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August 11, 2014 16:18
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KeyError: 'unset GREP_OPTIONS; qstat'
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# script | |
__author__ = "Ole Weidner" | |
__copyright__ = "Copyright 2012-2013, The SAGA Project" | |
__license__ = "MIT" | |
""" This examples shows how to run a job on a remote SGE cluster | |
using the 'SGE' job adaptor. | |
More information about the saga-python job API can be found at: | |
http://saga-project.github.com/saga-python/doc/library/job/index.html | |
""" | |
import sys | |
import saga | |
def main(): | |
try: | |
# Your ssh identity on the remote machine. | |
ctx = saga.Context("ssh") | |
# Change e.g., if you have a differnent username on the remote machine | |
#ctx.user_id = "your_ssh_username" | |
session = saga.Session() | |
session.add_context(ctx) | |
# Create a job service object that represent a remote pbs cluster. | |
# The keyword 'pbs' in the url scheme triggers the SGE adaptors | |
# and '+ssh' enables SGE remote access via SSH. | |
js = saga.job.Service("sge+ssh://joe2", | |
session=session) | |
# Next, we describe the job we want to run. A complete set of job | |
# description attributes can be found in the API documentation. | |
jd = saga.job.Description() | |
jd.environment = {'FILENAME': 'testfile'} | |
# jd.wall_time_limit = 1 # minutes | |
jd.executable = '/bin/touch' | |
jd.arguments = ['$FILENAME'] | |
# jd.total_cpu_count = 12 # for lonestar this has to be a multiple of 12 | |
# jd.spmd_variation = '12way' # translates to the qsub -pe flag | |
#jd.total_physical_memory = 1024 # Memory requirements in Megabyte | |
# jd.queue = "development" | |
# jd.project = "TG-MCB090174" | |
jd.working_directory = "/W5/sade/sge" | |
jd.output = "examplejob.out" | |
jd.error = "examplejob.err" | |
# Create a new job from the job description. The initial state of | |
# the job is 'New'. | |
touchjob = js.create_job(jd) | |
# Check our job's id and state | |
print "Job ID : %s" % (touchjob.id) | |
print "Job State : %s" % (touchjob.state) | |
# Now we can start our job. | |
print "\n...starting job...\n" | |
touchjob.run() | |
print "Job ID : %s" % (touchjob.id) | |
print "Job State : %s" % (touchjob.state) | |
# List all jobs that are known by the adaptor. | |
# This should show our job as well. | |
print "\nListing active jobs: " | |
for job in js.list(): | |
print " * %s" % job | |
# wait for our job to complete | |
print "\n...waiting for job...\n" | |
touchjob.wait() | |
print "Job State : %s" % (touchjob.state) | |
print "Exitcode : %s" % (touchjob.exit_code) | |
print "Exec. hosts : %s" % (touchjob.execution_hosts) | |
print "Create time : %s" % (touchjob.created) | |
print "Start time : %s" % (touchjob.started) | |
print "End time : %s" % (touchjob.finished) | |
js.close() | |
return 0 | |
except saga.SagaException, ex: | |
# Catch all saga exceptions | |
print "An exception occured: (%s) %s " % (ex.type, (str(ex))) | |
# Get the whole traceback in case of an exception - | |
# this can be helpful for debugging the problem | |
print " \n*** Backtrace:\n %s" % ex.traceback | |
return -1 | |
if __name__ == "__main__": | |
sys.exit(main()) | |
# The result | |
(sqmpy-env)pc-p282(/W5/sade/workspace/saga-samples) SAGA_VERBOSE=DEBUG python sge.py > log.log | |
2014:08:11 18:15:32 MainThread saga : [INFO ] saga-python version: 0.17 | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.myproxy | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.myproxy for saga.Context API with URL scheme(s) ['myproxy://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.x509 | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.x509 for saga.Context API with URL scheme(s) ['x509://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.ssh | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.ssh for saga.Context API with URL scheme(s) ['ssh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.userpass | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.userpass for saga.Context API with URL scheme(s) ['userpass://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_job | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Service API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Job API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_file | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_file for saga.namespace.Directory API with URL scheme(s) ['file://', 'local://', 'sftp://', 'gsisftp://', 'ssh://', 'gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_file for saga.namespace.Entry API with URL scheme(s) ['file://', 'local://', 'sftp://', 'gsisftp://', 'ssh://', 'gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_file for saga.filesystem.Directory API with URL scheme(s) ['file://', 'local://', 'sftp://', 'gsisftp://', 'ssh://', 'gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_file for saga.filesystem.File API with URL scheme(s) ['file://', 'local://', 'sftp://', 'gsisftp://', 'ssh://', 'gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_resource | |
2014:08:11 18:15:32 MainThread saga.Engine : [WARNING ] Skipping adaptor saga.adaptors.shell.shell_resource: beta versions are disabled (v0.1.beta) | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.redis.redis_advert | |
2014:08:11 18:15:32 MainThread saga.Engine : [WARNING ] Skipping adaptor saga.adaptors.redis.redis_advert: beta versions are disabled (v0.2.beta) | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.sge.sgejob | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Service API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Job API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.pbs.pbsjob | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Service API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Job API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.lsf.lsfjob | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Service API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Job API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://'] | |
2014:08:11 18:15:32 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.irods.irods_replica | |
2014:08:11 18:15:33 MainThread saga.Engine : [ERROR ] Skipping adaptor saga.adaptors.irods.irods_replica: failed self test: Could not run iRODS/ils. Check iRODSenvironment and certificates ('module' object has no attribute 'logger') (/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/irods/irods_replica.py +200 (sanity_check) : "environment and certificates (%s)" % ex)) | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.condor.condorjob | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Service API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Job API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.slurm.slurm_job | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Service API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.slurm.slurm_job for saga.job.Job API with URL scheme(s) ['slurm://', 'slurm+ssh://', 'slurm+gsissh://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.http.http_file | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.http.http_file for saga.namespace.Entry API with URL scheme(s) ['http://', 'https://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.http.http_file for saga.filesystem.File API with URL scheme(s) ['http://', 'https://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.aws.ec2_resource | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.aws.ec2_resource for saga.Context API with URL scheme(s) ['ec2://', 'ec2_keypair://', 'openstack://', 'eucalyptus://', 'euca://', 'aws://', 'amazon://', 'http://', 'https://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.aws.ec2_resource for saga.resource.Manager API with URL scheme(s) ['ec2://', 'ec2_keypair://', 'openstack://', 'eucalyptus://', 'euca://', 'aws://', 'amazon://', 'http://', 'https://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.aws.ec2_resource for saga.resource.Compute API with URL scheme(s) ['ec2://', 'ec2_keypair://', 'openstack://', 'eucalyptus://', 'euca://', 'aws://', 'amazon://', 'http://', 'https://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.loadl.loadljob | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Service API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://'] | |
2014:08:11 18:15:33 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Job API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://'] | |
2014:08:11 18:15:33 MainThread saga.saga.adaptor.ssh : [INFO ] default ssh key at /home/sade/.ssh/id_rsa | |
2014:08:11 18:15:33 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/authorized_keys (no public key: /home/sade/.ssh/authorized_keys.pub) | |
2014:08:11 18:15:33 MainThread saga.saga.adaptor.ssh : [INFO ] default ssh key at /home/sade/.ssh/id_dsa | |
2014:08:11 18:15:33 MainThread saga.saga.adaptor.ssh : [INFO ] default ssh key at /home/sade/.ssh/identity | |
2014:08:11 18:15:33 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/authorized_keys2 (no public key: /home/sade/.ssh/authorized_keys2.pub) | |
2014:08:11 18:15:33 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/known_hosts__ (no public key: /home/sade/.ssh/known_hosts__.pub) | |
2014:08:11 18:15:33 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/known_hosts (no public key: /home/sade/.ssh/known_hosts.pub) | |
2014:08:11 18:15:33 MainThread saga.DefaultSession : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_rsa.pub', 'UserKey' : '/home/sade/.ssh/id_rsa'} | |
2014:08:11 18:15:34 MainThread saga.ContextSSH : [INFO ] init SSH context for key at '/home/sade/.ssh/id_rsa' done | |
2014:08:11 18:15:34 MainThread saga.DefaultSession : [DEBUG ] default context [saga.adaptor.ssh ] : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_rsa.pub', 'UserKey' : '/home/sade/.ssh/id_rsa'} | |
2014:08:11 18:15:34 MainThread saga.DefaultSession : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_dsa.pub', 'UserKey' : '/home/sade/.ssh/id_dsa'} | |
2014:08:11 18:15:34 MainThread saga.ContextSSH : [INFO ] init SSH context for key at '/home/sade/.ssh/id_dsa' done | |
2014:08:11 18:15:34 MainThread saga.DefaultSession : [DEBUG ] default context [saga.adaptor.ssh ] : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_dsa.pub', 'UserKey' : '/home/sade/.ssh/id_dsa'} | |
2014:08:11 18:15:34 MainThread saga.DefaultSession : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/identity.pub', 'UserKey' : '/home/sade/.ssh/identity'} | |
2014:08:11 18:15:34 MainThread saga.ContextSSH : [INFO ] init SSH context for key at '/home/sade/.ssh/identity' done | |
2014:08:11 18:15:34 MainThread saga.DefaultSession : [DEBUG ] default context [saga.adaptor.ssh ] : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/identity.pub', 'UserKey' : '/home/sade/.ssh/identity'} | |
2014:08:11 18:15:34 MainThread saga.saga.Session : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh'} | |
2014:08:11 18:15:34 MainThread saga.PTYShell : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x3181d50> | |
2014:08:11 18:15:34 MainThread saga.PTYShell : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
2014:08:11 18:15:34 MainThread saga.PTYShell : [DEBUG ] open master pty for [ssh] [joe2] sade: /usr/bin/env TERM=vt100 "/usr/bin/ssh" -t -o IdentityFile=/home/sade/.ssh/id_rsa -o IdentityFile=/home/sade/.ssh/id_dsa -o IdentityFile=/home/sade/.ssh/identity -o ControlMaster=yes -o ControlPath=/tmp/saga_ssh_sade_%h_%p.ctrl joe2' | |
2014:08:11 18:15:34 MainThread saga.PTYShell : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x3191f50> | |
2014:08:11 18:15:34 MainThread saga.PTYShell : [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/home/sade/.ssh/id_rsa -o IdentityFile=/home/sade/.ssh/id_dsa -o IdentityFile=/home/sade/.ssh/identity -o ControlMaster=yes -o ControlPath=/tmp/saga_ssh_sade_%h_%p.ctrl joe2 | |
2014:08:11 18:15:34 MainThread saga.PTYShell : [DEBUG ] write: [ 3] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
2014:08:11 18:15:34 MainThread saga.PTYShell : [DEBUG ] read : [ 3] [ 86] (ControlSocket /tmp/saga_ssh_sade_joe2_22.ctrl already exists, disabling multiplexing\n) | |
2014:08:11 18:15:34 MainThread saga.PTYShell : [DEBUG ] read : [ 3] [ 199] (Last login: Mon Aug 11 18:15:24 2014 from pc-p282.iwm.fraunhofer.de\n*\n* --==## joe02.iwm.fhg.de ##==--\n*\n*\n* 2014/05/15, Xantaro/randy:\n* - installed gcc/4.9.0\n* - installed python/3.3.5\n\n\n) | |
2014:08:11 18:15:34 MainThread saga.PTYShell : [DEBUG ] read : [ 3] [ 566] ( \nCurrently Loaded Modulefiles:\n 1) gcc/4.5.2 3) intel/openmpi-1.6.3 5) netcdf/4.1.2-b1\n 2) intel/XE.1 4) hdf5/1.8.5-p1\n \n\n#################################################\n# #\n# Please check the wiki for conventions #\n# and other valuable information #\n# #\n# http://joe1/wiki #\n# #\n#################################################\n\n) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] got initial shell prompt (5) (ControlSocket /tmp/saga_ssh_sade_joe2_22.ctrl already exists, disabling multiplexing | |
Last login: Mon Aug 11 18:15:24 2014 from pc-p282.iwm.fraunhofer.de | |
* | |
* --==## joe02.iwm.fhg.de ##==-- | |
* | |
* | |
* 2014/05/15, Xantaro/randy: | |
* - installed gcc/4.9.0 | |
* - installed python/3.3.5 | |
Currently Loaded Modulefiles: | |
1) gcc/4.5.2 3) intel/openmpi-1.6.3 5) netcdf/4.1.2-b1 | |
2) intel/XE.1 4) hdf5/1.8.5-p1 | |
#################################################) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] Got initial shell prompt (5) (ControlSocket /tmp/saga_ssh_sade_joe2_22.ctrl already exists, disabling multiplexing | |
Last login: Mon Aug 11 18:15:24 2014 from pc-p282.iwm.fraunhofer.de | |
* | |
* --==## joe02.iwm.fhg.de ##==-- | |
* | |
* | |
* 2014/05/15, Xantaro/randy: | |
* - installed gcc/4.9.0 | |
* - installed python/3.3.5 | |
Currently Loaded Modulefiles: | |
1) gcc/4.5.2 3) intel/openmpi-1.6.3 5) netcdf/4.1.2-b1 | |
2) intel/XE.1 4) hdf5/1.8.5-p1 | |
#################################################) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x3191c10> | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/home/sade/.ssh/id_rsa -o IdentityFile=/home/sade/.ssh/id_dsa -o IdentityFile=/home/sade/.ssh/identity -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_sade_%h_%p.ctrl joe2 | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 77] (Control socket connect(/tmp/saga_ssh_sade_joe2_22.ctrl): Connection refused\n) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 199] (Last login: Mon Aug 11 18:15:34 2014 from pc-p282.iwm.fraunhofer.de\n*\n* --==## joe02.iwm.fhg.de ##==--\n*\n*\n* 2014/05/15, Xantaro/randy:\n* - installed gcc/4.9.0\n* - installed python/3.3.5\n\n\n) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 566] ( \nCurrently Loaded Modulefiles:\n 1) gcc/4.5.2 3) intel/openmpi-1.6.3 5) netcdf/4.1.2-b1\n 2) intel/XE.1 4) hdf5/1.8.5-p1\n \n\n#################################################\n# #\n# Please check the wiki for conventions #\n# and other valuable information #\n# #\n# http://joe1/wiki #\n# #\n#################################################\n\n) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] got initial shell prompt (5) (Control socket connect(/tmp/saga_ssh_sade_joe2_22.ctrl): Connection refused | |
Last login: Mon Aug 11 18:15:34 2014 from pc-p282.iwm.fraunhofer.de | |
* | |
* --==## joe02.iwm.fhg.de ##==-- | |
* | |
* | |
* 2014/05/15, Xantaro/randy: | |
* - installed gcc/4.9.0 | |
* - installed python/3.3.5 | |
Currently Loaded Modulefiles: | |
1) gcc/4.5.2 3) intel/openmpi-1.6.3 5) netcdf/4.1.2-b1 | |
2) intel/XE.1 4) hdf5/1.8.5-p1 | |
#################################################) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] Got initial shell prompt (5) (Control socket connect(/tmp/saga_ssh_sade_joe2_22.ctrl): Connection refused | |
Last login: Mon Aug 11 18:15:34 2014 from pc-p282.iwm.fraunhofer.de | |
* | |
* --==## joe02.iwm.fhg.de ##==-- | |
* | |
* | |
* 2014/05/15, Xantaro/randy: | |
* - installed gcc/4.9.0 | |
* - installed python/3.3.5 | |
Currently Loaded Modulefiles: | |
1) gcc/4.5.2 3) intel/openmpi-1.6.3 5) netcdf/4.1.2-b1 | |
2) intel/XE.1 4) hdf5/1.8.5-p1 | |
#################################################) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] running command shell: exec /bin/sh -i | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
2014:08:11 18:15:35 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
2014:08:11 18:15:36 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 1] (\n) | |
2014:08:11 18:15:36 MainThread saga.PTYShell : [DEBUG ] sent prompt trigger again (1) | |
2014:08:11 18:15:36 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 9] (joe2(~) $) | |
2014:08:11 18:15:36 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 21] ($PROMPT-0->PROMPT-0->) | |
2014:08:11 18:15:36 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 30] ( printf "SYNCHRONIZE_PROMPT\n"\n) | |
2014:08:11 18:15:36 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 30] (SYNCHRONIZE_PROMPT\nPROMPT-0->) | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] got new shell prompt | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] run_sync: which qdel | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 11] (which qdel\n) | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 38] (/opt/GE/2011.11p1/bin/linux-x64/qdel\n) | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->) | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] run_sync: qdel -help | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 11] (qdel -help\n) | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 585] (OGS/GE 2011.11p1\nusage: qdel [options] job_task_list\n [-f] force action\n [-help] print this help\n [-u user_list] delete all jobs of users specified in list\n job_task_list delete all jobs given in list\n\njob_task_list job_tasks[,job_tasks,...]\njob_tasks [job_id['.'task_id_range]|job_name|pattern][' -t 'task_id_range]\ntask_id_range task_id['-'task_id[':'step]]\nuser_list user[,user,...]\nPROMPT-0->) | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] run_sync: which qsub | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 11] (which qsub\n) | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 48] (/opt/GE/2011.11p1/bin/linux-x64/qsub\nPROMPT-0->) | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] run_sync: qsub -help | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 11] (qsub -help\n) | |
2014:08:11 18:15:37 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (OGS/GE 2011.11p1\nusage: qsub ... eadline initiation time\n [-) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (e path_list] ... to queue(s)\n [-notify] ) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( no ... ) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( consider following request ... account_name\ncomplex) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (_list complex[,comp ... cluster queue\nwc_host ) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 629] ( wildcard expression ... [:<socket>,<core>]\nPROMPT-0->) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] run_sync: which qconf | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (which qconf\n) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 49] (/opt/GE/2011.11p1/bin/linux-x64/qconf\nPROMPT-0->) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] run_sync: qconf -help | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (qconf -help\n) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (OGS/GE 2011.11p1\nusage: qconf ... w host group entry from file\n) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( [-arqs [rqs_list]] ... file\n [-at thread_name] ) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( add/start ... delete host) | |
2014:08:11 18:15:38 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( group entry\n [-drqs rqs_li ... s}] ) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( shutdown master|schedulin ... m) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (odify exec server\n [-Me fna ... e node_shares_list] ) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( modify sharetree node(s)\n ... n\n [-sckptl] ) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( show all ckpt ... show resource quota set(s)) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (\n [-srqsl] ... sharetree node(s)\n [-rsstno) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (de node_list] ... user[,user,...]\nobj_nm ) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 481] ( "queue"|"exechost"|"pe"|"ckpt"|"hostgroup"|"resource_quota"\nattr_nm (see man pages)\nobj_id_list objectname [ objectname ...]\nproject_list project[,project,...]\nevid_list all | evid[,evid,...]\nhost_list all | hostname[,hostname,...]\nobj_nm2 "queue"|"queue_domain"|"queue_instance"|"exechost"\nobj_nm3 "queue"\nthread_name "scheduler"|"jvm"\nPROMPT-0->) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] run_sync: which qacct | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (which qacct\n) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 39] (/opt/GE/2011.11p1/bin/linux-x64/qacct\n) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->) | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] run_sync: qacct -help | |
2014:08:11 18:15:39 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (qacct -help\n) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (OGS/GE 2011.11p1\nusage: qacct ... slots]] list ) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 328] ([matching] job slots\n [-t taskid[-taskid[:step]]] list all [matching] tasks (requires -j option)\n [[-f] acctfile] use alternate accounting file\n\n begin_time, end_time [[CC]YYMMDDhhmm[.SS]\n queue [cluster_queue|queue_instance|queue_domain|pattern]\nPROMPT-0->) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] run_sync: which qstat | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (which qstat\n) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 49] (/opt/GE/2011.11p1/bin/linux-x64/qstat\nPROMPT-0->) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] run_sync: qstat -help | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (qstat -help\n) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (OGS/GE 2011.11p1\nusage: qstat ... [-pe pe_list] ) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( select only queues wit ... have access\n [-urg] ) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 920] ( displ ... eue[,wc_queue,...]\nPROMPT-0->) | |
2014:08:11 18:15:40 MainThread saga.SGEJobService : [INFO ] Found SGE tools: {'qdel': {'path': '/opt/GE/2011.11p1/bin/linux-x64/qdel', 'version': 'OGS/GE 2011.11p1'}, 'qsub': {'path': '/opt/GE/2011.11p1/bin/linux-x64/qsub', 'version': 'OGS/GE 2011.11p1'}, 'qconf': {'path': '/opt/GE/2011.11p1/bin/linux-x64/qconf', 'version': 'OGS/GE 2011.11p1'}, 'qacct': {'path': '/opt/GE/2011.11p1/bin/linux-x64/qacct', 'version': 'OGS/GE 2011.11p1'}, 'qstat': {'path': '/opt/GE/2011.11p1/bin/linux-x64/qstat', 'version': 'OGS/GE 2011.11p1'}} | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] run_sync: /opt/GE/2011.11p1/bin/linux-x64/qconf -spl | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 43] (/opt/GE/2011.11p1/bin/linux-x64/qconf -spl\n) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 210] (abaqus\nabaqus_1\nabaqus_2\nabaqus_3\nabaqus_4\nabaqus_5\nabaqus_mpi\nlam\nmake\nmpich\nopenmpi\nopenmpi_16\nopenmpi_2\nopenmpi_32\nopenmpi_4\nopenmpi_64\nopenmpi_8\nopenmpi_sn\npvm\nsmp\ntobi_mpich\nPROMPT-0->) | |
2014:08:11 18:15:40 MainThread saga.SGEJobService : [DEBUG ] Available processing elements: ['abaqus', 'abaqus_1', 'abaqus_2', 'abaqus_3', 'abaqus_4', 'abaqus_5', 'abaqus_mpi', 'lam', 'make', 'mpich', 'openmpi', 'openmpi_16', 'openmpi_2', 'openmpi_32', 'openmpi_4', 'openmpi_64', 'openmpi_8', 'openmpi_sn', 'pvm', 'smp', 'tobi_mpich'] | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] run_sync: /opt/GE/2011.11p1/bin/linux-x64/qconf -sc | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 42] (/opt/GE/2011.11p1/bin/linux-x64/qconf -sc\n) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (#name shortcut ... NO 0:0:0 0\nh_) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (stack h_stack M ... 0 0\nmem_total ) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( mt MEMORY <= ... ta s_data MEM) | |
2014:08:11 18:15:40 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (ORY <= YES NO ... su MEMORY >= ) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 456] ( YES NO 0 0\ntmpdir tmp RESTRING == NO NO NONE 0\nvirtual_free vf MEMORY <= YES NO 0 0\nvirtual_total vt MEMORY <= YES NO 0 0\nvirtual_used vu MEMORY >= YES NO 0 0\n# >#< starts a comment but comments are not saved across edits --------\nPROMPT-0->) | |
2014:08:11 18:15:41 MainThread saga.SGEJobService : [DEBUG ] Optional memory attributes: [] | |
2014:08:11 18:15:41 MainThread saga.SGEJobService : [DEBUG ] Mandatory memory attributes: ['h_core', 'h_data', 'h_fsize', 'h_rss', 'h_stack', 'h_vmem', 'mem_free', 'mem_total', 'mem_used', 's_core', 's_data', 's_fsize', 's_rss', 's_stack', 's_vmem', 'swap_free', 'swap_rate', 'swap_rsvd', 'swap_total', 'swap_used', 'virtual_free', 'virtual_total', 'virtual_used'] | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] run_sync: /opt/GE/2011.11p1/bin/linux-x64/qconf -sconf | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 45] (/opt/GE/2011.11p1/bin/linux-x64/qconf -sconf\n) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (#global:\nexecd_spool_dir ... none\nexecd_params ) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1013] ( none\nreporting_ ... ,i,e,o,j,M,N,p,w\n\nPROMPT-0->) | |
2014:08:11 18:15:41 MainThread saga.SGEJobService : [INFO ] Accounting is enabled | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] run_sync: find $HOME/.saga/adaptors/sge_job -type f -mtime +30 -print -delete | wc -l | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 76] (find $HOME/.saga/adaptors/sge_job -type f -mtime +30 -print -delete | wc -l\n) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 13] (0\nPROMPT-0->) | |
2014:08:11 18:15:41 MainThread saga.SGEJobService : [INFO ] Purged 0 | |
temporary files | |
2014:08:11 18:15:41 MainThread saga.SGEJobService : [INFO ] Generated SGE script: | |
#!/bin/bash | |
#$ -S /bin/bash | |
#$ -V | |
#$ -v FILENAME=testfile | |
#$ -wd /W5/sade/sge | |
#$ -o examplejob.out | |
#$ -e examplejob.err | |
function aborted() { | |
echo Aborted with signal \$1. | |
echo \"signal: \$1\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
echo \"end_time: \$(LC_ALL=en_US.utf8 date '+%a %b %d %H:%M:%S %Y')\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
exit -1 | |
} | |
mkdir -p \$HOME/.saga/adaptors/sge_job | |
for sig in SIGHUP SIGINT SIGQUIT SIGTERM SIGUSR1 SIGUSR2; do trap \"aborted \$sig\" \$sig; done | |
echo \"hostname: \$HOSTNAME\" >\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
echo \"qsub_time: Mon Aug 11 18:15:41 2014\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
echo \"start_time: \$(LC_ALL=en_US.utf8 date '+%a %b %d %H:%M:%S %Y')\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
/bin/touch \$FILENAME | |
echo \"exit_status: \$?\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
echo \"end_time: \$(LC_ALL=en_US.utf8 date '+%a %b %d %H:%M:%S %Y')\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] run_sync: (test -d /W5/sade/sge && echo -n 0) || (mkdir -p /W5/sade/sge && echo -n 1) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 76] ((test -d /W5/sade/sge && echo -n 0) || (mkdir -p /W5/sade/sge && echo -n 1)\n) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1] (0) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] run_sync: (test -d && echo -n 0) || (mkdir -p && echo -n 1) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 52] ((test -d && echo -n 0) || (mkdir -p && echo -n 1)\n) | |
2014:08:11 18:15:41 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1] (0) | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->) | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] run_sync: (test -d && echo -n 0) || (mkdir -p && echo -n 1) | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 52] ((test -d && echo -n 0) || (mkdir -p && echo -n 1)\n) | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 11] (0PROMPT-0->) | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] run_sync: SCRIPTFILE=`mktemp -t SAGA-Python-SGEJobScript.XXXXXX` && echo " | |
#!/bin/bash | |
#$ -S /bin/bash | |
#$ -V | |
#$ -v FILENAME=testfile | |
#$ -wd /W5/sade/sge | |
#$ -o examplejob.out | |
#$ -e examplejob.err | |
function aborted() { | |
echo Aborted with signal \$1. | |
echo \"signal: \$1\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
echo \"end_time: \$(LC_ALL=en_US.utf8 date '+%a %b %d %H:%M:%S %Y')\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
exit -1 | |
} | |
mkdir -p \$HOME/.saga/adaptors/sge_job | |
for sig in SIGHUP SIGINT SIGQUIT SIGTERM SIGUSR1 SIGUSR2; do trap \"aborted \$sig\" \$sig; done | |
echo \"hostname: \$HOSTNAME\" >\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
echo \"qsub_time: Mon Aug 11 18:15:41 2014\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
echo \"start_time: \$(LC_ALL=en_US.utf8 date '+%a %b %d %H:%M:%S %Y')\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
/bin/touch \$FILENAME | |
echo \"exit_status: \$?\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID | |
echo \"end_time: \$(LC_ALL=en_US.utf8 date '+%a %b %d %H:%M:%S %Y')\" >>\$HOME/.saga/adaptors/sge_job/\$JOB_ID" > $SCRIPTFILE && /opt/GE/2011.11p1/bin/linux-x64/qsub -notify $SCRIPTFILE && rm -f $SCRIPTFILE | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 1130] (SCRIPTFILE=`mktemp -t SAGA-Pyt ... IPTFILE && rm -f $SCRIPTFILE\n) | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 72] (Your job 125834 ("SAGA-Python-SGEJobScript.wW6778") has been submitted\n) | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->) | |
2014:08:11 18:15:42 MainThread saga.SGEJobService : [INFO ] Submitted SGE job with id: [sge+ssh://joe2]-[125834] | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] run_sync: /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==125834) {{print $5,$6,$7,$8}}' | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 93] (/opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==125834) {{print $5,$6,$7,$8}}'\n) | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 26] (qw 08/11/2014 18:15:42 1\n) | |
2014:08:11 18:15:42 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->) | |
Traceback (most recent call last): | |
File "sge.py", line 99, in <module> | |
sys.exit(main()) | |
File "sge.py", line 68, in main | |
print "Job State : %s" % (touchjob.state) | |
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/job/job.py", line 542, in get_state | |
return self._adaptor.get_state (ttype=ttype) | |
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/cpi/decorators.py", line 51, in wrap_function | |
return sync_function (self, *args, **kwargs) | |
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/sge/sgejob.py", line 1235, in get_state | |
return self.js._job_get_state(self._id) | |
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/sge/sgejob.py", line 972, in _job_get_state | |
self.jobs[job_id] = self._job_get_info(job_id=job_id) | |
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/sge/sgejob.py", line 950, in _job_get_info | |
curr_info = self._retrieve_job(job_id) | |
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/sge/sgejob.py", line 890, in _retrieve_job | |
key_suffix=":") | |
File "/W5/sade/workspace/sqmpy-env/lib/python2.7/site-packages/saga_python-0.17-py2.7.egg/saga/adaptors/sge/sgejob.py", line 505, in __kvcmd_results | |
ret, out, _ = self.shell.run_sync('%s %s' % (self._commands[cmd]['path'], cmd_args)) | |
KeyError: 'unset GREP_OPTIONS; qstat' |
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