Maybe faster appveyor

.travis.yml

@@ -41,11 +41,11 @@ script:
   - # Run the testInstallation script
   - python -m simtk.testInstallation
   - # run all of the tests, making sure failures at this stage don't cause travis failures
-  - ctest -j2 -V || true
+  - ctest -j2 || true
   - # 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;
+  - if [ -s Testing/Temporary/LastTestsFailed.log ]; then ctest -I FailedTests.log; fi;
   - # run the python tests too
   - cd python/tests
   - pip install nose

CMakeLists.txt

@@ -122,7 +122,10 @@ ELSE (APPLE AND (NOT PNACL))
     IF (MSVC OR ANDROID OR PNACL)
         SET(EXTRA_COMPILE_FLAGS)
         IF (MSVC)
+            # Use warning level 2, not whatever warning level CMake picked.
             STRING(REGEX REPLACE "/W[0-4]" "/W2" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+            # Explicitly suppress warnings 4305 and 4244.
+            SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /wd4305 /wd4244")
         ENDIF (MSVC)
     ELSE (MSVC OR ANDROID OR PNACL)
         SET(EXTRA_COMPILE_FLAGS "-msse2")

appveyor.yml

@@ -28,16 +28,19 @@ install:
   - cd build
   - cmake -G "NMake Makefiles" %CMAKE_FLAGS% -LA ..
 
-build_script:
+# Run the build
   - cmake --build . --target install
   - cmake --build . --target PythonInstall
 
+build: false
 test_script:
-  - ctest && exit 0
-  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); 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
+  - ctest || exit 0
+  - python -c "import os; fn = os.path.join('Testing', 'Temporary', 'LastTestsFailed.log'); os.path.exists(fn) or exit(0); failed = [line.split(':')[0] for line in open(fn)]; print(','.join(x+','+x for x in failed))" > FailedTests.log
   - ps: >
-     If (Test-Path "FailedTests.log") {
-         ctest -V -I FailedTests.log
+     If (Test-Path "Testing\\Temporary\\LastTestsFailed.log") {
+         cat Testing\\Temporary\\LastTestsFailed.log
+         cat FailedTests.log
+         ctest -I FailedTests.log
      }
   - cd python\tests
   - nosetests -vv --processes=-1 --process-timeout=200

platforms/cuda/include/CudaNonbondedUtilities.h

@@ -142,8 +142,10 @@ public:
     void computeInteractions(int forceGroups);
     /**
      * Check to see if the neighbor list arrays are large enough, and make them bigger if necessary.
+     *
+     * @return true if the neighbor list needed to be enlarged.
      */
-    void updateNeighborListSize();
+    bool updateNeighborListSize();
     /**
      * Get the array containing the center of each atom block.
      */

platforms/cuda/src/CudaNonbondedUtilities.cpp

@@ -375,11 +375,16 @@ void CudaNonbondedUtilities::prepareInteractions(int forceGroups) {
 
     if (lastCutoff != kernels.cutoffDistance)
         forceRebuildNeighborList = true;
+    bool rebuild = false;
+    do {
         context.executeKernel(kernels.findBlockBoundsKernel, &findBlockBoundsArgs[0], context.getNumAtoms());
         blockSorter->sort(*sortedBlocks);
         context.executeKernel(kernels.sortBoxDataKernel, &sortBoxDataArgs[0], context.getNumAtoms());
         context.executeKernel(kernels.findInteractingBlocksKernel, &findInteractingBlocksArgs[0], context.getNumAtoms(), 256);
         forceRebuildNeighborList = false;
+        if (context.getComputeForceCount() == 1)
+            rebuild = updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
+    } while(rebuild);
     lastCutoff = kernels.cutoffDistance;
 }
 
@@ -389,18 +394,16 @@ void CudaNonbondedUtilities::computeInteractions(int forceGroups) {
     KernelSet& kernels = groupKernels[forceGroups];
     if (kernels.hasForces) {
         context.executeKernel(kernels.forceKernel, &forceArgs[0], numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
-        if (context.getComputeForceCount() == 1)
-            updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
     }
 }
 
-void CudaNonbondedUtilities::updateNeighborListSize() {
+bool CudaNonbondedUtilities::updateNeighborListSize() {
     if (!useCutoff)
-        return;
+        return false;
     unsigned int* pinnedInteractionCount = (unsigned int*) context.getPinnedBuffer();
     interactionCount->download(pinnedInteractionCount);
     if (pinnedInteractionCount[0] <= (unsigned int) maxTiles)
-        return;
+        return false;
 
     // The most recent timestep had too many interactions to fit in the arrays.  Make the arrays bigger to prevent
     // this from happening in the future.
@@ -422,6 +425,7 @@ void CudaNonbondedUtilities::updateNeighborListSize() {
         forceArgs[17] = &interactingAtoms->getDevicePointer();
     findInteractingBlocksArgs[7] = &interactingAtoms->getDevicePointer();
     forceRebuildNeighborList = true;
+    return true;
 }
 
 void CudaNonbondedUtilities::setUsePadding(bool padding) {

platforms/opencl/include/OpenCLNonbondedUtilities.h

@@ -154,8 +154,10 @@ public:
     void computeInteractions(int forceGroups);
     /**
      * Check to see if the neighbor list arrays are large enough, and make them bigger if necessary.
+     *
+     * @return true if the neighbor list needed to be enlarged.
      */
-    void updateNeighborListSize();
+    bool updateNeighborListSize();
     /**
      * Get the array containing the center of each atom block.
      */

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -341,6 +341,8 @@ void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) {
 
     if (lastCutoff != kernels.cutoffDistance)
         forceRebuildNeighborList = true;
+    bool rebuild = false;
+    do {
         setPeriodicBoxArgs(context, kernels.findBlockBoundsKernel, 1);
         context.executeKernel(kernels.findBlockBoundsKernel, context.getNumAtoms());
         blockSorter->sort(*sortedBlocks);
@@ -349,6 +351,9 @@ void OpenCLNonbondedUtilities::prepareInteractions(int forceGroups) {
         setPeriodicBoxArgs(context, kernels.findInteractingBlocksKernel, 0);
         context.executeKernel(kernels.findInteractingBlocksKernel, context.getNumAtoms(), interactingBlocksThreadBlockSize);
         forceRebuildNeighborList = false;
+        if (context.getComputeForceCount() == 1)
+            rebuild = updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
+    } while (rebuild);
     lastCutoff = kernels.cutoffDistance;
 }
 
@@ -360,18 +365,16 @@ void OpenCLNonbondedUtilities::computeInteractions(int forceGroups) {
         if (useCutoff)
             setPeriodicBoxArgs(context, kernels.forceKernel, 9);
         context.executeKernel(kernels.forceKernel, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
-        if (context.getComputeForceCount() == 1)
-            updateNeighborListSize(); // This is the first time step, so check whether our initial guess was large enough.
     }
 }
 
-void OpenCLNonbondedUtilities::updateNeighborListSize() {
+bool OpenCLNonbondedUtilities::updateNeighborListSize() {
     if (!useCutoff)
-        return;
+        return false;
     unsigned int* pinnedInteractionCount = (unsigned int*) context.getPinnedBuffer();
     interactionCount->download(pinnedInteractionCount);
     if (pinnedInteractionCount[0] <= (unsigned int) interactingTiles->getSize())
-        return;
+        return false;
 
     // The most recent timestep had too many interactions to fit in the arrays.  Make the arrays bigger to prevent
     // this from happening in the future.
@@ -395,6 +398,7 @@ void OpenCLNonbondedUtilities::updateNeighborListSize() {
         iter->second.findInteractingBlocksKernel.setArg<cl_uint>(9, maxTiles);
     }
     forceRebuildNeighborList = true;
+    return true;
 }
 
 void OpenCLNonbondedUtilities::setUsePadding(bool padding) {

wrappers/python/tests/TestAmberInpcrdFile.py

@@ -4,11 +4,18 @@ from simtk.openmm.app import *
 from simtk.openmm import *
 from simtk.unit import *
 import simtk.openmm.app.element as elem
+try:
+    from scipy.io import netcdf
+    SCIPY_IMPORT_FAILED = False
+except:
+    SCIPY_IMPORT_FAILED = True
+
 
 def compareByElement(array1, array2, cmp):
     for x, y in zip(array1, array2):
         cmp(x, y)
 
+
 class TestAmberInpcrdFile(unittest.TestCase):
     """Test the Amber inpcrd file parser"""
 
@@ -24,14 +31,11 @@ class TestAmberInpcrdFile(unittest.TestCase):
         compareByElement(inpcrd.boxVectors[0].value_in_unit(angstroms),
                          [30.2642725, 0.0, 0.0], cmp)
 
+    @unittest.skipIf(SCIPY_IMPORT_FAILED, "Scipy is not installed")
     def test_NetCDF(self):
         """ Test NetCDF restart file parsing """
         cmp = self.assertAlmostEqual
-        try:
-            from scipy.io import netcdf
-        except ImportError:
-            print('Not testing NetCDF file parser... scipy cannot be found')
-        else:
+
         inpcrd = AmberInpcrdFile('systems/amber.ncrst')
         self.assertEqual(len(inpcrd.positions), 2101)
         compareByElement(inpcrd.positions[0].value_in_unit(angstroms),

wrappers/python/tests/TestCheckpointReporter.py

 import os
 import unittest
 import tempfile
-import numpy as np
 from simtk.openmm import app
 import simtk.openmm as mm
 from simtk import unit
@@ -24,17 +23,19 @@ class TestCheckpointReporter(unittest.TestCase):
         self.simulation.step(1)
 
         # get the current positions
-        positions = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)._value
+        positions = self.simulation.context.getState(getPositions=True).getPositions()
+
         # now set the positions into junk...
-        self.simulation.context.setPositions(np.random.random(positions.shape))
+        self.simulation.context.setPositions([mm.Vec3(0, 0, 0)] * len(positions))
+
         # then reload the right positions from the checkpoint
         file.close()
         with open(file.name, 'rb') as f:
             self.simulation.context.loadCheckpoint(f.read())
         os.unlink(file.name)
 
-        newPositions = self.simulation.context.getState(getPositions=True).getPositions(asNumpy=True)._value
-        np.testing.assert_array_equal(positions, newPositions)
+        newPositions = self.simulation.context.getState(getPositions=True).getPositions()
+        self.assertSequenceEqual(positions, newPositions)
 
 if __name__ == '__main__':
     unittest.main()

wrappers/python/tests/TestNumpyCompatibility.py

 import unittest
-import numpy as np
-
 from simtk.openmm import app
 import simtk.openmm as mm
 from simtk import unit
+try:
+    import numpy as np
+    NUMPY_IMPORT_FAILED = False
+except ImportError:
+    NUMPY_IMPORT_FAILED = True
+
 
+@unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
 class TestNumpyCompatibility(unittest.TestCase):
 
     def setUp(self):
@@ -80,6 +85,8 @@ class TestNumpyCompatibility(unittest.TestCase):
         self.assertEqual(size, 10)
         np.testing.assert_array_almost_equal(energy, np.asarray(energy_out))
 
+
+@unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
 class TestNumpyUnits(unittest.TestCase):
 
     def setUp(self):