Merge pull request #178 from prabhuramachandran/fix-nnps-cache-bug

BUG: Fix massive leak with caching nnps.
pypr · Feb 27, 2019 · e57e9d4 · e57e9d4
2 parents 9d46b26 + 7b301a1
commit e57e9d4
Show file tree

Hide file tree

Showing 3 changed files with 28 additions and 4 deletions.
diff --git a/pysph/base/nnps_base.pxd b/pysph/base/nnps_base.pxd
@@ -246,7 +246,8 @@ cdef class NeighborCache:
     cdef UIntArray _start_stop
     cdef IntArray _cached
     cdef void **_neighbors
-    cdef list _neighbor_arrays
+    # This is made public purely for testing!
+    cdef public list _neighbor_arrays
     cdef int _last_avg_nbr_size
 
     cdef void get_neighbors_raw(self, size_t d_idx, UIntArray nbrs) nogil
@@ -265,7 +266,7 @@ cdef class NNPSBase:
     cdef public list pa_wrappers      # list of particle array wrappers
     cdef public int narrays           # Number of particle arrays
     cdef public bint use_cache        # Use cache or not.
-    cdef list cache                   # The neighbor cache.
+    cdef public list cache            # The neighbor cache.
     cdef int src_index, dst_index     # The current source and dest indices
 
     cdef public DomainManager domain  # Domain manager

diff --git a/pysph/base/nnps_base.pyx b/pysph/base/nnps_base.pyx
@@ -44,7 +44,7 @@ ELSE:
     cpdef int get_number_of_threads():
         return 1
     cpdef set_number_of_threads(int n):
-        print "OpenMP not available, cannot set number of threads."
+        print("OpenMP not available, cannot set number of threads.")
 
 
 IF UNAME_SYSNAME == "Windows":
@@ -1003,8 +1003,11 @@ cdef class NeighborCache:
         # This is an upper limit for the number of neighbors in a worst
         # case scenario.
         cdef size_t safety = 1024
+        cdef UIntArray arr
         for i in range(n_threads):
-            (<UIntArray>self._neighbors[i]).c_reserve(
+            arr = <UIntArray>self._neighbors[i]
+            arr.c_reset()
+            arr.c_reserve(
                 self._last_avg_nbr_size*np/n_threads + safety
             )
 

diff --git a/pysph/base/tests/test_nnps.py b/pysph/base/tests/test_nnps.py
@@ -1018,6 +1018,26 @@ def test_large_number_of_neighbors_linked_list():
     assert nbrs.length == len(x)
 
 
+def test_neighbor_cache_update_doesnt_leak():
+    # Given
+    x, y, z = numpy.random.random((3, 1000))
+    pa = get_particle_array(name='fluid', x=x, y=y, z=z, h=0.05)
+
+    nps = nnps.LinkedListNNPS(dim=3, particles=[pa], cache=True)
+    nps.set_context(0, 0)
+    nps.cache[0].find_all_neighbors()
+    old_length = sum(x.length for x in nps.cache[0]._neighbor_arrays)
+
+    # When
+    nps.update()
+    nps.set_context(0, 0)
+    nps.cache[0].find_all_neighbors()
+
+    # Then
+    new_length = sum(x.length for x in nps.cache[0]._neighbor_arrays)
+    assert new_length == old_length
+
+
 nnps_classes = [
     nnps.BoxSortNNPS,
     nnps.CellIndexingNNPS,