Merge pull request #1984 from peastman/cpu

LocalEnergyMinimizer switches to CPU if forces are getting clipped

openmmapi/src/LocalEnergyMinimizer.cpp

@@ -31,10 +31,12 @@
 
 #include "openmm/LocalEnergyMinimizer.h"
 #include "openmm/OpenMMException.h"
-#include "lbfgs.h"
 #include "openmm/Platform.h"
+#include "openmm/VerletIntegrator.h"
+#include "lbfgs.h"
 #include <cmath>
 #include <sstream>
+#include <string>
 #include <vector>
 #include <algorithm>
 
@@ -44,26 +46,43 @@ using namespace std;
 struct MinimizerData {
     Context& context;
     double k;
-    MinimizerData(Context& context, double k)
-        : context(context), k(k) {}
-};
-
-static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsfloatval_t *g, const int n, const lbfgsfloatval_t step) {
-    MinimizerData* data = reinterpret_cast<MinimizerData*>(instance);
-    Context& context = data->context;
-    const System& system = context.getSystem();
-    int numParticles = system.getNumParticles();
+    bool checkLargeForces;
+    VerletIntegrator cpuIntegrator;
+    Context* cpuContext;
+    MinimizerData(Context& context, double k) : context(context), k(k), cpuIntegrator(1.0), cpuContext(NULL) {
+        string platformName = context.getPlatform().getName();
+        checkLargeForces = (platformName == "CUDA" || platformName == "OpenCL");
+    }
+    ~MinimizerData() {
+        if (cpuContext != NULL)
+            delete cpuContext;
+    }
+    Context& getCpuContext() {
+        // Get an alternate context that runs on the CPU and doesn't place any limits
+        // on the magnitude of forces.
 
-    // Compute the force and energy for this configuration.
+        if (cpuContext == NULL) {
+            Platform* cpuPlatform;
+            try {
+                cpuPlatform = &Platform::getPlatformByName("CPU");
+            }
+            catch (...) {
+                cpuPlatform = &Platform::getPlatformByName("Reference");
+            }
+            cpuContext = new Context(context.getSystem(), cpuIntegrator, *cpuPlatform);
+            cpuContext->setState(context.getState(State::Positions | State::Velocities | State::Parameters));
+        }
+        return *cpuContext;
+    }
+};
 
-    vector<Vec3> positions(numParticles);
-    for (int i = 0; i < numParticles; i++)
-        positions[i] = Vec3(x[3*i], x[3*i+1], x[3*i+2]);
+static double computeForcesAndEnergy(Context& context, const vector<Vec3>& positions, lbfgsfloatval_t *g) {
     context.setPositions(positions);
     context.computeVirtualSites();
     State state = context.getState(State::Forces | State::Energy);
     const vector<Vec3>& forces = state.getForces();
-    for (int i = 0; i < numParticles; i++) {
+    const System& system = context.getSystem();
+    for (int i = 0; i < forces.size(); i++) {
         if (system.getParticleMass(i) == 0) {
             g[3*i] = 0.0;
             g[3*i+1] = 0.0;
@@ -75,7 +94,33 @@ static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsf
             g[3*i+2] = -forces[i][2];
         }
     }
-    double energy = state.getPotentialEnergy();
+    return state.getPotentialEnergy();
+}
+
+static lbfgsfloatval_t evaluate(void *instance, const lbfgsfloatval_t *x, lbfgsfloatval_t *g, const int n, const lbfgsfloatval_t step) {
+    MinimizerData* data = reinterpret_cast<MinimizerData*>(instance);
+    Context& context = data->context;
+    const System& system = context.getSystem();
+    int numParticles = system.getNumParticles();
+
+    // Compute the force and energy for this configuration.
+
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; i++)
+        positions[i] = Vec3(x[3*i], x[3*i+1], x[3*i+2]);
+    double energy = computeForcesAndEnergy(context, positions, g);
+    if (data->checkLargeForces) {
+        // The CUDA and OpenCL platforms accumulate forces in fixed point, so they
+        // can't handle very large forces.  Check for problematic forces (very large,
+        // infinite, or NaN) and if necessary recompute them on the CPU.
+
+        for (int i = 0; i < 3*numParticles; i++) {
+            if (!(fabs(g[i]) < 2e9)) {
+                energy = computeForcesAndEnergy(data->getCpuContext(), positions, g);
+                break;
+            }
+        }
+    }
 
     // Add harmonic forces for any constraints.
 
@@ -143,11 +188,11 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
         // Repeatedly minimize, steadily increasing the strength of the springs until all constraints are satisfied.
 
         double prevMaxError = 1e10;
+        MinimizerData data(context, k);
         while (true) {
             // Perform the minimization.
 
             lbfgsfloatval_t fx;
-            MinimizerData data(context, k);
             lbfgs(numParticles*3, x, &fx, evaluate, NULL, &data, &param);
 
             // Check whether all constraints are satisfied.
@@ -171,7 +216,7 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
             if (maxError >= prevMaxError)
                 break; // Further tightening the springs doesn't seem to be helping, so just give up.
             prevMaxError = maxError;
-            k *= 10;
+            data.k *= 10;
             if (maxError > 100*workingConstraintTol) {
                 // We've gotten far enough from a valid state that we might have trouble getting
                 // back, so reset to the original positions.

tests/TestLocalEnergyMinimizer.h

@@ -7,7 +7,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2018 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -38,6 +38,7 @@
 #include "openmm/VerletIntegrator.h"
 #include "openmm/VirtualSite.h"
 #include "sfmt/SFMT.h"
+#include <algorithm>
 #include <iostream>
 #include <vector>
 
@@ -196,6 +197,40 @@ void testVirtualSites() {
     ASSERT(forceNorm < 2*tolerance);
 }
 
+void testLargeForces() {
+    // Create a set of particles that are almost on top of each other so the initial
+    // forces are huge.
+    
+    const int numParticles = 10;
+    System system;
+    NonbondedForce* nonbonded = new NonbondedForce();
+    system.addForce(nonbonded);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        nonbonded->addParticle(1.0, 0.2, 1.0);
+    }
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; i++)
+        positions[i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*1e-10;
+
+    // Minimize it and verify that it didn't blow up.                                                                               
+
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    LocalEnergyMinimizer::minimize(context, 1.0);
+    State state = context.getState(State::Positions);
+    double maxdist = 0.0;
+    for (int i = 0; i < numParticles; i++) {
+        Vec3 r = state.getPositions()[i];
+        maxdist = max(maxdist, sqrt(r.dot(r)));
+    }
+    ASSERT(maxdist > 0.1);
+    ASSERT(maxdist < 10.0);
+}
+
 void runPlatformTests();
 
 int main(int argc, char* argv[]) {
@@ -204,6 +239,7 @@ int main(int argc, char* argv[]) {
         testHarmonicBonds();
         testLargeSystem();
         testVirtualSites();
+        testLargeForces();
         runPlatformTests();
     }
     catch(const exception& e) {