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<p>1 new commit in yt:</p>
<p><a href="https://bitbucket.org/yt_analysis/yt/commits/9c03543ba85f/">https://bitbucket.org/yt_analysis/yt/commits/9c03543ba85f/</a> Changeset: 9c03543ba85f Branch: yt User: ngoldbaum Date: 2016-03-24 18:29:09+00:00 Summary: Merged in xarthisius/yt (pull request #2036)</p>
<p>Fix memory leak in ARTIO Affected #: 2 files</p>
<p>diff -r 10bf552980ab547ece30ab77e8ccd522d440a74e -r 9c03543ba85f4f0aa07f2f0261724831cedfe754 yt/frontends/artio/_artio_caller.pyx --- a/yt/frontends/artio/_artio_caller.pyx +++ b/yt/frontends/artio/_artio_caller.pyx @@ -718,12 +718,13 @@</p>
<pre>cdef np.int64_t **pcount
cdef float **root_mesh_data
cdef np.int64_t nvars[2]</pre>
<p>+ cdef int cache_root_mesh</p>
<pre> def __init__(self, domain_dimensions, # cells
domain_left_edge,
domain_right_edge,
artio_fileset artio_handle,</pre>
<ul><li><p>sfc_start, sfc_end):</p></li></ul>
<p>+ sfc_start, sfc_end, int cache_root_mesh = 0):</p>
<pre>cdef int i
cdef np.int64_t sfc
self.sfc_start = sfc_start</pre>
<p>@@ -735,6 +736,7 @@</p>
<pre>self.oct_count = None
self.root_mesh_data = NULL
self.pcount = NULL</pre>
<p>+ self.cache_root_mesh = cache_root_mesh</p>
<pre> if artio_handle.has_particles:
self.pcount = <np.int64_t **> malloc(sizeof(np.int64_t*)</pre>
<p>@@ -789,10 +791,11 @@</p>
<pre> cdef float *grid_variables = <float *>malloc(
ngv * sizeof(float))
self.octree_handler = octree = ARTIOOctreeContainer(self)</pre>
<ul><li><p>self.root_mesh_data = <float **>malloc(sizeof(float *) * ngv)</p></li>
<li><p>for i in range(ngv):</p></li>
<li><p>self.root_mesh_data[i] = <float *>malloc(sizeof(float) * \</p></li>
<li><p>(self.sfc_end – self.sfc_start + 1))</p></li></ul>
<p>+ if self.cache_root_mesh == 1: + self.root_mesh_data = <float **>malloc(sizeof(float *) * ngv) + for i in range(ngv): + self.root_mesh_data[i] = <float *>malloc(sizeof(float) * \ + (self.sfc_end – self.sfc_start + 1))</p>
<pre># We want to pre-allocate an array of root pointers. In the future,
# this will be pre-determined by the ARTIO library. However, because
# realloc plays havoc with our tree searching, we can't utilize an</pre>
<p>@@ -808,7 +811,7 @@</p>
<pre> sfc, dpos, grid_variables, &num_oct_levels,
num_octs_per_level)
check_artio_status(status)</pre>
<ul><li><p>for i in range(ngv):</p></li></ul>
<p>+ for i in range(ngv * self.cache_root_mesh):</p>
<pre> self.root_mesh_data[i][sfc - self.sfc_start] = \
grid_variables[i]
if num_oct_levels > 0:</pre>
<p>@@ -823,7 +826,6 @@</p>
<pre>check_artio_status(status)
status = artio_grid_clear_sfc_cache(self.handle)
check_artio_status(status)</pre>
<p>–</p>
<pre> if self.artio_handle.has_particles:
num_particles_per_species = <int *>malloc(
sizeof(int)*num_species)</pre>
<p>@@ -1505,10 +1507,15 @@</p>
<pre>cdef np.int64_t sfc, num_cells, sfci = -1
cdef np.float64_t val
cdef double dpos[3]</pre>
<p>+ max_level = self.artio_handle.max_level + cdef int *num_octs_per_level = <int *>malloc( + (max_level + 1)*sizeof(int))</p>
<pre># We duplicate some of the grid_variables stuff here so that we can
# potentially release the GIL
nf = len(field_indices)
ngv = self.artio_handle.num_grid_variables</pre>
<p>+ cdef float *grid_variables = <float *>malloc( + ngv * sizeof(float))</p>
<pre>cdef np.ndarray[np.uint8_t, ndim=1, cast=True] mask
mask = self.mask(selector, -1)
num_cells = self._last_mask_sum</pre>
<p>@@ -1528,17 +1535,39 @@</p>
<pre># location based on the file index.
cdef int filled = 0
cdef float **mesh_data = self.range_handler.root_mesh_data</pre>
<ul><li><p>for sfc in range(self.sfc_start, self.sfc_end + 1):</p></li>
<li><p>if self.sfc_mask[sfc – self.sfc_start] == 0: continue</p></li>
<li><p>sfci += 1</p></li>
<li><p>if mask[sfci] == 0: continue</p></li>
<li><p>for i in range(nf):</p></li>
<li><p>field_vals[i][filled] = mesh_data[field_ind[i]][</p></li>
<li><p>sfc – self.sfc_start]</p></li>
<li><p>filled += 1</p></li></ul>
<p>+ if mesh_data == NULL: + status = artio_grid_cache_sfc_range(self.handle, self.sfc_start, + self.sfc_end) + check_artio_status(status) + for sfc in range(self.sfc_start, self.sfc_end + 1): + if self.sfc_mask[sfc – self.sfc_start] == 0: continue + sfci += 1 + if mask[sfci] == 0: continue + status = artio_grid_read_root_cell_begin( self.handle, + sfc, dpos, grid_variables, &num_oct_levels, + num_octs_per_level) + check_artio_status(status) + for i in range(nf): + field_vals[i][filled] = grid_variables[field_ind[i]] + filled += 1 + status = artio_grid_read_root_cell_end(self.handle) + check_artio_status(status) + status = artio_grid_clear_sfc_cache(self.handle) + check_artio_status(status) + else: + for sfc in range(self.sfc_start, self.sfc_end + 1): + if self.sfc_mask[sfc – self.sfc_start] == 0: continue + sfci += 1 + if mask[sfci] == 0: continue + for i in range(nf): + field_vals[i][filled] = mesh_data[field_ind[i]][ + sfc – self.sfc_start] + filled += 1</p>
<pre># Now we have all our sources.
free(field_ind)
free(field_vals)</pre>
<p>+ free(grid_variables) + free(num_octs_per_level)</p>
<pre> return tr
@cython.boundscheck(False)</pre>
<p>diff -r 10bf552980ab547ece30ab77e8ccd522d440a74e -r 9c03543ba85f4f0aa07f2f0261724831cedfe754 yt/frontends/artio/data_structures.py --- a/yt/frontends/artio/data_structures.py +++ b/yt/frontends/artio/data_structures.py @@ -164,6 +164,7 @@</p>
<pre> self.directory = os.path.dirname(self.index_filename)
self.max_level = ds.max_level</pre>
<p>+ self.range_handlers = {}</p>
<pre> self.float_type = np.float64
super(ARTIOIndex, self).__init__(ds, dataset_type)
</pre>
<p>@@ -251,11 +252,15 @@</p>
<pre>#v = np.array(list_sfc_ranges)
#list_sfc_ranges = [ (v.min(), v.max()) ]
for (start, end) in list_sfc_ranges:</pre>
<ul><li><p>range_handler = ARTIOSFCRangeHandler(</p></li>
<li><p>self.ds.domain_dimensions,</p></li>
<li><p>self.ds.domain_left_edge, self.ds.domain_right_edge,</p></li>
<li><p>self.ds._handle, start, end)</p></li>
<li><p>range_handler.construct_mesh()</p></li></ul>
<p>+ if (start, end) in self.range_handlers.keys(): + range_handler = self.range_handlers[(start, end)] + else: + range_handler = ARTIOSFCRangeHandler( + self.ds.domain_dimensions, + self.ds.domain_left_edge, self.ds.domain_right_edge, + self.ds._handle, start, end) + range_handler.construct_mesh() + self.range_handlers[(start, end)] = range_handler</p>
<pre>if nz != 2:
ci.append(ARTIORootMeshSubset(base_region, start, end,
range_handler.root_mesh_handler, self.ds))</pre>
<p>Repository URL: <a href="https://bitbucket.org/yt_analysis/yt/">https://bitbucket.org/yt_analysis/yt/</a></p>
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