Merge remote-tracking branch 'origin/master' into qc

d7569df2 · Peter Eastman · 4089b688 · 0c00acd2 · d7569df2 · d7569df2
Commit d7569df2 authored Jul 10, 2014 by Peter Eastman
20 changed files
--- a/.travis.yml
+++ b/.travis.yml
-language: cpp
-compiler:
-  - clang
+language: c

-before_install:
-  - sudo apt-get update -qq
-  - sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
-  - sudo apt-get install -qq swig doxygen llvm-3.3
-  - sudo apt-get install -qq python-numpy python-scipy python-nose
-  - export ASAN_SYMBOLIZER_PATH=/usr/bin/llvm-symbolizer-3.3
+install:
+  - source tools/ci/install.sh
+  - export PYTHONUNBUFFERED=true

 script:
-  - cmake -DCMAKE_INSTALL_PREFIX=$HOME/OpenMM .
-  - make
-  - make install
-  - sudo make PythonInstall
-  - # run all of the tests
-  - ctest -V
-  - # get a list of all of the failed tests into this stupid ctest format
-  - python -c 'fn = "Testing/Temporary/LastTestsFailed.log"; import os; os.path.exists(fn) or exit(0); l = [line.split(":")[0] for line in open(fn)]; triplets = zip(l, l, [","]*len(l)); print "".join(",".join(t) for t in triplets)' > FailedTests.log
-  - # rerun all of the failed tests
-  - if [ -s FailedTests.log ]; then ctest -V -I FailedTests.log; fi;
-  - # run the python tests too
-  - cd python/tests
-  - nosetests -vv
+  - export CC="clang++"
+  - source deactivate
+  - conda install --yes conda-build
+  - # Build the conda package, testing build before packaging.
+  - conda build tools/conda-recipe
+  - # Install the conda package locally.
+  - source activate $python
+  - conda install $HOME/miniconda/conda-bld/linux-64/openmm-dev-*
+  - conda list -e
+  - # Run the Python tests.
+  - pushd .
+  - cd wrappers/python/tests
+  - nosetests -vv --processes=-1 --process-timeout=200
+  - popd
+
+env:
+  global:
+    # encrypted BINSTAR_TOKEN for push of dev package to binstar
+    - secure: Qz3pEYXXFnNQ/WK+15ad4cdbLJvzgCIZRwKD9fLiS3CDO2ldAQWxzaz8RQOwqbFtZUWu7lQpr+GukNJz5p0w18QEto+BxLYG9aW5mjoc+F2vCjyWFjkwnJ/Z/3uBKTcr5x9Y7HKaPGivaJ4BNACifjt7cCpeVJzV6u2+bBgSoHc=
+
+  matrix:
+    - python=2.7  CONDA_PY=27
+    #- python=3.3  CONDA_PY=33
+
+after_success:
+  - echo "after_success"
+  - source tools/ci/after_success.sh
+
+
--- a/libraries/lepton/src/ParsedExpression.cpp
+++ b/libraries/lepton/src/ParsedExpression.cpp
@@ -269,7 +269,15 @@ ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const Expressio
                return ExpressionTreeNode(new Operation::Constant(dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()*getConstantValue(children[0])));
            if (children[0].getOperation().getId() == Operation::NEGATE) // Combine a multiply and a negate into a single multiply
                return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast<const Operation::MultiplyConstant*>(&node.getOperation())->getValue()), children[0].getChildren()[0]);
+            break;
        }
+        default:
+        {
+            // If operation ID is not one of the above,
+            // we don't substitute a simpler expression.
+            break;
+        }
+
    }
    return ExpressionTreeNode(node.getOperation().clone(), children);
 }

--- a/platforms/cuda/src/kernels/customGBEnergyN2.cu
+++ b/platforms/cuda/src/kernels/customGBEnergyN2.cu
@@ -190,7 +190,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
        
        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -203,7 +203,7 @@ extern "C" __global__ void computeN2Energy(unsigned long long* __restrict__ forc
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/cuda/src/kernels/customGBValueN2.cu
+++ b/platforms/cuda/src/kernels/customGBValueN2.cu
@@ -166,7 +166,7 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
        
        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -179,7 +179,7 @@ extern "C" __global__ void computeN2Value(const real4* __restrict__ posq, const
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/cuda/src/kernels/gbsaObc1.cu
+++ b/platforms/cuda/src/kernels/gbsaObc1.cu
@@ -226,7 +226,7 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa

        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -239,7 +239,7 @@ extern "C" __global__ void computeBornSum(unsigned long long* __restrict__ globa
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);
@@ -590,7 +590,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo

        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -603,7 +603,7 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/cuda/src/kernels/nonbonded.cu
+++ b/platforms/cuda/src/kernels/nonbonded.cu
@@ -333,7 +333,7 @@ extern "C" __global__ void computeNonbonded(
        bool includeTile = true;

        // Extract the coordinates of this tile.
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -346,7 +346,7 @@ extern "C" __global__ void computeNonbonded(
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/cuda/tests/TestCudaCustomIntegrator.cpp
+++ b/platforms/cuda/tests/TestCudaCustomIntegrator.cpp
@@ -292,6 +292,7 @@ void testWithThermostat() {
    system.addForce(forceField);
    AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
    system.addForce(thermostat);
+    integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
    Context context(system, integrator, platform);
    vector<Vec3> positions(numParticles);
    for (int i = 0; i < numParticles; ++i)
@@ -424,6 +425,7 @@ void testParameter() {
    integrator.addGlobalVariable("temp", 0);
    integrator.addComputeGlobal("temp", "AndersenTemperature");
    integrator.addComputeGlobal("AndersenTemperature", "temp*2");
+    integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
    Context context(system, integrator, platform);
    
    // See if the parameter is being used correctly.

--- a/platforms/cuda/tests/TestCudaMonteCarloAnisotropicBarostat.cpp
+++ b/platforms/cuda/tests/TestCudaMonteCarloAnisotropicBarostat.cpp
@@ -389,7 +389,7 @@ int main(int argc, char* argv[]) {
        testIdealGasAxis(1);
        testIdealGasAxis(2);
        testRandomSeed();
-        testEinsteinCrystal();
+        //testEinsteinCrystal();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;

--- a/platforms/opencl/src/kernels/customGBEnergyN2.cl
+++ b/platforms/opencl/src/kernels/customGBEnergyN2.cl
@@ -200,7 +200,7 @@ __kernel void computeN2Energy(

        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -213,7 +213,7 @@ __kernel void computeN2Energy(
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
+++ b/platforms/opencl/src/kernels/customGBEnergyN2_cpu.cl
@@ -216,7 +216,7 @@ __kernel void computeN2Energy(
        
        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -229,7 +229,7 @@ __kernel void computeN2Energy(
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/opencl/src/kernels/customGBValueN2.cl
+++ b/platforms/opencl/src/kernels/customGBValueN2.cl
@@ -174,7 +174,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*

        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -187,7 +187,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/opencl/src/kernels/customGBValueN2_cpu.cl
+++ b/platforms/opencl/src/kernels/customGBValueN2_cpu.cl
@@ -184,7 +184,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
        
        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -197,7 +197,7 @@ __kernel void computeN2Value(__global const real4* restrict posq, __local real4*
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/opencl/src/kernels/gbsaObc.cl
+++ b/platforms/opencl/src/kernels/gbsaObc.cl
@@ -186,7 +186,7 @@ __kernel void computeBornSum(

        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -199,7 +199,7 @@ __kernel void computeBornSum(
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);
@@ -574,7 +574,7 @@ __kernel void computeGBSAForce1(

        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -587,7 +587,7 @@ __kernel void computeGBSAForce1(
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/opencl/src/kernels/gbsaObc_cpu.cl
+++ b/platforms/opencl/src/kernels/gbsaObc_cpu.cl
@@ -192,7 +192,7 @@ __kernel void computeBornSum(

        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -205,7 +205,7 @@ __kernel void computeBornSum(
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);
@@ -607,7 +607,7 @@ __kernel void computeGBSAForce1(

        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -620,7 +620,7 @@ __kernel void computeGBSAForce1(
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/opencl/src/kernels/nonbonded.cl
+++ b/platforms/opencl/src/kernels/nonbonded.cl
@@ -213,7 +213,7 @@ __kernel void computeNonbonded(

        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -226,7 +226,7 @@ __kernel void computeNonbonded(
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/opencl/src/kernels/nonbonded_cpu.cl
+++ b/platforms/opencl/src/kernels/nonbonded_cpu.cl
@@ -230,7 +230,7 @@ __kernel void computeNonbonded(
        
        // Extract the coordinates of this tile.
        
-        unsigned int x, y;
+        int x, y;
        bool singlePeriodicCopy = false;
 #ifdef USE_CUTOFF
        if (numTiles <= maxTiles) {
@@ -243,7 +243,7 @@ __kernel void computeNonbonded(
        else
 #endif
        {
-            y = (unsigned int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
+            y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
            x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
            if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
                y += (x < y ? -1 : 1);

--- a/platforms/opencl/tests/TestOpenCLCustomIntegrator.cpp
+++ b/platforms/opencl/tests/TestOpenCLCustomIntegrator.cpp
@@ -292,6 +292,7 @@ void testWithThermostat() {
    system.addForce(forceField);
    AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);
    system.addForce(thermostat);
+    integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
    Context context(system, integrator, platform);
    vector<Vec3> positions(numParticles);
    for (int i = 0; i < numParticles; ++i)
@@ -424,6 +425,7 @@ void testParameter() {
    integrator.addGlobalVariable("temp", 0);
    integrator.addComputeGlobal("temp", "AndersenTemperature");
    integrator.addComputeGlobal("AndersenTemperature", "temp*2");
+    integrator.setRandomNumberSeed(thermostat->getRandomNumberSeed());
    Context context(system, integrator, platform);
    
    // See if the parameter is being used correctly.

--- a/platforms/opencl/tests/TestOpenCLMonteCarloAnisotropicBarostat.cpp
+++ b/platforms/opencl/tests/TestOpenCLMonteCarloAnisotropicBarostat.cpp
@@ -389,7 +389,7 @@ int main(int argc, char* argv[]) {
        testIdealGasAxis(1);
        testIdealGasAxis(2);
        testRandomSeed();
-        testEinsteinCrystal();
+        //testEinsteinCrystal();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;

--- a/platforms/reference/tests/TestReferenceMonteCarloAnisotropicBarostat.cpp
+++ b/platforms/reference/tests/TestReferenceMonteCarloAnisotropicBarostat.cpp
@@ -389,7 +389,7 @@ int main() {
        testIdealGasAxis(1);
        testIdealGasAxis(2);
        testRandomSeed();
-        testEinsteinCrystal();
+        //testEinsteinCrystal();
    }
    catch(const exception& e) {
        cout << "exception: " << e.what() << endl;

--- a/plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
+++ b/plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
@@ -126,7 +126,7 @@ public:
     *
     * @return the cutoff distance, measured in nm
     */
-    double getCutoffDistance(void) const;
+    double getCutoffDistance() const;

    /**
     * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use