // probe radius
-    double nonpolarEnergy = 4*PI_M*2.25936*extendedRadius*extendedRadius*std::pow(0.15/bornRadius, 6.0);
-    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
-    
-    // Change the parameters and see if it is still correct.
-    
-    forceField->setParticleParameters(0, 0.4, 0.25, 1);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Energy);
-    bornRadius = 0.25-0.009; // dielectric offset
-    bornEnergy = (-0.4*0.4/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
-    extendedRadius = 0.25+0.14;
-    nonpolarEnergy = 4*PI_M*2.25936*extendedRadius*extendedRadius*std::pow(0.25/bornRadius, 6.0);
-    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
-}
-
-void testGlobalSettings() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(2.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForce* forceField = new GBSAOBCForce();
-    forceField->addParticle(0.5, 0.15, 1);
-    const double soluteDielectric = 2.1;
-    const double solventDielectric = 35.0;
-    const double surfaceAreaEnergy = 0.75;
-    forceField->setSoluteDielectric(soluteDielectric);
-    forceField->setSolventDielectric(solventDielectric);
-    forceField->setSurfaceAreaEnergy(surfaceAreaEnergy);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, 0, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-    double bornRadius = 0.15-0.009; // dielectric offset
-    double eps0 = EPSILON0;
-    double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/soluteDielectric-1.0/solventDielectric)/bornRadius;
-    double extendedRadius = 0.15+0.14; // probe radius
-    double nonpolarEnergy = 4*PI_M*surfaceAreaEnergy*extendedRadius*extendedRadius*std::pow(0.15/bornRadius, 6.0);
-    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
-}
-
-void testCutoffAndPeriodic() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForce* gbsa = new GBSAOBCForce();
-    NonbondedForce* nonbonded = new NonbondedForce();
-    gbsa->addParticle(-1, 0.15, 1);
-    nonbonded->addParticle(-1, 1, 0);
-    gbsa->addParticle(1, 0.15, 1);
-    nonbonded->addParticle(1, 1, 0);
-    const double cutoffDistance = 3.0;
-    const double boxSize = 10.0;
-    nonbonded->setCutoffDistance(cutoffDistance);
-    gbsa->setCutoffDistance(cutoffDistance);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    system.addForce(gbsa);
-    system.addForce(nonbonded);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-
-    // Calculate the forces for both cutoff and periodic with two different atom positions.
-
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
-    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffNonPeriodic);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    State state1 = context.getState(State::Forces);
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
-    context.reinitialize();
-    context.setPositions(positions);
-    State state2 = context.getState(State::Forces);
-    positions[1][0]+= boxSize;
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
-    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffNonPeriodic);
-    context.reinitialize();
-    context.setPositions(positions);
-    State state3 = context.getState(State::Forces);
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
-    context.reinitialize();
-    context.setPositions(positions);
-    State state4 = context.getState(State::Forces);
-
-    // All forces should be identical, exception state3 which should be zero.
-
-    ASSERT_EQUAL_VEC(state1.getForces()[0], state2.getForces()[0], 0.01);
-    ASSERT_EQUAL_VEC(state1.getForces()[1], state2.getForces()[1], 0.01);
-    ASSERT_EQUAL_VEC(state1.getForces()[0], state4.getForces()[0], 0.01);
-    ASSERT_EQUAL_VEC(state1.getForces()[1], state4.getForces()[1], 0.01);
-    ASSERT_EQUAL_VEC(state3.getForces()[0], Vec3(0, 0, 0), 0.01);
-    ASSERT_EQUAL_VEC(state3.getForces()[1], Vec3(0, 0, 0), 0.01);
-}
-
-void testForce(int numParticles, NonbondedForce::NonbondedMethod method, GBSAOBCForce::NonbondedMethod method2) {
-    CpuPlatform platform;
-    ReferencePlatform reference;
-    System system;
-    GBSAOBCForce* gbsa = new GBSAOBCForce();
-    NonbondedForce* nonbonded = new NonbondedForce();
-    for (int i = 0; i < numParticles; ++i) {
-        system.addParticle(1.0);
-        double charge = i%2 == 0 ? -1 : 1;
-        gbsa->addParticle(charge, 0.15, 1);
-        nonbonded->addParticle(charge, 1, 0);
-    }
-    nonbonded->setNonbondedMethod(method);
-    gbsa->setNonbondedMethod(method2);
-    nonbonded->setCutoffDistance(3.0);
-    gbsa->setCutoffDistance(3.0);
-    int grid = (int) floor(0.5+pow(numParticles, 1.0/3.0));
-    if (method == NonbondedForce::CutoffPeriodic) {
-        double boxSize = (grid+1)*1.1;
-        system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    }
-    system.addForce(gbsa);
-    system.addForce(nonbonded);
-    LangevinIntegrator integrator1(0, 0.1, 0.01);
-    LangevinIntegrator integrator2(0, 0.1, 0.01);
-    Context context(system, integrator1, platform);
-    Context refContext(system, integrator2, reference);
-
-    // Set random (but uniformly distributed) positions for all the particles.
-
-    vector<Vec3> positions(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    for (int i = 0; i < grid; i++)
-        for (int j = 0; j < grid; j++)
-            for (int k = 0; k < grid; k++)
-                positions[i*grid*grid+j*grid+k] = Vec3(i*1.1, j*1.1, k*1.1);
-    for (int i = 0; i < numParticles; ++i)
-        positions[i] = positions[i] + Vec3(0.5*genrand_real2(sfmt), 0.5*genrand_real2(sfmt), 0.5*genrand_real2(sfmt));
-    context.setPositions(positions);
-    refContext.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    State refState = refContext.getState(State::Forces | State::Energy);
-
-    // Make sure the CPU and Reference platforms agree.
-
-    double norm = 0.0;
-    double diff = 0.0;
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 f = state.getForces()[i];
-        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
-        Vec3 delta = f-refState.getForces()[i];
-        diff += delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2];
-    }
-    norm = std::sqrt(norm);
-    diff = std::sqrt(diff);
-    ASSERT_EQUAL_TOL(0.0, diff, 0.001*norm);
-    ASSERT_EQUAL_TOL(state.getPotentialEnergy(), refState.getPotentialEnergy(), 1e-3);
-
-    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-    // (This doesn't work with cutoffs, since the energy changes discontinuously at the cutoff distance.)
-
-    if (method == NonbondedForce::NoCutoff)
-    {
-        const double delta = 0.3;
-        double step = 0.5*delta/norm;
-        vector<Vec3> positions2(numParticles), positions3(numParticles);
-        for (int i = 0; i < numParticles; ++i) {
-            Vec3 p = positions[i];
-            Vec3 f = state.getForces()[i];
-            positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-            positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
-        }
-        context.setPositions(positions2);
-        State state2 = context.getState(State::Energy);
-        context.setPositions(positions3);
-        State state3 = context.getState(State::Energy);
-        ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/delta, 1e-2)
-    }
-}
-
-int main() {
-    try {
-        if (!CpuPlatform::isProcessorSupported()) {
-            cout << "CPU is not supported.  Exiting." << endl;
-            return 0;
-        }
-        testSingleParticle();
-        testGlobalSettings();
-        testCutoffAndPeriodic();
-        for (int i = 5; i < 11; i++) {
-            testForce(i*i*i, NonbondedForce::NoCutoff, GBSAOBCForce::NoCutoff);
-            testForce(i*i*i, NonbondedForce::CutoffNonPeriodic, GBSAOBCForce::CutoffNonPeriodic);
-            testForce(i*i*i, NonbondedForce::CutoffPeriodic, GBSAOBCForce::CutoffPeriodic);
-        }
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }

platforms/cuda/CMakeLists.txt

@@ -13,9 +13,9 @@
 #----------------------------------------------------
 
 set(OPENMM_BUILD_CUDA_TESTS TRUE CACHE BOOL "Whether to build CUDA test cases")
-if(OPENMM_BUILD_CUDA_TESTS)
+if(BUILD_TESTING AND OPENMM_BUILD_CUDA_TESTS)
     SUBDIRS (tests)
-endif(OPENMM_BUILD_CUDA_TESTS)
+endif(BUILD_TESTING AND OPENMM_BUILD_CUDA_TESTS)
 
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.

platforms/cuda/include/CudaContext.h

@@ -30,6 +30,7 @@
 #include <map>
 #include <queue>
 #include <string>
+#include <utility>
 #define __CL_ENABLE_EXCEPTIONS
 #ifdef _MSC_VER
     // Prevent Windows from defining macros that interfere with other code.
@@ -538,6 +539,11 @@ public:
      */
     void invalidateMolecules();
 private:
+    /**
+     * Compute a sorted list of device indices in decreasing order of desirability
+     */
+    std::vector<int> getDevicePrecedence();
+
     struct Molecule;
     struct MoleculeGroup;
     class VirtualSiteInfo;

platforms/cuda/sharedTarget/CMakeLists.txt

@@ -18,7 +18,7 @@ SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE
 IF (APPLE)
     SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS} -F/Library/Frameworks -framework CUDA")
 ELSE (APPLE)
-    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 ENDIF (APPLE)
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})