updates to support memory leak reductions in biotissue

Author: jacobmerson

src/las.h

@@ -156,6 +156,14 @@ namespace las
      * @param cm The comm over which the vector is collective.
      */
     virtual Vec * create(unsigned lcl, unsigned bs, MPI_Comm cm) = 0;
+    /**
+     * Create a vector from an existing array
+     * @param data The array which the vector will use as data storage
+     * @param lcl The local number of rows (per-process in cm)
+     * @param bs The block size (should be the same over cm)
+     * @param cm The comm over which the vector is collective.
+     */
+    virtual Vec * create(scalar * data, unsigned lcl, unsigned bs, MPI_Comm cm)=0;
     virtual void destroy(Vec * v) = 0;
     /**
      * Create a vector suitable to act as the RHS vector to a

src/lasDense_impl.h

@@ -99,6 +99,10 @@ namespace las
     {
       return createVector(lcl);
     }
+    virtual Vec * create(scalar * data, unsigned lcl, unsigned, MPI_Comm)
+    {
+      return createVector(data, lcl);
+    }
     virtual void destroy(Vec * v)
     {
       destroyVector(v);

src/lasPETSc_impl.h

@@ -230,6 +230,15 @@ namespace las
     CHKERRABORT(LAS_COMM_WORLD, ierr);
     return reinterpret_cast<las::Vec*>(v);
   }
+  LAS_INLINE las::Vec * createPetscVector(scalar * data, unsigned l, unsigned bs, MPI_Comm cm = LAS_COMM_WORLD)
+  {
+    ::Vec * v = new ::Vec;
+    PetscErrorCode ierr = VecCreateMPIWithArray(cm, bs, l,PETSC_DECIDE,data, v);
+    CHKERRABORT(LAS_COMM_WORLD, ierr);
+    ierr = VecSetOption(*v,VEC_IGNORE_NEGATIVE_INDICES,PETSC_TRUE);
+    CHKERRABORT(LAS_COMM_WORLD, ierr);
+    return reinterpret_cast<las::Vec*>(v);
+  }
   LAS_INLINE void destroyPetscVec(las::Vec * v)
   {
     PetscErrorCode ierr = VecDestroy(getPetscVec(v));
@@ -255,6 +264,10 @@ namespace las
     {
       return createPetscVector(lcl,bs,cm);
     }
+    virtual Vec * create(scalar * data, unsigned lcl, unsigned bs, MPI_Comm cm)
+    {
+      return createPetscVector(data, lcl,bs,cm);
+    }
     virtual Vec * createRHS(Mat * m)
     {
       return createRHSVec(m);

src/lasSparse_impl.h

@@ -103,6 +103,10 @@ namespace las
     {
       return createVector(lcl);
     }
+    virtual Vec * create(scalar * data, unsigned lcl, unsigned, MPI_Comm)
+    {
+      return createVector(data, lcl);
+    }
     virtual void destroy(Vec * v) 
     {
       destroyVector(v);

src/lasSparskitExterns.cc

@@ -59,11 +59,14 @@ namespace las
     matrix.assign(matrix.size(),0.0);
   }
   void SparskitBuffers::resizeMatrixBuffer(int newSize) {
-    assert((newSize-matrixLength()) > 0);
-    heuristic_length = newSize;
-    matrix.resize(heuristic_length);
-    cols.resize(heuristic_length);
-    assert(cols.size() == heuristic_length);
-    assert(matrix.size() == heuristic_length);
+    // only support increasing the buffer size
+    if(newSize > matrixLength())
+    {
+      heuristic_length = newSize;
+      matrix.resize(heuristic_length);
+      cols.resize(heuristic_length);
+      assert(cols.size() == heuristic_length);
+      assert(matrix.size() == heuristic_length);
+    }
   }
 };

src/lasVec_impl.h

@@ -5,19 +5,30 @@
 #include <lasSys.h>
 #include <cassert>
 #include <cstring> // memset
+#include <iostream>
 namespace las
 {
   class lasVec
   {
   private:
     scalar * vls;
     int cnt;
+    // this is a data location that any negative indices will 
+    // sum into
+    scalar dummy_data;
   public:
     lasVec(int n)
       : vls(nullptr)
       , cnt(n)
+      , dummy_data(0)
+    {
+      alloc<Malloc>((void**)&vls,sizeof(scalar)*n);
+    }
+    lasVec(scalar * data, int n)
+      : vls(data)
+      , cnt(n)
+      , dummy_data(0)
     {
-      alloc<Malloc>((void**)&vls,sizeof(scalar)*(n+1));
     }
     ~lasVec()
     {
@@ -27,7 +38,7 @@ namespace las
     {
       assert(idx < cnt);
       if(idx < 0)
-        idx = cnt;
+        return dummy_data;
       return vls[idx];
     }
     void setVls(scalar * values) {
@@ -41,7 +52,8 @@ namespace las
     // too coupled to the implementation to leave external
     void zero()
     {
-      memset(&vls[0],0,sizeof(scalar)*(cnt+1));
+      memset(&vls[0],0,sizeof(scalar)*cnt);
+      dummy_data = 0;
     }
   };
   LAS_INLINE lasVec * getLASVec(Vec * v)
@@ -52,6 +64,10 @@ namespace las
   {
     return reinterpret_cast<Vec*>(new lasVec(n));
   }
+  LAS_INLINE Vec * createVector(scalar * data, unsigned n)
+  {
+    return reinterpret_cast<Vec*>(new lasVec(data,n));
+  }
   LAS_INLINE void destroyVector(Vec * v)
   {
     delete getLASVec(v);