1220 added timeout for process running

presg.py

@@ -278,7 +278,7 @@ def preSG1D(xr_sg, smdim):
     return sg
 
 
-def preSG(sg_xml, analysis, ppcmd='prevabs', solver='swiftcomp', write_input=True, scrnout=True):
+def preSG(sg_xml, analysis, ppcmd='prevabs', solver='swiftcomp', write_input=True, timeout=30, scrnout=True):
     """ Preprocessor of a structure gene.
 
     Parameters
@@ -331,12 +331,13 @@ def preSG(sg_xml, analysis, ppcmd='prevabs', solver='swiftcomp', write_input=Tru
             cmd.append('-' + analysis)
 
             # cmd = ' '.join(cmd)
-            if scrnout:
-                print('cmd:', cmd)
-                sbp.call(cmd)
-            else:
-                FNULL = open(os.devnull, 'w')
-                sbp.call(cmd, stdout=FNULL, stderr=sbp.STDOUT)
+            utl.run(cmd, timeout, scrnout)
+            # if scrnout:
+            #     print('cmd:', cmd)
+            #     sbp.call(cmd)
+            # else:
+            #     FNULL = open(os.devnull, 'w')
+            #     sbp.call(cmd, stdout=FNULL, stderr=sbp.STDOUT)
 
             return fn_sg_in, smdim
 

utils.py

@@ -1,11 +1,30 @@
 import os
+import sys
 import math
+import subprocess as sbp
 import numpy as np
-# import pandas as pd
 import xml.etree.ElementTree as et
 import msgpi.sg as sgm
 
 
+def run(cmd, timeout, scrnout):
+    # proc = sbp.Popen(cmd, stdout=sbp.PIPE, stderr=sbp.PIPE)
+    if scrnout:
+        # sbp.call(cmd)
+        proc = sbp.Popen(cmd)
+    else:
+        FNULL = open(os.devnull, 'w')
+        # sbp.call(cmd, stdout=FNULL, stderr=sbp.STDOUT)
+        proc = sbp.Popen(cmd, stdout=FNULL, stderr=sbp.STDOUT)
+
+    try:
+        stdout, stderr = proc.communicate(timeout=timeout)
+    except sbp.TimeoutExpired as e:
+        print('TimeoutExpired')
+        proc.kill()
+        print('Process killed')
+
+
 def tilde(v):
     """
     ~v_{ij} = -e_{ijk} * v_k