Closed jp43 closed 9 years ago
marksantcroos
commented
10 years ago NoSuccess: Error running job via 'qsub': qsub: option requires an argument -- 'A'
My guess is that somewhere in the stack somebody is setting an empty "project" or so ...
vivek-bala
commented
9 years ago I think if you set the allocation in the configuration file to your allocation on DaVinci (https://github.com/radical-cybertools/ExTASY/blob/devel/config/stampede.rcfg#L3), this error shouldn't come up. Also, there is not entry for DaVinci in the mdkernels package yet, so the proper modules for gromacs/lsdmap will not be loaded. I'll look up the documentation for the specific names and dependencies and add them.
jp43
commented
9 years ago Hi, thank you very much. It seems to work with the allocation number specified in the stampede.rcfg file. I actually added a new entry 'rice.davinci' in files lsdmap.json and gromacs.json in the mdkernels package installed on my laptop. So far, the MD simulations and the LSDMap finished correctly. More soon...
vivek-bala
commented
9 years ago Ah ok, good. Could you send me the entries in gromacs.json and lsdmap.json that you made ? I wasn't able to find any information about modules for lsdmap from the docs.
After successfully running the radical pilot simple-bot script on davinci, I got the following error message (with the DEBUG option) when running the gromacs GROMACS/LSDMap workflow (sorry it's kinda long):
2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] radical.pilot version: 0.20 (v0.20-154-g40cefe4@devel) 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] using database url mongodb://ec2-184-72-89-141.compute-1.amazonaws.com:27017/ 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] using database name radicalpilot 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/das4.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/epsrc.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/futuregrid.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/iu.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/local.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/lrz.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/ncar.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/radical.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/rice.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/configs/xsede.json 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] New Session created{'uid': '5435d27a71fc6f2a98f54602', 'created': datetime.datetime(2014, 10, 9, 0, 10, 34, 279769), 'database_auth': ':', 'database_name': 'radicalpilot', 'database_url': 'mongodb://ec2-184-72-89-141.compute-1.amazonaws.com:27017/radicalpilot', 'last_reconnect': None}. Session UID: 5435d27a71fc6f2a98f54602 2014:10:08 19:10:34 radical.pilot.MainProcess: [DEBUG ] Worker thread (ID: Thread-1[4362092544]) for PilotManager 5435d27a71fc6f2a98f54603 started. 2014:10:08 19:10:34 radical.pilot.MainProcess: [DEBUG ] saga.utils.PTYShell ('sftp://davinci.rice.edu/') 2014:10:08 19:10:34 radical.pilot.MainProcess: [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x1036746d0> 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] PTY prompt pattern: [\$#%>]]\s*$ 2014:10:08 19:10:34 radical.pilot.MainProcess: [DEBUG ] open master pty for [ssh] [jp43@davinci.rice.edu] jp43: /usr/bin/env TERM=vt100 "/usr/bin/ssh" -t -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=yes -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu' 2014:10:08 19:10:34 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x1036748d0> 2014:10:08 19:10:34 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=yes -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:34 radical.pilot.MainProcess: [DEBUG ] write: [ 6] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for PilotManager 5435d27a71fc6f2a98f54603. 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 581](Last login: Wed Oct 8 18:44:29 2014 from 10.86.79.85n-----------------------------------------------------------------------n Ken Kennedy Institute for Information Technology, Rice Universityn ===================================================================n Unauthorized access is prohibited.nn DAVINCI.RICE.EDUnn Questions and Problem Reports -> http://helpdesk.rice.edun Documentation and User News -> http://rcsg.rice.edu/davincin-----------------------------------------------------------------------n) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 77](Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependencyn) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 18]([jp43@login2 ~]$ $)
2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Wed Oct 8 18:44:29 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $)
2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Last login: Wed Oct 8 18:44:29 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x103674a50> 2014:10:08 19:10:35 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] write: [ 7] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 7] [ 581](Last login: Wed Oct 8 19:10:35 2014 from 10.86.79.85n-----------------------------------------------------------------------n Ken Kennedy Institute for Information Technology, Rice Universityn ===================================================================n Unauthorized access is prohibited.nn DAVINCI.RICE.EDUnn Questions and Problem Reports -> http://helpdesk.rice.edun Documentation and User News -> http://rcsg.rice.edu/davincin-----------------------------------------------------------------------n) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 7] [ 77](Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependencyn) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 7] [ 18]([jp43@login2 ~]$ $)
2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Wed Oct 8 19:10:35 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $)
2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Last login: Wed Oct 8 19:10:35 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] running command shell: exec /bin/sh -i 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] write: [ 7] [ 47](stty -echo ; unset HISTFILE ; exec /bin/sh -in) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 7] 1 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] write: [ 7] [ 100](unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/nulln) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 7] 10 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] got new shell prompt 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] run_sync: echo "WORKDIR: $SHARED_SCRATCH/$USER" 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] write: [ 7] [ 38](echo "WORKDIR: $SHARED_SCRATCH/$USER"n) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 7] [ 34](WORKDIR: /scratch/jp43nPROMPT-0-) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] Determined remote working directory for sftp://davinci.rice.edu/: '/scratch/jp43' 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] PTYShell del <saga.utils.pty_shell.PTYShell object at 0x1036746d0> 2014:10:08 19:10:35 radical.pilot.MainProcess: [INFO ] Launching ComputePilot {u'state': u'PendingLaunch', u'commands': [], u'description': {u'project': u'', u'resource': u'rice.davinci', u'queue': u'serial', u'sandbox': None, u'cleanup': None, u'pilot_agent_priv': None, u'access_schema': None, u'memory': None, u'cores': 12, u'runtime': 60}, u'sagajobid': None, u'started': None, u'cores_per_node': None, u'output_transfer_started': None, u'finished': None, u'submitted': datetime.datetime(2014, 10, 9, 0, 10, 35, 793000), u'output_transfer_finished': None, u'sandbox': u'sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/', u'pilotmanager': u'5435d27a71fc6f2a98f54603', u'unitmanager': None, u'heartbeat': None, u'statehistory': [{u'timestamp': datetime.datetime(2014, 10, 9, 0, 10, 35, 792000), u'state': u'PendingLaunch'}], u'input_transfer_started': None, u'_id': ObjectId('5435d27a71fc6f2a98f54604'), u'input_transfer_finished': None, u'nodes': None, u'log': []} 2014:10:08 19:10:35 radical.pilot.MainProcess: [INFO ] Using pilot agent /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/agent/radical-pilot-agent-multicore.py 2014:10:08 19:10:35 radical.pilot.MainProcess: [INFO ] Using bootstrapper /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/bootstrapper/default_bootstrapper.sh 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] Creating agent sandbox 'sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/'. 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] saga.fs.Directory ('sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/') 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x1036a7950> 2014:10:08 19:10:35 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] write: [ 8] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 8] [ 581](Last login: Wed Oct 8 19:10:35 2014 from 10.86.79.85n-----------------------------------------------------------------------n Ken Kennedy Institute for Information Technology, Rice Universityn ===================================================================n Unauthorized access is prohibited.nn DAVINCI.RICE.EDUnn Questions and Problem Reports -> http://helpdesk.rice.edun Documentation and User News -> http://rcsg.rice.edu/davincin-----------------------------------------------------------------------n) 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] PTYProcess del <saga.utils.pty_process.PTYProcess object at 0x103674a50> Pilot UID : 5435d27a71fc6f2a98f54604 2014:10:08 19:10:35 radical.pilot.MainProcess: [INFO ] Starting InputFileTransferWorker 2014:10:08 19:10:35 radical.pilot.MainProcess: [INFO ] Starting InputFileTransferWorker 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] Worker thread (ID: Thread-3[4408217600]) for UnitManager 5435d27b71fc6f2a98f54605 started. 2014:10:08 19:10:35 radical.pilot.MainProcess: [INFO ] Loaded scheduler: DirectSubmissionScheduler. 2014:10:08 19:10:35 radical.pilot.MainProcess: [DEBUG ] read : [ 8] [ 77](Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependencyn) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 8] [ 18]([jp43@login2 ~]$ $)
2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Wed Oct 8 19:10:35 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $)
2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Last login: Wed Oct 8 19:10:35 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] write: [ 8] [ 47](stty -echo ; unset HISTFILE ; exec /bin/sh -in) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 8] 1 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] write: [ 8] [ 100](unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/nulln) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 8] 10 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] write: [ 8] [ 153](mkdir -p '/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604' ; cd '/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604'n) 2014:10:08 19:10:36 radical.pilot.MainProcess: [INFO ] ComputePilot '5435d27a71fc6f2a98f54604' state changed from 'PendingLaunch' to 'Launching'. [Callback]: ComputePilot '5435d27a71fc6f2a98f54604' state changed to Launching. 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 5435d27b71fc6f2a98f54605. 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 5435d27b71fc6f2a98f54605. 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 5435d27b71fc6f2a98f54605. 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 5435d27b71fc6f2a98f54605. 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 8] 10 Loading kernel configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.mdkernels-0.1-py2.7.egg/radical/ensemblemd/mdkernels/configs/amber.json Loading kernel configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.mdkernels-0.1-py2.7.egg/radical/ensemblemd/mdkernels/configs/coco.json Loading kernel configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.mdkernels-0.1-py2.7.egg/radical/ensemblemd/mdkernels/configs/gromacs.json Loading kernel configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.mdkernels-0.1-py2.7.egg/radical/ensemblemd/mdkernels/configs/lsdmap.json Loading kernel configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.mdkernels-0.1-py2.7.egg/radical/ensemblemd/mdkernels/configs/mmpbsa.json Loading kernel configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.mdkernels-0.1-py2.7.egg/radical/ensemblemd/mdkernels/configs/namd.json Loading kernel configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.mdkernels-0.1-py2.7.egg/radical/ensemblemd/mdkernels/configs/sleep.json Loading kernel configurations from /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.mdkernels-0.1-py2.7.egg/radical/ensemblemd/mdkernels/configs/test.json Prepare grofiles.. 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] PTYProcess del <saga.utils.pty_process.PTYProcess object at 0x1036a7950> 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] Copying bootstrapper 'file://localhost//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/bootstrapper/default_bootstrapper.sh' to agent sandbox (sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/). 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x106f7a4d0> 2014:10:08 19:10:36 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 581](Last login: Wed Oct 8 19:10:35 2014 from 10.86.79.85n-----------------------------------------------------------------------n Ken Kennedy Institute for Information Technology, Rice Universityn ===================================================================n Unauthorized access is prohibited.nn DAVINCI.RICE.EDUnn Questions and Problem Reports -> http://helpdesk.rice.edun Documentation and User News -> http://rcsg.rice.edu/davincin-----------------------------------------------------------------------n) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 77](Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependencyn) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 18]([jp43@login2 ~]$ $)
2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Wed Oct 8 19:10:35 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $)
2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Last login: Wed Oct 8 19:10:35 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 47](stty -echo ; unset HISTFILE ; exec /bin/sh -in) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 17] 1 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 100](unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/nulln) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 17] 10 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x106f7a7d0> 2014:10:08 19:10:36 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/sftp -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 32](Connected to davinci.rice.edu.n) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 30](sftp> Invalid command.nsftp) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Connected to davinci.rice.edu. sftp> Invalid command. sftp> ) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Connected to davinci.rice.edu. sftp> Invalid command. sftp> ) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 238](mput "//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/bootstrapper/default_bootstrapper.sh" "/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604" nn) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 264](Uploading //Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/bootstrapper/default_bootstrapper.sh to /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/default_bootstrapper.shn) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 79](//Library/Frameworks/Python.framework/Version 0% 0 0.0KB/s --:-- ETA) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 81](//Library/Frameworks/Python.framework/Version 100% 14KB 14.1KB/s 00:00 n) 2014:10:08 19:10:36 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 12](sftp> sftp) Preprocessing time : 1.15126991272 Cycle 0 Starting Simulation 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start0.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start0.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out0.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out0.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start1.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start1.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out1.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out1.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start2.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start2.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out2.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out2.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start3.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start3.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out3.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out3.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start4.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start4.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out4.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out4.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start5.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start5.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out5.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out5.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start6.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start6.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out6.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out6.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start7.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start7.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out7.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out7.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start8.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start8.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out8.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out8.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start9.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start9.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out9.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out9.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start10.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start10.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out10.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out10.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start11.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start11.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out11.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out11.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start12.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start12.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out12.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out12.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start13.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start13.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out13.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out13.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start14.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start14.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out14.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out14.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '/Users/jordane/work/ExTASY/temp/start15.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/Users/jordane/work/ExTASY/temp/start15.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out15.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out15.gro', 'priority': 0}' 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] copy done: [] 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] Copying agent 'file://localhost//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/agent/radical-pilot-agent-multicore.py' to agent sandbox (sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/). 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 263](mput "//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/agent/radical-pilot-agent-multicore.py" "/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/radical-pilot-agent.py" nn) 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 265](Uploading //Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/agent/radical-pilot-agent-multicore.py to /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/radical-pilot-agent.pyn) 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 79](//Library/Frameworks/Python.framework/Version 0% 0 0.0KB/s --:-- ETA) 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 81](//Library/Frameworks/Python.framework/Version 100% 100KB 100.3KB/s 00:00 n) 2014:10:08 19:10:37 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 12](sftp> sftp) 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54607' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54607' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f5460b' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f5460b' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f5460c' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f5460c' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54614' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54614' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54611' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54611' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54612' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54612' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f5460d' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f5460d' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54606' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54606' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54615' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54615' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54608' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54608' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f5460e' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f5460e' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f5460a' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f5460a' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54610' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54610' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54613' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54613' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54609' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54609' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f5460f' state changed from 'New' to 'PendingInputStaging'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f5460f' state changed to PendingInputStaging. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] Creating ComputeUnit sandbox directory sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604//unit-5435d27d71fc6f2a98f54607. 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] saga.fs.Directory ('sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604//unit-5435d27d71fc6f2a98f54607') 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x108d913d0> 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 16] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 16] [ 581](Last login: Wed Oct 8 19:10:36 2014 from 10.86.79.85n-----------------------------------------------------------------------n Ken Kennedy Institute for Information Technology, Rice Universityn ===================================================================n Unauthorized access is prohibited.nn DAVINCI.RICE.EDUnn Questions and Problem Reports -> http://helpdesk.rice.edun Documentation and User News -> http://rcsg.rice.edu/davincin-----------------------------------------------------------------------n) 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] Creating ComputeUnit sandbox directory sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604//unit-5435d27d71fc6f2a98f5460b. 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] saga.fs.Directory ('sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604//unit-5435d27d71fc6f2a98f5460b') 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 16] [ 77](Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependencyn) 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f54607' state changed from 'PendingInputStaging' to 'StagingInput'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f54607' state changed to StagingInput. 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5435d27d71fc6f2a98f5460b' state changed from 'PendingInputStaging' to 'StagingInput'. [Callback]: ComputeUnit '5435d27d71fc6f2a98f5460b' state changed to StagingInput. 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 16] [ 18]([jp43@login2 ~]$ $)
2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Wed Oct 8 19:10:36 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $)
2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Last login: Wed Oct 8 19:10:36 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 16] [ 47](stty -echo ; unset HISTFILE ; exec /bin/sh -in) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x10340c510> 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 18] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 16] 1 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 16] [ 100](unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/nulln) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 16] 10 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 16] [ 23](test -d '/' && cd '/'n) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 581](Last login: Wed Oct 8 19:10:38 2014 from 10.86.79.85n-----------------------------------------------------------------------n Ken Kennedy Institute for Information Technology, Rice Universityn ===================================================================n Unauthorized access is prohibited.nn DAVINCI.RICE.EDUnn Questions and Problem Reports -> http://helpdesk.rice.edun Documentation and User News -> http://rcsg.rice.edu/davincin-----------------------------------------------------------------------n) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 16] 10 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 77](Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependencyn) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 18]([jp43@login2 ~]$ $)
2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Wed Oct 8 19:10:38 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $)
2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Last login: Wed Oct 8 19:10:38 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 18] [ 47](stty -echo ; unset HISTFILE ; exec /bin/sh -in) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 18] 1 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 18] [ 100](unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/nulln) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 18] 10 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 18] [ 23](test -d '/' && cd '/'n) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 16] [ 108](mkdir -p '/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/unit-5435d27d71fc6f2a98f54607'n) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 18] 10 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 16] 10 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] Processing input file transfers for ComputeUnit 5435d27d71fc6f2a98f54607 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] write: [ 18] [ 108](mkdir -p '/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/unit-5435d27d71fc6f2a98f5460b'n) 2014:10:08 19:10:38 radical.pilot.MainProcess: [DEBUG ] read : [ 18] 10 2014:10:08 19:10:38 radical.pilot.MainProcess: [INFO ] Processing input file transfers for ComputeUnit 5435d27d71fc6f2a98f5460b 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] Transferring input file file://localhost//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh -> sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604//unit-5435d27d71fc6f2a98f54607/run.sh 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] saga.fs.File ('file://localhost//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh') 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] copy done: [] 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] Transferring input file file://localhost//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh -> sftp://davinci.rice.edu/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604//unit-5435d27d71fc6f2a98f5460b/run.sh 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] saga.fs.File ('file://localhost//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh') 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] saga.job.Service ('pbs+ssh://davinci.rice.edu/') 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 290](mput "//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh" "/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/unit-5435d27d71fc6f2a98f54607/run.sh" nn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 292](Uploading //Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh to /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/unit-5435d27d71fc6f2a98f54607/run.shn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 79](//Library/Frameworks/Python.framework/Version 0% 0 0.0KB/s --:-- ETA) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x108da0510> 2014:10:08 19:10:39 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 581](Last login: Wed Oct 8 19:10:38 2014 from 10.86.79.85n-----------------------------------------------------------------------n Ken Kennedy Institute for Information Technology, Rice Universityn ===================================================================n Unauthorized access is prohibited.nn DAVINCI.RICE.EDUnn Questions and Problem Reports -> http://helpdesk.rice.edun Documentation and User News -> http://rcsg.rice.edu/davincin-----------------------------------------------------------------------n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 81](//Library/Frameworks/Python.framework/Version 100% 1547 1.5KB/s 00:00 n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 12](sftp> sftp) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 77](Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependencyn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 18]([jp43@login2 ~]$ $)
2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Wed Oct 8 19:10:38 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $)
2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Last login: Wed Oct 8 19:10:38 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 47](stty -echo ; unset HISTFILE ; exec /bin/sh -in) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x103424650> 2014:10:08 19:10:39 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_sshjordane%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 26] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] 1 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 100](unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/nulln) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] 10 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 11](which qdeln) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 26] [ 581](Last login: Wed Oct 8 19:10:39 2014 from 10.86.79.85n-----------------------------------------------------------------------n Ken Kennedy Institute for Information Technology, Rice Universityn ===================================================================n Unauthorized access is prohibited.nn DAVINCI.RICE.EDUnn Questions and Problem Reports -> http://helpdesk.rice.edun Documentation and User News -> http://rcsg.rice.edu/davincin-----------------------------------------------------------------------n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] 25 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 11](which qsubn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] 25 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 15](qsub --versionn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 26](version: 2.5.9nPROMPT-0-) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 15](which pbsnodesn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] 29 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 19](pbsnodes --versionn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 26](version: 2.5.9nPROMPT-0-) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 12](which qstatn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] 26 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 16](qstat --versionn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 26](version: 2.5.9nPROMPT-0-) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 12](which aprunn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 480](which: no aprun in %28/opt/apps/vmd/1.9.1-gpu/bin:/opt/apps/intel/2013.1.039/bin:/opt/apps/netcdf/4.1.3/bin:/opt/apps/netcdf/4.1.3/deps/hdf5/1.8.7/bin:/opt/apps/openmpi/1.6.5-intel/bin:/opt/apps/intel/2013.1.046/bin:/opt/apps/fltk/1.3.0/bin:/opt/apps/cuda/5.0.35/bin:/opt/apps/matlab/2011a/bin:/home/jp43/local/bin:/home/jp43/util:/home/jp43/lsdm:/home/jp43/matlab:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bin:/opt/apps/moab/current/bin%29nPROMPT-1-) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 76](unset GREP_OPTIONS; /usr/bin/pbsnodes -a | grep -E "%28np|pcpu%29[[:blank:]]*="n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [INFO ] Scheduled ComputeUnits [] for execution on ComputePilot '5435d27a71fc6f2a98f54604'. 2014:10:08 19:10:39 radical.pilot.MainProcess: [INFO ] 0 units remain unscheduled 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 26] [ 77](Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependencyn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 1024](np = 12n np = 12n ... np = 12n np = 12n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 1024](np = 12n np = 12n ... np = 12n np = 12n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 1024](np = 12n np = 12n n ... np = 16n np = 16n n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 158](p = 16n np = 16n np = 16n np = 16n np = 16n np = 16n np = 16n np = 16n np = 16n np = 16n np = 16nPROMPT-0-) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] Bootstrap command line: /bin/bash ['-l', 'default_bootstrapper.sh', "-n radicalpilot -s 5435d27a71fc6f2a98f54602 -p 5435d27a71fc6f2a98f54604 -t 60 -d 10 -c 12 -v 0.20 -m ec2-184-72-89-141.compute-1.amazonaws.com:27017 -a : -e 'module load openmpi' -l TORQUE -j SSH -k MPIEXEC "] 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] Submitting SAGA job with description: {'Queue': 'serial', 'Executable': '/bin/bash', 'WorkingDirectory': '/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604', 'Project': '', 'WallTimeLimit': 60, 'Arguments': ['-l', 'default_bootstrapper.sh', "-n radicalpilot -s 5435d27a71fc6f2a98f54602 -p 5435d27a71fc6f2a98f54604 -t 60 -d 10 -c 12 -v 0.20 -m ec2-184-72-89-141.compute-1.amazonaws.com:27017 -a : -e 'module load openmpi' -l TORQUE -j SSH -k MPIEXEC "], 'Error': 'AGENT.STDERR', 'Output': 'AGENT.STDOUT', 'TotalCPUCount': 12} 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 26] [ 18]([jp43@login2 ~]$ $) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 76](mkdir -p /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604n)
2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Wed Oct 8 19:10:39 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $)
2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Last login: Wed Oct 8 19:10:39 2014 from 10.86.79.85
Ken Kennedy Institute for Information Technology, Rice University
Loading cuda/5.0.35 fltk/1.3.0 netcdf/4.1.3 intel/2013.1.039 for dependency [jp43@login2 ~]$ $) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 26] [ 47](stty -echo ; unset HISTFILE ; exec /bin/sh -in) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] 10 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 25] [ 903](SCRIPTFILE=
mktemp -t SAGA-Pyt ... IPTFILE && rm -f $SCRIPTFILEn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 26] [ 1]($) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 26] [ 100](unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/nulln) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 26] [ 10](PROMPT-0-) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x108d7a0d0> 2014:10:08 19:10:39 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/sftp -o IdentityFile=/Users/jordane/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_jordane_%h_%p.jp43.ctrl jp43@davinci.rice.edu 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 27] [ 33](export PS1='$' ; set prompt='$'n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 25] [ 52](qsub: option requires an argument -- 'A'nPROMPT-1-) 2014:10:08 19:10:39 radical.pilot.MainProcess: [ERROR ] Pilot launching failed: Error running job via 'qsub': qsub: option requires an argument -- 'A' . Commandline was: SCRIPTFILE=mktemp -t SAGA-Python-PBSJobScript.XXXXXX` && echo "!/bin/bash
PBS -V
PBS -o /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/AGENT.STDOUT
PBS -e /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/AGENT.STDERR
PBS -l walltime=1:0:00
PBS -q serial
PBS -A
PBS -l nodes=1:ppn=12
export PBS_O_WORKDIR=/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604 mkdir -p /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604 cd /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604 /bin/bash -l default_bootstrapper.sh -n radicalpilot -s 5435d27a71fc6f2a98f54602 -p 5435d27a71fc6f2a98f54604 -t 60 -d 10 -c 12 -v 0.20 -m ec2-184-72-89-141.compute-1.amazonaws.com:27017 -a : -e 'module load openmpi' -l TORQUE -j SSH -k MPIEXEC " > $SCRIPTFILE && /usr/bin/qsub $SCRIPTFILE && rm -f $SCRIPTFILE (/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/saga_python-0.20-py2.7.egg/saga/adaptors/pbs/pbsjob.py +99 (log_error_and_raise) : raise exception(message)) Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/controller/pilot_launcher_worker.py", line 464, in run pilotjob.run() File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/saga_python-0.20-py2.7.egg/saga/job/job.py", line 397, in run return self._adaptor.run (ttype=ttype) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/saga_python-0.20-py2.7.egg/saga/adaptors/cpi/decorators.py", line 51, in wrap_function return sync_function (self, _args, *_kwargs) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/saga_python-0.20-py2.7.egg/saga/adaptors/pbs/pbsjob.py", line 1105, in run self._id = self.js._job_run(self._api()) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/saga_python-0.20-py2.7.egg/saga/adaptors/pbs/pbsjob.py", line 630, in _job_run log_error_and_raise(message, saga.NoSuccess, self._logger) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/saga_python-0.20-py2.7.egg/saga/adaptors/pbs/pbsjob.py", line 99, in log_error_and_raise raise exception(message) NoSuccess: Error running job via 'qsub': qsub: option requires an argument -- 'A' . Commandline was: SCRIPTFILE=
mktemp -t SAGA-Python-PBSJobScript.XXXXXX&& echo "!/bin/bash
PBS -V
PBS -o /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/AGENT.STDOUT
PBS -e /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/AGENT.STDERR
PBS -l walltime=1:0:00
PBS -q serial
PBS -A
PBS -l nodes=1:ppn=12
export PBS_O_WORKDIR=/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604 mkdir -p /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604 cd /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604 /bin/bash -l default_bootstrapper.sh -n radicalpilot -s 5435d27a71fc6f2a98f54602 -p 5435d27a71fc6f2a98f54604 -t 60 -d 10 -c 12 -v 0.20 -m ec2-184-72-89-141.compute-1.amazonaws.com:27017 -a : -e 'module load openmpi' -l TORQUE -j SSH -k MPIEXEC " > $SCRIPTFILE && /usr/bin/qsub $SCRIPTFILE && rm -f $SCRIPTFILE (/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/saga_python-0.20-py2.7.egg/saga/adaptors/pbs/pbsjob.py +99 (log_error_and_raise) : raise exception(message))
2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 27] [ 32](Connected to davinci.rice.edu.n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 27] 6 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Connected to davinci.rice.edu. sftp> ) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Connected to davinci.rice.edu. sftp> ) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] write: [ 27] [ 290](mput "//Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh" "/scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/unit-5435d27d71fc6f2a98f5460b/run.sh" nn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 27] [ 24](Invalid command.nsftp) 2014:10:08 19:10:39 radical.pilot.MainProcess: [INFO ] ComputePilot '5435d27a71fc6f2a98f54604' state changed from 'Launching' to 'Failed'. [Callback]: ComputePilot '5435d27a71fc6f2a98f54604' state changed to Failed. pilot manager controller thread caught system exit -- forcing application shutdown 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 27] [ 292](Uploading //Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh to /scratch/jp43/radical.pilot.sandbox/pilot-5435d27a71fc6f2a98f54604/unit-5435d27d71fc6f2a98f5460b/run.shn) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 27] [ 79](//Library/Frameworks/Python.framework/Version 0% 0 0.0KB/s --:-- ETA) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 27] [ 81](//Library/Frameworks/Python.framework/Version 100% 1547 1.5KB/s 00:00 n) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] read : [ 27] [ 12](sftp> sftp) 2014:10:08 19:10:39 radical.pilot.MainProcess: [DEBUG ] copy done: ['Uploading', '//Library/Frameworks/Python.framework/Version', 'sftp>'] Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/bin/extasy", line 9, in
load_entry_point('radical.ensemblemd.extasy==0.1', 'console_scripts', 'extasy')()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/runme.py", line 130, in main
Simulator(umgr,RPconfig,Kconfig,i)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.ensemblemd.extasy-0.1-py2.7.egg/radical/ensemblemd/extasy/bin/Simulator/Gromacs/simulator.py", line 56, in Simulator
umgr.wait_units()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/unit_manager.py", line 646, in wait_units
units = self.get_units (unit_ids)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/unit_manager.py", line 587, in get_units
units = ComputeUnit._get(unit_ids=unit_ids, unit_manager_obj=self)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/compute_unit.py", line 114, in _get
unit_ids=unit_ids
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/radical.pilot-0.20-py2.7.egg/radical/pilot/db/database.py", line 497, in get_compute_units
for obj in cursor:
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymongo-2.7.2-py2.7-macosx-10.9-intel.egg/pymongo/cursor.py", line 1058, in next
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymongo-2.7.2-py2.7-macosx-10.9-intel.egg/pymongo/cursor.py", line 1002, in _refresh
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymongo-2.7.2-py2.7-macosx-10.9-intel.egg/pymongo/cursor.py", line 915, in send_message
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymongo-2.7.2-py2.7-macosx-10.9-intel.egg/pymongo/mongo_client.py", line 1198, in _send_message_with_response
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymongo-2.7.2-py2.7-macosx-10.9-intel.egg/pymongo/mongo_client.py", line 1175, in __send_and_receive
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymongo-2.7.2-py2.7-macosx-10.9-intel.egg/pymongo/mongo_client.py", line 1167, in receive_message_on_socket
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymongo-2.7.2-py2.7-macosx-10.9-intel.egg/pymongo/mongo_client.py", line 1146, in __receive_data_on_socket
KeyboardInterrupt