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February 26, 2015 14:04
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extasy.log of grlsdmap workflow - default files
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| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] radical.pilot version: 0.23 (v0.23) | |
| 2015:02:26 14:00:31 21243 MainThread saga : [INFO ] saga-python version: v0.26 | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.myproxy | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.myproxy for saga.Context API with URL scheme(s) ['myproxy://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.x509 | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.x509 for saga.Context API with URL scheme(s) ['x509://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.ssh | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.ssh for saga.Context API with URL scheme(s) ['ssh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.userpass | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.userpass for saga.Context API with URL scheme(s) ['userpass://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_job | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Service API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.shell.shell_job for saga.job.Job API with URL scheme(s) ['fork://', 'local://', 'ssh://', 'gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_file | |
| 2015:02:26 14:00:31 21243 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://'] | |
| 2015:02:26 14:00:31 21243 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://'] | |
| 2015:02:26 14:00:31 21243 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://'] | |
| 2015:02:26 14:00:31 21243 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://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.shell.shell_resource | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [WARNING ] Skipping adaptor saga.adaptors.shell.shell_resource: beta versions are disabled (v0.1.beta) | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.redis.redis_advert | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [WARNING ] Skipping adaptor saga.adaptors.redis.redis_advert 1: module loading failed: No module named redis | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.sge.sgejob | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Service API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.sge.sgejob for saga.job.Job API with URL scheme(s) ['sge://', 'sge+ssh://', 'sge+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.pbs.pbsjob | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Service API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.pbs.pbsjob for saga.job.Job API with URL scheme(s) ['pbs://', 'pbs+ssh://', 'pbs+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.lsf.lsfjob | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Service API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.lsf.lsfjob for saga.job.Job API with URL scheme(s) ['lsf://', 'lsf+ssh://', 'lsf+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.condor.condorjob | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Service API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.condor.condorjob for saga.job.Job API with URL scheme(s) ['condor://', 'condor+ssh://', 'condor+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.slurm.slurm_job | |
| 2015:02:26 14:00:31 21243 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://'] | |
| 2015:02:26 14:00:31 21243 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://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.http.http_file | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.http.http_file for saga.namespace.Entry API with URL scheme(s) ['http://', 'https://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.http.http_file for saga.filesystem.File API with URL scheme(s) ['http://', 'https://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.aws.ec2_resource | |
| 2015:02:26 14:00:31 21243 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://'] | |
| 2015:02:26 14:00:31 21243 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://'] | |
| 2015:02:26 14:00:31 21243 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://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.loadl.loadljob | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Service API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.loadl.loadljob for saga.job.Job API with URL scheme(s) ['loadl://', 'loadl+ssh://', 'loadl+gsissh://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.globus_online.go_file | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Directory API with URL scheme(s) ['go://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.globus_online.go_file for saga.namespace.Entry API with URL scheme(s) ['go://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.Directory API with URL scheme(s) ['go://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.globus_online.go_file for saga.filesystem.File API with URL scheme(s) ['go://'] | |
| 2015:02:26 14:00:31 21243 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /users/ardita/.ssh/known_hosts.old (no public key: /users/ardita/.ssh/known_hosts.old.pub) | |
| 2015:02:26 14:00:31 21243 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /users/ardita/.ssh/k.dat (no public key: /users/ardita/.ssh/k.dat.pub) | |
| 2015:02:26 14:00:31 21243 MainThread saga.saga.adaptor.ssh : [INFO ] default ssh key at /users/ardita/.ssh/id_rsa | |
| 2015:02:26 14:00:31 21243 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /users/ardita/.ssh/environment (no public key: /users/ardita/.ssh/environment.pub) | |
| 2015:02:26 14:00:31 21243 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /users/ardita/.ssh/known_hosts (no public key: /users/ardita/.ssh/known_hosts.pub) | |
| 2015:02:26 14:00:31 21243 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /users/ardita/.ssh/authorized_keys (no public key: /users/ardita/.ssh/authorized_keys.pub) | |
| 2015:02:26 14:00:31 21243 MainThread saga.saga.adaptor.ssh : [INFO ] ignore ssh key at /users/ardita/.ssh/config (no public key: /users/ardita/.ssh/config.pub) | |
| 2015:02:26 14:00:31 21243 MainThread saga.ContextSSH : [INFO ] init SSH context for key at '/users/ardita/.ssh/id_rsa' done | |
| 2015:02:26 14:00:31 21243 MainThread saga.DefaultSession : [DEBUG ] default context [saga.adaptor.ssh ] : {'LifeTime' : '-1', 'Type' : 'ssh', 'UserCert' : '/users/ardita/.ssh/id_rsa.pub', 'UserKey' : '/users/ardita/.ssh/id_rsa'} | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] using database url mongodb://extasy:extasyproject@extasy-db.epcc.ed.ac.uk/radicalpilot | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] using database path radicalpilot | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for nersc.hopper | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for futuregrid.sierra | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for futuregrid.alamo | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for futuregrid.hotel | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for futuregrid.india | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for lrz.supermuc | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for epsrc.archer | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for rice.biou | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for rice.davinci | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for local.localhost | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for radical.tutorial | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for das4.fs2 | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for ncar.yellowstone | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for iu.bigred2 | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for iu.quarry | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for xsede.stampede | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for xsede.trestles | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for xsede.gordon | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for xsede.blacklight | |
| 2015:02:26 14:00:31 radical.pilot.MainProcess: [INFO ] Loaded resource configurations for xsede.lonestar | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [INFO ] New Session created{'uid': '54ef26fff8cdba52fb1ccf5d', 'created': datetime.datetime(2015, 2, 26, 14, 0, 31, 878594), 'database_auth': 'extasy:extasyproject', 'database_name': 'radicalpilot', 'database_url': 'mongodb://extasy:extasyproject@extasy-db.epcc.ed.ac.uk/radicalpilot', 'last_reconnect': None}. | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [DEBUG ] Worker thread (ID: Thread-1[139931242460928]) for PilotManager 54ef2700f8cdba52fb1ccf5e started. | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [WARNING ] using alias 'xsede.stampede' for deprecated resource key 'stampede.tacc.utexas.edu' | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [DEBUG ] saga.utils.PTYShell ('sftp://stampede.tacc.utexas.edu/') | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444d601310> | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [DEBUG ] open master pty for [ssh] [ardi@stampede.tacc.utexas.edu] ardi: /usr/bin/env TERM=vt100 "/usr/bin/ssh" -t -o IdentityFile=/users/ardita/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_ardita_%h_%p.ardi.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 ardi@stampede.tacc.utexas.edu' | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444e10da50> | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/users/ardita/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_ardita_%h_%p.ardi.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 ardi@stampede.tacc.utexas.edu | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [DEBUG ] write: [ 5] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:00:32 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for PilotManager 54ef2700f8cdba52fb1ccf5e. | |
| 2015:02:26 14:00:33 radical.pilot.MainProcess: [DEBUG ] write: [ 5] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:33 radical.pilot.MainProcess: [DEBUG ] write: [ 5] [ 28] ( printf 'HELLO_%d_SAGA\n' 1\n) | |
| 2015:02:26 14:00:34 radical.pilot.MainProcess: [DEBUG ] write: [ 5] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:34 radical.pilot.MainProcess: [DEBUG ] write: [ 5] [ 28] ( printf 'HELLO_%d_SAGA\n' 2\n) | |
| 2015:02:26 14:00:35 radical.pilot.MainProcess: [DEBUG ] write: [ 5] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:35 radical.pilot.MainProcess: [DEBUG ] write: [ 5] [ 28] ( printf 'HELLO_%d_SAGA\n' 3\n) | |
| 2015:02:26 14:00:35 radical.pilot.MainProcess: [DEBUG ] read : [ 5] [ 2396] (Last login: Thu Feb 26 05:18:5 ... __________________________\n\n) | |
| 2015:02:26 14:00:35 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Thu Feb 26 05:18:59 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:00:35 radical.pilot.MainProcess: [DEBUG ] waiting for prompt trigger HELLO_3_SAGA: (5) (Last login: Thu Feb 26 05:18:59 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [DEBUG ] read : [ 5] [ 244] (----------------------- Project balances for user ardi ------------------------\n| Name Avail SUs Expires | Name Avail SUs Expires |\n| TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | \n) | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [DEBUG ] read : [ 5] [ 405] (-------------------------- Disk quotas for user ardi --------------------------\n| Disk Usage (GB) Limit %Used File Usage Limit %Used |\n| /home1 0.1 5.0 2.37 5069 150000 3.38 |\n| /work 9.3 1024.0 0.91 619813 3000000 20.66 |\n-------------------------------------------------------------------------------\n) | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [DEBUG ] read : [ 5] [ 249] (\nTip 62 (See "module help tacc_tips" for features or how to disable)\n\n The man-pages are divided into sections: section (1) are commands; section (2) are system functions, section (3) are library functions. (e.g. man 2 time; man 3 strlen)\n\n) | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [DEBUG ] read : [ 5] [ 69] (login2.stampede(1)$ $$HELLO_1_SAGA\n$$HELLO_2_SAGA\n$$HELLO_3_SAGA\n$) | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [DEBUG ] got shell prompt trigger (4) ( | |
| See "man slurm" or the Stampede user guide for more detailed information. | |
| --> To see all the software that is available across all compilers and | |
| mpi stacks, issue: "module spider" | |
| --> To see which software packages are available with your currently loaded | |
| compiler and mpi stack, issue: "module avail" | |
| --> Stampede has three parallel file systems: $HOME (permanent, | |
| quota'd, backed-up) $WORK (permanent, quota'd, not backed-up) and | |
| $SCRATCH (high-speed purged storage). The "cdw" and "cds" aliases | |
| are provided as a convenience to change to your $WORK and $SCRATCH | |
| directories, respectively. | |
| ______________________________________________________________________________ | |
| ----------------------- Project balances for user ardi ------------------------ | |
| | Name Avail SUs Expires | Name Avail SUs Expires | | |
| | TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | | |
| -------------------------- Disk quotas for user ardi -------------------------- | |
| | Disk Usage (GB) Limit %Used File Usage Limit %Used | | |
| | /home1 0.1 5.0 2.37 5069 150000 3.38 | | |
| | /work 9.3 1024.0 0.91 619813 3000000 20.66 | | |
| ------------------------------------------------------------------------------- | |
| Tip 62 (See "module help tacc_tips" for features or how to disable) | |
| The man-pages are divided into sections: section (1) are commands; section (2) are system functions, section (3) are library functions. (e.g. man 2 time; man 3 strlen) | |
| login2.stampede(1)$ $$HELLO_1_SAGA | |
| $$HELLO_2_SAGA | |
| $$HELLO_3_SAGA) | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444d601850> | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/users/ardita/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_ardita_%h_%p.ardi.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 ardi@stampede.tacc.utexas.edu | |
| 2015:02:26 14:00:36 radical.pilot.MainProcess: [DEBUG ] write: [ 6] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:00:37 radical.pilot.MainProcess: [DEBUG ] write: [ 6] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:37 radical.pilot.MainProcess: [DEBUG ] write: [ 6] [ 28] ( printf 'HELLO_%d_SAGA\n' 1\n) | |
| 2015:02:26 14:00:38 radical.pilot.MainProcess: [DEBUG ] write: [ 6] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:38 radical.pilot.MainProcess: [DEBUG ] write: [ 6] [ 28] ( printf 'HELLO_%d_SAGA\n' 2\n) | |
| 2015:02:26 14:00:38 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 2396] (Last login: Thu Feb 26 06:25:5 ... __________________________\n\n) | |
| 2015:02:26 14:00:38 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Thu Feb 26 06:25:55 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:00:38 radical.pilot.MainProcess: [DEBUG ] waiting for prompt trigger HELLO_2_SAGA: (5) (Last login: Thu Feb 26 06:25:55 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 244] (----------------------- Project balances for user ardi ------------------------\n| Name Avail SUs Expires | Name Avail SUs Expires |\n| TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | \n) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 405] (-------------------------- Disk quotas for user ardi --------------------------\n| Disk Usage (GB) Limit %Used File Usage Limit %Used |\n| /home1 0.1 5.0 2.37 5069 150000 3.38 |\n| /work 9.3 1024.0 0.91 619813 3000000 20.66 |\n-------------------------------------------------------------------------------\n) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 143] (\nTip 106 (See "module help tacc_tips" for features or how to disable)\n\n To find broken symlinks do:\n $ find . -type l -xtype l\n\n) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 53] (login1.stampede(1)$ $$HELLO_1_SAGA\n$$HELLO_2_SAGA\n$) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] got shell prompt trigger (4) ( | |
| See "man slurm" or the Stampede user guide for more detailed information. | |
| --> To see all the software that is available across all compilers and | |
| mpi stacks, issue: "module spider" | |
| --> To see which software packages are available with your currently loaded | |
| compiler and mpi stack, issue: "module avail" | |
| --> Stampede has three parallel file systems: $HOME (permanent, | |
| quota'd, backed-up) $WORK (permanent, quota'd, not backed-up) and | |
| $SCRATCH (high-speed purged storage). The "cdw" and "cds" aliases | |
| are provided as a convenience to change to your $WORK and $SCRATCH | |
| directories, respectively. | |
| ______________________________________________________________________________ | |
| ----------------------- Project balances for user ardi ------------------------ | |
| | Name Avail SUs Expires | Name Avail SUs Expires | | |
| | TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | | |
| -------------------------- Disk quotas for user ardi -------------------------- | |
| | Disk Usage (GB) Limit %Used File Usage Limit %Used | | |
| | /home1 0.1 5.0 2.37 5069 150000 3.38 | | |
| | /work 9.3 1024.0 0.91 619813 3000000 20.66 | | |
| ------------------------------------------------------------------------------- | |
| Tip 106 (See "module help tacc_tips" for features or how to disable) | |
| To find broken symlinks do: | |
| $ find . -type l -xtype l | |
| login1.stampede(1)$ $$HELLO_1_SAGA | |
| $$HELLO_2_SAGA) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] write: [ 6] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 1] ($) | |
| 2015:02:26 14:00:39 radical.pilot.MainProcess: [DEBUG ] flush: [ 6] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] write: [ 6] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] got new shell prompt | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] flush: [ 6] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] flush: [ 6] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] run_sync: echo "WORKDIR: $WORK" | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] write: [ 6] [ 22] (echo "WORKDIR: $WORK"\n) | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] read : [ 6] [ 37] (WORKDIR: /work/02998/ardi\nPROMPT-0->) | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Determined remote working directory for sftp://stampede.tacc.utexas.edu/: '/work/02998/ardi' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] PTYShell del <saga.utils.pty_shell.PTYShell object at 0x7f444d601310> | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [INFO ] Launching ComputePilot {u'state': u'PendingLaunch', u'commands': [], u'description': {u'project': u'TG-MCB090174', u'resource': u'stampede.tacc.utexas.edu', u'queue': u'normal', u'sandbox': None, u'cleanup': None, u'pilot_agent_priv': None, u'access_schema': None, u'memory': None, u'cores': 16, 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(2015, 2, 26, 14, 0, 40, 556000), u'output_transfer_finished': None, u'sandbox': u'sftp://stampede.tacc.utexas.edu/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/', u'pilotmanager': u'54ef2700f8cdba52fb1ccf5e', u'unitmanager': None, u'heartbeat': None, u'statehistory': [{u'timestamp': datetime.datetime(2015, 2, 26, 14, 0, 40, 554000), u'state': u'PendingLaunch'}], u'input_transfer_started': None, u'_id': ObjectId('54ef2700f8cdba52fb1ccf5f'), u'input_transfer_finished': None, u'nodes': None, u'log': []} | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [WARNING ] using alias 'xsede.stampede' for deprecated resource key 'stampede.tacc.utexas.edu' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [INFO ] Using pilot agent /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/agent/radical-pilot-agent-multicore.py | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [INFO ] Using bootstrapper /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Copying bootstrapper 'file://localhost//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh' to agent sandbox (sftp://stampede.tacc.utexas.edu/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f//default_bootstrapper.sh). | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] init_instance file://localhost//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c27c0d0> | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] open master pty for [sh] [localhost] ardita: /usr/bin/env TERM=vt100 "/bin/tcsh" -i' | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444e179990> | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 7] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] PTYProcess del <saga.utils.pty_process.PTYProcess object at 0x7f444d601850> | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [INFO ] Starting InputFileTransferWorker | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [INFO ] Starting InputFileTransferWorker | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Worker thread (ID: Thread-3[139931190011648]) for UnitManager 54ef2708f8cdba52fb1ccf60 started. | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [INFO ] Loaded scheduler: DirectSubmissionScheduler. | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/grlsd-on-stampede_26Feb/grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///grompp.mdp', 'priority': 0}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/grlsd-on-stampede_26Feb/topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///topol.top', 'priority': 0}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/grlsd-on-stampede_26Feb/config.ini', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///config.ini', 'priority': 0}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/gro.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///gro.py', 'priority': 0}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/spliter.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///spliter.py', 'priority': 0}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/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}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/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}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/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}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/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}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/../../Analyzer/LSDMap/select.py', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///select.py', 'priority': 0}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/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}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/grlsd-on-stampede_26Feb/backup/iter-1/0_input.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter-1/0_input.gro', 'priority': 0}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Completing entry '{'action': 'Transfer', 'source': 'file:///users/ardita/grlsd-on-stampede_26Feb/backup/iter-1/weight.w', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'staging:///iter-1/weight.w', 'priority': 0}' | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 54ef2708f8cdba52fb1ccf60. | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 54ef2708f8cdba52fb1ccf60. | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 54ef2708f8cdba52fb1ccf60. | |
| 2015:02:26 14:00:40 radical.pilot.MainProcess: [DEBUG ] Connected to MongoDB. Serving requests for UnitManager 54ef2708f8cdba52fb1ccf60. | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 3] ( \n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 47] (Removable media:\n /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 3] ( \n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 244] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:00:40 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 3] ( \n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 7] [ 82] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n$) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444c37b610> | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 11] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:00:41 radical.pilot.MainProcess: [INFO ] ComputePilot '54ef2700f8cdba52fb1ccf5f' state changed from 'PendingLaunch' to 'Launching'. | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 3] ( \n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 47] (Removable media:\n /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 3] ( \n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 275] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \nCurrently Loaded Modulefiles:\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 3] ( \n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 81] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 1] ($) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 11] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] flush: [ 11] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 11] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] flush: [ 11] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 11] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] flush: [ 11] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] flush: [ 11] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:41 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c37b950> | |
| 2015:02:26 14:00:41 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:00:41 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444e13ae50> | |
| 2015:02:26 14:00:41 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/users/ardita/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_ardita_%h_%p.ardi.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 ardi@stampede.tacc.utexas.edu | |
| 2015:02:26 14:00:41 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] run_sync: true; test -r '//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh' | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 11] [ 123] (true; test -r '//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh'\n) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:41 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] file initialized (0)() | |
| 2015:02:26 14:00:42 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:42 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 28] ( printf 'HELLO_%d_SAGA\n' 1\n) | |
| 2015:02:26 14:00:43 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:43 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 28] ( printf 'HELLO_%d_SAGA\n' 2\n) | |
| 2015:02:26 14:00:44 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 2396] (Last login: Thu Feb 26 06:25:4 ... __________________________\n\n) | |
| 2015:02:26 14:00:44 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Thu Feb 26 06:25:41 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:00:44 radical.pilot.MainProcess: [DEBUG ] waiting for prompt trigger HELLO_2_SAGA: (5) (Last login: Thu Feb 26 06:25:41 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 244] (----------------------- Project balances for user ardi ------------------------\n| Name Avail SUs Expires | Name Avail SUs Expires |\n| TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | \n) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 405] (-------------------------- Disk quotas for user ardi --------------------------\n| Disk Usage (GB) Limit %Used File Usage Limit %Used |\n| /home1 0.1 5.0 2.37 5069 150000 3.38 |\n| /work 9.3 1024.0 0.91 619813 3000000 20.66 |\n-------------------------------------------------------------------------------\n) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 163] (\nTip 21 (See "module help tacc_tips" for features or how to disable)\n\n You can find all installed bio codes by executing\n $ module keyword bio\n\n) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 53] (login4.stampede(1)$ $$HELLO_1_SAGA\n$$HELLO_2_SAGA\n$) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] got shell prompt trigger (4) ( | |
| See "man slurm" or the Stampede user guide for more detailed information. | |
| --> To see all the software that is available across all compilers and | |
| mpi stacks, issue: "module spider" | |
| --> To see which software packages are available with your currently loaded | |
| compiler and mpi stack, issue: "module avail" | |
| --> Stampede has three parallel file systems: $HOME (permanent, | |
| quota'd, backed-up) $WORK (permanent, quota'd, not backed-up) and | |
| $SCRATCH (high-speed purged storage). The "cdw" and "cds" aliases | |
| are provided as a convenience to change to your $WORK and $SCRATCH | |
| directories, respectively. | |
| ______________________________________________________________________________ | |
| ----------------------- Project balances for user ardi ------------------------ | |
| | Name Avail SUs Expires | Name Avail SUs Expires | | |
| | TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | | |
| -------------------------- Disk quotas for user ardi -------------------------- | |
| | Disk Usage (GB) Limit %Used File Usage Limit %Used | | |
| | /home1 0.1 5.0 2.37 5069 150000 3.38 | | |
| | /work 9.3 1024.0 0.91 619813 3000000 20.66 | | |
| ------------------------------------------------------------------------------- | |
| Tip 21 (See "module help tacc_tips" for features or how to disable) | |
| You can find all installed bio codes by executing | |
| $ module keyword bio | |
| login4.stampede(1)$ $$HELLO_1_SAGA | |
| $$HELLO_2_SAGA) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:00:45 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 1] ($) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:45 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:00:46 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:46 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:00:46 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:46 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c37bc10> | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444e1687d0> | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 14] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:00:46 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:00:46 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 3] ( \n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 18] (Removable media:\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 29] ( /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 3] ( \n) | |
| 2015:02:26 14:00:46 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 275] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \nCurrently Loaded Modulefiles:\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 3] ( \n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 82] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n$) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 14] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] flush: [ 14] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 14] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] flush: [ 14] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 14] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 14] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] flush: [ 14] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c38d150> | |
| 2015:02:26 14:00:46 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:00:46 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444e168810> | |
| 2015:02:26 14:00:46 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/users/ardita/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_ardita_%h_%p.ardi.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 ardi@stampede.tacc.utexas.edu | |
| 2015:02:26 14:00:46 radical.pilot.MainProcess: [DEBUG ] write: [ 15] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:00:47 radical.pilot.MainProcess: [DEBUG ] write: [ 15] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:47 radical.pilot.MainProcess: [DEBUG ] write: [ 15] [ 28] ( printf 'HELLO_%d_SAGA\n' 1\n) | |
| 2015:02:26 14:00:48 radical.pilot.MainProcess: [DEBUG ] write: [ 15] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:48 radical.pilot.MainProcess: [DEBUG ] write: [ 15] [ 28] ( printf 'HELLO_%d_SAGA\n' 2\n) | |
| 2015:02:26 14:00:49 radical.pilot.MainProcess: [DEBUG ] read : [ 15] [ 2396] (Last login: Thu Feb 26 06:42:1 ... __________________________\n\n) | |
| 2015:02:26 14:00:49 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Thu Feb 26 06:42:18 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:00:49 radical.pilot.MainProcess: [DEBUG ] waiting for prompt trigger HELLO_2_SAGA: (5) (Last login: Thu Feb 26 06:42:18 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] read : [ 15] [ 244] (----------------------- Project balances for user ardi ------------------------\n| Name Avail SUs Expires | Name Avail SUs Expires |\n| TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | \n) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] read : [ 15] [ 405] (-------------------------- Disk quotas for user ardi --------------------------\n| Disk Usage (GB) Limit %Used File Usage Limit %Used |\n| /home1 0.1 5.0 2.37 5069 150000 3.38 |\n| /work 9.3 1024.0 0.91 619815 3000000 20.66 |\n-------------------------------------------------------------------------------\n) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] read : [ 15] [ 275] (\nTip 118 (See "module help tacc_tips" for features or how to disable)\n\n Want to know what MACROS are predefined by the GCC and Intel compilers? Do\n $ gcc -dM -E - < /dev/null > gcc_defined_macros.txt\n $ icc -dM -E - < /dev/null > icc_defined_macros.txt\n\n) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] read : [ 15] [ 53] (login3.stampede(1)$ $$HELLO_1_SAGA\n$$HELLO_2_SAGA\n$) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] got shell prompt trigger (4) ( | |
| See "man slurm" or the Stampede user guide for more detailed information. | |
| --> To see all the software that is available across all compilers and | |
| mpi stacks, issue: "module spider" | |
| --> To see which software packages are available with your currently loaded | |
| compiler and mpi stack, issue: "module avail" | |
| --> Stampede has three parallel file systems: $HOME (permanent, | |
| quota'd, backed-up) $WORK (permanent, quota'd, not backed-up) and | |
| $SCRATCH (high-speed purged storage). The "cdw" and "cds" aliases | |
| are provided as a convenience to change to your $WORK and $SCRATCH | |
| directories, respectively. | |
| ______________________________________________________________________________ | |
| ----------------------- Project balances for user ardi ------------------------ | |
| | Name Avail SUs Expires | Name Avail SUs Expires | | |
| | TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | | |
| -------------------------- Disk quotas for user ardi -------------------------- | |
| | Disk Usage (GB) Limit %Used File Usage Limit %Used | | |
| | /home1 0.1 5.0 2.37 5069 150000 3.38 | | |
| | /work 9.3 1024.0 0.91 619815 3000000 20.66 | | |
| ------------------------------------------------------------------------------- | |
| Tip 118 (See "module help tacc_tips" for features or how to disable) | |
| Want to know what MACROS are predefined by the GCC and Intel compilers? Do | |
| $ gcc -dM -E - < /dev/null > gcc_defined_macros.txt | |
| $ icc -dM -E - < /dev/null > icc_defined_macros.txt | |
| login3.stampede(1)$ $$HELLO_1_SAGA | |
| $$HELLO_2_SAGA) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:00:50 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] write: [ 15] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] read : [ 15] [ 1] ($) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] flush: [ 15] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] write: [ 15] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] read : [ 15] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:50 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] flush: [ 15] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] flush: [ 15] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c38d510> | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444e102090> | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 16] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:00:50 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/ | |
| 2015:02:26 14:00:50 radical.pilot.MainProcess: [DEBUG ] write: [ 15] [ 80] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/\n) | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 3] ( \n) | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:00:50 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:00:51 radical.pilot.MainProcess: [DEBUG ] read : [ 15] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:51 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 18] (Removable media:\n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 29] ( /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 3] ( \n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 275] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \nCurrently Loaded Modulefiles:\n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 3] ( \n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 82] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n$) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 16] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:00:51 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444c38d7d0> | |
| 2015:02:26 14:00:51 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/sftp -o IdentityFile=/users/ardita/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_ardita_%h_%p.ardi.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 ardi@stampede.tacc.utexas.edu | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:00:51 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 43] (Connecting to stampede.tacc.utexas.edu...\n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 16] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 16] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 16] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 16] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 16] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:51 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 16] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:51 radical.pilot.MainProcess: [DEBUG ] flush: [ 15] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Connecting to stampede.tacc.utexas.edu... | |
| sftp> ) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Connecting to stampede.tacc.utexas.edu... | |
| sftp> ) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444c38de10> | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/sftp -o IdentityFile=/users/ardita/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_ardita_%h_%p.ardi.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 ardi@stampede.tacc.utexas.edu | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 43] (Connecting to stampede.tacc.utexas.edu...\n) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 211] (mput "//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/default_bootstrapper.sh"\n) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 216] (mput "//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pil ot/bootstrapper/default_bootstrapper.sh" "/work/02998/ardi/radical.pilot.sandbox /pilot-54ef2700f8cdba52fb1ccf5f/default_bootstrapper.sh"\n) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 215] (Uploading //users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/default_bootstrapper.sh\n) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (//users/ardita/ExTASY-tools/lib/python2.7/sit 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:00:54 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (//users/ardita/ExTASY-tools/lib/python2.7/sit 100% 14KB 14.3KB/s 00:00 \n) | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '//users/ardita/ExTASY-tools/lib/python2.7/sit', 'sftp>'] | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] Copying agent 'file://localhost//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/agent/radical-pilot-agent-multicore.py' to agent sandbox (sftp://stampede.tacc.utexas.edu/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/). | |
| 2015:02:26 14:00:55 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] init_instance file://localhost//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/agent/radical-pilot-agent-multicore.py | |
| 2015:02:26 14:00:55 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] flush: [ 11] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:55 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] run_sync: true; test -r '//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/agent/radical-pilot-agent-multicore.py' | |
| 2015:02:26 14:00:55 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] write: [ 11] [ 125] (true; test -r '//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/agent/radical-pilot-agent-multicore.py'\n) | |
| 2015:02:26 14:00:55 21243 PilotLauncherWorker-1 saga.ShellFile : [DEBUG ] read : [ 11] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:55 21243 PilotLauncherWorker-1 saga.ShellFile : [INFO ] file initialized (0)() | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 212] (mput "//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/agent/radical-pilot-agent-multicore.py" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/radical-pilot-agent.py"\n) | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 217] (mput "//users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pil ot/agent/radical-pilot-agent-multicore.py" "/work/02998/ardi/radical.pilot.sandb ox/pilot-54ef2700f8cdba52fb1ccf5f/radical-pilot-agent.py"\n) | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 216] (Uploading //users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/pilot/agent/radical-pilot-agent-multicore.py to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/radical-pilot-agent.py\n) | |
| 2015:02:26 14:00:55 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (//users/ardita/ExTASY-tools/lib/python2.7/sit 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:00:56 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (//users/ardita/ExTASY-tools/lib/python2.7/sit 100% 104KB 103.8KB/s 00:01 ) | |
| 2015:02:26 14:00:56 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 2] (\n) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '//users/ardita/ExTASY-tools/lib/python2.7/sit', 'sftp>'] | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] saga.job.Service ('slurm+ssh://stampede.tacc.utexas.edu/') | |
| 2015:02:26 14:00:57 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] Opening shell of type: ssh://stampede.tacc.utexas.edu | |
| 2015:02:26 14:00:57 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c38dc10> | |
| 2015:02:26 14:00:57 21243 PilotLauncherWorker-1 saga.SLURMJobService : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 6] (sftp> ) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Connecting to stampede.tacc.utexas.edu... | |
| sftp> ) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Connecting to stampede.tacc.utexas.edu... | |
| sftp> ) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] flush: [ 18] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444dd0ae90> | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/ssh -t -o IdentityFile=/users/ardita/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_ardita_%h_%p.ardi.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 ardi@stampede.tacc.utexas.edu | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] flush: [ 18] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] write: [ 18] [ 153] (mput "/users/ardita/grlsd-on-stampede_26Feb/grompp.mdp" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/grompp.mdp"\n) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 156] (mput "/users/ardita/grlsd-on-stampede_26Feb/grompp.mdp" "/work/02998/ardi /radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/grompp.mdp"\n) | |
| 2015:02:26 14:00:57 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 157] (Uploading /users/ardita/grlsd-on-stampede_26Feb/grompp.mdp to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/grompp.mdp\n) | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 79] (/users/ardita/grlsd-on-stampede_26Feb/grompp. 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 81] (/users/ardita/grlsd-on-stampede_26Feb/grompp. 100% 1409 1.4KB/s 00:00 \n) | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [DEBUG ] read : [ 18] [ 6] (sftp> ) | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/grlsd-on-stampede_26Feb/grompp.', 'sftp>'] | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:00:58 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 28] ( printf 'HELLO_%d_SAGA\n' 1\n) | |
| 2015:02:26 14:00:58 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:00:58 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:00:58 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444ddd9710> | |
| 2015:02:26 14:00:58 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:00:59 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 51] ( export PS1='$' > /dev/null 2>&1 || set prompt='$'\n) | |
| 2015:02:26 14:00:59 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 28] ( printf 'HELLO_%d_SAGA\n' 2\n) | |
| 2015:02:26 14:00:59 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 2396] (Last login: Thu Feb 26 08:00:4 ... __________________________\n\n) | |
| 2015:02:26 14:00:59 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Last login: Thu Feb 26 08:00:44 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:00:59 radical.pilot.MainProcess: [DEBUG ] waiting for prompt trigger HELLO_2_SAGA: (5) (Last login: Thu Feb 26 08:00:44 2015 from poirot.pharm.nottingham.ac.uk | |
| ------------------------------------------------------------------------------ | |
| 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> | |
| ) | |
| 2015:02:26 14:01:00 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 244] (----------------------- Project balances for user ardi ------------------------\n| Name Avail SUs Expires | Name Avail SUs Expires |\n| TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | \n) | |
| 2015:02:26 14:01:00 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 405] (-------------------------- Disk quotas for user ardi --------------------------\n| Disk Usage (GB) Limit %Used File Usage Limit %Used |\n| /home1 0.1 5.0 2.37 5069 150000 3.38 |\n| /work 9.3 1024.0 0.91 619818 3000000 20.66 |\n-------------------------------------------------------------------------------\n) | |
| 2015:02:26 14:01:00 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 329] (\nTip 66 (See "module help tacc_tips" for features or how to disable)\n\n Did you know that you can edit the command line with emacs or vi commands? By default, bash uses emacs style editing. Use "set -o vi" to switch to vi style. See www.gnu.org/software/bash/manual/html_node/Command-Line-Editing.html for more details.\n\n) | |
| 2015:02:26 14:01:00 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 53] (login4.stampede(1)$ $$HELLO_1_SAGA\n$$HELLO_2_SAGA\n$) | |
| 2015:02:26 14:01:00 radical.pilot.MainProcess: [DEBUG ] got shell prompt trigger (4) ( | |
| See "man slurm" or the Stampede user guide for more detailed information. | |
| --> To see all the software that is available across all compilers and | |
| mpi stacks, issue: "module spider" | |
| --> To see which software packages are available with your currently loaded | |
| compiler and mpi stack, issue: "module avail" | |
| --> Stampede has three parallel file systems: $HOME (permanent, | |
| quota'd, backed-up) $WORK (permanent, quota'd, not backed-up) and | |
| $SCRATCH (high-speed purged storage). The "cdw" and "cds" aliases | |
| are provided as a convenience to change to your $WORK and $SCRATCH | |
| directories, respectively. | |
| ______________________________________________________________________________ | |
| ----------------------- Project balances for user ardi ------------------------ | |
| | Name Avail SUs Expires | Name Avail SUs Expires | | |
| | TG-MCB090174 138809 2015-09-30 | TG-TRA140016 -81080 2015-05-06 | | |
| -------------------------- Disk quotas for user ardi -------------------------- | |
| | Disk Usage (GB) Limit %Used File Usage Limit %Used | | |
| | /home1 0.1 5.0 2.37 5069 150000 3.38 | | |
| | /work 9.3 1024.0 0.91 619818 3000000 20.66 | | |
| ------------------------------------------------------------------------------- | |
| Tip 66 (See "module help tacc_tips" for features or how to disable) | |
| Did you know that you can edit the command line with emacs or vi commands? By default, bash uses emacs style editing. Use "set -o vi" to switch to vi style. See www.gnu.org/software/bash/manual/html_node/Command-Line-Editing.html for more details. | |
| login4.stampede(1)$ $$HELLO_1_SAGA | |
| $$HELLO_2_SAGA) | |
| 2015:02:26 14:01:00 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:01:00 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) ( | |
| $) | |
| 2015:02:26 14:01:00 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:00 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:00 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444c38d710> | |
| 2015:02:26 14:01:00 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:00 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 20] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 3] ( \n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 1] ($) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 47] (Removable media:\n /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 3] ( \n) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 244] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 3] ( \n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 81] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 1] ($) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 20] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 20] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:01 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 20] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 20] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] Verifying existence of remote SLURM tools. | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 20] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 20] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:01 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 20] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] run_sync: which squeue | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 13] (which squeue\n) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 27] (/usr/bin/squeue\nPROMPT-0->) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] run_sync: which sbatch | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 13] (which sbatch\n) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 151] (mput "/users/ardita/grlsd-on-stampede_26Feb/topol.top" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/topol.top"\n) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 154] (mput "/users/ardita/grlsd-on-stampede_26Feb/topol.top" "/work/02998/ardi/ radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/topol.top"\n) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 27] (/usr/bin/sbatch\nPROMPT-0->) | |
| 2015:02:26 14:01:01 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:02 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] run_sync: which scancel | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 14] (which scancel\n) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 155] (Uploading /users/ardita/grlsd-on-stampede_26Feb/topol.top to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/topol.top\n) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 28] (/usr/bin/scancel\nPROMPT-0->) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/grlsd-on-stampede_26Feb/topol.t 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:02 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] run_sync: which scontrol | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 15] (which scontrol\n) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/grlsd-on-stampede_26Feb/topol.t 100% 6674 6.5KB/s 00:00 \n) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 29] (/usr/bin/scontrol\nPROMPT-0->) | |
| 2015:02:26 14:01:02 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] got cmd prompt (0)(/usr/bin/scontrol | |
| ) | |
| 2015:02:26 14:01:02 21243 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 | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/grlsd-on-stampede_26Feb/topol.t', 'sftp>'] | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:02 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] run_sync: whoami | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 7] (whoami\n) | |
| 2015:02:26 14:01:02 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 16] (ardi\nPROMPT-0->) | |
| 2015:02:26 14:01:02 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] Username detected as: ardi | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] Bootstrap command line: /bin/bash ['-l', 'default_bootstrapper.sh', "-n radicalpilot -s 54ef26fff8cdba52fb1ccf5d -p 54ef2700f8cdba52fb1ccf5f -t 60 -c 16 -v 0.23 -m extasy-db.epcc.ed.ac.uk:27017 -a extasy:extasyproject -i /opt/apps/python/epd/7.3.2/bin/python -e 'module purge' -e 'module load TACC' -e 'module load cluster' -e 'module load Linux' -e 'module load mvapich2' -e 'module load python/2.7.3-epd-7.3.2' -e 'module unload xalt' -e 'export TACC_DELETE_FILES=TRUE' -l SLURM -j SSH -k IBRUN -d 10 -b"] | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] Submitting SAGA job with description: {'Queue': 'normal', 'Executable': '/bin/bash', 'WorkingDirectory': '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/', 'Project': 'TG-MCB090174', 'WallTimeLimit': 60, 'Arguments': ['-l', 'default_bootstrapper.sh', "-n radicalpilot -s 54ef26fff8cdba52fb1ccf5d -p 54ef2700f8cdba52fb1ccf5f -t 60 -c 16 -v 0.23 -m extasy-db.epcc.ed.ac.uk:27017 -a extasy:extasyproject -i /opt/apps/python/epd/7.3.2/bin/python -e 'module purge' -e 'module load TACC' -e 'module load cluster' -e 'module load Linux' -e 'module load mvapich2' -e 'module load python/2.7.3-epd-7.3.2' -e 'module unload xalt' -e 'export TACC_DELETE_FILES=TRUE' -l SLURM -j SSH -k IBRUN -d 10 -b"], 'Error': 'AGENT.STDERR', 'Output': 'AGENT.STDOUT', 'TotalCPUCount': 16} | |
| 2015:02:26 14:01:02 21243 PilotLauncherWorker-1 saga.SLURMJobService : [WARNING ] number_of_processes not specified in submitted SLURM job description -- defaulting to 1 per total_cpu_count! (16) | |
| 2015:02:26 14:01:02 21243 PilotLauncherWorker-1 saga.SLURMJobService : [INFO ] Creating working directory /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/ | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:02 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:02 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c344610> | |
| 2015:02:26 14:01:02 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:02 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444dd1f9d0> | |
| 2015:02:26 14:01:02 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:02 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 21] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:02 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/ | |
| 2015:02:26 14:01:02 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 80] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 3] ( \n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:03 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:03 21243 PilotLauncherWorker-1 saga.SLURMJobService : [INFO ] SLURM script generated: | |
| #!/bin/sh | |
| #SBATCH -J "SAGAPythonSLURMJob" | |
| #SBATCH --ntasks=16 | |
| #SBATCH --cpus-per-task=1 | |
| #SBATCH -D /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/ | |
| #SBATCH -o AGENT.STDOUT | |
| #SBATCH -e AGENT.STDERR | |
| #SBATCH -t 01:00:00 | |
| #SBATCH -p normal | |
| #SBATCH -A TG-MCB090174 | |
| /bin/bash -l default_bootstrapper.sh -n radicalpilot -s 54ef26fff8cdba52fb1ccf5d -p 54ef2700f8cdba52fb1ccf5f -t 60 -c 16 -v 0.23 -m extasy-db.epcc.ed.ac.uk:27017 -a extasy:extasyproject -i /opt/apps/python/epd/7.3.2/bin/python -e 'module purge' -e 'module load TACC' -e 'module load cluster' -e 'module load Linux' -e 'module load mvapich2' -e 'module load python/2.7.3-epd-7.3.2' -e 'module unload xalt' -e 'export TACC_DELETE_FILES=TRUE' -l SLURM -j SSH -k IBRUN -d 10 -b | |
| 2015:02:26 14:01:03 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 18] (Removable media:\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 29] ( /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 3] ( \n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 244] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 3] ( \n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 53] (ardita@poirot 101% export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 29] (export: Command not found.\n$) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i2015:02:26 14:01:03 radical.pilot.MainProcess: [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444c3447d0> | |
| 2015:02:26 14:01:03 radical.pilot.MainProcess: [INFO ] running: /usr/bin/env TERM=vt100 /usr/bin/sftp -o IdentityFile=/users/ardita/.ssh/id_rsa -o ControlMaster=no -o ControlPath=/tmp/saga_ssh_ardita_%h_%p.ardi.ctrl -o TCPKeepAlive=no -o ServerAliveInterval=10 -o ServerAliveCountMax=20 ardi@stampede.tacc.utexas.edu | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 21] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:03 radical.pilot.MainProcess: [DEBUG ] read : [ 22] [ 43] (Connecting to stampede.tacc.utexas.edu...\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 21] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 21] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 21] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 21] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 21] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:03 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 21] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:03 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:03 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:03 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:03 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 153] (mput "/users/ardita/grlsd-on-stampede_26Feb/config.ini" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/config.ini"\n) | |
| 2015:02:26 14:01:03 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 156] (mput "/users/ardita/grlsd-on-stampede_26Feb/config.ini" "/work/02998/ardi /radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/config.ini"\n) | |
| 2015:02:26 14:01:04 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 157] (Uploading /users/ardita/grlsd-on-stampede_26Feb/config.ini to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/config.ini\n) | |
| 2015:02:26 14:01:04 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/grlsd-on-stampede_26Feb/config. 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:04 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/grlsd-on-stampede_26Feb/config. 100% 264 0.3KB/s 00:00 \n) | |
| 2015:02:26 14:01:04 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:04 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/grlsd-on-stampede_26Feb/config.', 'sftp>'] | |
| 2015:02:26 14:01:04 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:04 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:04 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:04 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:04 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:04 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:04 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c344f50> | |
| 2015:02:26 14:01:04 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:06 radical.pilot.MainProcess: [DEBUG ] read : [ 22] [ 6] (sftp> ) | |
| 2015:02:26 14:01:06 radical.pilot.MainProcess: [DEBUG ] got initial shell prompt (5) (Connecting to stampede.tacc.utexas.edu... | |
| sftp> ) | |
| 2015:02:26 14:01:06 radical.pilot.MainProcess: [DEBUG ] Got initial shell prompt (5) (Connecting to stampede.tacc.utexas.edu... | |
| sftp> ) | |
| 2015:02:26 14:01:06 radical.pilot.MainProcess: [DEBUG ] flush: [ 22] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444dcb1110> | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 23] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:06 radical.pilot.MainProcess: [DEBUG ] flush: [ 22] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 3] ( \n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:06 radical.pilot.MainProcess: [DEBUG ] write: [ 22] [ 49] (mput "/tmp/tmp_Obdz3f.slurm" "tmp_Obdz3f.slurm"\n) | |
| 2015:02:26 14:01:06 radical.pilot.MainProcess: [DEBUG ] read : [ 22] [ 50] (mput "/tmp/tmp_Obdz3f.slurm" "tmp_Obdz3f.slurm"\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 47] (Removable media:\n /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 3] ( \n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 244] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 3] ( \n) | |
| 2015:02:26 14:01:06 radical.pilot.MainProcess: [DEBUG ] read : [ 22] [ 71] (Uploading /tmp/tmp_Obdz3f.slurm to /home1/02998/ardi/tmp_Obdz3f.slurm\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 53] (ardita@poirot 101% export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 29] (export: Command not found.\n$) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 23] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 23] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:06 radical.pilot.MainProcess: [DEBUG ] read : [ 22] [ 79] (/tmp/tmp_Obdz3f.slurm 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 23] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:06 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 23] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:07 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:07 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 23] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:07 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 23] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:07 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 23] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] read : [ 22] [ 81] (/tmp/tmp_Obdz3f.slurm 100% 769 0.8KB/s 00:01 \n) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] read : [ 22] [ 6] (sftp> ) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/tmp/tmp_Obdz3f.slurm', 'sftp>'] | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:07 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] run_sync: cat 'tmp_Obdz3f.slurm' | sbatch && rm -vf 'tmp_Obdz3f.slurm' | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 61] (cat 'tmp_Obdz3f.slurm' | sbatch && rm -vf 'tmp_Obdz3f.slurm'\n) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 213] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/gro.py" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/gro.py"\n) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 218] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ense mblemd/extasy/bin/Preprocessor/Gromacs/gro.py" "/work/02998/ardi/radical.pilot.s andbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/gro.py"\n) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 203] (-----------------------------------------------------------------\n Welcome to the Stampede Supercomputer \n-----------------------------------------------------------------\n\n) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 217] (Uploading /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/gro.py to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/gro.py\n) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 81] (--> Verifying valid submit host (login4)...OK\n--> Verifying valid jobname...OK\n) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/ExTASY-tools/lib/python2.7/site 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:07 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/ExTASY-tools/lib/python2.7/site 100% 846 0.8KB/s 00:00 \n) | |
| 2015:02:26 14:01:08 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:08 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/ExTASY-tools/lib/python2.7/site', 'sftp>'] | |
| 2015:02:26 14:01:08 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:08 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:08 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:08 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c344ad0> | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444dcc2c90> | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 24] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 3] ( \n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 18] (Removable media:\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 29] ( /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 3] ( \n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 244] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 3] ( \n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 81] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 1] ($) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 24] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 24] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 24] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:08 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 24] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:09 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:09 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 24] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:09 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 24] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:09 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 24] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:09 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:09 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:09 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:09 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 221] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/spliter.py" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/spliter.py"\n) | |
| 2015:02:26 14:01:09 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 226] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ense mblemd/extasy/bin/Preprocessor/Gromacs/spliter.py" "/work/02998/ardi/radical.pil ot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/spliter.py"\n) | |
| 2015:02:26 14:01:09 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 225] (Uploading /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Preprocessor/Gromacs/spliter.py to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/spliter.py\n) | |
| 2015:02:26 14:01:09 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/ExTASY-tools/lib/python2.7/site 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:09 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/ExTASY-tools/lib/python2.7/site 100% 1398 1.4KB/s 00:00 \n) | |
| 2015:02:26 14:01:10 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:10 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/ExTASY-tools/lib/python2.7/site', 'sftp>'] | |
| 2015:02:26 14:01:10 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:10 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:10 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:10 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c355350> | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444dcc2cd0> | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 25] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 3] ( \n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 47] (Removable media:\n /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 3] ( \n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 244] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 3] ( \n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 81] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 1] ($) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 25] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 25] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 25] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 25] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 25] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 25] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:10 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 25] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:11 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:11 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:11 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:11 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 210] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.py" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/run.py"\n) | |
| 2015:02:26 14:01:11 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 215] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ense mblemd/extasy/bin/Simulator/Gromacs/run.py" "/work/02998/ardi/radical.pilot.sand box/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/run.py"\n) | |
| 2015:02:26 14:01:11 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 214] (Uploading /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.py to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/run.py\n) | |
| 2015:02:26 14:01:11 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/ExTASY-tools/lib/python2.7/site 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:11 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/ExTASY-tools/lib/python2.7/site 100% 2509 2.5KB/s 00:00 \n) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/ExTASY-tools/lib/python2.7/site', 'sftp>'] | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 38] (--> Enforcing max jobs per user...OK\n) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 70] (--> Verifying availability of your home dir (/home1/02998/ardi)...OK\n) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 69] (--> Verifying availability of your work dir (/work/02998/ardi)...OK\n) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 75] (--> Verifying availability of your scratch dir (/scratch/02998/ardi)...OK\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 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)...) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 4] (OK\n) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 29] (Submitted batch job 4909583\n) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 38] (removed `tmp_Obdz3f.slurm'\nPROMPT-0->) | |
| 2015:02:26 14:01:12 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] staged/submit SLURM script (/tmp/tmp_Obdz3f.slurm) (tmp_Obdz3f.slurm) (0) | |
| 2015:02:26 14:01:12 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] started job [slurm+ssh://stampede.tacc.utexas.edu/]-[4909583] | |
| 2015:02:26 14:01:12 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] Batch system output: | |
| ----------------------------------------------------------------- | |
| Welcome to the Stampede Supercomputer | |
| ----------------------------------------------------------------- | |
| --> Verifying valid submit host (login4)...OK | |
| --> Verifying valid jobname...OK | |
| --> Enforcing max jobs per user...OK | |
| --> Verifying availability of your home dir (/home1/02998/ardi)...OK | |
| --> Verifying availability of your work dir (/work/02998/ardi)...OK | |
| --> Verifying availability of your scratch dir (/scratch/02998/ardi)...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 4909583 | |
| removed `tmp_Obdz3f.slurm' | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c355f10> | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444c355ed0> | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 26] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:12 21243 PilotLauncherWorker-1 saga.SLURMJobService : [DEBUG ] run_sync: scontrol show job 4909583 | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 26] (scontrol show job 4909583\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 3] ( \n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 891] (JobId=4909583 Name=SAGAPythonS ... 8cdba52fb1ccf5f/\n\nPROMPT-0->) | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [DEBUG ] SAGA job submitted with job id [slurm+ssh://stampede.tacc.utexas.edu/]-[4909583] | |
| 2015:02:26 14:01:12 radical.pilot.MainProcess: [INFO ] ComputePilot '54ef2700f8cdba52fb1ccf5f' state changed from 'Launching' to 'PendingActive'. | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 18] (Removable media:\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 29] ( /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 3] ( \n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 244] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 3] ( \n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 53] (ardita@poirot 101% export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 28] (export: Command not found.\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 1] ($) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 26] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 26] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 26] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 26] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 26] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 26] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:12 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 26] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:13 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:13 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:13 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:13 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 224] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/pre_analyze.py" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/pre_analyze.py"\n) | |
| 2015:02:26 14:01:13 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 229] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ense mblemd/extasy/bin/Analyzer/LSDMap/pre_analyze.py" "/work/02998/ardi/radical.pilo t.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/pre_analyze.py"\n) | |
| 2015:02:26 14:01:13 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 228] (Uploading /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/pre_analyze.py to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/pre_analyze.py\n) | |
| 2015:02:26 14:01:13 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/ExTASY-tools/lib/python2.7/site 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:13 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/ExTASY-tools/lib/python2.7/site 100% 426 0.4KB/s 00:00 \n) | |
| 2015:02:26 14:01:14 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:14 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/ExTASY-tools/lib/python2.7/site', 'sftp>'] | |
| 2015:02:26 14:01:14 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:14 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:14 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:14 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c35c950> | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444dcdc690> | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 27] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 3] ( \n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 18] (Removable media:\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 29] ( /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 3] ( \n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 244] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 3] ( \n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 53] (ardita@poirot 101% export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 28] (export: Command not found.\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 1] ($) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 27] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 27] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 27] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 27] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 27] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 27] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:14 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 27] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 226] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/run_analyzer.sh" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/run_analyzer.sh"\n) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 231] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ense mblemd/extasy/bin/Analyzer/LSDMap/run_analyzer.sh" "/work/02998/ardi/radical.pil ot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/run_analyzer.sh"\n) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 230] (Uploading /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/run_analyzer.sh to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/run_analyzer.sh\n) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/ExTASY-tools/lib/python2.7/site 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/ExTASY-tools/lib/python2.7/site 100% 99 0.1KB/s 00:00 \n) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/ExTASY-tools/lib/python2.7/site', 'sftp>'] | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:15 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:16 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:16 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c35cf10> | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444dc6d0d0> | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 28] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 3] ( \n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 47] (Removable media:\n /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 3] ( \n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 241] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 3] ( \n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 3] ( \n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 82] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n$) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 28] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 28] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 28] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 28] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 28] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 28] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:16 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 28] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 226] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/post_analyze.py" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/post_analyze.py"\n) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 231] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ense mblemd/extasy/bin/Analyzer/LSDMap/post_analyze.py" "/work/02998/ardi/radical.pil ot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/post_analyze.py"\n) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 230] (Uploading /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/post_analyze.py to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/post_analyze.py\n) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/ExTASY-tools/lib/python2.7/site 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/ExTASY-tools/lib/python2.7/site 100% 1025 1.0KB/s 00:00 \n) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/ExTASY-tools/lib/python2.7/site', 'sftp>'] | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:17 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:18 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:18 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c35c8d0> | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444dcdc6d0> | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 29] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 48] ( \nWelcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 47] (Removable media:\n /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 3] ( \n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 241] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 3] ( \n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 3] ( \n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 82] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n$) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 29] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 29] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 29] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 29] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 29] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 29] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:18 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 29] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 214] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/select.py" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/select.py"\n) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 219] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ense mblemd/extasy/bin/Analyzer/LSDMap/select.py" "/work/02998/ardi/radical.pilot.san dbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/select.py"\n) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 218] (Uploading /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/select.py to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/select.py\n) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/ExTASY-tools/lib/python2.7/site 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/ExTASY-tools/lib/python2.7/site 100% 3536 3.5KB/s 00:00 \n) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/ExTASY-tools/lib/python2.7/site', 'sftp>'] | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:19 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:20 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:20 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c355b10> | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444c35c310> | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 30] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 48] ( \nWelcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 2400 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 47] (Removable media:\n /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 3] ( \n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 241] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 3] ( \n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 3] ( \n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 82] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n$) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 2400 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 2400 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 30] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 30] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 30] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 30] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 30] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 30] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:20 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 30] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 224] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/reweighting.py" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/reweighting.py"\n) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 229] (mput "/users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ense mblemd/extasy/bin/Analyzer/LSDMap/reweighting.py" "/work/02998/ardi/radical.pilo t.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/reweighting.py"\n) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 228] (Uploading /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/extasy/bin/Analyzer/LSDMap/reweighting.py to /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/reweighting.py\n) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 79] (/users/ardita/ExTASY-tools/lib/python2.7/site 0% 0 0.0KB/s --:-- ETA) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 81] (/users/ardita/ExTASY-tools/lib/python2.7/site 100% 8918 8.7KB/s 00:00 \n) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 6] (sftp> ) | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] copy done: ['mput', 'Uploading', '/users/ardita/ExTASY-tools/lib/python2.7/site', 'sftp>'] | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [INFO ] Operating from staging | |
| 2015:02:26 14:01:21 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' | |
| 2015:02:26 14:01:22 radical.pilot.MainProcess: [DEBUG ] write: [ 13] [ 370] (mkdir -p /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && cd /work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area && mkdir -p '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area' ; cd '/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area'\n) | |
| 2015:02:26 14:01:22 radical.pilot.MainProcess: [DEBUG ] read : [ 13] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellDirectory : [DEBUG ] initialized directory (0)() | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellDirectory : [DEBUG ] PTYShell init <saga.utils.pty_shell.PTYShell object at 0x7f444c398250> | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellDirectory : [INFO ] PTY prompt pattern: [\$#%>\]]\s*$ | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] PTYProcess init <saga.utils.pty_process.PTYProcess object at 0x7f444e1020d0> | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [INFO ] running: /usr/bin/env TERM=vt100 /bin/tcsh -i | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 31] [ 33] ( export PS1='$' ; set prompt='$'\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 3] ( \n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 45] (Welcome to poirot.pharm.nottingham.ac.uk\n \n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 46] (Operating System: CentOS release 6.6 (Final)\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 94] (CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz\n 8 3601 MHz x86_64 Processors\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 63] (Main memory size: 15874 Mbytes\nSwap memory size: 8007 Mbytes\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 47] (Removable media:\n /dev/sr0: CDDVDW SH-222BB\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 3] ( \n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 244] (Disk quotas for user ardita (uid 1285): \n Filesystem blocks quota limit grace files quota limit grace\nlund.pharm.nottingham.ac.uk:/users/\n 394G 400G 1812G 115k 0 0 \n \n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 31] (Currently Loaded Modulefiles:\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 73] ( 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 3] ( \n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 41] (Condor queue: 0 jobs currently in queue\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 131] ( \nFor information about this machine and software available on it go to:\n http://holmes.cancres.nottingham.ac.uk/facilities/\n \n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 82] (ardita@poirot 101% export PS1='$' ; set prompt='$'\nexport: Command not found.\n$) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] Got initial shell prompt (5) ( | |
| Welcome to poirot.pharm.nottingham.ac.uk | |
| Operating System: CentOS release 6.6 (Final) | |
| CPU: GenuineIntel Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz | |
| 8 3601 MHz x86_64 Processors | |
| Main memory size: 15874 Mbytes | |
| Swap memory size: 8007 Mbytes | |
| Removable media: | |
| /dev/sr0: CDDVDW SH-222BB | |
| Disk quotas for user ardita (uid 1285): | |
| Filesystem blocks quota limit grace files quota limit grace | |
| lund.pharm.nottingham.ac.uk:/users/ | |
| 394G 400G 1812G 115k 0 0 | |
| Currently Loaded Modulefiles: | |
| 1) sysinit 2) intel/14.0.3 3) python/2.7.8 4) geany/1.24.1 | |
| Condor queue: 0 jobs currently in queue | |
| For information about this machine and software available on it go to: | |
| http://holmes.cancres.nottingham.ac.uk/facilities/ | |
| ardita@poirot 101% export PS1='$' ; set prompt='$' | |
| export: Command not found. | |
| $) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellDirectory : [DEBUG ] running command shell: exec /bin/sh -i | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 31] [ 47] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 48] ( stty -echo ; unset HISTFILE ; exec /bin/sh -i\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 8] (sh-4.1$ ) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 31] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 31] [ 100] ( unset PROMPT_COMMAND ; unset HISTFILE ; PS1='PROMPT-$?->'; PS2=''; export PS1 PS2 2>&1 >/dev/null\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellDirectory : [DEBUG ] got new shell prompt | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 31] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellDirectory : [DEBUG ] run_sync: cd /users/ardita/grlsd-on-stampede_26Feb | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] write: [ 31] [ 41] (cd /users/ardita/grlsd-on-stampede_26Feb\n) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] read : [ 31] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:22 21243 MainThread saga.ShellFile : [DEBUG ] flush: [ 31] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:22 radical.pilot.MainProcess: [DEBUG ] flush: [ 13] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] flush: [ 17] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] write: [ 17] [ 176] (mput "/users/ardita/grlsd-on-stampede_26Feb/backup/iter-1/0_input.gro" "/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_area/iter-1/0_input.gro"\n) | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] read : [ 17] [ 284] (mput "/users/ardita/grlsd-on-stampede_26Feb/backup/iter-1/0_input.gro" "/ work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_are a/iter-1/0_input.gro"\nstat /users/ardita/grlsd-on-stampede_26Feb/backup/iter-1/0_input.gro: No such file or directory\nsftp> ) | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] DoesNotExist: file copy failed: mput "/users/ardita/grlsd-on-stampede_26Feb/backup/iter-1/0_input.gro" "/ work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_are a/iter-1/0_input.gro" | |
| stat /users/ardita/grlsd-on-stampede_26Feb/backup/iter-1/0_input.gro: No such file or directory | |
| sftp> | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] session 54ef26fff8cdba52fb1ccf5d closing | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] session 54ef26fff8cdba52fb1ccf5d closes pmgr 54ef2700f8cdba52fb1ccf5e | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pmgr 54ef2700f8cdba52fb1ccf5e closing | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pmgr 54ef2700f8cdba52fb1ccf5e cancel worker Thread-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pworker Thread-1 stops launcher PilotLauncherWorker-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] launcher PilotLauncherWorker-1 stopping | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] launcher PilotLauncherWorker-1 stopped | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pworker Thread-1 stopped launcher PilotLauncherWorker-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pmgr 54ef2700f8cdba52fb1ccf5e canceled worker Thread-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] Reconnected to existing ComputePilot {'uid': '54ef2700f8cdba52fb1ccf5f', 'stdout': None, 'start_time': None, 'resource_detail': {'cores_per_node': None, 'nodes': None}, 'submission_time': datetime.datetime(2015, 2, 26, 14, 0, 40, 556000), 'logfile': None, 'resource': u'stampede.tacc.utexas.edu', 'log': [<radical.pilot.logentry.Logentry object at 0x7f444d601290>, <radical.pilot.logentry.Logentry object at 0x7f444d601490>, <radical.pilot.logentry.Logentry object at 0x7f444d601150>, <radical.pilot.logentry.Logentry object at 0x7f444d601190>, <radical.pilot.logentry.Logentry object at 0x7f444d6011d0>, <radical.pilot.logentry.Logentry object at 0x7f444d6010d0>], 'sandbox': u'sftp://stampede.tacc.utexas.edu/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/', 'state': u'PendingActive', 'stop_time': None, 'stderr': None} | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pmgr 54ef2700f8cdba52fb1ccf5e cancels pilot 54ef2700f8cdba52fb1ccf5f | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [INFO ] Sent 'COMMAND_CANCEL_PILOT' command to pilots ['54ef2700f8cdba52fb1ccf5f']. | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [WARNING ] actively cancel pilot 54ef2700f8cdba52fb1ccf5f? state: PendingActive | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [INFO ] actively cancel pilot 54ef2700f8cdba52fb1ccf5f ([slurm+ssh://stampede.tacc.utexas.edu/]-[4909583], slurm+ssh://stampede.tacc.utexas.edu/) | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] flush: [ 19] [ ] (flush pty read cache) | |
| 2015:02:26 14:01:23 21243 MainThread saga.SLURMJobService : [DEBUG ] run_sync: scancel 4909583 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] write: [ 19] [ 16] (scancel 4909583\n) | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] read : [ 19] [ 10] (PROMPT-0->) | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] Reconnected to existing ComputePilot {'uid': '54ef2700f8cdba52fb1ccf5f', 'stdout': None, 'start_time': None, 'resource_detail': {'cores_per_node': None, 'nodes': None}, 'submission_time': datetime.datetime(2015, 2, 26, 14, 0, 40, 556000), 'logfile': None, 'resource': u'stampede.tacc.utexas.edu', 'log': [<radical.pilot.logentry.Logentry object at 0x7f444c2a8090>, <radical.pilot.logentry.Logentry object at 0x7f444c2a8050>, <radical.pilot.logentry.Logentry object at 0x7f444c2a8110>, <radical.pilot.logentry.Logentry object at 0x7f444c2a8150>, <radical.pilot.logentry.Logentry object at 0x7f444c2a8190>, <radical.pilot.logentry.Logentry object at 0x7f444c2a81d0>], 'sandbox': u'sftp://stampede.tacc.utexas.edu/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/', 'state': 'Canceling', 'stop_time': None, 'stderr': None} | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pmgr 54ef2700f8cdba52fb1ccf5e wait for pilot 54ef2700f8cdba52fb1ccf5f (Canceling) | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [DEBUG ] Reconnected to existing ComputePilot {'uid': '54ef2700f8cdba52fb1ccf5f', 'stdout': None, 'start_time': None, 'resource_detail': {'cores_per_node': None, 'nodes': None}, 'submission_time': datetime.datetime(2015, 2, 26, 14, 0, 40, 556000), 'logfile': None, 'resource': u'stampede.tacc.utexas.edu', 'log': [<radical.pilot.logentry.Logentry object at 0x7f444c2a8050>, <radical.pilot.logentry.Logentry object at 0x7f444c2a8110>, <radical.pilot.logentry.Logentry object at 0x7f444c2a8150>, <radical.pilot.logentry.Logentry object at 0x7f444c2a8190>, <radical.pilot.logentry.Logentry object at 0x7f444c2a81d0>, <radical.pilot.logentry.Logentry object at 0x7f444c2a8210>], 'sandbox': u'sftp://stampede.tacc.utexas.edu/work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/', 'state': 'Canceling', 'stop_time': None, 'stderr': None} | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pmgr 54ef2700f8cdba52fb1ccf5e canceled pilot 54ef2700f8cdba52fb1ccf5f | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pmgr 54ef2700f8cdba52fb1ccf5e stops worker Thread-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pworker Thread-1 stopping | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pworker Thread-1 stops launcher PilotLauncherWorker-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] launcher PilotLauncherWorker-1 stopping | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] launcher PilotLauncherWorker-1 stopped | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pworker Thread-1 stopped launcher PilotLauncherWorker-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pworker Thread-1 stopped | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pmgr 54ef2700f8cdba52fb1ccf5e stopped worker Thread-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] pmgr 54ef2700f8cdba52fb1ccf5e closed | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] session 54ef26fff8cdba52fb1ccf5d closed pmgr None | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] session 54ef26fff8cdba52fb1ccf5d closes umgr 54ef2708f8cdba52fb1ccf60 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stopping | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stops itransfer InputFileTransferWorker-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] itransfer InputFileTransferWorker-1 stopping | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] itransfer InputFileTransferWorker-1 stopped | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stopped itransfer InputFileTransferWorker-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stops itransfer InputFileTransferWorker-2 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] itransfer InputFileTransferWorker-2 stopping | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] itransfer InputFileTransferWorker-2 stopped | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stopped itransfer InputFileTransferWorker-2 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stops otransfer OutputFileTransferWorker-1 | |
| 2015:02:26 14:01:23 radical.pilot.MainProcess: [ERROR ] otransfer OutputFileTransferWorker-1 stopping | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [ERROR ] otransfer OutputFileTransferWorker-1 stopped | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stopped otransfer OutputFileTransferWorker-1 | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stops otransfer OutputFileTransferWorker-2 | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [ERROR ] otransfer OutputFileTransferWorker-2 stopping | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [ERROR ] otransfer OutputFileTransferWorker-2 stopped | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stopped otransfer OutputFileTransferWorker-2 | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [ERROR ] uworker Thread-3 stopped | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [INFO ] Closed UnitManager 54ef2708f8cdba52fb1ccf60. | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [ERROR ] session 54ef26fff8cdba52fb1ccf5d closed umgr None | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [INFO ] Deleted session 54ef26fff8cdba52fb1ccf5d from database. | |
| 2015:02:26 14:01:24 radical.pilot.MainProcess: [ERROR ] session None closed | |
| ExTASY version : 0.1.3-beta-1-g2cdf59c | |
| Session UID: 54ef26fff8cdba52fb1ccf5d | |
| Pilot UID : 54ef2700f8cdba52fb1ccf5f | |
| Loading kernel configurations from /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/gromacs.json | |
| Loading kernel configurations from /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/amber.json | |
| Loading kernel configurations from /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/mmpbsa.json | |
| Loading kernel configurations from /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/test.json | |
| Loading kernel configurations from /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/coco.json | |
| Loading kernel configurations from /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/lsdmap.json | |
| Loading kernel configurations from /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/sleep.json | |
| Loading kernel configurations from /users/ardita/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/namd.json | |
| Preprocessing stage .... | |
| [Callback]: ComputePilot '54ef2700f8cdba52fb1ccf5f' state changed to Launching. | |
| [Callback]: ComputePilot '54ef2700f8cdba52fb1ccf5f' state changed to PendingActive. | |
| An error occurred: file copy failed: mput "/users/ardita/grlsd-on-stampede_26Feb/backup/iter-1/0_input.gro" "/ work/02998/ardi/radical.pilot.sandbox/pilot-54ef2700f8cdba52fb1ccf5f/staging_are a/iter-1/0_input.gro" | |
| stat /users/ardita/grlsd-on-stampede_26Feb/backup/iter-1/0_input.gro: No such file or directory | |
| sftp> (/users/ardita/ExTASY-tools/lib/python2.7/site-packages/saga/utils/pty_shell.py +1010 (run_copy_to) : raise se.DoesNotExist._log (info['logger'], "file copy failed: %s" % str(out))) | |
| Closing session, exiting now ... |
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