Merge pull request #1287 from deeptools/overcommitted_cpus

Overcommitted cpus

CHANGES.txt

@@ -5,6 +5,8 @@
 * initiate deprecation of tight_layout in plotheatmap, in favor of constrained_layout. Minor changes in paddings, etc can occur (but for the better).
 * documentation changes to improve ESS tab, table constraints have been lifted & sphinx_rtd_theme to v2.0.0
 * upload artifact in gh test runner pinned to 3
+* Try to get the number of processors from sched_getaffinity, to avoid using to many in job submissions for example. #1199
+* Fix typo in estimateScaleFactor that fixes broken argparsing. #1286
 
 3.5.4
 * error handling and cases for bwAverage with >2 samples

deeptools/estimateScaleFactor.py

@@ -98,7 +98,7 @@ def main(args=None):
     between to samples
 
     """
-    args = parseArguments().parse_args(args)
+    args = parseArguments(args)
     if len(args.bamfiles) > 2:
         print("SES method to estimate scale factors only works for two samples")
         exit(0)

deeptools/parserCommon.py

@@ -1,6 +1,7 @@
 import argparse
 import os
 from importlib.metadata import version
+import multiprocessing
 
 
 def check_float_0_1(value):
@@ -341,8 +342,12 @@ def getParentArgParse(args=None, binSize=True, blackList=True):
 
 
 def numberOfProcessors(string):
-    import multiprocessing
-    availProc = multiprocessing.cpu_count()
+    try:
+        # won't work on macOS or windows
+        # limit threads to what is available (e.g. grid submissions, issue #1199)
+        availProc = len(os.sched_getaffinity(0))
+    except AttributeError:
+        availProc = multiprocessing.cpu_count()
 
     if string == "max/2":  # default case
         # by default half of the available processors are used