Attempt setting env var HDF5_USE_FILE_LOCKING to false when opening n…

…etcdf file on failure
choderalab · May 30, 2019 · 27c43ce · 27c43ce
1 parent 53170a1
commit 27c43ce
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/openmmtools/multistate/multistatereporter.py b/openmmtools/multistate/multistatereporter.py
@@ -375,6 +375,10 @@ def _open_dataset_robustly(self, *args, n_attempts=5, sleep_time=2,
                              'in {} seconds'.format(attempt+1, n_attempts, sleep_time))
                 time.sleep(sleep_time)
 
+        # At the very last attempt, we try setting the environment variable
+        # controlling the locking mechanism of HDF5 (see choderalab/yank#1165).
+        if n_attempts > 1:
+            os.environ['HDF5_USE_FILE_LOCKING'] = 'FALSE'
 
         # Last attempt finally raises any error.
         return netcdf.Dataset(*args, **kwargs)