Crashing nipype with memory consumption

output.txt

Top 1 lines
#1: traits/has_traits.py:3008: 1.3 KiB
    if not meta_eval( getattr( trait, meta_name ) ):37 other: 14.1 KiB
Total allocated size: 15.3 KiB

Top 1 lines
#1: testnipype.py:50: 8388608.0 KiB
    large_str = ' ' * (8 * 1024**3)94 other: 362.5 KiB
Total allocated size: 8388970.6 KiB

Top 1 lines
#1: testnipype.py:50: 8388608.0 KiB
    large_str = ' ' * (8 * 1024**3)110 other: 383.4 KiB
Total allocated size: 8388991.4 KiB

Top 1 lines
#1: testnipype.py:50: 8388608.0 KiB
    large_str = ' ' * (8 * 1024**3)132 other: 17046.6 KiB
Total allocated size: 8405654.6 KiB

171121-15:37:05,797 workflow INFO:
	 Workflow work settings: ['check', 'execution', 'logging', 'monitoring']
171121-15:40:46,671 workflow INFO:
	 Running serially.
171121-15:40:46,685 workflow INFO:
	 [Node] Setting-up "work.node09999" in "/tmp/tmp4qftuz_6/work/node09999".
171121-15:40:46,687 workflow INFO:
	 [Node] Running "node09999" ("nipype.interfaces.base.CommandLine"), a CommandLine Interface with command:
ls -lah.
171121-15:40:46,693 interface WARNING:
	 Could not get linked libraries for "ls".
171121-15:40:46,698 workflow WARNING:
	 [Node] Exception "work.node09999" (/tmp/tmp4qftuz_6/work/node09999)
171121-15:40:46,698 workflow ERROR:
	 Node node09999 failed to run on host dendrite.
171121-15:40:46,699 workflow ERROR:
	 Saving crash info to /home/oesteban/tmp/test/crash-20171121-154046-oesteban-node09999-eafd76be-694b-4b85-8dbd-eee2fda53494.pklz
Traceback (most recent call last):
  File "/home/oesteban/workspace/nipype/nipype/pipeline/plugins/linear.py", line 43, in run
    node.run(updatehash=updatehash)
  File "/home/oesteban/workspace/nipype/nipype/pipeline/engine/nodes.py", line 405, in run
    self._run_interface(execute=True)
  File "/home/oesteban/workspace/nipype/nipype/pipeline/engine/nodes.py", line 508, in _run_interface
    self._result = self._run_command(execute)
  File "/home/oesteban/workspace/nipype/nipype/pipeline/engine/nodes.py", line 640, in _run_command
    result = self._interface.run()
  File "/home/oesteban/workspace/nipype/nipype/interfaces/base.py", line 1089, in run
    runtime = self._run_interface(runtime)
  File "/home/oesteban/workspace/nipype/nipype/interfaces/base.py", line 1664, in _run_interface
    runtime = run_command(runtime, output=self.terminal_output)
  File "/home/oesteban/workspace/nipype/nipype/interfaces/base.py", line 1392, in run_command
    close_fds=True)
  File "/home/oesteban/.anaconda3/lib/python3.6/subprocess.py", line 707, in __init__
    restore_signals, start_new_session)
  File "/home/oesteban/.anaconda3/lib/python3.6/subprocess.py", line 1260, in _execute_child
    restore_signals, start_new_session, preexec_fn)
OSError: [Errno 12] Cannot allocate memory

testnipype.py

import os
import linecache
from nipype.interfaces import base as nib, utility as niu
from nipype.pipeline import engine as pe
from nipype.pipeline import plugins as pp
from time import sleep
import tracemalloc

tracemalloc.start()


def display_top(group_by='lineno', limit=1):
    snapshot = tracemalloc.take_snapshot()
    snapshot = snapshot.filter_traces((
        tracemalloc.Filter(False, "<frozen importlib._bootstrap>"),
        tracemalloc.Filter(False, "<unknown>"),
    ))
    top_stats = snapshot.statistics(group_by)

    msg = "Top %s lines\n" % limit
    for index, stat in enumerate(top_stats[:limit], 1):
        frame = stat.traceback[0]
        # replace "/path/to/module/file.py" with "module/file.py"
        filename = os.sep.join(frame.filename.split(os.sep)[-2:])
        msg += ("#%s: %s:%s: %.1f KiB\n"
              % (index, filename, frame.lineno, stat.size / 1024))
        line = linecache.getline(frame.filename, frame.lineno).strip()
        if line:
            msg += '    %s' % line

    other = top_stats[limit:]
    if other:
        size = sum(stat.size for stat in other)
        msg += "%s other: %.1f KiB\n" % (len(other), size / 1024)
    total = sum(stat.size for stat in top_stats)
    msg += "Total allocated size: %.1f KiB\n" % (total / 1024)
    return msg


# import hunter
# hunter.trace(threading_support=True)
# plugin = pp.multiproc.MultiProcPlugin()

iface = nib.CommandLine(command='ls -lah')
# iface.run()

# n1 = pe.Node(iface, name='sleep')

print(display_top())
large_str = ' ' * (8 * 1024**3)
print(display_top())
wf = pe.Workflow(name='work')
print(display_top())
wf.add_nodes([pe.Node(iface, name='node%05d' % i) for i in range(10000)])
print(display_top())
# res = wf.run(plugin='MultiProc', plugin_args={'maxtasksperchild': None})
res = wf.run()
print(display_top())
large_str += ' ' # So that the garbage collector does not clean it
print(large_str[:10], large_str[-10:])