I'm using OpenMP to parallelize some union operation on Boost::geometry polygons (BPolygon
).
However I am stumbling over very strange exceptions that only occur from time to time (despite my RNGs being seeded with the same seed) so I wonder whether I'm ignoring some undefined behaviors with OpenMP parallelization and containers...
The code is part of a large and rather complex ensemble so I cannot really provide a MWE but the relevant parts are as follow:
std::unordered_map<size_t, std::vector<std::vector<BPolygon>>> container;
#pragma omp parallel
{
std::vector<BPolygon> vec_geom;
#pragma omp for
for (size_t gid : gids)
{
[...]
auto iter_block, iter_block_end;
container[gid] = std::vector<std::vector<BPolygon>>();
while (iter_block != iter_block_end)
{
auto iter_node = neurite_it->second->nodes_cbegin();
auto iter_node_end = neurite_it->second->nodes_cend();
// store the union in vec_geom
vec_geom.clear();
while (iter_node != iter_node_end)
{
cascading_union(node_it->second, vec_geom);
iter_node++;
}
// add the union to the container
container[gid].push_back(vec_geom);
iter_block++;
}
}
}
with the cascading union function being
void cascading_union(TNodePtr n, std::vector<BPolygon> &vec_geom)
{
auto range = n->segment_range();
auto seg_it = range.begin();
auto seg_end = range.end();
std::vector<BPolygon> vec, vec_tmp;
BPolygon poly1, poly2;
// container associated to `range` cannot be modified so
// we store the first unions in a new vector
while (seg_it != seg_end)
{
poly1 = *((*seg_it).get());
seg_it++;
if (seg_it != seg_end)
{
poly2 = *((*seg_it).get());
bg::union_(poly1, poly2, vec_tmp);
vec.push_back(vec_tmp[0]);
vec_tmp.clear();
}
else
{
vec.push_back(poly1);
}
}
stype imax(vec.size()), imax2;
// cascading union on final vector
while (imax > 1)
{
imax2 = 0;
for (stype i=0; i < imax; i += 2)
{
poly1 = vec[i];
if (i + 1 < imax)
{
poly2 = vec[i + 1];
bg::union_(poly1, poly2, vec_tmp);
vec[imax2] = vec_tmp[0];
vec_tmp.clear();
}
else
{
vec[imax2] = poly1;
}
imax2++;
}
vec.resize(imax2);
imax = imax2;
}
if (imax > 0)
{
vec_geom.push_back(vec.back());
}
}
The type of errors that are encounter are:
container[gid] = std::vector<std::vector<BPolygon>>();
munmap_chunk(): invalid pointer
(precise location unknown)cascading_union
:bg::union_
free(): invalid next size (fast)
(precise location unknown)malloc(): unaligned tcache chunk detected
(precise location unknown)Please let me know if full backtraces would be useful.
I am wondering whether, though containers are supposed to be thread-safe, it could be an issue with the fact that here I'm dealing with variable size objects inside the container.
Note: these errors stem from a recent restructuring, so I think that there is no issue with the polygons or underlying structures because the errors were absent from previous implementations.
Thank to the comments, I realized that my idea about containers being thread-safe was wrong (well they are safe to read but not to modify).
Assignments and call to push_back
must be wrapped in
#pragma omp critical