Job starts but fails

[TensorDuck]

As you can see below, the job starts but then fails to generate any output files and exits. I can't identify an error in the .log file.

This is the example using lsdmap and dmdmd. The output I got was here:

ExTASY version :  0.1-20-g347657f
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/coco.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/namd.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/sleep.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/amber.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/test.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/lsdmap.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/mmpbsa.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/gromacs.json
Session UID: rp.session.jchen-Vostro-260.extasy.016694.0003
Pilot UID       : pilot.0000
Preprocessing stage ....
[Callback]: ComputePilot 'pilot.0000' state changed to Launching.
[Callback]: ComputeUnit 'unit.000000' state changed to PendingInputStaging.
[Callback]: ComputeUnit 'unit.000000' state changed to PendingAgentInputStaging.
[Callback]: ComputePilot 'pilot.0000' state changed to PendingActive.
[Callback]: ComputeUnit 'unit.000000' state changed to AgentStagingInput.
[Callback]: ComputePilot 'pilot.0000' state changed to Active.
[Callback]: ComputeUnit 'unit.000000' state changed to Executing.
[Callback]: ComputeUnit 'unit.000000' state changed to PendingAgentOutputStaging.
[Callback]: ComputeUnit 'unit.000000' state changed to Done.
Cycle : 0
Starting Simulation
An error occurred: 'stampede.tacc.utexas.edu'
Closing session, exiting now ...
[Callback]: ComputePilot 'pilot.0000' state changed to Canceled.

The extasy.log shows this:

2015:09:16 16:14:42 5484   MainThread   saga                  : [INFO    ] saga-python          version: 0.35
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] radical.pilot        version: 0.35
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.myproxy
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.myproxy for saga.Context API with URL scheme(s) ['myproxy://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.x509
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.x509 for saga.Context API with URL scheme(s) ['x509://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.ssh
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.ssh for saga.Context API with URL scheme(s) ['ssh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.context.userpass
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.context.userpass for saga.Context API with URL scheme(s) ['userpass://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_job
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Service API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Job API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_file
2015:09:16 16:14:42 5484   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://']
2015:09:16 16:14:42 5484   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://']
2015:09:16 16:14:42 5484   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://']
2015:09:16 16:14:42 5484   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://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.shell.shell_resource
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [WARNING ] Skipping adaptor saga.adaptors.shell.shell_resource: beta versions are disabled (v0.1.beta)
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.redis.redis_advert
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [WARNING ] Skipping adaptor saga.adaptors.redis.redis_advert 1: module loading failed: No module named redis
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.sge.sgejob
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Service API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Job API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.pbs.pbsjob
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Service API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Job API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.lsf.lsfjob
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Service API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Job API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.condor.condorjob
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Service API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Job API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.slurm.slurm_job
2015:09:16 16:14:42 5484   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://']
2015:09:16 16:14:42 5484   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://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.http.http_file
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.http.http_file for saga.namespace.Entry API with URL scheme(s) ['http://', 'https://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.http.http_file for saga.filesystem.File API with URL scheme(s) ['http://', 'https://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.aws.ec2_resource
2015:09:16 16:14:42 5484   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://']
2015:09:16 16:14:42 5484   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://']
2015:09:16 16:14:42 5484   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://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.loadl.loadljob
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Service API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Job API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.globus_online.go_file
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Directory API with URL scheme(s) ['go://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Entry API with URL scheme(s) ['go://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.Directory API with URL scheme(s) ['go://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.File API with URL scheme(s) ['go://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.torque.torquejob
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.torque.torquejob for saga.job.Service API with URL scheme(s) ['torque://', 'torque+ssh://', 'torque+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.torque.torquejob for saga.job.Job API with URL scheme(s) ['torque://', 'torque+ssh://', 'torque+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Loading  adaptor saga.adaptors.pbspro.pbsprojob
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbspro.pbsprojob for saga.job.Service API with URL scheme(s) ['pbspro://', 'pbspro+ssh://', 'pbspro+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.Engine           : [INFO    ] Register adaptor saga.adaptors.pbspro.pbsprojob for saga.job.Job API with URL scheme(s) ['pbspro://', 'pbspro+ssh://', 'pbspro+gsissh://']
2015:09:16 16:14:42 5484   MainThread   saga.saga.adaptor.ssh : [INFO    ] ignore ssh key at /home/extasy/.ssh/known_hosts (no public key: /home/extasy/.ssh/known_hosts.pub)
2015:09:16 16:14:42 5484   MainThread   saga.saga.adaptor.ssh : [WARNING ] ignore  ssh key at /home/extasy/.ssh/id_rsa (requires passphrase)
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] using database url  mongodb://extasy:extasyproject@extasy-db.epcc.ed.ac.uk/radicalpilot
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] using database path radicalpilot
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/stfc.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for stfc.joule
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/radical.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for radical.tutorial
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/rice.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for rice.biou
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for rice.davinci
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/local.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for local.localhost
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/aliases.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/nersc.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.hopper_ccm
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.hopper
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.edison
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for nersc.edison_ccm
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/xsede.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.blacklight
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.supermic
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.lonestar
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.comet
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.stampede
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.trestles
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for xsede.gordon
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/futuregrid.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.xray
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.echo
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.india
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.bravo
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.xray_ccm
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for futuregrid.delta
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ornl.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ornl.titan
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/epsrc.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for epsrc.archer
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ncsa.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncsa.bw_ccm
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncsa.bw
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/ncar.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for ncar.yellowstone
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/das4.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for das4.fs2
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/lrz.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for lrz.supermuc
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/configs/iu.json
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for iu.bigred2
2015:09:16 16:14:42 5484   MainThread   radical.pilot         : [INFO    ] Load resource configurations for iu.bigred2_ccm
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [INFO    ] New Session created {'uid': 'rp.session.jchen-Vostro-260.extasy.016694.0003', 'created': datetime.datetime(2015, 9, 16, 21, 14, 42, 677473), 'database_auth': 'extasy:extasyproject', 'database_name': 'radicalpilot', 'database_url': 'mongodb://extasy:extasyproject@extasy-db.epcc.ed.ac.uk/radicalpilot', 'connected': None}.
2015:09:16 16:14:43 5484   Thread-1     radical.pilot         : [DEBUG   ] Worker thread (ID: Thread-1[140178053281536]) for PilotManager 55f9dbc3ee1f52156c89f242 started.
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [WARNING ] using alias 'xsede.stampede' for deprecated resource key 'stampede.tacc.utexas.edu'
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [DEBUG   ] saga.utils.PTYShell ('ssh://stampede.tacc.utexas.edu/')
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbf959910>
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [DEBUG   ] open master pty for [ssh] [jc49@stampede.tacc.utexas.edu] jc49: /usr/bin/env TERM=vt100  "/usr/bin/ssh" -t  -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no  -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu'
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc09e7d90>
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [INFO    ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu
2015:09:16 16:14:43 5484   MainThread   radical.pilot         : [DEBUG   ] write: [    5] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    5] [ 2380] (Last login: Wed Sep 16 16:02:0 ... __________________________\n\n)
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] got initial shell prompt (6) (Last login: Wed Sep 16 16:02:07 2015 from 128.42.90.115
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--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] Got initial shell prompt (6) (Last login: Wed Sep 16 16:02:07 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbf959710>
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [INFO    ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] write: [    6] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    6] [ 2380] (Last login: Wed Sep 16 16:14:4 ... __________________________\n\n)
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] got initial shell prompt (6) (Last login: Wed Sep 16 16:14:44 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] Got initial shell prompt (6) (Last login: Wed Sep 16 16:14:44 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] write: [    6] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:44 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Connected to MongoDB. Serving requests for PilotManager 55f9dbc3ee1f52156c89f242.
2015:09:16 16:14:44 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    6] [  243] (----------------------- Project balances for user jc49 ------------------------\n| Name           Avail SUs     Expires |                                      |\n| TG-MCB090174       53573  2015-09-30 |                                      |\n)
2015:09:16 16:14:45 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    6] [  486] (-------------------------- Disk quotas for user jc49 --------------------------\n| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |\n| /home1              0.1       5.0     2.88         6405      150000    4.27 |\n| /work               0.0    1024.0     0.00         3588     3000000    0.12 |\n| /scratch            0.0       0.0     0.00            3           0    0.00 |\n-------------------------------------------------------------------------------\n)
2015:09:16 16:14:45 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    6] [  220] (\nTip 107   (See "module help tacc_tips" for features or how to disable)\n\n   A complex if then else block in a shell script can be written on one line as:\n      $ [[ test ]] && if_true_do_this || otherwise_to_that\n\n)
2015:09:16 16:14:45 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    6] [  383] (Lmod Warning:  One or more\nmodules in your default  collection\nhave changed: "TACC". \nTo rebuild the collection, load the modules you wish then do:\n  $ module save default\nIf you no longer want this module collection do:\n  rm ~/.lmod.d/default\n\nFor more information execute 'module help' or see www.tacc.utexas.edu/tacc-projects/lmod/user-guide/loading-modules\n\n)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    6] [   21] (login3.stampede(1)$ $)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [    6] [     ] (flush pty read cache)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    6] [    1] ($)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [WARNING ] flush: [    6] [    1] (discard data: '$')
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] write: [    6] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    6] [   10] (PROMPT-0->)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] got new shell prompt
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [    6] [     ] (flush pty read cache)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [    6] [     ] (flush pty read cache)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] run_sync: echo "WORKDIR: $WORK"
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] write: [    6] [   22] (echo "WORKDIR: $WORK"\n)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] read : [    6] [   37] (WORKDIR: /work/03531/jc49\nPROMPT-0->)
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] Determined remote working directory for ssh://stampede.tacc.utexas.edu/: '/work/03531/jc49'
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] PTYShell del  <saga.utils.pty_shell.PTYShell object at 0x7f7dbf959910>
2015:09:16 16:14:46 5484   MainThread   radical.pilot         : [DEBUG   ] PTYProcess del  <saga.utils.pty_process.PTYProcess object at 0x7f7dbf959710>
2015:09:16 16:14:47 5484   InputFileTransferWorker-1 radical.pilot         : [INFO    ] Starting InputFileTransferWorker
2015:09:16 16:14:47 5484   InputFileTransferWorker-2 radical.pilot         : [INFO    ] Starting InputFileTransferWorker
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [INFO    ] Launching ComputePilot pilot.0000
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [WARNING ] using alias 'xsede.stampede' for deprecated resource key 'stampede.tacc.utexas.edu'
2015:09:16 16:14:47 5484   Thread-3     radical.pilot         : [DEBUG   ] Worker thread (ID: Thread-3[140177666209536]) for UnitManager 55f9dbc6ee1f52156c89f243 started.
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [INFO    ] Loaded scheduler: DirectSubmissionScheduler.
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc280b50>
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0a176d0>
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [INFO    ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   12] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [ 2380] (Last login: Wed Sep 16 16:14:4 ... __________________________\n\n)
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] got initial shell prompt (6) (Last login: Wed Sep 16 16:14:44 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Got initial shell prompt (6) (Last login: Wed Sep 16 16:14:44 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   12] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/09-09-extasy_tutorial/grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///grompp.mdp', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/09-09-extasy_tutorial/topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///topol.top', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/09-09-extasy_tutorial/config.ini', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///config.ini', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/gro.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///gro.py', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/spliter.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///spliter.py', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Simulator/Gromacs/run.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///run.py', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/pre_analyze.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///pre_analyze.py', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/run_analyzer.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///run_analyzer.sh', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/post_analyze.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///post_analyze.py', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/selection.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///selection.py', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/reweighting.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///reweighting.py', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/09-09-extasy_tutorial/lsdm.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///lsdm.py', 'priority': 0}'
2015:09:16 16:14:47 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Transfer', 'source': 'file:///home/extasy/ExTASY/09-09-extasy_tutorial/input.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///input.gro', 'priority': 0}'
2015:09:16 16:14:47 5484   Thread-1     radical.pilot         : [INFO    ] ComputePilot 'pilot.0000' state changed from 'PendingLaunch' to 'Launching'.
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [  243] (----------------------- Project balances for user jc49 ------------------------\n| Name           Avail SUs     Expires |                                      |\n| TG-MCB090174       53573  2015-09-30 |                                      |\n)
2015:09:16 16:14:47 5484   InputFileTransferWorker-1 radical.pilot         : [DEBUG   ] Connected to MongoDB. Serving requests for UnitManager 55f9dbc6ee1f52156c89f243.
2015:09:16 16:14:47 5484   InputFileTransferWorker-2 radical.pilot         : [DEBUG   ] Connected to MongoDB. Serving requests for UnitManager 55f9dbc6ee1f52156c89f243.
2015:09:16 16:14:47 5484   OutputFileTransferWorker-2 radical.pilot         : [DEBUG   ] Connected to MongoDB. Serving requests for UnitManager 55f9dbc6ee1f52156c89f243.
2015:09:16 16:14:47 5484   OutputFileTransferWorker-1 radical.pilot         : [DEBUG   ] Connected to MongoDB. Serving requests for UnitManager 55f9dbc6ee1f52156c89f243.
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [  486] (-------------------------- Disk quotas for user jc49 --------------------------\n| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |\n| /home1              0.1       5.0     2.88         6405      150000    4.27 |\n| /work               0.0    1024.0     0.00         3588     3000000    0.12 |\n| /scratch            0.0       0.0     0.00            3           0    0.00 |\n-------------------------------------------------------------------------------\n)
2015:09:16 16:14:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [  158] (\nTip 102   (See "module help tacc_tips" for features or how to disable)\n\n   To bypass any alias and shell function for any executable do "command foo".\n\n)
2015:09:16 16:14:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [  383] (Lmod Warning:  One or more\nmodules in your default  collection\nhave changed: "TACC". \nTo rebuild the collection, load the modules you wish then do:\n  $ module save default\nIf you no longer want this module collection do:\n  rm ~/.lmod.d/default\n\nFor more information execute 'module help' or see www.tacc.utexas.edu/tacc-projects/lmod/user-guide/loading-modules\n\n)
2015:09:16 16:14:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [   21] (login3.stampede(1)$ $)
2015:09:16 16:14:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [    1] ($)
2015:09:16 16:14:48 5484   PilotLauncherWorker-1 radical.pilot         : [WARNING ] flush: [   12] [    1] (discard data: '$')
2015:09:16 16:14:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   12] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:14:49 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)2015:09:16 16:14:49 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc295d10>
2015:09:16 16:14:49 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$

2015:09:16 16:14:49 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:49 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0a17710>
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [INFO    ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   10] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [ 2380] (Last login: Wed Sep 16 16:14:4 ... __________________________\n\n)
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [DEBUG   ] got initial shell prompt (6) (Last login: Wed Sep 16 16:14:47 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [DEBUG   ] Got initial shell prompt (6) (Last login: Wed Sep 16 16:14:47 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:49 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   10] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:49 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/ && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/ &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/'
2015:09:16 16:14:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   12] [  430] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/ && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/ &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/'\n)
2015:09:16 16:14:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [  243] (----------------------- Project balances for user jc49 ------------------------\n| Name           Avail SUs     Expires |                                      |\n| TG-MCB090174       53573  2015-09-30 |                                      |\n)
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [  486] (-------------------------- Disk quotas for user jc49 --------------------------\n| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |\n| /home1              0.1       5.0     2.88         6405      150000    4.27 |\n| /work               0.0    1024.0     0.00         3589     3000000    0.12 |\n| /scratch            0.0       0.0     0.00            3           0    0.00 |\n-------------------------------------------------------------------------------\n)
2015:09:16 16:14:49 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [  221] (\nTip 80   (See "module help tacc_tips" for features or how to disable)\n\n   Want to know detailed information about a file do: "stat your_file_or_dir" to find out the create, access and modify times, permission etc.\n\n)
2015:09:16 16:14:50 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [  383] (Lmod Warning:  One or more\nmodules in your default  collection\nhave changed: "TACC". \nTo rebuild the collection, load the modules you wish then do:\n  $ module save default\nIf you no longer want this module collection do:\n  rm ~/.lmod.d/default\n\nFor more information execute 'module help' or see www.tacc.utexas.edu/tacc-projects/lmod/user-guide/loading-modules\n\n)
2015:09:16 16:14:50 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [   21] (login3.stampede(1)$ $)
2015:09:16 16:14:50 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   10] [     ] (flush pty read cache)
2015:09:16 16:14:50 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [    1] ($)
2015:09:16 16:14:50 5484   MainThread   radical.pilot         : [WARNING ] flush: [   10] [    1] (discard data: '$')
2015:09:16 16:14:50 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   10] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:50 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [   10] (PROMPT-0->)
2015:09:16 16:14:50 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:50 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   10] [     ] (flush pty read cache)
2015:09:16 16:14:50 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   10] [     ] (flush pty read cache)
2015:09:16 16:14:50 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:14:50 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc295e90>
2015:09:16 16:14:50 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:50 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:50 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:50 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] open master pty for [sh] [localhost] extasy: /usr/bin/env TERM=vt100  "/bin/bash"  -i'
2015:09:16 16:14:50 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbc295f10>
2015:09:16 16:14:50 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:50 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] write: [   13] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   13] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbc2a51d0>
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] write: [   14] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:14:51 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   10] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   14] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] write: [   14] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   14] [    1] ($)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:51 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [   10] (PROMPT-0->)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc2a52d0>
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   14] [    1] ($)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [WARNING ] flush: [   14] [    1] (discard data: '$')
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0980d90>
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   15] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   15] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   15] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   15] [    1] ($)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   15] [     ] (flush pty read cache)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   15] [    1] ($)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   15] [    1] (discard data: '$')
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] write: [   14] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   14] [   10] (PROMPT-0->)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   15] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   15] [   10] (PROMPT-0->)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   15] [     ] (flush pty read cache)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] write: [   14] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   14] [   10] (PROMPT-0->)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   15] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   15] [   10] (PROMPT-0->)
2015:09:16 16:14:51 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   15] [     ] (flush pty read cache)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 radical.pilot         : [INFO    ] Using bootstrapper /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Copying bootstrapper 'file://localhost/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh' to agent sandbox (<saga.filesystem.directory.Directory object at 0x7f7dbdaba550>).
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:51 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/09-09-extasy_tutorial/grompp.mdp to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./grompp.mdp
2015:09:16 16:14:51 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   10] [     ] (flush pty read cache)
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbc2a5b50>
2015:09:16 16:14:51 5484   PilotLauncherWorker-1 radical.pilot         : [INFO    ] running: /usr/bin/env TERM=vt100 /usr/bin/sftp -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   40] (Connected to stampede.tacc.utexas.edu.\n)
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] got initial shell prompt (6) (Connected to stampede.tacc.utexas.edu.
sftp> )
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Got initial shell prompt (6) (Connected to stampede.tacc.utexas.edu.
sftp> )
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:52 5484   MainThread   radical.pilot         : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbc2a5e90>
2015:09:16 16:14:52 5484   MainThread   radical.pilot         : [INFO    ] running: /usr/bin/env TERM=vt100 /usr/bin/sftp -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   16] [  243] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/default_bootstrapper.sh"\n)
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [  250] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/pilot/bootstrapper/default_bootstrapper.sh" "/work/03531/jc49/radical.pilot.sa ndbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/default_bootstra pper.sh"\n)
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [  247] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/default_bootstrapper.sh\n)
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100%   43KB  43.5KB/s   00:00    \n)
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Copying sdist 'file://localhost/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/utils/radical.utils-0.35.tar.gz' to sandbox (sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/).
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:52 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   16] [  234] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/utils/radical.utils-0.35.tar.gz" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/radical.utils-0.35.tar.gz"\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [  239] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/utils/radical.utils-0.35.tar.gz" "/work/03531/jc49/radical.pilot.sandbox/rp.se ssion.jchen-Vostro-260.extasy.016694.0003-pilot.0000/radical.utils-0.35.tar.gz"\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [  238] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/utils/radical.utils-0.35.tar.gz to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/radical.utils-0.35.tar.gz\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100%   95KB  94.8KB/s   00:00    \n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Copying sdist 'file://localhost/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/saga/saga-python-0.35.tar.gz' to sandbox (sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/).
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   17] [   40] (Connected to stampede.tacc.utexas.edu.\n)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   17] [    6] (sftp> )
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] got initial shell prompt (6) (Connected to stampede.tacc.utexas.edu.
sftp> )
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] Got initial shell prompt (6) (Connected to stampede.tacc.utexas.edu.
sftp> )
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   17] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   16] [  221] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/saga/saga-python-0.35.tar.gz" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/saga-python-0.35.tar.gz"\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [  226] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/saga/s aga-python-0.35.tar.gz" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen -Vostro-260.extasy.016694.0003-pilot.0000/saga-python-0.35.tar.gz"\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [  225] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/saga/saga-python-0.35.tar.gz to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/saga-python-0.35.tar.gz\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   17] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100%  440KB 439.8KB/s   00:00    \n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Copying sdist 'file://localhost/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/controller/..//radical.pilot-0.35.tar.gz' to sandbox (sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/).
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   17] [  184] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/grompp.mdp" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/grompp.mdp"\n)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   17] [  189] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/grompp.mdp" "/work/03531/ jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot. 0000/staging_area/grompp.mdp"\n)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   17] [  188] (Uploading /home/extasy/ExTASY/09-09-extasy_tutorial/grompp.mdp to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/grompp.mdp\n)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   17] [   79] (/home/extasy/ExTASY/09-09-extasy_tutorial/gro   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   17] [   81] (/home/extasy/ExTASY/09-09-extasy_tutorial/gro 100% 1409     1.4KB/s   00:00    \n)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   17] [    6] (sftp> )
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/09-09-extasy_tutorial/gro', 'sftp>']
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   10] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   10] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:14:53 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   10] [   10] (PROMPT-0->)
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc2ac250>
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0996890>
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   18] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   18] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   18] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   18] [    1] ($)
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   18] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   18] [    1] ($)
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   18] [    1] (discard data: '$')
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   16] [  234] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/radical.pilot-0.35.tar.gz" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/radical.pilot-0.35.tar.gz"\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   15] (mput  "/home/ex)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   57] (tasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radi)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   48] (ca l/pilot/radical.pilot-0.35.tar.gz" "/work/03)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   44] (531/jc49/radical.pilot.sandbox/rp.se ssion.)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   41] (jchen-Vostro-260.extasy.016694.0003-pilot)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   34] (.0000/radical.pilot-0.35.tar.gz"\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [  238] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/radical.pilot-0.35.tar.gz to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/radical.pilot-0.35.tar.gz\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100%  316KB 315.6KB/s   00:00    \n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   18] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   18] [   10] (PROMPT-0->)
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:53 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   18] [     ] (flush pty read cache)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] PTYShell del  <saga.utils.pty_shell.PTYShell object at 0x7f7dbc295e90>
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 saga.ShellDirectory   : [DEBUG   ] PTYProcess del  <saga.utils.pty_process.PTYProcess object at 0x7f7dbc2a51d0>
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] saga.job.Service ('slurm+ssh://stampede.tacc.utexas.edu/')
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] Opening shell of type: ssh://stampede.tacc.utexas.edu
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc2a5910>
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc09968d0>
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [INFO    ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:53 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   82] (mux_client_request_session: session request failed: Session open refused by peer\n)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   18] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   18] [   10] (PROMPT-0->)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   18] [     ] (flush pty read cache)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/09-09-extasy_tutorial/topol.top to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./topol.top
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  182] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/topol.top" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/topol.top"\n)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  187] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/topol.top" "/work/03531/j c49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0 000/staging_area/topol.top"\n)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  186] (Uploading /home/extasy/ExTASY/09-09-extasy_tutorial/topol.top to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/topol.top\n)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/09-09-extasy_tutorial/top   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/09-09-extasy_tutorial/top 100% 6674     6.5KB/s   00:00    \n)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/09-09-extasy_tutorial/top', 'sftp>']
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:14:54 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc2ac650>
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:54 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [  113] (ControlSocket /tmp/saga_ssh_extasy_stampede.tacc.utexas.edu_22.jc49.ctrl already exists, disabling multiplexing\n)
2015:09:16 16:14:54 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [ 2380] (Last login: Wed Sep 16 16:11:1 ... __________________________\n\n)
2015:09:16 16:14:54 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] got initial shell prompt (6) (mux_client_request_session: session request failed: Session open refused by peer
ControlSocket /tmp/saga_ssh_extasy_stampede.tacc.utexas.edu_22.jc49.ctrl already exists, disabling multiplexing
Last login: Wed Sep 16 16:11:10 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:54 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Got initial shell prompt (6) (mux_client_request_session: session request failed: Session open refused by peer
ControlSocket /tmp/saga_ssh_extasy_stampede.tacc.utexas.edu_22.jc49.ctrl already exists, disabling multiplexing
Last login: Wed Sep 16 16:11:10 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:14:54 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:54 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0a17690>
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   19] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   19] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   19] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   19] [    1] ($)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   19] [     ] (flush pty read cache)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   19] [    1] ($)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   19] [    1] (discard data: '$')
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   19] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   19] [   10] (PROMPT-0->)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   19] [     ] (flush pty read cache)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   19] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   19] [   10] (PROMPT-0->)
2015:09:16 16:14:54 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   19] [     ] (flush pty read cache)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/09-09-extasy_tutorial/config.ini to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./config.ini
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:55 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [  243] (----------------------- Project balances for user jc49 ------------------------\n| Name           Avail SUs     Expires |                                      |\n| TG-MCB090174       53573  2015-09-30 |                                      |\n)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  184] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/config.ini" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/config.ini"\n)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  189] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/config.ini" "/work/03531/ jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot. 0000/staging_area/config.ini"\n)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  188] (Uploading /home/extasy/ExTASY/09-09-extasy_tutorial/config.ini to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/config.ini\n)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/09-09-extasy_tutorial/con   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/09-09-extasy_tutorial/con 100%  264     0.3KB/s   00:00    \n)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/09-09-extasy_tutorial/con', 'sftp>']
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc2acdd0>
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0935b90>
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   20] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   20] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   20] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   20] [    1] ($)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   20] [     ] (flush pty read cache)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   20] [    1] ($)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   20] [    1] (discard data: '$')
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   20] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   20] [   10] (PROMPT-0->)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   20] [     ] (flush pty read cache)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   20] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   20] [   10] (PROMPT-0->)
2015:09:16 16:14:55 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   20] [     ] (flush pty read cache)
2015:09:16 16:14:55 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [  486] (-------------------------- Disk quotas for user jc49 --------------------------\n| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |\n| /home1              0.1       5.0     2.88         6405      150000    4.27 |\n| /work               0.0    1024.0     0.00         3596     3000000    0.12 |\n| /scratch            0.0       0.0     0.00            3           0    0.00 |\n-------------------------------------------------------------------------------\n)
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/gro.py to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./gro.py
2015:09:16 16:14:55 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:55 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [  228] (\nTip 144   (See "module help tacc_tips" for features or how to disable)\n\n   You can make sure a parameter has a value by putting this in a shell script:\n      param=${param:-$(read -p "Enter parameter: "; echo "$REPLY")}\n\n)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  246] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/gro.py" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/gro.py"\n)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  253] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/ensemblemd/extasy/bin/Preprocessor/Gromacs/gro.py" "/work/03531/jc49/radical.p ilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_a rea/gro.py"\n)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  250] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/gro.py to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/gro.py\n)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100%  780     0.8KB/s   00:00    \n)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc23b6d0>
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0935bd0>
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   21] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   21] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   21] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   21] [    1] ($)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   21] [     ] (flush pty read cache)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   21] [    1] ($)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   21] [    1] (discard data: '$')
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   21] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   21] [   10] (PROMPT-0->)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   21] [     ] (flush pty read cache)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   21] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   21] [   10] (PROMPT-0->)
2015:09:16 16:14:56 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   21] [     ] (flush pty read cache)
2015:09:16 16:14:56 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [  383] (Lmod Warning:  One or more\nmodules in your default  collection\nhave changed: "TACC". \nTo rebuild the collection, load the modules you wish then do:\n  $ module save default\nIf you no longer want this module collection do:\n  rm ~/.lmod.d/default\n\nFor more information execute 'module help' or see www.tacc.utexas.edu/tacc-projects/lmod/user-guide/loading-modules\n\n)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/spliter.py to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./spliter.py
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:56 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  254] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/spliter.py" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/spliter.py"\n)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  261] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/ensemblemd/extasy/bin/Preprocessor/Gromacs/spliter.py" "/work/03531/jc49/radic al.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/stagi ng_area/spliter.py"\n)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  258] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/spliter.py to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/spliter.py\n)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100% 1398     1.4KB/s   00:00    \n)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   21] (login1.stampede(1)$ $)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [    1] ($)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [WARNING ] flush: [   14] [    1] (discard data: '$')
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc2ac4d0>
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbc2ac0d0>
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   22] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   10] (PROMPT-0->)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] got new shell prompt
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   22] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   22] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   22] [    1] ($)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   22] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   22] [    1] ($)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   22] [    1] (discard data: '$')
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] Verifying existence of remote SLURM tools.
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   22] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   22] [   10] (PROMPT-0->)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   22] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: which squeue
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [   13] (which squeue\n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   27] (/usr/bin/squeue\nPROMPT-0->)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   22] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   22] [   10] (PROMPT-0->)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   22] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: which sbatch
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [   13] (which sbatch\n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   27] (/usr/bin/sbatch\nPROMPT-0->)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Simulator/Gromacs/run.py to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./run.py
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: which scancel
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [   14] (which scancel\n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   28] (/usr/bin/scancel\nPROMPT-0->)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: which scontrol
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [   15] (which scontrol\n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   29] (/usr/bin/scontrol\nPROMPT-0->)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] got cmd prompt (0)(/usr/bin/scontrol
)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] No username provided in URL slurm+ssh://stampede.tacc.utexas.edu/, so we are going to find it with whoami
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: whoami
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [    7] (whoami\n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   16] (jc49\nPROMPT-0->)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] Username detected as: jc49
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Bootstrap command line: /bin/bash ['-l default_bootstrapper.sh', " -b 'radical.utils-0.35.tar.gz:saga-python-0.35.tar.gz:radical.pilot-0.35.tar.gz' -c '16' -d '10' -g '/work/03531/jc49/radical.pilot.sandbox/ve_stampede' -j 'SSH' -k 'MPIRUN_RSH' -l 'SLURM' -m 'extasy-db.epcc.ed.ac.uk:27017' -n 'radicalpilot' -o 'POPEN' -p 'pilot.0000' -q 'CONTINUOUS' -r '60' -s 'rp.session.jchen-Vostro-260.extasy.016694.0003' -t 'multicore' -u 'create' -v 'local' -a 'extasy:extasyproject' -e 'module purge' -e 'module load TACC' -e 'module load intel/15.0.2' -e 'module load python/2.7.9' -e 'module unload xalt' -e 'export TACC_DELETE_FILES=TRUE'"]
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  243] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.py" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/run.py"\n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Submitting SAGA job with description: {'Queue': 'normal', 'Executable': '/bin/bash', 'TotalPhysicalMemory': None, 'WorkingDirectory': '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/', 'Project': 'TG-MCB090174', 'WallTimeLimit': 60, 'Arguments': ['-l default_bootstrapper.sh', " -b 'radical.utils-0.35.tar.gz:saga-python-0.35.tar.gz:radical.pilot-0.35.tar.gz' -c '16' -d '10' -g '/work/03531/jc49/radical.pilot.sandbox/ve_stampede' -j 'SSH' -k 'MPIRUN_RSH' -l 'SLURM' -m 'extasy-db.epcc.ed.ac.uk:27017' -n 'radicalpilot' -o 'POPEN' -p 'pilot.0000' -q 'CONTINUOUS' -r '60' -s 'rp.session.jchen-Vostro-260.extasy.016694.0003' -t 'multicore' -u 'create' -v 'local' -a 'extasy:extasyproject' -e 'module purge' -e 'module load TACC' -e 'module load intel/15.0.2' -e 'module load python/2.7.9' -e 'module unload xalt' -e 'export TACC_DELETE_FILES=TRUE'"], 'ProcessesPerHost': None, 'Error': 'agent.err', 'Output': 'agent.out', 'TotalCPUCount': 16}
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  497] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/ensemblemd/extasy/bin/Simulator/Gromacs/run.py" "/work/03531/jc49/radical.pilo t.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area /run.py"\nUploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.py to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/run.py\n)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] number_of_processes not specified in submitted SLURM job description -- defaulting to 1 per total_cpu_count! (16)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100% 4351     4.3KB/s   00:00    \n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [INFO    ] Creating working directory /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [  107] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/\n)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   10] (PROMPT-0->)
2015:09:16 16:14:57 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [INFO    ] SLURM script generated:
#!/bin/sh

#SBATCH -J "SAGAPythonSLURMJob"
#SBATCH --ntasks=16
#SBATCH -D /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/
#SBATCH -o agent.out
#SBATCH -e agent.err
#SBATCH -t 01:00:00
#SBATCH -p normal
#SBATCH -A TG-MCB090174

## EXEC
/bin/bash -l default_bootstrapper.sh  -b 'radical.utils-0.35.tar.gz:saga-python-0.35.tar.gz:radical.pilot-0.35.tar.gz' -c '16' -d '10' -g '/work/03531/jc49/radical.pilot.sandbox/ve_stampede' -j 'SSH' -k 'MPIRUN_RSH' -l 'SLURM' -m 'extasy-db.epcc.ed.ac.uk:27017' -n 'radicalpilot' -o 'POPEN' -p 'pilot.0000' -q 'CONTINUOUS' -r '60' -s 'rp.session.jchen-Vostro-260.extasy.016694.0003' -t 'multicore' -u 'create' -v 'local' -a 'extasy:extasyproject' -e 'module purge' -e 'module load TACC' -e 'module load intel/15.0.2' -e 'module load python/2.7.9' -e 'module unload xalt' -e 'export TACC_DELETE_FILES=TRUE'

2015:09:16 16:14:57 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:14:57 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc23b050>
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbc2a5a90>
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:57 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   23] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   23] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   23] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   23] [    1] ($)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   23] [     ] (flush pty read cache)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   23] [    1] ($)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   23] [    1] (discard data: '$')
2015:09:16 16:14:58 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbc23bc10>
2015:09:16 16:14:58 5484   PilotLauncherWorker-1 radical.pilot         : [INFO    ] running: /usr/bin/env TERM=vt100 /usr/bin/sftp -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu
2015:09:16 16:14:58 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   24] [   82] (mux_client_request_session: session request failed: Session open refused by peer\n)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   23] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   23] [   10] (PROMPT-0->)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   23] [     ] (flush pty read cache)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   23] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   23] [   10] (PROMPT-0->)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   23] [     ] (flush pty read cache)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/pre_analyze.py to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./pre_analyze.py
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:58 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   24] [  113] (ControlSocket /tmp/saga_ssh_extasy_stampede.tacc.utexas.edu_22.jc49.ctrl already exists, disabling multiplexing\n)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  257] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/pre_analyze.py" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/pre_analyze.py"\n)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  264] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/ensemblemd/extasy/bin/Analyzer/LSDMap/pre_analyze.py" "/work/03531/jc49/radica l.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/stagin g_area/pre_analyze.py"\n)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  261] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/pre_analyze.py to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/pre_analyze.py\n)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100%  618     0.6KB/s   00:00    \n)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:14:58 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc2668d0>
2015:09:16 16:14:58 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   24] [   40] (Connected to stampede.tacc.utexas.edu.\n)
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   24] [    6] (sftp> )
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] got initial shell prompt (6) (mux_client_request_session: session request failed: Session open refused by peer
ControlSocket /tmp/saga_ssh_extasy_stampede.tacc.utexas.edu_22.jc49.ctrl already exists, disabling multiplexing
Connected to stampede.tacc.utexas.edu.
sftp> )
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Got initial shell prompt (6) (mux_client_request_session: session request failed: Session open refused by peer
ControlSocket /tmp/saga_ssh_extasy_stampede.tacc.utexas.edu_22.jc49.ctrl already exists, disabling multiplexing
Connected to stampede.tacc.utexas.edu.
sftp> )
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   24] [     ] (flush pty read cache)
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0a3cf90>
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   25] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   25] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   25] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   25] [    1] ($)
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   25] [     ] (flush pty read cache)
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   25] [    1] ($)
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   25] [    1] (discard data: '$')
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   24] [     ] (flush pty read cache)
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   25] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   25] [   10] (PROMPT-0->)
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:14:59 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   25] [     ] (flush pty read cache)
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   24] [   86] (mput  "/home/extasy/.saga/adaptors/shell//staging.140178004531472" "tmp_KCcxLS.slurm"\n)
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   24] [   89] (mput  "/home/extasy/.saga/adaptors/shell//staging.140178004531472" "tmp_KC cxLS.slurm"\n)
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   24] [  108] (Uploading /home/extasy/.saga/adaptors/shell//staging.140178004531472 to /home1/03531/jc49/tmp_KCcxLS.slurm\n)
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   24] [   79] (/home/extasy/.saga/adaptors/shell//staging.14   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   24] [   81] (/home/extasy/.saga/adaptors/shell//staging.14 100%  891     0.9KB/s   00:00    \n)
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   24] [    6] (sftp> )
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/.saga/adaptors/shell//staging.14', 'sftp>']
2015:09:16 16:14:59 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   25] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   25] [   10] (PROMPT-0->)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   25] [     ] (flush pty read cache)
2015:09:16 16:15:00 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: sbatch 'tmp_KCcxLS.slurm'; rm -vf 'tmp_KCcxLS.slurm'
2015:09:16 16:15:00 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [   53] (sbatch 'tmp_KCcxLS.slurm'; rm -vf 'tmp_KCcxLS.slurm'\n)
2015:09:16 16:15:00 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [  203] (-----------------------------------------------------------------\n              Welcome to the Stampede Supercomputer              \n-----------------------------------------------------------------\n\n)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/run_analyzer.sh to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./run_analyzer.sh
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:00 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   81] (--> Verifying valid submit host (login1)...OK\n--> Verifying valid jobname...OK\n)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  259] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/run_analyzer.sh" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/run_analyzer.sh"\n)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  266] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/ensemblemd/extasy/bin/Analyzer/LSDMap/run_analyzer.sh" "/work/03531/jc49/radic al.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/stagi ng_area/run_analyzer.sh"\n)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  263] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/run_analyzer.sh to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/run_analyzer.sh\n)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100%   99     0.1KB/s   00:00    \n)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc1ef1d0>
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0232090>
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   26] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   26] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   26] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   26] [    1] ($)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   26] [     ] (flush pty read cache)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   26] [    1] ($)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   26] [    1] (discard data: '$')
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   26] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   26] [   10] (PROMPT-0->)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   26] [     ] (flush pty read cache)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   26] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   26] [   10] (PROMPT-0->)
2015:09:16 16:15:00 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   26] [     ] (flush pty read cache)
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/post_analyze.py to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./post_analyze.py
2015:09:16 16:15:00 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  259] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/post_analyze.py" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/post_analyze.py"\n)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  266] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/ensemblemd/extasy/bin/Analyzer/LSDMap/post_analyze.py" "/work/03531/jc49/radic al.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/stagi ng_area/post_analyze.py"\n)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  263] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/post_analyze.py to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/post_analyze.py\n)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100% 1028     1.0KB/s   00:00    \n)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc1efdd0>
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0243ed0>
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   27] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   27] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   27] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   27] [    1] ($)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   27] [     ] (flush pty read cache)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   27] [    1] ($)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   27] [    1] (discard data: '$')
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   27] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   27] [   10] (PROMPT-0->)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   27] [     ] (flush pty read cache)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   27] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   27] [   10] (PROMPT-0->)
2015:09:16 16:15:01 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   27] [     ] (flush pty read cache)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/selection.py to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./selection.py
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:01 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  253] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/selection.py" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/selection.py"\n)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  260] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/ensemblemd/extasy/bin/Analyzer/LSDMap/selection.py" "/work/03531/jc49/radical. pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_ area/selection.py"\n)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  257] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/selection.py to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/selection.py\n)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100% 3536     3.5KB/s   00:00    \n)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc1f64d0>
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc0249050>
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   28] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   28] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   28] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   28] [    1] ($)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   28] [     ] (flush pty read cache)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   28] [    1] ($)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   28] [    1] (discard data: '$')
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   28] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   28] [   10] (PROMPT-0->)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   28] [     ] (flush pty read cache)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   28] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   28] [   10] (PROMPT-0->)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   28] [     ] (flush pty read cache)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/reweighting.py to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./reweighting.py
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  257] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/reweighting.py" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/reweighting.py"\n)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  264] (mput  "/home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radica l/ensemblemd/extasy/bin/Analyzer/LSDMap/reweighting.py" "/work/03531/jc49/radica l.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/stagin g_area/reweighting.py"\n)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  261] (Uploading /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/reweighting.py to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/reweighting.py\n)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/ExTASY-tools/lib/python2.   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/ExTASY-tools/lib/python2. 100% 8918     8.7KB/s   00:00    \n)
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/ExTASY-tools/lib/python2.', 'sftp>']
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:02 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:15:02 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc1f6e10>
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbc1f6f10>
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   29] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   29] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   29] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   29] [    1] ($)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   29] [     ] (flush pty read cache)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   29] [    1] ($)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   29] [    1] (discard data: '$')
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   29] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   29] [   10] (PROMPT-0->)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   29] [     ] (flush pty read cache)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   29] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   29] [   10] (PROMPT-0->)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   29] [     ] (flush pty read cache)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/09-09-extasy_tutorial/lsdm.py to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./lsdm.py
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  178] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/lsdm.py" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/lsdm.py"\n)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  183] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/lsdm.py" "/work/03531/jc4 9/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.000 0/staging_area/lsdm.py"\n)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  182] (Uploading /home/extasy/ExTASY/09-09-extasy_tutorial/lsdm.py to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/lsdm.py\n)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/09-09-extasy_tutorial/lsd   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/09-09-extasy_tutorial/lsd 100%   14KB  14.3KB/s   00:00    \n)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/09-09-extasy_tutorial/lsd', 'sftp>']
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   12] [  478] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area'\n)
2015:09:16 16:15:03 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc1f6590>
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc09b52d0>
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   30] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   30] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   30] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   30] [    1] ($)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   30] [     ] (flush pty read cache)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   30] [    1] ($)
2015:09:16 16:15:03 5484   MainThread   saga.ShellDirectory   : [WARNING ] flush: [   30] [    1] (discard data: '$')
2015:09:16 16:15:04 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   30] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:15:04 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   30] [   10] (PROMPT-0->)
2015:09:16 16:15:04 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:15:04 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   30] [     ] (flush pty read cache)
2015:09:16 16:15:04 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:15:04 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] write: [   30] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:15:04 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] read : [   30] [   10] (PROMPT-0->)
2015:09:16 16:15:04 5484   MainThread   saga.ShellDirectory   : [DEBUG   ] flush: [   30] [     ] (flush pty read cache)
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [INFO    ] Transferring file:///home/extasy/ExTASY/09-09-extasy_tutorial/input.gro to sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/./input.gro
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   16] [     ] (flush pty read cache)
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   16] [  182] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/input.gro" "/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/input.gro"\n)
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  187] (mput  "/home/extasy/ExTASY/09-09-extasy_tutorial/input.gro" "/work/03531/j c49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0 000/staging_area/input.gro"\n)
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [  186] (Uploading /home/extasy/ExTASY/09-09-extasy_tutorial/input.gro to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/input.gro\n)
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   79] (/home/extasy/ExTASY/09-09-extasy_tutorial/inp   0%    0     0.0KB/s   --:-- ETA)
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [   81] (/home/extasy/ExTASY/09-09-extasy_tutorial/inp 100% 1047KB   1.0MB/s   00:00    \n)
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   16] [    6] (sftp> )
2015:09:16 16:15:04 5484   MainThread   radical.pilot         : [DEBUG   ] copy done: ['mput', 'Uploading', '/home/extasy/ExTASY/09-09-extasy_tutorial/inp', 'sftp>']
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'staging:///spliter.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'spliter.py', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'staging:///input.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'input.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start0.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start0.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start1.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start1.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start2.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start2.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start3.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start3.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start4.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start4.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start5.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start5.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start6.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start6.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start7.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start7.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start8.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start8.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start9.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start9.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start10.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start10.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start11.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start11.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start12.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start12.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start13.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start13.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start14.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start14.gro', 'priority': 0}'
2015:09:16 16:15:05 5484   MainThread   radical.pilot         : [DEBUG   ] Completing entry '{'action': 'Link', 'source': 'temp/start15.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter0/start15.gro', 'priority': 0}'
2015:09:16 16:15:06 5484   MainThread   radical.pilot         : [INFO    ] Scheduled ComputeUnits [unit.000000 (Scheduling     : python ['spliter.py', '16', 'input.gro']) (140178004273680)] on ComputePilot 'pilot.0000'.
2015:09:16 16:15:06 5484   MainThread   radical.pilot         : [INFO    ] 0 units remain unscheduled
2015:09:16 16:15:06 5484   Thread-3     radical.pilot         : [INFO    ] RUN ComputeUnit 'unit.000000' state changed from 'Scheduling' to 'PendingInputStaging'.
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 radical.pilot         : [DEBUG   ] InputStagingController: unit found: unit.000000
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 radical.pilot         : [INFO    ] InputStagingController: Creating ComputeUnit sandbox directory sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000//unit.000000.
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 radical.pilot         : [DEBUG   ] saga.fs.Directory ('sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000//unit.000000')
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 radical.pilot         : [DEBUG   ] flush: [   12] [     ] (flush pty read cache)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] run_sync: mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000 && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000 &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000'
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 radical.pilot         : [DEBUG   ] write: [   12] [  474] (mkdir -p /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000 && cd /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000 &&  mkdir -p '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000' ;  cd '/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000'\n)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 radical.pilot         : [DEBUG   ] read : [   12] [   10] (PROMPT-0->)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] initialized directory (0)()
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc266f90>
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dc09aae10>
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [INFO    ] running: /usr/bin/env TERM=vt100 /bin/bash -i
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] write: [   32] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   32] [   56] (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] Got initial shell prompt (6) (extasy@jchen-Vostro-260:~/ExTASY/09-09-extasy_tutorial$ )
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] write: [   32] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   32] [    1] ($)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] flush: [   32] [     ] (flush pty read cache)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   32] [    1] ($)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [WARNING ] flush: [   32] [    1] (discard data: '$')
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] write: [   32] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   32] [   10] (PROMPT-0->)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] got new shell prompt
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] flush: [   32] [     ] (flush pty read cache)
2015:09:16 16:15:07 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   38] (--> Enforcing max jobs per user...OK\n)
2015:09:16 16:15:07 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   70] (--> Verifying availability of your home dir (/home1/03531/jc49)...OK\n)
2015:09:16 16:15:07 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   69] (--> Verifying availability of your work dir (/work/03531/jc49)...OK\n)
2015:09:16 16:15:07 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   75] (--> Verifying availability of your scratch dir (/scratch/03531/jc49)...OK\n)
2015:09:16 16:15:07 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [  202] (--> Verifying valid ssh keys...OK\n--> Verifying access to desired queue (normal)...OK\n--> Verifying job request is within current queue limits...OK\n--> Checking available allocation (TG-MCB090174)...)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] run_sync: cd /home/extasy/ExTASY/09-09-extasy_tutorial
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] write: [   32] [   45] (cd /home/extasy/ExTASY/09-09-extasy_tutorial\n)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] read : [   32] [   10] (PROMPT-0->)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 saga.ShellDirectory   : [DEBUG   ] flush: [   32] [     ] (flush pty read cache)
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 radical.pilot         : [INFO    ] InputStagingController: Processing input file transfers for ComputeUnit unit.000000
2015:09:16 16:15:07 5484   InputFileTransferWorker-1 radical.pilot         : [DEBUG   ] InputStagingController: unit.000000 : push to agent
2015:09:16 16:15:07 5484   Thread-3     radical.pilot         : [INFO    ] RUN ComputeUnit 'unit.000000' state changed from 'PendingInputStaging' to 'PendingAgentInputStaging'.
2015:09:16 16:15:08 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [    4] (OK\n)
2015:09:16 16:15:08 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   29] (Submitted batch job 5767425\n)
2015:09:16 16:15:08 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [   38] (removed `tmp_KCcxLS.slurm'\nPROMPT-0->)
2015:09:16 16:15:08 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] staged/submit SLURM script (tmp_KCcxLS.slurm) (0)
2015:09:16 16:15:08 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] started job [slurm+ssh://stampede.tacc.utexas.edu/]-[5767425]
2015:09:16 16:15:08 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] Batch system output:
-----------------------------------------------------------------
              Welcome to the Stampede Supercomputer              
-----------------------------------------------------------------

--> Verifying valid submit host (login1)...OK
--> Verifying valid jobname...OK
--> Enforcing max jobs per user...OK
--> Verifying availability of your home dir (/home1/03531/jc49)...OK
--> Verifying availability of your work dir (/work/03531/jc49)...OK
--> Verifying availability of your scratch dir (/scratch/03531/jc49)...OK
--> Verifying valid ssh keys...OK
--> Verifying access to desired queue (normal)...OK
--> Verifying job request is within current queue limits...OK
--> Checking available allocation (TG-MCB090174)...OK
Submitted batch job 5767425
removed `tmp_KCcxLS.slurm'

2015:09:16 16:15:08 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:15:09 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: scontrol show job 5767425
2015:09:16 16:15:09 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   14] [   26] (scontrol show job 5767425\n)
2015:09:16 16:15:09 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   14] [ 1277] (JobId=5767425 JobName=SAGAPyth ... .0000//agent.out\n\nPROMPT-0->)
2015:09:16 16:15:09 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] SAGA job submitted with job id [slurm+ssh://stampede.tacc.utexas.edu/]-[5767425]
2015:09:16 16:15:10 5484   Thread-1     radical.pilot         : [INFO    ] ComputePilot 'pilot.0000' state changed from 'Launching' to 'PendingActive'.
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [INFO    ] Performing periodical health check for pilot.0000 (SAGA job id [slurm+ssh://stampede.tacc.utexas.edu/]-[5767425])
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] Opening shell of type: ssh://stampede.tacc.utexas.edu
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f7dbc1ef410>
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [INFO    ] PTY prompt pattern: [\$#%>\]]\s*$
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [INFO    ] ssh copy  mode set to 'sftp'
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [INFO    ] ssh share mode set to 'auto'
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f7dbf959ad0>
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [INFO    ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o ControlMaster=auto -o ControlPath=/tmp/saga_ssh_extasy_%h_%p.jc49.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 jc49@stampede.tacc.utexas.edu
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   33] ( export PS1='$' ; set prompt='$'\n)
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [   82] (mux_client_request_session: session request failed: Session open refused by peer\n)
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [  113] (ControlSocket /tmp/saga_ssh_extasy_stampede.tacc.utexas.edu_22.jc49.ctrl already exists, disabling multiplexing\n)
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [ 2380] (Last login: Wed Sep 16 16:03:4 ... __________________________\n\n)
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] got initial shell prompt (6) (mux_client_request_session: session request failed: Session open refused by peer
ControlSocket /tmp/saga_ssh_extasy_stampede.tacc.utexas.edu_22.jc49.ctrl already exists, disabling multiplexing
Last login: Wed Sep 16 16:03:42 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] Got initial shell prompt (6) (mux_client_request_session: session request failed: Session open refused by peer
ControlSocket /tmp/saga_ssh_extasy_stampede.tacc.utexas.edu_22.jc49.ctrl already exists, disabling multiplexing
Last login: Wed Sep 16 16:03:42 2015 from 128.42.90.115
------------------------------------------------------------------------------
                   Welcome to the Stampede Supercomputer
      Texas Advanced Computing Center, The University of Texas at Austin
------------------------------------------------------------------------------

              ** Unauthorized use/access is prohibited. **

If you log on to this computer system, you acknowledge your awareness
of and concurrence with the UT Austin Acceptable Use Policy. The
University will prosecute violators to the full extent of the law.

TACC Usage Policies:
http://www.tacc.utexas.edu/user-services/usage-policies/
______________________________________________________________________________

Questions and Problem Reports:

--> XD Projects:     help@xsede.org (email)
--> TACC Projects:   portal.tacc.utexas.edu (web)

Documentation:  http://www.tacc.utexas.edu/user-services/user-guides/
User News:      http://www.tacc.utexas.edu/user-services/user-news/
______________________________________________________________________________

Welcome to Stampede, *please* read these important system notes:

--> Stampede is currently running the SLURM resource manager to
    schedule all compute resources. Example SLURM job scripts are
    available on the system at /share/doc/slurm

    To run an interactive shell, issue: 
          srun -p development -t 0:30:00 -n 32 --pty /bin/bash -l

    To submit a batch job, issue:       sbatch job.mpi 
    To show all queued jobs, issue:     showq
    To kill a queued job, issue:        scancel <jobId>
)
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] running command shell:         exec /bin/sh -i
2015:09:16 16:15:45 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n)
2015:09:16 16:15:46 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [  243] (----------------------- Project balances for user jc49 ------------------------\n| Name           Avail SUs     Expires |                                      |\n| TG-MCB090174       53573  2015-09-30 |                                      |\n)
2015:09:16 16:15:46 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [  486] (-------------------------- Disk quotas for user jc49 --------------------------\n| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |\n| /home1              0.1       5.0     2.88         6405      150000    4.27 |\n| /work               0.0    1024.0     0.00         4229     3000000    0.14 |\n| /scratch            0.0       0.0     0.00            3           0    0.00 |\n-------------------------------------------------------------------------------\n)
2015:09:16 16:15:46 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [  155] (\nTip 113   (See "module help tacc_tips" for features or how to disable)\n\n   To print a random number between 1 and X do:\n      $ echo $[RANDOM%X+1]\n\n)
2015:09:16 16:15:46 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:46 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   99] (unset PROMPT_COMMAND ;  unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n)
2015:09:16 16:15:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [    1] (\n)
2015:09:16 16:15:47 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] sent prompt trigger again (1)
2015:09:16 16:15:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [  383] (Lmod Warning:  One or more\nmodules in your default  collection\nhave changed: "TACC". \nTo rebuild the collection, load the modules you wish then do:\n  $ module save default\nIf you no longer want this module collection do:\n  rm ~/.lmod.d/default\n\nFor more information execute 'module help' or see www.tacc.utexas.edu/tacc-projects/lmod/user-guide/loading-modules\n\n)
2015:09:16 16:15:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [   21] (login2.stampede(1)$ $)
2015:09:16 16:15:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [   21] ($PROMPT-0->PROMPT-0->)
2015:09:16 16:15:47 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   29] (printf "SYNCHRONIZE_PROMPT\n"\n)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [   30] (SYNCHRONIZE_PROMPT\nPROMPT-0->)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] got new shell prompt
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] Verifying existence of remote SLURM tools.
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: which squeue
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   13] (which squeue\n)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [   27] (/usr/bin/squeue\nPROMPT-0->)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: which sbatch
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   13] (which sbatch\n)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [   27] (/usr/bin/sbatch\nPROMPT-0->)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: which scancel
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   14] (which scancel\n)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [   28] (/usr/bin/scancel\nPROMPT-0->)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: which scontrol
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   15] (which scontrol\n)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [   29] (/usr/bin/scontrol\nPROMPT-0->)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] got cmd prompt (0)(/usr/bin/scontrol
)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] No username provided in URL slurm+ssh://stampede.tacc.utexas.edu/, so we are going to find it with whoami
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: whoami
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [    7] (whoami\n)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [   16] (jc49\nPROMPT-0->)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] Username detected as: jc49
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: scontrol show job 5767425
2015:09:16 16:15:48 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   26] (scontrol show job 5767425\n)
2015:09:16 16:15:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [ 1326] (JobId=5767425 JobName=SAGAPyth ... .0000//agent.out\n\nPROMPT-0->)
2015:09:16 16:15:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] flush: [   33] [     ] (flush pty read cache)
2015:09:16 16:15:49 5484   PilotLauncherWorker-1 saga.SLURMJobService  : [DEBUG   ] run_sync: scontrol show job 5767425
2015:09:16 16:15:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] write: [   33] [   26] (scontrol show job 5767425\n)
2015:09:16 16:15:49 5484   PilotLauncherWorker-1 radical.pilot         : [DEBUG   ] read : [   33] [ 1326] (JobId=5767425 JobName=SAGAPyth ... .0000//agent.out\n\nPROMPT-0->)
2015:09:16 16:15:49 5484   PilotLauncherWorker-1 radical.pilot         : [INFO    ] pilot pilot.0000 seems alive and well
2015:09:16 16:15:50 5484   Thread-3     radical.pilot         : [INFO    ] RUN ComputeUnit 'unit.000000' state changed from 'PendingAgentInputStaging' to 'AgentStagingInput'.
2015:09:16 16:15:50 5484   Thread-1     radical.pilot         : [INFO    ] ComputePilot 'pilot.0000' state changed from 'PendingActive' to 'Active'.
2015:09:16 16:15:51 5484   Thread-3     radical.pilot         : [INFO    ] RUN ComputeUnit 'unit.000000' state changed from 'AgentStagingInput' to 'Executing'.
2015:09:16 16:15:53 5484   Thread-3     radical.pilot         : [INFO    ] RUN ComputeUnit 'unit.000000' state changed from 'Executing' to 'PendingAgentOutputStaging'.
2015:09:16 16:15:54 5484   OutputFileTransferWorker-2 radical.pilot         : [INFO    ] OFTW CU found, progressing ...
2015:09:16 16:15:54 5484   OutputFileTransferWorker-2 radical.pilot         : [DEBUG   ] OutputStagingController: unit found: unit.000000
2015:09:16 16:15:54 5484   OutputFileTransferWorker-2 radical.pilot         : [INFO    ] OutputStagingController: Processing output file transfers for ComputeUnit unit.000000
2015:09:16 16:15:54 5484   Thread-3     radical.pilot         : [INFO    ] RUN ComputeUnit 'unit.000000' state changed from 'PendingAgentOutputStaging' to 'Done'.
2015:09:16 16:15:54 5484   MainThread   radical.pilot         : [DEBUG   ] session rp.session.jchen-Vostro-260.extasy.016694.0003 closing
2015:09:16 16:15:54 5484   MainThread   radical.pilot         : [DEBUG   ] session rp.session.jchen-Vostro-260.extasy.016694.0003 closes   pmgr   55f9dbc3ee1f52156c89f242
2015:09:16 16:15:54 5484   MainThread   radical.pilot         : [DEBUG   ] pmgr    55f9dbc3ee1f52156c89f242 closing
2015:09:16 16:15:54 5484   MainThread   radical.pilot         : [DEBUG   ] pmgr    55f9dbc3ee1f52156c89f242 cancel   worker Thread-1
2015:09:16 16:15:54 5484   MainThread   radical.pilot         : [DEBUG   ] pworker Thread-1 stops   launcher PilotLauncherWorker-1
2015:09:16 16:15:54 5484   MainThread   radical.pilot         : [DEBUG   ] launcher PilotLauncherWorker-1 stopping
2015:09:16 16:15:55 5484   MainThread   radical.pilot         : [DEBUG   ] launcher PilotLauncherWorker-1 stopped
2015:09:16 16:15:55 5484   MainThread   radical.pilot         : [DEBUG   ] pworker Thread-1 stopped launcher PilotLauncherWorker-1
2015:09:16 16:15:55 5484   MainThread   radical.pilot         : [DEBUG   ] pmgr    55f9dbc3ee1f52156c89f242 canceled worker Thread-1
2015:09:16 16:15:55 5484   MainThread   radical.pilot         : [DEBUG   ] Reconnected to existing ComputePilot {'uid': 'pilot.0000', 'stdout': None, 'start_time': datetime.datetime(2015, 9, 16, 21, 15, 49, 108000), 'resource_detail': {'cores_per_node': 16, 'nodes': [u'c401-001']}, 'submission_time': datetime.datetime(2015, 9, 16, 21, 14, 46, 575000), 'logfile': None, 'resource': u'stampede.tacc.utexas.edu', 'log': [<radical.pilot.logentry.Logentry object at 0x7f7dbc1f6a90>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f6850>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f6510>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f6a50>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f6b50>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f62d0>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f6fd0>], 'sandbox': u'sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/', 'state': u'Active', 'stop_time': None, 'stderr': None}
2015:09:16 16:15:55 5484   MainThread   radical.pilot         : [DEBUG   ] pmgr    55f9dbc3ee1f52156c89f242 cancels  pilot  pilot.0000
2015:09:16 16:15:55 5484   MainThread   radical.pilot         : [INFO    ] Sent 'COMMAND_CANCEL_PILOT' command to pilots ['pilot.0000'].
2015:09:16 16:15:55 5484   MainThread   radical.pilot         : [WARNING ] actively cancel pilot pilot.0000 state: Active
2015:09:16 16:15:55 5484   MainThread   radical.pilot         : [DEBUG   ] delay to actively cancel pilot pilot.0000: state Active
2015:09:16 16:16:00 5484   Thread-1     radical.pilot         : [INFO    ] ComputePilot 'pilot.0000' state changed from 'Active' to 'Canceled'.
2015:09:16 16:16:05 5484   MainThread   radical.pilot         : [INFO    ] actively cancel pilot pilot.0000 (delayed) ([slurm+ssh://stampede.tacc.utexas.edu/]-[5767425], slurm+ssh://stampede.tacc.utexas.edu/)
2015:09:16 16:16:05 5484   MainThread   radical.pilot         : [DEBUG   ] flush: [   14] [     ] (flush pty read cache)
2015:09:16 16:16:05 5484   MainThread   saga.SLURMJobService  : [DEBUG   ] run_sync: scancel 5767425
2015:09:16 16:16:05 5484   MainThread   radical.pilot         : [DEBUG   ] write: [   14] [   16] (scancel 5767425\n)
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] read : [   14] [   95] (scancel: error: slurm_kill_job2() failed Job/step already completing or completed\nPROMPT-255->)
2015:09:16 16:16:07 5484   MainThread   saga.SLURMJobService  : [ERROR   ] NoSuccess: Could not cancel job 5767425 because: scancel: error: slurm_kill_job2() failed Job/step already completing or completed

2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [WARNING ] delayed pilot cancelation failed. This is not necessarily a problem.
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] Reconnected to existing ComputePilot {'uid': 'pilot.0000', 'stdout': u"[... CONTENT SHORTENED ...]\n/ve_stampede/lib/python2.7/plat-linux2', '/work/03531/jc49/radical.pilot.sandbox/ve_stampede/lib/python2.7/lib-tk', '/work/03531/jc49/radical.pilot.sandbox/ve_stampede/lib/python2.7/lib-old', '/work/03531/jc49/radical.pilot.sandbox/ve_stampede/lib/python2.7/lib-dynload', '/opt/apps/intel15/python/2.7.9/lib/python2.7', '/opt/apps/intel15/python/2.7.9/lib/python2.7/plat-linux2', '/opt/apps/intel15/python/2.7.9/lib/python2.7/lib-tk']\npython: 2.7.9 (default, Apr 27 2015, 09:07:35) \n[GCC Intel(R) C++ gcc 4.4 mode]\nutils : 0.35  : /work/03531/jc49/radical.pilot.sandbox/ve_stampede/rp_install/lib/python2.7/site-packages/radical/utils/__init__.pyc\nsaga  : 0.35  : /work/03531/jc49/radical.pilot.sandbox/ve_stampede/rp_install/lib/python2.7/site-packages/saga/__init__.pyc\npilot : 0.35  : /work/03531/jc49/radical.pilot.sandbox/ve_stampede/rp_install/lib/python2.7/site-packages/radical/pilot/__init__.pyc\n        type  : multicore\n        gitid : $Id$\n\n---------------------------------------------------------------------\n\n", 'start_time': datetime.datetime(2015, 9, 16, 21, 15, 49, 108000), 'resource_detail': {'cores_per_node': 16, 'nodes': [u'c401-001']}, 'submission_time': datetime.datetime(2015, 9, 16, 21, 14, 46, 575000), 'logfile': u"[... CONTENT SHORTENED ...]\n.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/iter0/start15.gro\n2015-09-16 16:15:52,734 - radical.pilot.agent - INFO - Link'ed /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000/temp/start15.gro to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/iter0/start15.gro - success\n2015-09-16 16:15:52,914 - radical.pilot.agent - DEBUG - bulk update result: {'nModified': 1, 'nUpserted': 0, 'nMatched': 1, 'writeErrors': [], 'upserted': [], 'writeConcernErrors': [], 'nRemoved': 0, 'nInserted': 0}\n2015-09-16 16:15:53,967 - radical.pilot.agent - DEBUG - bulk update result: {'nModified': 1, 'nUpserted': 0, 'nMatched': 1, 'writeErrors': [], 'upserted': [], 'writeConcernErrors': [], 'nRemoved': 0, 'nInserted': 0}\n2015-09-16 16:15:59,406 - radical.pilot.agent - WARNING - CANCEL received. Terminating.\n2015-09-16 16:15:59,573 - radical.pilot.agent - WARNING - Terminated (_terminate set).\n", 'resource': u'stampede.tacc.utexas.edu', 'log': [<radical.pilot.logentry.Logentry object at 0x7f7dbc295ed0>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f6b50>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f6fd0>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f62d0>, <radical.pilot.logentry.Logentry object at 0x7f7dbc1f6a50>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280f50>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280dd0>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280f90>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280f10>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280ed0>, <radical.pilot.logentry.Logentry object at 0x7f7dbf9596d0>], 'sandbox': u'sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/', 'state': u'Canceled', 'stop_time': datetime.datetime(2015, 9, 16, 21, 15, 59, 573000), 'stderr': u"[... CONTENT SHORTENED ...]\n52 60859  StageoutWorker-0 radical.pilot.agent   : [INFO    ] Link'ed /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000/temp/start15.gro to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/iter0/start15.gro - success\n2015:09:16 16:15:52 60859  UpdateWorker-0 radical.pilot.agent   : [DEBUG   ] bulk update result: {'nModified': 1, 'nUpserted': 0, 'nMatched': 1, 'writeErrors': [], 'upserted': [], 'writeConcernErrors': [], 'nRemoved': 0, 'nInserted': 0}\n2015:09:16 16:15:53 60859  UpdateWorker-0 radical.pilot.agent   : [DEBUG   ] bulk update result: {'nModified': 1, 'nUpserted': 0, 'nMatched': 1, 'writeErrors': [], 'upserted': [], 'writeConcernErrors': [], 'nRemoved': 0, 'nInserted': 0}\n2015:09:16 16:15:59 60859  HeartbeatMonitor radical.pilot.agent   : [WARNING ] CANCEL received. Terminating.\n2015:09:16 16:15:59 60859  MainThread   radical.pilot.agent   : [WARNING ] Terminated (_terminate set).\n"}
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] pmgr    55f9dbc3ee1f52156c89f242 wait for pilot  pilot.0000 (Canceled)
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] Reconnected to existing ComputePilot {'uid': 'pilot.0000', 'stdout': u"[... CONTENT SHORTENED ...]\n/ve_stampede/lib/python2.7/plat-linux2', '/work/03531/jc49/radical.pilot.sandbox/ve_stampede/lib/python2.7/lib-tk', '/work/03531/jc49/radical.pilot.sandbox/ve_stampede/lib/python2.7/lib-old', '/work/03531/jc49/radical.pilot.sandbox/ve_stampede/lib/python2.7/lib-dynload', '/opt/apps/intel15/python/2.7.9/lib/python2.7', '/opt/apps/intel15/python/2.7.9/lib/python2.7/plat-linux2', '/opt/apps/intel15/python/2.7.9/lib/python2.7/lib-tk']\npython: 2.7.9 (default, Apr 27 2015, 09:07:35) \n[GCC Intel(R) C++ gcc 4.4 mode]\nutils : 0.35  : /work/03531/jc49/radical.pilot.sandbox/ve_stampede/rp_install/lib/python2.7/site-packages/radical/utils/__init__.pyc\nsaga  : 0.35  : /work/03531/jc49/radical.pilot.sandbox/ve_stampede/rp_install/lib/python2.7/site-packages/saga/__init__.pyc\npilot : 0.35  : /work/03531/jc49/radical.pilot.sandbox/ve_stampede/rp_install/lib/python2.7/site-packages/radical/pilot/__init__.pyc\n        type  : multicore\n        gitid : $Id$\n\n---------------------------------------------------------------------\n\n", 'start_time': datetime.datetime(2015, 9, 16, 21, 15, 49, 108000), 'resource_detail': {'cores_per_node': 16, 'nodes': [u'c401-001']}, 'submission_time': datetime.datetime(2015, 9, 16, 21, 14, 46, 575000), 'logfile': u"[... CONTENT SHORTENED ...]\n.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/iter0/start15.gro\n2015-09-16 16:15:52,734 - radical.pilot.agent - INFO - Link'ed /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000/temp/start15.gro to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/iter0/start15.gro - success\n2015-09-16 16:15:52,914 - radical.pilot.agent - DEBUG - bulk update result: {'nModified': 1, 'nUpserted': 0, 'nMatched': 1, 'writeErrors': [], 'upserted': [], 'writeConcernErrors': [], 'nRemoved': 0, 'nInserted': 0}\n2015-09-16 16:15:53,967 - radical.pilot.agent - DEBUG - bulk update result: {'nModified': 1, 'nUpserted': 0, 'nMatched': 1, 'writeErrors': [], 'upserted': [], 'writeConcernErrors': [], 'nRemoved': 0, 'nInserted': 0}\n2015-09-16 16:15:59,406 - radical.pilot.agent - WARNING - CANCEL received. Terminating.\n2015-09-16 16:15:59,573 - radical.pilot.agent - WARNING - Terminated (_terminate set).\n", 'resource': u'stampede.tacc.utexas.edu', 'log': [<radical.pilot.logentry.Logentry object at 0x7f7dbc1f6a50>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280f50>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280dd0>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280f90>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280f10>, <radical.pilot.logentry.Logentry object at 0x7f7dbc280ed0>, <radical.pilot.logentry.Logentry object at 0x7f7dbc295d90>, <radical.pilot.logentry.Logentry object at 0x7f7dbc295ed0>, <radical.pilot.logentry.Logentry object at 0x7f7dbc295f90>, <radical.pilot.logentry.Logentry object at 0x7f7dbf959690>, <radical.pilot.logentry.Logentry object at 0x7f7dbf9596d0>], 'sandbox': u'sftp://stampede.tacc.utexas.edu/work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/', 'state': u'Canceled', 'stop_time': datetime.datetime(2015, 9, 16, 21, 15, 59, 573000), 'stderr': u"[... CONTENT SHORTENED ...]\n52 60859  StageoutWorker-0 radical.pilot.agent   : [INFO    ] Link'ed /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/unit.000000/temp/start15.gro to /work/03531/jc49/radical.pilot.sandbox/rp.session.jchen-Vostro-260.extasy.016694.0003-pilot.0000/staging_area/iter0/start15.gro - success\n2015:09:16 16:15:52 60859  UpdateWorker-0 radical.pilot.agent   : [DEBUG   ] bulk update result: {'nModified': 1, 'nUpserted': 0, 'nMatched': 1, 'writeErrors': [], 'upserted': [], 'writeConcernErrors': [], 'nRemoved': 0, 'nInserted': 0}\n2015:09:16 16:15:53 60859  UpdateWorker-0 radical.pilot.agent   : [DEBUG   ] bulk update result: {'nModified': 1, 'nUpserted': 0, 'nMatched': 1, 'writeErrors': [], 'upserted': [], 'writeConcernErrors': [], 'nRemoved': 0, 'nInserted': 0}\n2015:09:16 16:15:59 60859  HeartbeatMonitor radical.pilot.agent   : [WARNING ] CANCEL received. Terminating.\n2015:09:16 16:15:59 60859  MainThread   radical.pilot.agent   : [WARNING ] Terminated (_terminate set).\n"}
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] pmgr    55f9dbc3ee1f52156c89f242 canceled pilot  pilot.0000
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] pmgr    55f9dbc3ee1f52156c89f242 stops    worker Thread-1
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] pworker Thread-1 stopping
2015:09:16 16:16:07 5484   Thread-1     radical.pilot         : [DEBUG   ] pworker Thread-1 stops   launcher PilotLauncherWorker-1
2015:09:16 16:16:07 5484   Thread-1     radical.pilot         : [DEBUG   ] launcher PilotLauncherWorker-1 stopping
2015:09:16 16:16:07 5484   Thread-1     radical.pilot         : [DEBUG   ] launcher PilotLauncherWorker-1 stopped
2015:09:16 16:16:07 5484   Thread-1     radical.pilot         : [DEBUG   ] pworker Thread-1 stopped launcher PilotLauncherWorker-1
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] pworker Thread-1 stopped
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] pmgr    55f9dbc3ee1f52156c89f242 stopped  worker Thread-1
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] pmgr    55f9dbc3ee1f52156c89f242 closed
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] session rp.session.jchen-Vostro-260.extasy.016694.0003 closed   pmgr   None
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] session rp.session.jchen-Vostro-260.extasy.016694.0003 closes   umgr   55f9dbc6ee1f52156c89f243
2015:09:16 16:16:07 5484   MainThread   radical.pilot         : [DEBUG   ] uworker  Thread-3 stopping
2015:09:16 16:16:08 5484   Thread-3     radical.pilot         : [DEBUG   ] uworker Thread-3 stops   itransfer InputFileTransferWorker-1
2015:09:16 16:16:08 5484   Thread-3     radical.pilot         : [DEBUG   ] itransfer InputFileTransferWorker-1 stopping
2015:09:16 16:16:09 5484   Thread-3     radical.pilot         : [DEBUG   ] itransfer InputFileTransferWorker-1 stopped
2015:09:16 16:16:09 5484   Thread-3     radical.pilot         : [DEBUG   ] uworker Thread-3 stopped itransfer InputFileTransferWorker-1
2015:09:16 16:16:09 5484   Thread-3     radical.pilot         : [DEBUG   ] uworker Thread-3 stops   itransfer InputFileTransferWorker-2
2015:09:16 16:16:09 5484   Thread-3     radical.pilot         : [DEBUG   ] itransfer InputFileTransferWorker-2 stopping
2015:09:16 16:16:09 5484   Thread-3     radical.pilot         : [DEBUG   ] itransfer InputFileTransferWorker-2 stopped
2015:09:16 16:16:09 5484   Thread-3     radical.pilot         : [DEBUG   ] uworker Thread-3 stopped itransfer InputFileTransferWorker-2
2015:09:16 16:16:09 5484   Thread-3     radical.pilot         : [DEBUG   ] uworker Thread-3 stops   otransfer OutputFileTransferWorker-1
2015:09:16 16:16:09 5484   Thread-3     radical.pilot         : [DEBUG   ] otransfer OutputFileTransferWorker-1 stopping
2015:09:16 16:16:10 5484   Thread-3     radical.pilot         : [DEBUG   ] otransfer OutputFileTransferWorker-1 stopped
2015:09:16 16:16:10 5484   Thread-3     radical.pilot         : [DEBUG   ] uworker Thread-3 stopped otransfer OutputFileTransferWorker-1
2015:09:16 16:16:10 5484   Thread-3     radical.pilot         : [DEBUG   ] uworker Thread-3 stops   otransfer OutputFileTransferWorker-2
2015:09:16 16:16:10 5484   Thread-3     radical.pilot         : [DEBUG   ] otransfer OutputFileTransferWorker-2 stopping
2015:09:16 16:16:10 5484   Thread-3     radical.pilot         : [DEBUG   ] otransfer OutputFileTransferWorker-2 stopped
2015:09:16 16:16:10 5484   Thread-3     radical.pilot         : [DEBUG   ] uworker Thread-3 stopped otransfer OutputFileTransferWorker-2
2015:09:16 16:16:10 5484   MainThread   radical.pilot         : [DEBUG   ] uworker  Thread-3 stopped
2015:09:16 16:16:10 5484   MainThread   radical.pilot         : [INFO    ] Closed UnitManager 55f9dbc6ee1f52156c89f243.
2015:09:16 16:16:10 5484   MainThread   radical.pilot         : [DEBUG   ] session rp.session.jchen-Vostro-260.extasy.016694.0003 closed   umgr   None
2015:09:16 16:16:10 5484   MainThread   radical.pilot         : [DEBUG   ] session rp.session.jchen-Vostro-260.extasy.016694.0003 closed

[vivek-bala]

Could you tell me what you have as the remote host in config file ? Is it stampede.tacc.utexas.edu(incorrect) or xsede.stampede(correct) ?

[vivek-bala]

possibly #187

[TensorDuck]

Using xsede.stampede fixes the problem. Now the gromacs-lsdmap workflow works as expected. Thanks!