Changeset 18453

Timestamp:

08/21/14 09:20:51 (11 years ago)

Author:

Mathieu Morlighem

Message:

BUG: fixed memory leak in bamg and in InterpFromMeshToMesh2d, python needs to make a COPY of the data in WriteData just like matlab otherwise we cannot delete the data after the WriteData call and matlab leaks

Location:

issm/trunk-jpl/src

Files:

• c/bamg/Mesh.cpp (modified) (3 diffs)
• c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp (modified) (5 diffs)
• wrappers/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp (modified) (1 diff)
• wrappers/python/io/WritePythonData.cpp (modified) (4 diffs)

issm/trunk-jpl/src/c/bamg/Mesh.cpp

@@ -227 +227 @@
                 /*Original code from Frederic Hecht <hecht@ann.jussieu.fr> (BAMG v1.01, Mesh2.cpp/Triangles)*/
 
-                //if (vertices)             delete [] vertices;
-                if (edges)                delete [] edges;
-                if (triangles)            delete [] triangles;
-                if (quadtree)             delete    quadtree;
-                //if (orderedvertices)                delete [] orderedvertices;
-                if (subdomains)           delete []  subdomains;
-                if (VerticesOnGeomEdge)   delete [] VerticesOnGeomEdge;
-                if (VerticesOnGeomVertex) delete [] VerticesOnGeomVertex;
-                if (VertexOnBThVertex)    delete [] VertexOnBThVertex;
-                if (VertexOnBThEdge)      delete [] VertexOnBThEdge;
-
-                if (&Gh) {
+                if(vertices)             delete [] vertices;
+                if(edges)                delete [] edges;
+                if(triangles)            delete [] triangles;
+                if(quadtree)             delete    quadtree;
+                if(orderedvertices)      delete [] orderedvertices;
+                if(subdomains)           delete []  subdomains;
+                if(VerticesOnGeomEdge)   delete [] VerticesOnGeomEdge;
+                if(VerticesOnGeomVertex) delete [] VerticesOnGeomVertex;
+                if(VertexOnBThVertex)    delete [] VertexOnBThVertex;
+                if(VertexOnBThEdge)      delete [] VertexOnBThEdge;
+
+                if(&Gh){
                         if (Gh.NbRef>0) Gh.NbRef--;
                         else if (Gh.NbRef==0) delete &Gh;
                 }
-                if (&BTh && (&BTh != this)) {
+                if(&BTh && (&BTh != this)){
                         if (BTh.NbRef>0) BTh.NbRef--;
                         else if (BTh.NbRef==0) delete &BTh;
@@ -2726 +2726 @@
 
                 /*Allocate if maxnbv_in>0*/
-                if (maxnbv_in) {
+                if(maxnbv_in){
                         vertices=new BamgVertex[maxnbv];
                         _assert_(vertices);
@@ -2734 +2734 @@
                         _assert_(triangles);
                 }
-                else {
+                else{
                         vertices=NULL;
                         orderedvertices=NULL;

issm/trunk-jpl/src/c/modules/InterpFromMeshToMesh2dx/InterpFromMeshToMesh2dx.cpp

@@ -49 +49 @@
 
         /*read background mesh*/
-        Mesh Th(index_data,x_data,y_data,nods_data,nels_data); 
+        Mesh* Th=new Mesh(index_data,x_data,y_data,nods_data,nels_data); 
 
         /*Get reference number (for subdomains)*/
-        long* reft = xNew<long>(Th.nbt);
-        Th.TriangleReferenceList(reft);
-        Th.CreateSingleVertexToTriangleConnectivity();
+        long* reft = xNew<long>(Th->nbt);
+        Th->TriangleReferenceList(reft);
+        Th->CreateSingleVertexToTriangleConnectivity();
 
         /*Get domain boundaries*/
@@ -79 +79 @@
                 /*Get current point coordinates*/
                 r.x=x_interp[i]; r.y=y_interp[i];
-                I2 I=Th.R2ToI2(r);
+                I2 I=Th->R2ToI2(r);
 
                 /*Find triangle holding r/I*/
-                Triangle &tb=*Th.TriangleFindFromCoord(I,dete);
+                Triangle &tb=*Th->TriangleFindFromCoord(I,dete);
 
                 /*point inside convex*/
@@ -92 +92 @@
                         areacoord[2]= (double) dete[2]/tb.det;
                         /*3 vertices of the triangle*/
-                        i0=Th.GetId(tb[0]);
-                        i1=Th.GetId(tb[1]);
-                        i2=Th.GetId(tb[2]);
+                        i0=Th->GetId(tb[0]);
+                        i1=Th->GetId(tb[1]);
+                        i2=Th->GetId(tb[2]);
                         /*triangle number*/
-                        it=Th.GetId(tb);
+                        it=Th->GetId(tb);
 
                         /*Inside convex but outside mesh*/
@@ -120 +120 @@
                                 areacoord[OppositeVertex[k]] = 1 - aa -bb;
                                 //3 vertices of the triangle
-                                i0=Th.GetId(tc[0]);
-                                i1=Th.GetId(tc[1]);
-                                i2=Th.GetId(tc[2]);
+                                i0=Th->GetId(tc[0]);
+                                i1=Th->GetId(tc[1]);
+                                i2=Th->GetId(tc[2]);
                                 //triangle number
-                                it=Th.GetId(tc);
+                                it=Th->GetId(tc);
                         }
                 }
@@ -145 +145 @@
 
         /*clean-up and return*/
+        delete Th;
         xDelete<long>(reft);
         *pdata_interp=data_interp;

issm/trunk-jpl/src/wrappers/InterpFromMeshToMesh2d/InterpFromMeshToMesh2d.cpp

@@ -76 +76 @@
 
         /*end module: */
+        xDelete<int>(index);
+        xDelete<double>(x_data);
+        xDelete<double>(y_data);
+        xDelete<double>(data);
+        xDelete<double>(x_interp);
+        xDelete<double>(y_interp);
+        xDelete<double>(data_interp);
+        delete options;
         MODULEEND();
 }

issm/trunk-jpl/src/wrappers/python/io/WritePythonData.cpp

@@ -35 +35 @@
         PyObject* array=NULL;
 
-        dims[0]=(npy_intp)M;
-        dims[1]=(npy_intp)N;
-        array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,matrix);
+        /*copy matrix: */
+        double* matrix_python=xNew<double>(M*N);
+        memcpy(matrix_python,matrix,M*N*sizeof(double));
+
+        dims[0]=(npy_intp)M;
+        dims[1]=(npy_intp)N;
+        array=PyArray_SimpleNewFromData(2,dims,NPY_DOUBLE,matrix_python);
 
         PyTuple_SetItem(tuple, index, array);
@@ -47 +51 @@
         PyObject* array=NULL;
 
-        /*intermediary:*/
-        long* lmatrix=NULL;
-        int i;
-
         /*transform into long matrix: */
-        lmatrix=xNew<long>(M*N);
-        for(i=0;i<M*N;i++)lmatrix[i]=(long)matrix[i];
+        long* lmatrix=xNew<long>(M*N);
+        for(int i=0;i<M*N;i++)lmatrix[i]=(long)matrix[i];
 
         dims[0]=(npy_intp)M;
@@ -67 +67 @@
         PyObject* array=NULL;
 
-        dims[0]=(npy_intp)M;
-        dims[1]=(npy_intp)N;
-        array=PyArray_SimpleNewFromData(2,dims,NPY_BOOL,matrix);
+        /*copy matrix: */
+        bool* matrix_python=xNew<bool>(M*N);
+        memcpy(matrix_python,matrix,M*N*sizeof(bool));
+
+        dims[0]=(npy_intp)M;
+        dims[1]=(npy_intp)N;
+        array=PyArray_SimpleNewFromData(2,dims,NPY_BOOL,matrix_python);
 
         PyTuple_SetItem(tuple, index, array);
@@ -76 +80 @@
 void WriteData(PyObject* py_tuple, int index, double* vector, int M){
 
-        double   *buffer = NULL;
         npy_intp  dim   = 10;
         PyObject *array = NULL;
 
-        /*Copy vector*/
-        buffer=xNew<double>(M);
-        for(int i=0;i<M;i++)buffer[i]=vector[i];
+
+        /*copy vector: */
+        double* vector_python=xNew<double>(M);
+        memcpy(vector_python,vector,M*sizeof(double));
 
         dim=(npy_intp)M;
-        array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,buffer);
+        array=PyArray_SimpleNewFromData(1,&dim,NPY_DOUBLE,vector_python);
 
         PyTuple_SetItem(py_tuple, index, array);