Merge pull request #349 from EricDeveaud/master

use available processor for process not all on host

src/megahit

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # -------------------------------------------------------------------------
 # MEGAHIT
@@ -19,7 +19,6 @@
 # -------------------------------------------------------------------------
 
 
-from __future__ import print_function
 
 import getopt
 import json
@@ -375,7 +374,7 @@ def parse_option(argv):
         elif option == '--max-tip-len':
             opt.max_tip_len = int(value)
         elif option == '--merge-level':
-            (opt.merge_len, opt.merge_similar) = map(float, value.split(','))
+            (opt.merge_len, opt.merge_similar) = list(map(float, value.split(',')))
             opt.merge_len = int(opt.merge_len)
         elif option == '--prune-level':
             opt.prune_level = int(value)
@@ -553,12 +552,12 @@ def check_and_correct_option():
         raise Usage('--low-local-ratio should be in (0, 0.5].')
     if opt.cleaning_rounds <= 0:
         raise Usage('--cleaning-rounds must be >= 1')
-    if opt.num_cpu_threads > multiprocessing.cpu_count():
-        logger.warning('Maximum number of available CPU thread is %d.' % multiprocessing.cpu_count())
-        logger.warning('Number of thread is reset to the %d.' % multiprocessing.cpu_count())
-        opt.num_cpu_threads = multiprocessing.cpu_count()
+    if opt.num_cpu_threads > len(os.sched_getaffinity(0)):
+        logger.warning('Maximum number of available CPU thread is %d.' % len(os.sched_getaffinity(0)))
+        logger.warning('Number of thread is reset to the %d.' % len(os.sched_getaffinity(0)))
+        opt.num_cpu_threads = len(os.sched_getaffinity(0))
     if opt.num_cpu_threads == 0:
-        opt.num_cpu_threads = multiprocessing.cpu_count()
+        opt.num_cpu_threads = len(os.sched_getaffinity(0))
     if opt.prune_depth < 0 and opt.prune_level < 3:
         opt.prune_depth = opt.min_count
     if opt.bubble_level < 0: