Fixed errors in which destructors were executed in the wrong order

olla/src/Kernel.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -41,6 +41,7 @@ Kernel::Kernel(KernelImpl* impl) : impl(impl) {
 }
 
 Kernel::Kernel(const Kernel& copy) : impl(copy.impl) {
+    if (impl)
         impl->referenceCount++;
 }
 
@@ -53,7 +54,13 @@ Kernel::~Kernel() {
 }
 
 Kernel& Kernel::operator=(const Kernel& copy) {
+    if (impl) {
+        impl->referenceCount--;
+        if (impl->referenceCount == 0)
+            delete impl;
+    }
     impl = copy.impl;
+    if (impl)
         impl->referenceCount++;
     return *this;
 }

openmmapi/src/ContextImpl.cpp

@@ -118,6 +118,14 @@ ContextImpl::ContextImpl(Context& owner, System& system, Integrator& integrator,
 ContextImpl::~ContextImpl() {
     for (int i = 0; i < (int) forceImpls.size(); ++i)
         delete forceImpls[i];
+    
+    // Make sure all kernels get properly deleted before contextDestroyed() is called.
+    
+    initializeForcesKernel = Kernel();
+    kineticEnergyKernel = Kernel();
+    updateStateDataKernel = Kernel();
+    applyConstraintsKernel = Kernel();
+    virtualSitesKernel = Kernel();
     platform->contextDestroyed(*this);
 }
 

platforms/cuda2/src/CudaContext.cpp

@@ -229,7 +229,6 @@ CudaContext::~CudaContext() {
     string errorMessage = "Error deleting Context";
     if (contextIsValid)
         CHECK_RESULT(cuCtxDestroy(context));
-    contextIsValid = false;
 }
 
 void CudaContext::initialize() {