Merge pull request #138 from MannLabs/dev_mp

Fix Out of Bounds issue upon multiple multiprocessing worker runs

Author: sophiamaedler

src/scportrait/pipeline/segmentation/segmentation.py

@@ -742,7 +742,6 @@ def _resolve_sharding(self, sharding_plan):
             local_hf = h5py.File(local_output, "r")
             local_hdf_labels = local_hf.get(self.DEFAULT_MASK_NAME)[:]
 
-            print(type(local_hdf_labels))
             shifted_map, edge_labels = shift_labels(
                 local_hdf_labels,
                 class_id_shift,
@@ -902,8 +901,9 @@ def _resolve_sharding(self, sharding_plan):
         if not self.deep_debug:
             self._cleanup_shards(sharding_plan)
 
-    def _initializer_function(self, gpu_id_list):
+    def _initializer_function(self, gpu_id_list, n_processes):
         current_process().gpu_id_list = gpu_id_list
+        current_process().n_processes = n_processes
 
     def _perform_segmentation(self, shard_list):
         # get GPU status
@@ -921,7 +921,7 @@ def _perform_segmentation(self, shard_list):
             with mp.get_context(self.context).Pool(
                 processes=self.n_processes,
                 initializer=self._initializer_function,
-                initargs=[self.gpu_id_list],
+                initargs=[self.gpu_id_list, self.n_processes],
             ) as pool:
                 list(
                     tqdm(

src/scportrait/pipeline/segmentation/workflows.py

@@ -15,6 +15,7 @@
 from skimage.filters import median
 from skimage.morphology import binary_erosion, dilation, disk, erosion
 from skimage.segmentation import watershed
+import _multiprocessing
 
 from scportrait.pipeline._utils.segmentation import (
     contact_filter,
@@ -1353,6 +1354,9 @@ def _check_gpu_status(self):
             gpu_id_list = current.gpu_id_list
             cpu_id = int(cpu_name[cpu_name.find("-") + 1 :]) - 1
 
+            if cpu_id >= len(gpu_id_list):
+                cpu_id = cpu_id%current.n_processes
+
             # track gpu_id and update GPU status
             self.gpu_id = gpu_id_list[cpu_id]
             self.status = "multi_GPU"