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mehdisadeghi/gist:06c81930eec6cb97d21f

Created August 13, 2014 10:16
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sge debug output
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gistfile1.py
(sqmpy-env)pc-p282(/W5/sade/workspace/saga-samples) SAGA_VERBOSE=DEBUG python sge.py
2014:08:13 12:15:01 MainThread saga : [INFO ] saga-python version: 0.17
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.myproxy
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.myproxy for saga.Context API with URL scheme(s) ['myproxy://']
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.x509
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.x509 for saga.Context API with URL scheme(s) ['x509://']
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.ssh
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.ssh for saga.Context API with URL scheme(s) ['ssh://']
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.userpass
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.userpass for saga.Context API with URL scheme(s) ['userpass://']
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_job
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Service API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Job API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_file
2014:08:13 12:15:01 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://']
2014:08:13 12:15:01 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://']
2014:08:13 12:15:01 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://']
2014:08:13 12:15:01 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://']
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_resource
2014:08:13 12:15:01 MainThread saga.Engine : [WARNING ] Skipping adaptor saga.adaptors.shell.shell_resource: beta versions are disabled (v0.1.beta)
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.redis.redis_advert
2014:08:13 12:15:01 MainThread saga.Engine : [WARNING ] Skipping adaptor saga.adaptors.redis.redis_advert: beta versions are disabled (v0.2.beta)
2014:08:13 12:15:01 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.sge.sgejob
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Service API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Job API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.pbs.pbsjob
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Service API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Job API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.lsf.lsfjob
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Service API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Job API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.irods.irods_replica
2014:08:13 12:15:02 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))
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.condor.condorjob
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Service API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Job API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.slurm.slurm_job
2014:08:13 12:15:02 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://']
2014:08:13 12:15:02 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://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.http.http_file
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.http.http_file for saga.namespace.Entry API with URL scheme(s) ['http://', 'https://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.http.http_file for saga.filesystem.File API with URL scheme(s) ['http://', 'https://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.aws.ec2_resource
2014:08:13 12:15:02 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://']
2014:08:13 12:15:02 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://']
2014:08:13 12:15:02 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://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.loadl.loadljob
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Service API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2014:08:13 12:15:02 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Job API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2014:08:13 12:15:02 MainThread saga.saga.adaptor.ssh : [INFO ] default ssh key at /home/sade/.ssh/id_rsa
2014:08:13 12:15:02 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/authorized_keys (no public key: /home/sade/.ssh/authorized_keys.pub)
2014:08:13 12:15:02 MainThread saga.saga.adaptor.ssh : [INFO ] default ssh key at /home/sade/.ssh/id_dsa
2014:08:13 12:15:02 MainThread saga.saga.adaptor.ssh : [INFO ] default ssh key at /home/sade/.ssh/identity
2014:08:13 12:15:02 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/authorized_keys2 (no public key: /home/sade/.ssh/authorized_keys2.pub)
2014:08:13 12:15:02 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/known_hosts__ (no public key: /home/sade/.ssh/known_hosts__.pub)
2014:08:13 12:15:02 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /home/sade/.ssh/known_hosts (no public key: /home/sade/.ssh/known_hosts.pub)
2014:08:13 12:15:03 MainThread saga.DefaultSession : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_rsa.pub', 'UserKey' : '/home/sade/.ssh/id_rsa'}
2014:08:13 12:15:03 MainThread saga.ContextSSH : [INFO ] init SSH context for key at '/home/sade/.ssh/id_rsa' done
2014:08:13 12:15:03 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'}
2014:08:13 12:15:03 MainThread saga.DefaultSession : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/id_dsa.pub', 'UserKey' : '/home/sade/.ssh/id_dsa'}
2014:08:13 12:15:03 MainThread saga.ContextSSH : [INFO ] init SSH context for key at '/home/sade/.ssh/id_dsa' done
2014:08:13 12:15:03 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'}
2014:08:13 12:15:03 MainThread saga.DefaultSession : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/identity.pub', 'UserKey' : '/home/sade/.ssh/identity'}
2014:08:13 12:15:03 MainThread saga.ContextSSH : [INFO ] init SSH context for key at '/home/sade/.ssh/identity' done
2014:08:13 12:15:03 MainThread saga.DefaultSession : [DEBUG ] default context [saga.adaptor.ssh ] : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/home/sade/.ssh/identity.pub', 'UserKey' : '/home/sade/.ssh/identity'}
2014:08:13 12:15:03 MainThread saga.saga.Session : [DEBUG ] adding context : {'LifeTime' : '-1', 'Type' : 'ssh'}
2014:08:13 12:15:03 MainThread saga.PTYShell : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x1a0ee10>
2014:08:13 12:15:03 MainThread saga.PTYShell : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$
2014:08:13 12:15:03 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'
2014:08:13 12:15:03 MainThread saga.PTYShell : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x1a2b5d0>
2014:08:13 12:15:03 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
2014:08:13 12:15:03 MainThread saga.PTYShell : [DEBUG ] write: [ 3] [ 33] ( export PS1='$' ; set prompt='$'\n)
2014:08:13 12:15:03 MainThread saga.PTYShell : [DEBUG ] read : [ 3] [ 86] (ControlSocket /tmp/saga_ssh_sade_joe2_22.ctrl already exists, disabling multiplexing\n)
2014:08:13 12:15:03 MainThread saga.PTYShell : [DEBUG ] read : [ 3] [ 199] (Last login: Wed Aug 13 12:14:27 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)
2014:08:13 12:15:04 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)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] got initial shell prompt (5) (ControlSocket /tmp/saga_ssh_sade_joe2_22.ctrl already exists, disabling multiplexing
Last login: Wed Aug 13 12:14:27 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
#################################################)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] Got initial shell prompt (5) (ControlSocket /tmp/saga_ssh_sade_joe2_22.ctrl already exists, disabling multiplexing
Last login: Wed Aug 13 12:14:27 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
#################################################)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x1a2ba50>
2014:08:13 12:15:04 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
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 33] ( export PS1='$' ; set prompt='$'\n)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 77] (Control socket connect(/tmp/saga_ssh_sade_joe2_22.ctrl): Connection refused\n)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 199] (Last login: Wed Aug 13 12:15:03 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)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 3] ( \n)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 563] (Currently 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)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] got initial shell prompt (5) (Control socket connect(/tmp/saga_ssh_sade_joe2_22.ctrl): Connection refused
Last login: Wed Aug 13 12:15:03 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
#################################################)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] Got initial shell prompt (5) (Control socket connect(/tmp/saga_ssh_sade_joe2_22.ctrl): Connection refused
Last login: Wed Aug 13 12:15:03 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
#################################################)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] running command shell: exec /bin/sh -i
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2014:08:13 12:15:04 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (joe2(~) $$)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] got new shell prompt
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] run_sync: which qdel
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 11] (which qdel\n)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 48] (/opt/GE/2011.11p1/bin/linux-x64/qdel\nPROMPT-0->)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] run_sync: qdel -help
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 11] (qdel -help\n)
2014:08:13 12:15:05 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->)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] run_sync: which qsub
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 11] (which qsub\n)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 38] (/opt/GE/2011.11p1/bin/linux-x64/qsub\n)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] run_sync: qsub -help
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 11] (qsub -help\n)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (OGS/GE 2011.11p1\nusage: qsub ... eadline initiation time\n [-)
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (e path_list] ... to queue(s)\n [-notify] )
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( no ... )
2014:08:13 12:15:05 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( consider following request ... account_name\ncomplex)
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (_list complex[,comp ... cluster queue\nwc_host )
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 629] ( wildcard expression ... [:<socket>,<core>]\nPROMPT-0->)
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] run_sync: which qconf
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (which qconf\n)
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 49] (/opt/GE/2011.11p1/bin/linux-x64/qconf\nPROMPT-0->)
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] run_sync: qconf -help
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (qconf -help\n)
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (OGS/GE 2011.11p1\nusage: qconf ... w host group entry from file\n)
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( [-arqs [rqs_list]] ... file\n [-at thread_name] )
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( add/start ... delete host)
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( group entry\n [-drqs rqs_li ... s}] )
2014:08:13 12:15:06 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( shutdown master|schedulin ... m)
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (odify exec server\n [-Me fna ... e node_shares_list] )
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( modify sharetree node(s)\n ... n\n [-sckptl] )
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( show all ckpt ... show resource quota set(s))
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (\n [-srqsl] ... sharetree node(s)\n [-rsstno)
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (de node_list] ... user[,user,...]\nobj_nm )
2014:08:13 12:15:07 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->)
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] run_sync: which qacct
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (which qacct\n)
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 39] (/opt/GE/2011.11p1/bin/linux-x64/qacct\n)
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] run_sync: qacct -help
2014:08:13 12:15:07 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (qacct -help\n)
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (OGS/GE 2011.11p1\nusage: qacct ... slots]] list )
2014:08:13 12:15:08 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->)
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] run_sync: which qstat
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (which qstat\n)
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 49] (/opt/GE/2011.11p1/bin/linux-x64/qstat\nPROMPT-0->)
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] run_sync: qstat -help
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 12] (qstat -help\n)
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (OGS/GE 2011.11p1\nusage: qstat ... [-pe pe_list] )
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( select only queues wit ... have access\n [-urg] )
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 920] ( displ ... eue[,wc_queue,...]\nPROMPT-0->)
2014:08:13 12:15:08 MainThread saga.SGEJobService : [INFO ] Found SGE tools: {'qdel': {'path': 'unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qdel', 'version': 'OGS/GE 2011.11p1'}, 'qsub': {'path': 'unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qsub', 'version': 'OGS/GE 2011.11p1'}, 'qconf': {'path': 'unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qconf', 'version': 'OGS/GE 2011.11p1'}, 'qacct': {'path': 'unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qacct', 'version': 'OGS/GE 2011.11p1'}, 'qstat': {'path': 'unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat', 'version': 'OGS/GE 2011.11p1'}}
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qconf -spl
2014:08:13 12:15:08 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 63] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qconf -spl\n)
2014:08:13 12:15:09 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->)
2014:08:13 12:15:09 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']
2014:08:13 12:15:09 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qconf -sc
2014:08:13 12:15:09 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 62] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qconf -sc\n)
2014:08:13 12:15:09 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (#name shortcut ... NO 0:0:0 0\nh_)
2014:08:13 12:15:09 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (stack h_stack M ... 0 0\nmem_total )
2014:08:13 12:15:09 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] ( mt MEMORY <= ... ta s_data MEM)
2014:08:13 12:15:09 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (ORY <= YES NO ... su MEMORY >= )
2014:08:13 12:15:09 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->)
2014:08:13 12:15:09 MainThread saga.SGEJobService : [DEBUG ] Optional memory attributes: []
2014:08:13 12:15:09 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']
2014:08:13 12:15:09 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qconf -sconf
2014:08:13 12:15:09 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 65] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qconf -sconf\n)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1024] (#global:\nexecd_spool_dir ... none\nexecd_params )
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1013] ( none\nreporting_ ... ,i,e,o,j,M,N,p,w\n\nPROMPT-0->)
2014:08:13 12:15:10 MainThread saga.SGEJobService : [INFO ] Accounting is enabled
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] run_sync: find $HOME/.saga/adaptors/sge_job -type f -mtime +30 -print -delete | wc -l
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 76] (find $HOME/.saga/adaptors/sge_job -type f -mtime +30 -print -delete | wc -l\n)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 13] (0\nPROMPT-0->)
2014:08:13 12:15:10 MainThread saga.SGEJobService : [INFO ] Purged 0
temporary files
Job ID : None
Job State : New
...starting job...
2014:08:13 12:15:10 MainThread saga.SGEJobService : [INFO ] Generated SGE script:
#!/bin/bash
#$ -S /bin/bash
#$ -V
#$ -v FILENAME=/home/sade/sqmpy/7/in.flow.couette
#$ -wd /home/sade/sqmpy/7/
#$ -o examplejob.out
#$ -e examplejob.err
#$ -l h_rt=0:1:00
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: Wed Aug 13 12:15:10 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
/home/sade/sqmpy/7/submit_LMP.sh \$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
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] run_sync: (test -d /home/sade/sqmpy/7/ && echo -n 0) || (mkdir -p /home/sade/sqmpy/7/ && echo -n 1)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 90] ((test -d /home/sade/sqmpy/7/ && echo -n 0) || (mkdir -p /home/sade/sqmpy/7/ && echo -n 1)\n)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1] (0)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] run_sync: (test -d && echo -n 0) || (mkdir -p && echo -n 1)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 52] ((test -d && echo -n 0) || (mkdir -p && echo -n 1)\n)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1] (0)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] run_sync: (test -d && echo -n 0) || (mkdir -p && echo -n 1)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 52] ((test -d && echo -n 0) || (mkdir -p && echo -n 1)\n)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 1] (0)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] run_sync: SCRIPTFILE=`mktemp -t SAGA-Python-SGEJobScript.XXXXXX` && echo "
#!/bin/bash
#$ -S /bin/bash
#$ -V
#$ -v FILENAME=/home/sade/sqmpy/7/in.flow.couette
#$ -wd /home/sade/sqmpy/7/
#$ -o examplejob.out
#$ -e examplejob.err
#$ -l h_rt=0:1:00
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: Wed Aug 13 12:15:10 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
/home/sade/sqmpy/7/submit_LMP.sh \$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 && unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qsub -notify $SCRIPTFILE && rm -f $SCRIPTFILE
2014:08:13 12:15:10 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 1223] (SCRIPTFILE=`mktemp -t SAGA-Pyt ... IPTFILE && rm -f $SCRIPTFILE\n)
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 82] (Your job 126378 ("SAGA-Python-SGEJobScript.l30213") has been submitted\nPROMPT-0->)
2014:08:13 12:15:11 MainThread saga.SGEJobService : [INFO ] Submitted SGE job with id: [sge+ssh://joe2]-[126378]
Job ID : [sge+ssh://joe2]-[126378]
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 36] (qw 08/13/2014 12:15:11 1\nPROMPT-0->)
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 98] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\nPROMPT-0->)
2014:08:13 12:15:11 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Pending, returncode=None, exec_hosts=joe2, create_time=Wed Aug 13 12:15:11 2014, start_time=None, end_time=None, gone=False]
Job State : Pending
Listing active jobs:
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | grep `whoami`
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 94] (unset GREP_OPTIONS; unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | grep `whoami`\n)
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 458] ( 126374 0.51815 SAGA-Pytho sade qw 08/13/2014 12:03:55 12 \n 125833 0.50213 SAGA-Pytho sade Eqw 08/11/2014 18:13:14 1 \n 125834 0.50213 SAGA-Pytho sade Eqw 08/11/2014 18:15:42 1 \n 126378 0.00000 SAGA-Pytho sade qw 08/13/2014 12:15:11 1 \nPROMPT-0->)
* [sge+ssh://joe2]-[126374]
* [sge+ssh://joe2]-[125833]
* [sge+ssh://joe2]-[125834]
* [sge+ssh://joe2]-[126378]
...waiting for job...
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:11 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:12 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 36] (qw 08/13/2014 12:15:11 1\nPROMPT-0->)
2014:08:13 12:15:12 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:12 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:12 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 98] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\nPROMPT-0->)
2014:08:13 12:15:12 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Pending, returncode=None, exec_hosts=joe2, create_time=Wed Aug 13 12:15:11 2014, start_time=None, end_time=None, gone=False]
2014:08:13 12:15:12 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:12 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:13 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 36] (qw 08/13/2014 12:15:11 1\nPROMPT-0->)
2014:08:13 12:15:13 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:13 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:13 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 88] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\n)
2014:08:13 12:15:13 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:13 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Pending, returncode=None, exec_hosts=joe2, create_time=Wed Aug 13 12:15:11 2014, start_time=None, end_time=None, gone=False]
2014:08:13 12:15:14 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:14 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:14 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 36] (qw 08/13/2014 12:15:11 1\nPROMPT-0->)
2014:08:13 12:15:14 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:14 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:14 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 98] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\nPROMPT-0->)
2014:08:13 12:15:14 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Pending, returncode=None, exec_hosts=joe2, create_time=Wed Aug 13 12:15:11 2014, start_time=None, end_time=None, gone=False]
2014:08:13 12:15:15 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:15 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:15 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 36] (qw 08/13/2014 12:15:11 1\nPROMPT-0->)
2014:08:13 12:15:15 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:15 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:15 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 98] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\nPROMPT-0->)
2014:08:13 12:15:15 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Pending, returncode=None, exec_hosts=joe2, create_time=Wed Aug 13 12:15:11 2014, start_time=None, end_time=None, gone=False]
2014:08:13 12:15:16 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:16 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:16 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 36] (qw 08/13/2014 12:15:11 1\nPROMPT-0->)
2014:08:13 12:15:16 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:16 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:16 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 98] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\nPROMPT-0->)
2014:08:13 12:15:16 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Pending, returncode=None, exec_hosts=joe2, create_time=Wed Aug 13 12:15:11 2014, start_time=None, end_time=None, gone=False]
2014:08:13 12:15:17 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:17 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:17 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 26] (qw 08/13/2014 12:15:11 1\n)
2014:08:13 12:15:17 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:17 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:17 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:17 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 98] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\nPROMPT-0->)
2014:08:13 12:15:17 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Pending, returncode=None, exec_hosts=joe2, create_time=Wed Aug 13 12:15:11 2014, start_time=None, end_time=None, gone=False]
2014:08:13 12:15:18 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:18 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:18 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 36] (qw 08/13/2014 12:15:11 1\nPROMPT-0->)
2014:08:13 12:15:18 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:18 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:18 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 98] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\nPROMPT-0->)
2014:08:13 12:15:18 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Pending, returncode=None, exec_hosts=joe2, create_time=Wed Aug 13 12:15:11 2014, start_time=None, end_time=None, gone=False]
2014:08:13 12:15:19 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:19 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:19 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 36] (qw 08/13/2014 12:15:11 1\nPROMPT-0->)
2014:08:13 12:15:19 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:19 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:19 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 98] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\nPROMPT-0->)
2014:08:13 12:15:19 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Pending, returncode=None, exec_hosts=joe2, create_time=Wed Aug 13 12:15:11 2014, start_time=None, end_time=None, gone=False]
2014:08:13 12:15:19 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:19 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:20 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 59] (r 08/13/2014 12:15:20 abaqus@node106.iwm.fhg.de\nPROMPT-0->)
2014:08:13 12:15:20 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'
2014:08:13 12:15:20 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 107] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat -j 126378 | grep -E 'submission_time|sge_o_host'\n)
2014:08:13 12:15:20 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 98] (submission_time: Wed Aug 13 12:15:11 2014\nsge_o_host: joe2\nPROMPT-0->)
2014:08:13 12:15:20 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Running, returncode=None, exec_hosts=node106.iwm.fhg.de, create_time=Wed Aug 13 12:15:11 2014, start_time=Wed Aug 13 12:15:20 2014, end_time=None, gone=False]
2014:08:13 12:15:20 MainThread saga.PTYShell : [DEBUG ] run_sync: unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'
2014:08:13 12:15:20 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 113] (unset GREP_OPTIONS; /opt/GE/2011.11p1/bin/linux-x64/qstat | tail -n+3 | awk '($1==126378) {{print $5,$6,$7,$8}}'\n)
2014:08:13 12:15:21 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:21 MainThread saga.PTYShell : [DEBUG ] run_sync: cat $HOME/.saga/adaptors/sge_job/126378
2014:08:13 12:15:21 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 40] (cat $HOME/.saga/adaptors/sge_job/126378\n)
2014:08:13 12:15:21 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 159] (hostname: node106.iwm.fhg.de\nqsub_time: Wed Aug 13 12:15:10 2014\nstart_time: Wed Aug 13 12:15:20 2014\nexit_status: 126\nend_time: Wed Aug 13 12:15:20 2014\n)
2014:08:13 12:15:21 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
2014:08:13 12:15:21 MainThread saga.SGEJobService : [DEBUG ] job_info(126378)=[state=Done, returncode=126, exec_hosts=node106.iwm.fhg.de, create_time=Wed Aug 13 12:15:10 2014, start_time=Wed Aug 13 12:15:20 2014, end_time=Wed Aug 13 12:15:20 2014, gone=False]
2014:08:13 12:15:21 MainThread saga.PTYShell : [DEBUG ] run_sync: rm $HOME/.saga/adaptors/sge_job/126378
2014:08:13 12:15:21 MainThread saga.PTYShell : [DEBUG ] write: [ 4] [ 39] (rm $HOME/.saga/adaptors/sge_job/126378\n)
2014:08:13 12:15:21 MainThread saga.PTYShell : [DEBUG ] read : [ 4] [ 10] (PROMPT-0->)
Job State : Done
Exitcode : 126
Exec. hosts : node106.iwm.fhg.de
Create time : Wed Aug 13 12:15:10 2014
Start time : Wed Aug 13 12:15:20 2014
End time : Wed Aug 13 12:15:20 2014
2014:08:13 12:15:21 Dummy-1 saga.PTYShell : [DEBUG ] PTYShell del <saga.utils.pty_shell.PTYShell object at 0x1a0ee10>
2014:08:13 12:15:21 Dummy-1 saga.PTYShell : [DEBUG ] PTYProcess del <saga.utils.pty_process.PTYProcess object at 0x1a2ba50>
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