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Makefile

@@ -36,6 +36,7 @@ INSTALL_FILES=VERSION mjf.init \
               mjf.sh.torque mjf.csh.torque mjf-get-total-cpu.torque \
               mjf.sh.htcondor mjf.csh.htcondor mjf-get-total-cpu.htcondor \
               mjf-job-wrapper make-jobfeatures.htcondor \
+              mjf.sh.gridengine mjf.csh.gridengine make-jobfeatures.gridengine \
               mjf.sh.onlymf mjf.csh.onlymf \
               DIRACbenchmark.py db12.init
 
@@ -113,6 +114,24 @@ htcondor-rpm: mjf-scripts.tgz
 	  --define "_topdir $(shell pwd)/RPMTMP" \
 	  --buildroot $(shell pwd)/RPMTMP/BUILDROOT mjf-htcondor.spec
 
+gridengine-install: $(INSTALL_FILES) install
+	mkdir -p $(RPM_BUILD_ROOT)/usr/sbin 
+	cp mjf.sh.gridengine \
+           $(RPM_BUILD_ROOT)/etc/profile.d/mjf.sh
+	cp mjf.csh.gridengine \
+           $(RPM_BUILD_ROOT)/etc/profile.d/mjf.csh
+	cp make-jobfeatures.gridengine \
+           $(RPM_BUILD_ROOT)/usr/sbin/make-jobfeatures
+
+gridengine-rpm: mjf-scripts.tgz
+	rm -Rf RPMTMP
+	mkdir -p RPMTMP/SOURCES RPMTMP/SPECS RPMTMP/BUILD \
+         RPMTMP/SRPMS RPMTMP/RPMS/noarch RPMTMP/BUILDROOT
+	cp -f mjf-scripts.tgz RPMTMP/SOURCES        
+	export MJF_VERSION=$(VERSION) ; rpmbuild -ba \
+	  --define "_topdir $(shell pwd)/RPMTMP" \
+	  --buildroot $(shell pwd)/RPMTMP/BUILDROOT mjf-gridengine.spec
+
 db12-install: $(INSTALL_FILES)
 	mkdir -p $(RPM_BUILD_ROOT)/etc/rc.d/init.d \
                  $(RPM_BUILD_ROOT)/etc/db12 \

make-jobfeatures.gridengine

+#!/usr/bin/python
+#
+#  make-jobfeatures script for Machine/Job Features on Grid Engine
+#
+#  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.
+
+#  Create $JOBFEATURES files following the Machine/Job Features 
+#  specification in HSF-TN-2016-02
+#
+#  This script creates the $JOBFEATURES directory at 
+#  /tmp/mjf-$USER/jobfeatures-$JOB_ID 
+#  and attempts to populate it from OS/batch information
+#  and from $MACHINEFEATURES=/etc/machinefeatures
+#
+#  If the following variables are present in /var/run/mjf or 
+#  /etc/sysconfig/mjf then they are used as defaults if not 
+#  obtainable from Grid Engine:
+#
+#  - allocated_cpu
+#  - wall_limit_secs
+#  - cpu_limit_secs
+#  - max_rss_bytes
+#  - max_swap_bytes
+#  - scratch_limit_bytes
+#  - hs06_job
+#  - db12_job
+#
+#  Values in /var/run/mjf are preferred over /etc/sysconfig/mjf.
+#
+#  The following per-cpu values in either mjf file will be used
+#  to calculate the corresponding per-job values if not given in
+#  either file or obtainable from Grid Engine:
+# 
+#  - cpu_limit_secs_per_cpu
+#  - max_rss_bytes_per_cpu
+#  - max_swap_bytes_per_cpu
+#  - scratch_limit_bytes_per_cpu
+#
+#  Additionally you can set mjf_tmp_dir in those files to use a 
+#  directory other than /tmp for the mjf-$USER directories.
+#
+
+import os
+import re
+import pwd
+import sys
+import stat
+import time
+
+os.umask(0022)
+
+try:
+  job_id = os.environ['JOB_ID']
+except:
+  sys.stderr.write('Could not get Grid Engine $JOB_ID - exiting make-jobfeatures\n')
+  sys.exit(10)
+
+# Values in /var/run/mjf take precedence
+try:
+  fromRun = open('/var/run/mjf','r').read()
+except:
+  fromRun = ''
+
+# Also look in persistent /etc/sysconfig/mjf
+try:
+  fromSysconfig = open('/etc/sysconfig/mjf','r').read()
+except:
+  fromSysconfig = ''  
+
+mjfTmpDir = '/tmp'
+
+if 'mjf_tmp_dir=' in fromRun + fromSysconfig:
+  try:
+    matchObject = re.search("mjf_tmp_dir=(.*)", fromRun + '\n' + fromSysconfig)
+    mjfTmpDir = matchObject.group(1)
+  except:
+    pass
+
+try:
+  userName = pwd.getpwuid(os.getuid())[0]
+except:
+  userName = str(os.getuid())
+
+# First make sure the mjfTmpDir/mjf-$USER directory exists
+try:
+  os.mkdir(mjfTmpDir + '/mjf-' + userName)
+except:
+  # Ok if exists already
+  pass
+
+try: 
+  userDirStat = os.stat(mjfTmpDir + '/mjf-' + userName)
+except:
+  print mjfTmpDir + '/mjf-' + userName + ' could not be created'
+  sys.exit(12)
+
+# Check it is owned by us
+if userDirStat.st_uid != os.getuid() or userDirStat.st_gid != os.getgid():
+  print mjfTmpDir + '/mjf-' + userName + ' has the wrong UID/GID'
+  sys.exit(13)
+
+# Ensure the right permissions
+os.chmod(mjfTmpDir + '/mjf-' + userName, 
+         stat.S_IRWXU + stat.S_IRGRP + stat.S_IXGRP + stat.S_IROTH + stat.S_IXOTH)
+
+# Now the directory for this job (but with # -> _)
+jobfeaturesDir = mjfTmpDir + '/mjf-' + userName + '/jobfeatures-' + job_id
+
+if os.path.exists(jobfeaturesDir):
+  # Silently exit if has been created already
+  sys.exit(0)
+
+try:
+  os.mkdir(jobfeaturesDir)
+except:
+  print 'Failed to create ' + jobfeaturesDir
+  sys.exit(14)
+
+open(jobfeaturesDir + '/job_id', 'w').write(job_id)
+
+jobfeatures = {}
+jobfeatures['allocated_cpu'] = 1
+  
+jobstart_secs = int(time.time())
+open(jobfeaturesDir + '/jobstart_secs', 'w').write(str(jobstart_secs))
+
+# Get any defaults for these (integer) values
+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]*)", fromRun + '\n' + fromSysconfig)
+      jobfeatures[key] = int(matchObject.group(1))
+    except:
+      pass
+
+# Look for $NSLOTS for the number of CPUs allocated
+try:
+  jobfeatures['allocated_cpu'] = int(os.environ['NSLOTS'])
+except:
+  pass
+
+# Look for any per-cpu values given in either file
+for key in ['cpu_limit_secs', 'max_rss_bytes', 
+            'max_swap_bytes', 'scratch_limit']:
+
+  if key + '_per_cpu=' in fromRun + fromSysconfig:
+    try:
+      matchObject = re.search(key + "_per_cpu=([0-9]*)", fromRun + '\n' + fromSysconfig)
+
+      if key not in jobfeatures:
+        jobfeatures[key] = int(matchObject.group(1)) * jobfeatures['allocated_cpu']
+    except:
+      pass
+
+#
+#
+# Get jobfeatures['wall_limit_secs'] here, somehow?
+#
+#
+
+
+if not 'cpu_limit_secs' in jobfeatures and 'wall_limit_secs' in jobfeatures:
+  # If not given in mjf files, we create a CPU seconds limit from wallclock 
+  # and allocated CPUs/processors
+  jobfeatures['cpu_limit_secs'] = jobfeatures['wall_limit_secs'] * jobfeatures['allocated_cpu']
+
+# Write out if these have been set from files or prologue.user arguments
+for key in ['allocated_cpu', 'wall_limit_secs', 'cpu_limit_secs',
+            'max_rss_bytes', 'max_swap_bytes', 'scratch_limit_bytes']:
+
+  if key in jobfeatures:
+    open(jobfeaturesDir + '/' + key, 'w').write(str(jobfeatures[key]))
+
+# Try to get/calculate hs06_job
+hs06_job = None
+
+if 'hs06_job=' in fromRun + fromSysconfig:
+  try:
+    matchObject = re.search("hs06_job=([0-9.]*)", fromRun + '\n' + fromSysconfig)
+    hs06_job = float(matchObject.group(1))
+  except:
+    pass
+
+if not hs06_job:
+  try:
+    hs06 = float(open('/etc/machinefeatures/hs06','r').readline())
+  except:
+    hs06 = None
+
+  try:
+    total_cpu = int(open('/etc/machinefeatures/total_cpu','r').readline())
+  except:
+    total_cpu = None
+
+  if hs06 and total_cpu:
+    # Simple pro-rata allocation of total hs06 depending on processors for this job
+    hs06_job = (jobfeatures['allocated_cpu'] * hs06) / total_cpu
+    
+if hs06_job:
+  # We got it from somewhere
+  open(jobfeaturesDir + '/hs06_job', 'w').write('%.2f' % hs06_job)
+
+# Try to get/calculate db12_job
+db12_job = None
+
+if 'db12_job=' in fromRun + fromSysconfig:
+  try:
+    matchObject = re.search("db12_job=([0-9.]*)", fromRun + '\n' + fromSysconfig)
+    db12_job = float(matchObject.group(1))
+  except:
+    pass
+
+if not db12_job:
+  try:
+    db12 = float(open('/etc/machinefeatures/db12','r').readline())
+  except:
+    db12 = None
+
+  try:
+    total_cpu = int(open('/etc/machinefeatures/total_cpu','r').readline())
+  except:
+    total_cpu = None
+
+  if db12 and total_cpu:
+    # Simple pro-rata allocation of total db12 depending on processors for this job
+    db12_job = (jobfeatures['allocated_cpu'] * db12) / total_cpu
+    
+if db12_job:
+  # We got it from somewhere
+  open(jobfeaturesDir + '/db12_job', 'w').write('%.2f' % db12_job)
+
+# We output $JOBFEATURES in case the calling script needs it
+print jobfeaturesDir
+
+ 
\ No newline at end of file

make-jobfeatures.htcondor

@@ -56,7 +56,7 @@
 #
 #  The following per-cpu values in either mjf file will be used
 #  to calculate the corresponding per-job values if not given in
-#  either file or obtainable from PBS/Torque:
+#  either file or obtainable from HTCondor:
 # 
 #  - cpu_limit_secs_per_cpu
 #  - max_rss_bytes_per_cpu

mjf.csh.gridengine

+mjf_tmp_dir=/tmp
+if ( -r /etc/sysconfig/mjf ) then
+  source /var/sysconfig/mjf
+endif
+if ( -r /var/run/mjf ) then
+  source /var/run/mjf
+endif
+if ( -d /etc/machinefeatures ) then
+  setenv MACHINEFEATURES /etc/machinefeatures
+endif
+setenv JOBFEATURES `/usr/sbin/make-jobfeatures`

mjf.sh.gridengine

+mjf_tmp_dir=/tmp
+if [ -r /etc/sysconfig/mjf ] ; then
+ . /etc/sysconfig/mjf
+fi
+if [ -r /var/run/mjf ] ; then
+ . /etc/sysconfig/mjf
+fi
+if [ -d /etc/machinefeatures ] ; then
+  export MACHINEFEATURES=/etc/machinefeatures
+fi
+export JOBFEATURES=`/usr/sbin/make-jobfeatures`