ashkurti
ashkurti
/ grlsdmapFails
Created
October 3, 2014 10:43
Gromacs /Lsdmap on Stampede fails - Linux/Stampede platform
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| [ExTASY-toolsOct2] ardita@poirot 187% extasy --RPconfig stampede.rcfg --Kconfig gromacslsdmap.wcfg | |
| Session UID: 542e7955f8cdba2fce5f0321 | |
| Pilot UID : 542e7958f8cdba2fce5f0323 | |
| [Callback]: ComputePilot '542e7958f8cdba2fce5f0323' state changed to Launching. | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/gromacs.json | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/amber.json | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/mmpbsa.json | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/test.json | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/coco.json | |
| Loading kernel configurations from /users/ardita/Ex |
ashkurti
/ gist:9345b8dd5ab2b363fd03
Created
October 3, 2014 15:42
DEBUG activated for gromacs/lsdmap workflow that fails in linux/stampede platform
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| [ExTASY-toolsOct2] ardita@poirot 201% extasy --RPconfig stampede.rcfg --Kconfig gromacslsdmap.wcfg | |
| 2014:10:03 16:41:15 radical.pilot.MainProcess: [INFO ] radical.pilot version: 0.20 | |
| 2014:10:03 16:41:15 radical.pilot.MainProcess: [INFO ] using database url mongodb://ec2-184-72-89-141.compute-1.amazonaws.com:27017/ | |
| 2014:10:03 16:41:15 radical.pilot.MainProcess: [INFO ] using database name radicalpilot | |
| 2014:10:03 16:41:15 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/localhost.json | |
| 2014:10:03 16:41:15 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/futuregrid.json | |
| 2014:10:03 16:41:15 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/lrz.json | |
| 2014:10:03 16:41:16 radical.pilot.MainProcess |
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| [ExTASY-toolsOct2] ardita@tirith 114% extasy --RPconfig stampede.rcfg --Kconfig gromacslsdmap.wcfg | |
| Session UID: 5430103554737d225a00a395 | |
| Pilot UID : 5430103954737d225a00a397 | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/gromacs.json | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/amber.json | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/mmpbsa.json | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/test.json | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/coco.json | |
| Loading kernel configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/mdkernels/configs/ls |
ashkurti
/ gist:60c522c3ef1f285aba19
Created
October 4, 2014 17:01
Bag of Tasks fails locally (linux environment) - without debug
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| [ExTASY-toolsOct2] ardita@jekyll 114% echo $RADICAL_PILOT_DBURL | |
| mongodb://ec2-184-72-89-141.compute-1.amazonaws.com:27017/ | |
| [ExTASY-toolsOct2] ardita@jekyll 115% python local_simple_bot.py | |
| Initializing Pilot Manager ... | |
| Submitting Compute Pilot to Pilot Manager ... | |
| [Callback]: ComputePilot 'None' state: Launching. | |
| Initializing Unit Manager ... | |
| Registering Compute Pilot with Unit Manager ... | |
| Submit Compute Units to Unit Manager ... | |
| [Callback]: ComputeUnit '5430225be14fa23fd85b64d2' state: PendingExecution. |
ashkurti
/ gist:63ce36ffbe7ea67bf7fa
Created
October 4, 2014 17:05
Bag of Tasks fails locally (linux environment) - with debug
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| [ExTASY-toolsOct2] ardita@jekyll 120% python local_simple_bot.py | |
| 2014:10:04 18:03:26 radical.pilot.MainProcess: [INFO ] radical.pilot version: 0.20 | |
| 2014:10:04 18:03:26 radical.pilot.MainProcess: [INFO ] using database url mongodb://ec2-184-72-89-141.compute-1.amazonaws.com:27017/ | |
| 2014:10:04 18:03:26 radical.pilot.MainProcess: [INFO ] using database name radicalpilot | |
| 2014:10:04 18:03:26 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/localhost.json | |
| 2014:10:04 18:03:26 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/futuregrid.json | |
| 2014:10:04 18:03:26 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/lrz.json | |
| 2014:10:04 18:03:26 radical.pilot.MainProcess: [INFO ] Loaded resource config |
ashkurti
/ gist:921846ca66b94214af6a
Created
October 4, 2014 17:10
Bag of tasks fails locally (linux environment) - simple_bot.py not modified
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| [ExTASY-toolsOct2] ardita@jekyll 125% python simple_bot.py | |
| 2014:10:04 18:09:07 radical.pilot.MainProcess: [INFO ] radical.pilot version: 0.20 | |
| 2014:10:04 18:09:07 radical.pilot.MainProcess: [INFO ] using database url mongodb://ec2-184-72-89-141.compute-1.amazonaws.com:27017/ | |
| 2014:10:04 18:09:07 radical.pilot.MainProcess: [INFO ] using database name radicalpilot | |
| 2014:10:04 18:09:07 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/localhost.json | |
| 2014:10:04 18:09:07 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/futuregrid.json | |
| 2014:10:04 18:09:07 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/lrz.json | |
| 2014:10:04 18:09:07 radical.pilot.MainProcess: [INFO ] Loaded resource configuratio |
ashkurti
/ BotFailsRemotelyDebug
Created
October 4, 2014 17:56
Bag of Tasks fails locally (linux environment) - with debug
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| [ExTASY-toolsOct2] ardita@jekyll 137% python remote_simple_bot.py | |
| 2014:10:04 18:29:42 radical.pilot.MainProcess: [INFO ] radical.pilot version: 0.20 | |
| 2014:10:04 18:29:43 radical.pilot.MainProcess: [INFO ] using database url mongodb://ec2-184-72-89-141.compute-1.amazonaws.com:27017/ | |
| 2014:10:04 18:29:43 radical.pilot.MainProcess: [INFO ] using database name radicalpilot | |
| 2014:10:04 18:29:43 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/localhost.json | |
| 2014:10:04 18:29:43 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/futuregrid.json | |
| 2014:10:04 18:29:43 radical.pilot.MainProcess: [INFO ] Loaded resource configurations from /users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/configs/lrz.json | |
| 2014:10:04 18:29:43 radical.pilot.MainProcess: [INFO ] Loaded resource confi |
ashkurti
/ gist:1d900a91fdcc9b702165
Created
October 6, 2014 10:07
Gromacs /Lsdmap on Stampede fails - Linux/Stampede platform - ACTIVE DEBUG
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| ... | |
| 2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}' | |
| 2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out40.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out40.gro', 'priority': 0}' | |
| 2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh > run.sh' into dict '{'action': 'Transfer', 'source': '/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'run.sh', 'priority': 0}' | |
| 2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start41.gro > start.gro' into dic |
ashkurti
/ gist:71841867fa71a4c86edb
Created
October 6, 2014 13:37
Amber/Coco workflow on ARCHER - STDERR of the failed compute unit
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| ardi@eslogin003:/work/e290/e290/ardi/radical.pilot.sandbox/pilot-5432858754737d534315377b/unit-5432865b54737d5343153785> more STDERR | |
| Traceback (most recent call last): | |
| Traceback (most recent call last): | |
| File "pycoco.py", line 97, in <module> | |
| Traceback (most recent call last): | |
| File "pycoco.py", line 97, in <module> | |
| File "pycoco.py", line 97, in <module> | |
| Traceback (most recent call last): | |
| Traceback (most recent call last): | |
| File "pycoco.py", line 97, in <module> |
ashkurti
/ coco_amber_stampede
Created
November 5, 2014 11:27
Output of the coco amber workflow on stampede including the debug option - November 5
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| [ExTASY-tools] ardita@tirith 123% extasy --RPconfig stampede.rcfg --Kconfig cocoamber.wcfg > extasy.log | |
| 2014:11:05 11:23:46 radical.pilot.MainProcess: [INFO ] radical.pilot version: 0.21 (v0.21) | |
| 2014:11:05 11:23:46 18883 MainThread saga : [INFO ] saga-python version: 0.22 | |
| 2014:11:05 11:23:46 18883 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.myproxy | |
| 2014:11:05 11:23:46 18883 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.myproxy for saga.Context API with URL scheme(s) ['myproxy://'] | |
| 2014:11:05 11:23:46 18883 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.x509 | |
| 2014:11:05 11:23:46 18883 MainThread saga.Engine : [INFO ] Register adaptor saga.adaptors.context.x509 for saga.Context API with URL scheme(s) ['x509://'] | |
| 2014:11:05 11:23:46 18883 MainThread saga.Engine : [INFO ] Loading adaptor saga.adaptors.context.ssh | |
| 2014:11:05 11: |
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