Merge pull request #343 from rmcgibbo/test-cpu-settle

[WIP] TestCpuSettle segfault on travis

.travis.yml

@@ -5,13 +5,14 @@ compiler:
 before_install:
   - sudo apt-get update -qq
   - sudo apt-get install -qq libpcre3 libpcre3-dev gromacs
-  - sudo apt-get install -qq swig doxygen
+  - 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
 
 script:
-  - cmake -DCMAKE_INSTALL_PREFIX=~/OpenMM . 
-  - make 
-  - make test 
+  - cmake -DCMAKE_INSTALL_PREFIX=~/OpenMM -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS_DEBUG="-g -fsanitize=address -fno-omit-frame-pointer -O2" .
+  - make
+  - make test
   - make install
   - ls ~/OpenMM/include
   - export LD_LIBRARY_PATH=~/OpenMM/lib/

platforms/cpu/src/CpuSETTLE.cpp

@@ -41,7 +41,9 @@ public:
             inverseMasses(inverseMasses), tolerance(tolerance), threadSettle(threadSettle) {
     }
     void execute(ThreadPool& threads, int threadIndex) {
-        threadSettle[threadIndex]->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
+        if (threadIndex < threadSettle.size()) {
+            threadSettle[threadIndex]->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
+        }
     }
     vector<OpenMM::RealVec>& atomCoordinates;
     vector<OpenMM::RealVec>& atomCoordinatesP;