From bd7f00cc4c6135b715e425d1ab67a4e175aa77ef Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sat, 28 Oct 2017 10:04:39 -0700
Subject: [PATCH] [ENH] Close file descriptors

When running large nipype graphs, the open file-descriptors end up provoking OSError 12 (could not allocate memory).
---
 nipype/interfaces/base.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py
index f8e845d944..7f586d4923 100644
--- a/nipype/interfaces/base.py
+++ b/nipype/interfaces/base.py
@@ -1373,7 +1373,9 @@ def run_command(runtime, output=None, timeout=0.01):
                     stderr=stderr,
                     shell=True,
                     cwd=runtime.cwd,
-                    env=env)
+                    env=env,
+                    close_fds=True,
+    )
     result = {
         'stdout': [],
         'stderr': [],
@@ -1421,12 +1423,14 @@ def _process(drain=0):
         proc.wait()
         if outfile is not None:
             stdout.flush()
+            stdout.close()
             with open(outfile, 'rb') as ofh:
                 stdoutstr = ofh.read()
             result['stdout'] = read_stream(stdoutstr, logger=iflogger)
 
         if errfile is not None:
             stderr.flush()
+            stderr.close()
             with open(errfile, 'rb') as efh:
                 stderrstr = efh.read()
             result['stderr'] = read_stream(stderrstr, logger=iflogger)