Adds memory cleanup functions for some Omega classes (#45)

* Adds memory cleanup functions for some Omega classes

For Omega classes that store all instances, this adds some
erase/clear functions to clean up memory before the yakl finalize
call. Updates developer guide to note the requirement for this cleanup.

components/omega/doc/devGuide/Decomp.md

@@ -104,3 +104,15 @@ yakl::c::parallel_for( yakl::c::Bounds<2>(NCellsOwned,MaxEdges),
   }
 });
 ```
+
+Any defined decomposition can be removed by name using
+```c++
+Decomp::erase(Name);
+```
+and all decompositions *must* be removed before the yakl finalize call using
+```c++
+Decomp::clear();
+```
+which destroys all host and device arrays before YAKL finalizes and removes
+the memory pool in which all the arrays are allocated. Failure to call clear
+before `yakl::finalize()` will result in an error.

components/omega/doc/devGuide/MachEnv.md

@@ -59,7 +59,9 @@ Because the new environments are subsets of the default environment, one
 additional function `OMEGA::MachEnv::isMember()` is provided so that
 non-member tasks can be excluded from calculations. The retrieval functions
 call from non-member tasks will return invalid values. Finally, there is
-a `removeEnv` function that can delete any defined environment.
+a `removeEnv(Name)` function that can delete any individual defined
+environment by name and a `removeAll()` function that cleans up by
+removing all defined environments.
 
 As a class that is basically a container for the environment parameters,
 the implementation is a simple class with several scalar data members and

components/omega/src/base/Decomp.cpp

@@ -630,30 +630,30 @@ Decomp::Decomp(
 
    // Create device copies of all arrays
 
-   // NCellsHalo = NCellsHaloH.createDeviceCopy();
-   // CellID     = CellIDH.createDeviceCopy();
-   // CellLoc    = CellLocH.createDeviceCopy();
+   NCellsHalo = NCellsHaloH.createDeviceCopy();
+   CellID     = CellIDH.createDeviceCopy();
+   CellLoc    = CellLocH.createDeviceCopy();
 
-   // NEdgesHalo = NEdgesHaloH.createDeviceCopy();
-   // EdgeID     = EdgeIDH.createDeviceCopy();
-   // EdgeLoc    = EdgeLocH.createDeviceCopy();
+   NEdgesHalo = NEdgesHaloH.createDeviceCopy();
+   EdgeID     = EdgeIDH.createDeviceCopy();
+   EdgeLoc    = EdgeLocH.createDeviceCopy();
 
-   // NVerticesHalo = NVerticesHaloH.createDeviceCopy();
-   // VertexID      = VertexIDH.createDeviceCopy();
-   // VertexLoc     = VertexLocH.createDeviceCopy();
+   NVerticesHalo = NVerticesHaloH.createDeviceCopy();
+   VertexID      = VertexIDH.createDeviceCopy();
+   VertexLoc     = VertexLocH.createDeviceCopy();
 
-   // CellsOnCell    = CellsOnCellH.createDeviceCopy();
-   // EdgesOnCell    = EdgesOnCellH.createDeviceCopy();
-   // VerticesOnCell = VerticesOnCellH.createDeviceCopy();
-   // NEdgesOnCell    = NEdgesOnCellH.createDeviceCopy();
+   CellsOnCell    = CellsOnCellH.createDeviceCopy();
+   EdgesOnCell    = EdgesOnCellH.createDeviceCopy();
+   VerticesOnCell = VerticesOnCellH.createDeviceCopy();
+   NEdgesOnCell   = NEdgesOnCellH.createDeviceCopy();
 
-   // CellsOnEdge     = CellsOnEdgeH.createDeviceCopy();
-   // EdgesOnEdge     = EdgesOnEdgeH.createDeviceCopy();
-   // VerticesOnEdge  = VerticesOnEdgeH.createDeviceCopy();
-   // NEdgesOnEdge    = NEdgesOnEdgeH.createDeviceCopy();
+   CellsOnEdge    = CellsOnEdgeH.createDeviceCopy();
+   EdgesOnEdge    = EdgesOnEdgeH.createDeviceCopy();
+   VerticesOnEdge = VerticesOnEdgeH.createDeviceCopy();
+   NEdgesOnEdge   = NEdgesOnEdgeH.createDeviceCopy();
 
-   // CellsOnVertex = CellsOnVertexH.createDeviceCopy();
-   // EdgesOnVertex = EdgesOnVertexH.createDeviceCopy();
+   CellsOnVertex = CellsOnVertexH.createDeviceCopy();
+   EdgesOnVertex = EdgesOnVertexH.createDeviceCopy();
 
    // Assign this as the default decomposition
    AllDecomps.emplace(Name, *this);
@@ -666,9 +666,30 @@ Decomp::Decomp(
 
 Decomp::~Decomp() {
 
-   // TODO: add deletes for all arrays and remove from AllDecomps map
+   // No operations needed, YAKL arrays removed when no longer in scope
 
-} // end removeEnv
+} // end decomp destructor
+
+//------------------------------------------------------------------------------
+// Removes a decomposition from list and destroys it
+
+void Decomp::erase(std::string InName // [in] name of decomp to remove
+) {
+
+   AllDecomps.erase(InName); // removes the decomp from the list (map) and in
+                             // the process, calls the destructor
+
+} // end decomp erase
+
+//------------------------------------------------------------------------------
+// Removes all decompositions to clean up before exit
+
+void Decomp::clear() {
+
+   AllDecomps.clear(); // removes all decomps from the list (map) and in
+                       // the process, calls the destructors for each
+
+} // end decomp clear
 
 // Retrieval functions
 //------------------------------------------------------------------------------

components/omega/src/base/Decomp.h

@@ -232,6 +232,13 @@ class Decomp {
    /// Destructor - deallocates all memory and deletes a Decomp.
    ~Decomp();
 
+   /// Erase - removes a defined decomposition
+   static void erase(std::string InName ///< [in] name of decomp to remove
+   );
+
+   /// Clear - removes all defined decompositions to clean up
+   static void clear();
+
    // Retrieval functions
 
    /// Retrieves a pointer the default decomposition. The preference is

components/omega/src/base/MachEnv.cpp

@@ -402,6 +402,15 @@ void MachEnv::removeEnv(const std::string Name // [in] name of env to remove
 
 } // end removeEnv
 
+//------------------------------------------------------------------------------
+// Remove all environments
+
+void MachEnv::removeAll() {
+
+   AllEnvs.clear(); // removes all environments by removing them from map
+
+} // end removeAll
+
 // Retrieval functions
 //------------------------------------------------------------------------------
 // Get default environment

components/omega/src/base/MachEnv.h

@@ -118,6 +118,9 @@ class MachEnv {
    removeEnv(const std::string Name ///< [in] name of environment to remove
    );
 
+   /// Removes all MachEnvs to clean up
+   static void removeAll();
+
    // Retrieval functions
 
    /// Retrieve the default environment

components/omega/test/CMakeLists.txt

@@ -234,6 +234,7 @@ set_tests_properties(
   MACHINE_ENV_TEST
   BROADCAST_TEST
   LOGGING_TEST
+  DECOMP_TEST
   IO_TEST
   YAKL_TEST
   PROPERTIES FAIL_REGULAR_EXPRESSION "FAIL"

components/omega/test/base/DecompTest.cpp

@@ -130,9 +130,10 @@ int main(int argc, char *argv[]) {
                RefSumVertices);
    }
 
-   // Test that device arrays are identical
+   // Clean up
+   OMEGA::Decomp::clear();
+   OMEGA::MachEnv::removeAll();
 
-   // MPI_Status status;
    if (Err == 0)
       LOG_INFO("DecompTest: Successful completion");
    yakl::finalize();

components/omega/test/base/MachEnvTest.cpp

@@ -449,11 +449,9 @@ int main(int argc, char *argv[]) {
    }
 #endif
 
-   // finalize environments
+   // finalize and clean up environments (test both removal functions)
    OMEGA::MachEnv::removeEnv("Contig");
-   OMEGA::MachEnv::removeEnv("Contig2");
-   OMEGA::MachEnv::removeEnv("Stride");
-   OMEGA::MachEnv::removeEnv("Subset");
+   OMEGA::MachEnv::removeAll();
 
    // MPI_Status status;
    MPI_Finalize();