[MOAB-dev] commit/MOAB: danwu: When reading cell variables with Zoltan partition and mixed elements options, the conversion from global cell index to local cell index is incorrect (only works for trivial partition) and causes vector buffer overflow. Fixed this bug with some other minor changes.
commits-noreply at bitbucket.org
commits-noreply at bitbucket.org
Tue Oct 29 12:31:44 CDT 2013
1 new commit in MOAB:
https://bitbucket.org/fathomteam/moab/commits/3422c95f7ce3/
Changeset: 3422c95f7ce3
Branch: master
User: danwu
Date: 2013-10-29 18:31:28
Summary: When reading cell variables with Zoltan partition and mixed elements options, the conversion from global cell index to local cell index is incorrect (only works for trivial partition) and causes vector buffer overflow. Fixed this bug with some other minor changes.
Affected #: 1 file
diff --git a/src/io/NCHelperMPAS.cpp b/src/io/NCHelperMPAS.cpp
index 404619d..550988b 100644
--- a/src/io/NCHelperMPAS.cpp
+++ b/src/io/NCHelperMPAS.cpp
@@ -221,7 +221,7 @@ ErrorCode NCHelperMPAS::check_existing_mesh()
nLocalCells = localGidCells.size();
if (numCellGroups > 1) {
- // Restore cellHandleToGlobalID
+ // Restore cellHandleToGlobalID map
Range::const_iterator rit;
int i;
for (rit = local_cells.begin(), i = 0; rit != local_cells.end(); ++rit, i++)
@@ -756,10 +756,11 @@ ErrorCode NCHelperMPAS::read_ucd_variable_to_nonset_async(std::vector<ReadNC::Va
ERRORR(rval, "Failed to iterate tag on owned faces.");
for (int j = 0; j < count; j++) {
- int cell_idx = cellHandleToGlobalID[*(iter + j)]; // Global cell index
- cell_idx -= localGidCells[0]; // Local cell index
+ int global_cell_idx = cellHandleToGlobalID[*(iter + j)]; // Global cell index, 1 based
+ int local_cell_idx = localGidCells.index(global_cell_idx); // Local cell index, 0 based
+ assert(local_cell_idx != -1);
for (int level = 0; level < vdatas[i].numLev; level++)
- ((double*) ptr)[j * vdatas[i].numLev + level] = tmpdoubledata[cell_idx * vdatas[i].numLev + level];
+ ((double*) ptr)[j * vdatas[i].numLev + level] = tmpdoubledata[local_cell_idx * vdatas[i].numLev + level];
}
iter += count;
@@ -900,10 +901,11 @@ ErrorCode NCHelperMPAS::read_ucd_variable_to_nonset(std::vector<ReadNC::VarData>
ERRORR(rval, "Failed to iterate tag on owned faces.");
for (int j = 0; j < count; j++) {
- int cell_idx = cellHandleToGlobalID[*(iter + j)]; // Global cell index
- cell_idx -= localGidCells[0]; // Local cell index
+ int global_cell_idx = cellHandleToGlobalID[*(iter + j)]; // Global cell index, 1 based
+ int local_cell_idx = localGidCells.index(global_cell_idx); // Local cell index, 0 based
+ assert(local_cell_idx != -1);
for (int level = 0; level < vdatas[i].numLev; level++)
- ((double*) ptr)[j * vdatas[i].numLev + level] = tmpdoubledata[cell_idx * vdatas[i].numLev + level];
+ ((double*) ptr)[j * vdatas[i].numLev + level] = tmpdoubledata[local_cell_idx * vdatas[i].numLev + level];
}
iter += count;
@@ -1275,9 +1277,9 @@ ErrorCode NCHelperMPAS::create_local_edges(EntityHandle start_vertex,
int verticesOnEdgeVarId;
// Read vertices on each local edge, to get edge connectivity
- // Utilize the memory storage pointed by conn_arr_edges
success = NCFUNC(inq_varid)(_fileId, "verticesOnEdge", &verticesOnEdgeVarId);
ERRORS(success, "Failed to get variable id of verticesOnEdge.");
+ // Utilize the memory storage pointed by conn_arr_edges
int* vertices_on_local_edges = (int*) conn_arr_edges;
#ifdef PNETCDF_FILE
nb_reads = localGidEdges.psize();
@@ -1315,12 +1317,12 @@ ErrorCode NCHelperMPAS::create_local_edges(EntityHandle start_vertex,
#endif
// Populate connectivity for local edges
- // Convert in-place from int to EntityHandle type (backward)
+ // Convert in-place from int to EntityHandle type (reading backward is the trick)
for (int edge_vert = nLocalEdges * 2 - 1; edge_vert >= 0; edge_vert--) {
- EntityHandle global_vert_id = vertices_on_local_edges[edge_vert]; // 1 based
- int vert_idx = localGidVerts.index(global_vert_id); // 0 based
- assert(vert_idx != -1);
- conn_arr_edges[edge_vert] = start_vertex + vert_idx;
+ int global_vert_idx = vertices_on_local_edges[edge_vert]; // Global vertex index, 1 based
+ int local_vert_idx = localGidVerts.index(global_vert_idx); // Local vertex index, 0 based
+ assert(local_vert_idx != -1);
+ conn_arr_edges[edge_vert] = start_vertex + local_vert_idx;
}
return MB_SUCCESS;
@@ -1375,16 +1377,17 @@ ErrorCode NCHelperMPAS::create_local_cells(const std::vector<int>& vertices_on_l
// Set connectivity array with proper local vertices handles
for (int j = 0; j < num_group_cells; j++) {
- int cell_idx = (int)local_cells_with_n_edges[num_edges_per_cell][j]; // Global cell index
+ int global_cell_idx = (int)local_cells_with_n_edges[num_edges_per_cell][j]; // Global cell index, 1 based
+ int local_cell_idx = localGidCells.index(global_cell_idx); // Local cell index, 0 based
+ assert(local_cell_idx != -1);
- if (numCellGroups > 1)
- cellHandleToGlobalID[start_element + j] = cell_idx;
-
- cell_idx = localGidCells.index(cell_idx);
- assert(cell_idx != -1);
+ if (numCellGroups > 1) {
+ // Populate cellHandleToGlobalID map to read cell variables
+ cellHandleToGlobalID[start_element + j] = global_cell_idx;
+ }
for (int k = 0; k < num_edges_per_cell; k++) {
- EntityHandle global_vert_id = vertices_on_local_cells[cell_idx * maxEdgesPerCell + k];
+ EntityHandle global_vert_id = vertices_on_local_cells[local_cell_idx * maxEdgesPerCell + k];
int idx_vertex = localGidVerts.index(global_vert_id);
assert(idx_vertex != -1);
conn_arr_local_cells_with_n_edges[num_edges_per_cell][j * num_edges_per_cell + k] =
@@ -1431,12 +1434,12 @@ ErrorCode NCHelperMPAS::create_padded_local_cells(const std::vector<int>& vertic
// Set connectivity array with proper local vertices handles
// vertices_on_local_cells array was already corrected to have the last vertices padded
// no need for extra checks considering
- for (int cell_idx = 0; cell_idx < nLocalCells; cell_idx++) {
+ for (int local_cell_idx = 0; local_cell_idx < nLocalCells; local_cell_idx++) {
for (int i = 0; i < maxEdgesPerCell; i++) {
- EntityHandle global_vert_id = vertices_on_local_cells[cell_idx * maxEdgesPerCell + i]; // 1 based
- int local_vert_idx = localGidVerts.index(global_vert_id); // 0 based
+ EntityHandle global_vert_idx = vertices_on_local_cells[local_cell_idx * maxEdgesPerCell + i]; // Global vertex index, 1 based
+ int local_vert_idx = localGidVerts.index(global_vert_idx); // Local vertex index, 0 based
assert(local_vert_idx != -1);
- conn_arr_local_cells[cell_idx * maxEdgesPerCell + i] = start_vertex + local_vert_idx;
+ conn_arr_local_cells[local_cell_idx * maxEdgesPerCell + i] = start_vertex + local_vert_idx;
}
}
@@ -1650,13 +1653,13 @@ ErrorCode NCHelperMPAS::create_gather_set_cells(EntityHandle gather_set, EntityH
ERRORR(rval, "Failed to add cells to the gather set.");
for (int j = 0; j < num_group_cells; j++) {
- int cell_idx = gather_cells_with_n_edges[num_edges_per_cell][j]; // Global cell index
- cell_idx--; // 1 based -> 0 based
+ int gather_cell_idx = gather_cells_with_n_edges[num_edges_per_cell][j]; // Global cell index, 1 based
+ gather_cell_idx--; // 1 based -> 0 based
for (int k = 0; k < num_edges_per_cell; k++)
// Connectivity array is shifted by where the gather set vertices start
conn_arr_gather_cells_with_n_edges[num_edges_per_cell][j * num_edges_per_cell + k] =
- (gather_set_start_vertex - 1) + vertices_on_gather_cells[cell_idx * maxEdgesPerCell + k];
+ (gather_set_start_vertex - 1) + vertices_on_gather_cells[gather_cell_idx * maxEdgesPerCell + k];
}
}
}
@@ -1720,16 +1723,16 @@ ErrorCode NCHelperMPAS::create_padded_gather_set_cells(EntityHandle gather_set,
rval = mbImpl->add_entities(gather_set, gather_cells_range);
ERRORR(rval, "Failed to add cells to the gather set.");
- for (int cell_idx = 0; cell_idx < nCells; cell_idx++) {
- int num_edges = num_edges_on_gather_cells[cell_idx];
+ for (int gather_cell_idx = 0; gather_cell_idx < nCells; gather_cell_idx++) {
+ int num_edges = num_edges_on_gather_cells[gather_cell_idx];
for (int i = 0; i < num_edges; i++)
// Connectivity array is shifted by where the gather set vertices start
- conn_arr_gather_cells[cell_idx * maxEdgesPerCell + i] = (gather_set_start_vertex - 1) + vertices_on_gather_cells[cell_idx * maxEdgesPerCell + i];
+ conn_arr_gather_cells[gather_cell_idx * maxEdgesPerCell + i] = (gather_set_start_vertex - 1) + vertices_on_gather_cells[gather_cell_idx * maxEdgesPerCell + i];
// Padding: fill connectivity array with last vertex handle
- EntityHandle last_vert_id = conn_arr_gather_cells[cell_idx * maxEdgesPerCell + num_edges - 1];
+ EntityHandle last_vert_handle = conn_arr_gather_cells[gather_cell_idx * maxEdgesPerCell + num_edges - 1];
for (int i = num_edges; i < maxEdgesPerCell; i++)
- conn_arr_gather_cells[cell_idx * maxEdgesPerCell + i] = last_vert_id;
+ conn_arr_gather_cells[gather_cell_idx * maxEdgesPerCell + i] = last_vert_handle;
}
return MB_SUCCESS;
Repository URL: https://bitbucket.org/fathomteam/moab/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
More information about the moab-dev
mailing list