Fill out prologue.user and add epilogue.user

Makefile

@@ -31,7 +31,7 @@
 
 include VERSION
 
-INSTALL_FILES=VERSION prologue.user mjf.init mjf.sh mjf.csh
+INSTALL_FILES=VERSION prologue.user epilogue.user mjf.init mjf.sh mjf.csh
           
 TGZ_FILES=$(INSTALL_FILES) Makefile mjf-torque.spec
 
@@ -46,7 +46,7 @@ install: $(INSTALL_FILES)
 	mkdir -p $(RPM_BUILD_ROOT)/var/lib/torque/mom_priv \
 	         $(RPM_BUILD_ROOT)/etc/rc.d/init.d \
 	         $(RPM_BUILD_ROOT)/etc/profile.d
-	cp prologue.user  \
+	cp prologue.user epilogue.user \
 	   $(RPM_BUILD_ROOT)/var/lib/torque/mom_priv
 	cp mjf.init \
 	   $(RPM_BUILD_ROOT)/etc/rc.d/init.d/mjf

epilogue.user

+#!/bin/sh
+#
+#  epilogue.user script for Machine/Job Features on Torque/PBS
+#
+#  Andrew McNab, University of Manchester.
+#  Copyright (c) 2016. All rights reserved.
+#
+#  Redistribution and use in source and binary forms, with or
+#  without modification, are permitted provided that the following
+#  conditions are met:
+#
+#    o Redistributions of source code must retain the above
+#      copyright notice, this list of conditions and the following
+#      disclaimer. 
+#    o Redistributions in binary form must reproduce the above
+#      copyright notice, this list of conditions and the following
+#      disclaimer in the documentation and/or other materials
+#      provided with the distribution. 
+#
+#  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+#  CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+#  INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+#  DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
+#  BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+#  EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+#  TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+#  DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+#  ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+#  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+#  OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+#  POSSIBILITY OF SUCH DAMAGE.
+
+# Remove $JOBFEATURES directory for this job where the directory
+# is at $HOME/jobfeatures-$PBS_JOBID
+
+if [ "$PBS_JOBID" != "" -a -d "$HOME/jobfeatures-$PBS_JOBID" ] ; then
+  rm -Rf "$HOME/jobfeatures-$PBS_JOBID" 
+fi

prologue.user

@@ -30,6 +30,25 @@
 #  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
 #  OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 #  POSSIBILITY OF SUCH DAMAGE.
+
+#  Create $JOBFEATURES files following the Machine/Job Features 
+#  specification in HSF-TN-2016-02
+#
+#  This script creates the $JOBFEATURES directory at 
+#  $HOME/jobfeatures-$PBS_JOBID and attempts to populate it
+#  from Torque/PBS information and from 
+#  $MACHINEFEATURES=/etc/machinefeatures
+#
+#  If the following variables are present in /var/run/mjf or 
+#  /etc/sysconfig/mjf then they are preferred:
+#
+#  - hs06_job
+#  - allocated_cpu
+#  - wall_limit_secs
+#  - cpu_limit_secs
+#  - max_rss_bytes
+#  - max_swap_bytes
+#  - scratch_limit_bytes
 #
 
 import os
@@ -37,27 +56,23 @@ import re
 import sys
 import time
 
-#
-# PROGRAM MAIN !!!
-# 
-
-
-homdeDir = os.path.expanduser('~')
+homeDir = os.path.expanduser('~')
 
 job_id = os.environ['PBS_JOBID']
 
-jobfeaturesDir = homeDir + '/jobfeatures-' + jobID
-
+jobfeaturesDir = homeDir + '/jobfeatures-' + job_id
 os.mkdir(jobfeaturesDir)
 
 open(jobfeaturesDir + '/job_id', 'w').write(job_id)
 
+jobfeatures = {}
+
 try:
-  allocated_cpu = int(os.environ['PBS_NUM_PPN'])
+  jobfeatures['allocated_cpu'] = int(os.environ['PBS_NUM_PPN'])
 except:
-  allocated_cpu = 1
+  jobfeatures['allocated_cpu'] = 1
   
-open(jobfeaturesDir + '/job_id', 'w').write(str(allocated_cpu))
+open(jobfeaturesDir + '/job_id', 'w').write(str(jobfeatures['allocated_cpu']))
 
 try:
   hs06 = float(open('/etc/machinefeatures/hs06','r').readline())
@@ -71,14 +86,88 @@ except:
   
 if hs06 and total_cpu:
   # Simple pro-rata allocation of total hs06 depending on processors for this job
-  hs06_job = (allocated_cpu * hs06) / total_cpu
-  open(jobfeaturesDir + '/hs06_job', 'w').write(str(hs06_job))
+  hs06_job = (jobfeatures['allocated_cpu'] * hs06) / total_cpu
+else:
+  hs06_job = None
+
+jobstart_secs = int(time.time())
+open(jobfeaturesDir + '/jobstart_secs', 'w').write(str(jobstart_secs))
+
+jobfeatures['wall_limit_secs'] = None
+jobfeatures['cpu_limits_secs'] = None
+jobfeatures['max_rss_bytes']   = None
+jobfeatures['max_swap_bytes']  = None
 
 try: 
-  qstatResult = os.popen('qstat -f ' + jobID,'r').read()
+  qstatResult = os.popen('qstat -f ' + job_id,'r').read()
 except:
+  # Ok if not possible (qstat not installed? Not allowed to use it?)
   pass
+else:
+  try:
+    wallMatchObject = re.search(' *Resource_List.walltime = ([0-9]*):([0-9]*):([0-9]*)', qstatResult)
+    jobfeatures['wall_limit_secs'] = int(wallMatchObject.group(1)) * 3600 + int(wallMatchObject.group(2)) * 60 + int(wallMatchObject.group(3))
+  except:
+    pass
 
-jobstart_secs = int(time.time())
-open(jobfeaturesDir + '/jobstart_secs', 'w').write(str(jobstart_secs))
+  try:
+    cpuMatchObject = re.search(' *Resource_List.cput = ([0-9]*):([0-9]*):([0-9]*)', qstatResult)
+    jobfeatures['cpu_limit_secs'] = int(cpuMatchObject.group(1)) * 3600 + int(cpuMatchObject.group(2)) * 60 + int(cpuMatchObject.group(3))
+  except:
+    pass
+
+  try:
+    rssMatchObject = re.search(' *Resource_List.mem = ([0-9]*)([a-z]*)', qstatResult)
+    rssInt  = int(rssMatchObject.group(1))
+    rssUnit = rssMatchObject.group(2)
+  except:
+    pass
+  else:    
+    if rssUnit == 'gb':
+      jobfeatures['max_rss_bytes'] = rssInt * 1000000000
+    elif rssUnit == 'mb':
+      jobfeatures['max_rss_bytes'] = rssInt * 1000000
+    elif rssUnit == 'kb':
+      jobfeatures['max_rss_bytes'] = rssInt * 1000
+    elif rssUnit == 'b':
+      # Is this the right name??
+      jobfeatures['max_rss_bytes'] = rssInt
+
+# Values in /var/run/mjf take precedence
+try:
+  fromRun = open('/var/run/mjf','r').read()
+except:
+  fromRun = ''
+
+# Also look in persistent /etc/sysconfig/mjf
+try:
+  fromSysconfig = open('/etc/sysconfig/mjf','r').read()
+except:
+  fromSysconfig = ''  
+
+# hs06_job is a float so special handling
+if 'hs06_job=' in fromRun + fromSysconfig:
+  try:
+    matchObject = re.search(key + "=([0-9.]*)", fromSysconfig + fromRun)
+    hs06_job = float(matchObject.group(1))
+  except:
+    pass
+    
+  if hs06_job:
+    # Has been defined here or before
+    open(jobfeaturesDir + '/hs06_job', 'w').write('%.2f' % hs06_job)
+
+# The rest are integers so handle with a list
+for key in ['allocated_cpu', 'wall_limit_secs', 'cpu_limit_secs',
+            'max_rss_bytes', 'max_swap_bytes', 'scratch_limit_bytes']:
+
+  if key + '=' in fromRun + fromSysconfig:
+    try:
+      matchObject = re.search(key + "=([0-9]*)", fromSysconfig + fromRun)
+      jobfeatures[key] = int(matchObject.group(1))
+    except:
+      pass
+
+  if key in jobfeatures:
+    open(jobfeaturesDir + '/' + key, 'w').write(str(jobfeatures[key]))