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ashkurti/gist:1d900a91fdcc9b702165

Created October 6, 2014 10:07
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Gromacs /Lsdmap on Stampede fails - Linux/Stampede platform - ACTIVE DEBUG
Raw
gistfile1.txt
...
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 dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start41.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out41.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out41.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/start42.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start42.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out42.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out42.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/start43.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start43.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out43.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out43.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/start44.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start44.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out44.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out44.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/start45.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start45.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out45.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out45.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/start46.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start46.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out46.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out46.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/start47.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start47.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out47.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out47.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/start48.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start48.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out48.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out48.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/start49.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start49.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out49.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out49.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/start50.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start50.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out50.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out50.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/start51.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start51.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out51.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out51.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/start52.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start52.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out52.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out52.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/start53.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start53.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out53.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out53.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/start54.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start54.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:28 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 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 > out54.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out54.gro', 'priority': 0}'
2014:10:06 11:05:29 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 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start55.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start55.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out55.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out55.gro', 'priority': 0}'
2014:10:06 11:05:29 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 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start56.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start56.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out56.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out56.gro', 'priority': 0}'
2014:10:06 11:05:29 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 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start57.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start57.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out57.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out57.gro', 'priority': 0}'
2014:10:06 11:05:29 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 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start58.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start58.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out58.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out58.gro', 'priority': 0}'
2014:10:06 11:05:29 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 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start59.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start59.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out59.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out59.gro', 'priority': 0}'
2014:10:06 11:05:29 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 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start60.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start60.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out60.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out60.gro', 'priority': 0}'
2014:10:06 11:05:29 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 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start61.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start61.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out61.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out61.gro', 'priority': 0}'
2014:10:06 11:05:29 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 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start62.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start62.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out62.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out62.gro', 'priority': 0}'
2014:10:06 11:05:29 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 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '/users/ardita/grlsd-on-stampede/temp/start63.gro > start.gro' into dict '{'action': 'Transfer', 'source': '/users/ardita/grlsd-on-stampede/temp/start63.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'start.gro', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './grompp.mdp' into dict '{'action': 'Transfer', 'source': './grompp.mdp', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'grompp.mdp', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string './topol.top' into dict '{'action': 'Transfer', 'source': './topol.top', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'topol.top', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string '' into dict '{'action': 'Transfer', 'source': '', 'flags': ['CreateParents', 'SkipFailed'], 'target': '', 'priority': 0}'
2014:10:06 11:05:29 radical.pilot.MainProcess: [DEBUG ] Converting string 'out.gro > out63.gro' into dict '{'action': 'Transfer', 'source': 'out.gro', 'flags': ['CreateParents', 'SkipFailed'], 'target': 'out63.gro', 'priority': 0}'
2014:10:06 11:05:30 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc27' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc27' state changed to PendingInputStaging.
2014:10:06 11:05:30 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc54' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc54' state changed to PendingInputStaging.
2014:10:06 11:05:30 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc3c' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc3c' state changed to PendingInputStaging.
2014:10:06 11:05:30 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc55' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc55' state changed to PendingInputStaging.
2014:10:06 11:05:30 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc40' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc40' state changed to PendingInputStaging.
2014:10:06 11:05:30 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc3a' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc3a' state changed to PendingInputStaging.
2014:10:06 11:05:30 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc56' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc56' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc3b' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc3b' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc51' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc51' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc2d' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc2d' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc2e' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc2e' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc21' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc21' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc38' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc38' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc29' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc29' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc3d' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc3d' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc42' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc42' state changed to PendingInputStaging.
2014:10:06 11:05:31 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc52' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc52' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc2b' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc2b' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc17' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc17' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc3f' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc3f' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc31' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc31' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc4d' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc4d' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc2c' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc2c' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc33' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc33' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc53' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc53' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc43' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc43' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc19' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc19' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc34' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc34' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc4f' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc4f' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc45' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc45' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc1a' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc1a' state changed to PendingInputStaging.
2014:10:06 11:05:32 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc4a' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc4a' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc1b' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc1b' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc2f' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc2f' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc30' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc30' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc46' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc46' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc47' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc47' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc32' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc32' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc1e' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc1e' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc48' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc48' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc37' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc37' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc25' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc25' state changed to PendingInputStaging.
2014:10:06 11:05:33 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc2a' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc2a' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc39' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc39' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc35' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc35' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc49' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc49' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc1f' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc1f' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc4c' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc4c' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc36' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc36' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc4b' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc4b' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc18' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc18' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc41' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc41' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc20' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc20' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc1c' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc1c' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc44' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc44' state changed to PendingInputStaging.
2014:10:06 11:05:34 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc28' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc28' state changed to PendingInputStaging.
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc26' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc26' state changed to PendingInputStaging.
2014:10:06 11:05:35 radical.pilot.MainProcess: [DEBUG ] Copying bootstrapper 'file://localhost//users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/bootstrapper/default_bootstrapper.sh' to agent sandbox (sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15/).
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc22' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc22' state changed to PendingInputStaging.
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc23' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc23' state changed to PendingInputStaging.
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc4e' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc4e' state changed to PendingInputStaging.
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc24' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc24' state changed to PendingInputStaging.
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc3e' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc3e' state changed to PendingInputStaging.
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc1d' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc1d' state changed to PendingInputStaging.
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc50' state changed from 'New' to 'PendingInputStaging'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc50' state changed to PendingInputStaging.
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] Creating ComputeUnit sandbox directory sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15//unit-5432696854737d58ea7cdc27.
2014:10:06 11:05:35 radical.pilot.MainProcess: [DEBUG ] saga.fs.Directory ('sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15//unit-5432696854737d58ea7cdc27')
2014:10:06 11:05:35 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696854737d58ea7cdc27' state changed from 'PendingInputStaging' to 'StagingInput'.
[Callback]: ComputeUnit '5432696854737d58ea7cdc27' state changed to StagingInput.
2014:10:06 11:05:36 radical.pilot.MainProcess: [INFO ] Creating ComputeUnit sandbox directory sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15//unit-5432696954737d58ea7cdc54.
2014:10:06 11:05:36 radical.pilot.MainProcess: [DEBUG ] saga.fs.Directory ('sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15//unit-5432696954737d58ea7cdc54')
2014:10:06 11:05:36 radical.pilot.MainProcess: [INFO ] RUN ComputeUnit '5432696954737d58ea7cdc54' state changed from 'PendingInputStaging' to 'StagingInput'.
[Callback]: ComputeUnit '5432696954737d58ea7cdc54' state changed to StagingInput.
2014:10:06 11:05:39 radical.pilot.MainProcess: [INFO ] Processing input file transfers for ComputeUnit 5432696954737d58ea7cdc54
2014:10:06 11:05:39 radical.pilot.MainProcess: [DEBUG ] Transferring input file file://localhost//users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh -> sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15//unit-5432696954737d58ea7cdc54/run.sh
2014:10:06 11:05:39 radical.pilot.MainProcess: [DEBUG ] saga.fs.File ('file://localhost//users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh')
2014:10:06 11:05:39 radical.pilot.MainProcess: [INFO ] Processing input file transfers for ComputeUnit 5432696854737d58ea7cdc27
2014:10:06 11:05:40 radical.pilot.MainProcess: [DEBUG ] Transferring input file file://localhost//users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh -> sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15//unit-5432696854737d58ea7cdc27/run.sh
2014:10:06 11:05:40 radical.pilot.MainProcess: [DEBUG ] saga.fs.File ('file://localhost//users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/run.sh')
2014:10:06 11:05:41 radical.pilot.MainProcess: [INFO ] Scheduled ComputeUnits [] for execution on ComputePilot '5432696554737d58ea7cdc15'.
2014:10:06 11:05:41 radical.pilot.MainProcess: [INFO ] 0 units remain unscheduled
2014:10:06 11:05:43 radical.pilot.MainProcess: [DEBUG ] Copying agent 'file://localhost//users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/agent/radical-pilot-agent-multicore.py' to agent sandbox (sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15/).
2014:10:06 11:05:44 radical.pilot.MainProcess: [DEBUG ] Transferring input file file://localhost//users/ardita/grlsd-on-stampede/temp/start16.gro -> sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15//unit-5432696854737d58ea7cdc27/start.gro
2014:10:06 11:05:44 radical.pilot.MainProcess: [DEBUG ] saga.fs.File ('file://localhost//users/ardita/grlsd-on-stampede/temp/start16.gro')
2014:10:06 11:05:46 radical.pilot.MainProcess: [DEBUG ] saga.job.Service ('slurm+ssh://stampede.tacc.utexas.edu')
2014:10:06 11:05:46 radical.pilot.MainProcess: [INFO ] Error: Insufficient system resources: Insufficient system resources: read from process failed '[Errno 5] Input/output error' : (Shared connection to stampede.tacc.utexas.edu closed.
) ((Shared connection to stampede.tacc.utexas.edu closed.
)) (/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_exceptions.py +59 (translate_exception) : e = se.NoSuccess ("Insufficient system resources: %s" % cmsg)). Traceback (most recent call last):
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/controller/input_file_transfer_worker.py", line 149, in run
input_file.copy(target)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/namespace/entry.py", line 276, in copy
ret = self._adaptor.copy_self (tgt_url, flags, ttype=ttype)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/adaptors/cpi/decorators.py", line 51, in wrap_function
return sync_function (self, *args, **kwargs)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/adaptors/shell/shell_file.py", line 1151, in copy_self
with self.lm.lease (lease_tgt, self.shell_creator, tgt) \
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/utils/lease_manager.py", line 206, in lease
obj = self._create_object (pool_id, creator, args)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/utils/lease_manager.py", line 146, in _create_object
obj = _LeaseObject (self, creator, args)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/utils/lease_manager.py", line 27, in __init__
self.obj = creator (*args)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/adaptors/shell/shell_file.py", line 965, in _shell_creator
return sups.PTYShell (url, self.session, self._logger)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_shell.py", line 228, in __init__
self.pty_shell = self.factory.run_shell (self.pty_info)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_shell_factory.py", line 418, in run_shell
self._initialize_pty (sh_slave, info, is_shell=True)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_shell_factory.py", line 384, in _initialize_pty
raise ptye.translate_exception (e)
NoSuccess: Insufficient system resources: Insufficient system resources: read from process failed '[Errno 5] Input/output error' : (Shared connection to stampede.tacc.utexas.edu closed.
) ((Shared connection to stampede.tacc.utexas.edu closed.
)) (/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_exceptions.py +59 (translate_exception) : e = se.NoSuccess ("Insufficient system resources: %s" % cmsg))
2014:10:06 11:05:46 radical.pilot.MainProcess: [DEBUG ] Transferring input file file://localhost//users/ardita/grlsd-on-stampede/grompp.mdp -> sftp://stampede.tacc.utexas.edu/work/02998/ardi/pilot-5432696554737d58ea7cdc15//unit-5432696854737d58ea7cdc27/grompp.mdp
2014:10:06 11:05:46 radical.pilot.MainProcess: [DEBUG ] saga.fs.File ('file://localhost//users/ardita/grlsd-on-stampede/grompp.mdp')
2014:10:06 11:05:46 radical.pilot.MainProcess: [ERROR ] Pilot launching failed: Insufficient system resources: Insufficient system resources: read from process failed '[Errno 5] Input/output error' : (Shared connection to stampede.tacc.utexas.edu closed.
) ((Shared connection to stampede.tacc.utexas.edu closed.
)) (/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_exceptions.py +59 (translate_exception) : e = se.NoSuccess ("Insufficient system resources: %s" % cmsg))
Traceback (most recent call last):
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/controller/pilot_launcher_worker.py", line 372, in run
js = saga.job.Service(job_service_url, session=self._session)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/job/service.py", line 115, in __init__
url, session, ttype=_ttype)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/base.py", line 99, in __init__
self._init_task = self._adaptor.init_instance (adaptor_state, *args, **kwargs)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/adaptors/cpi/decorators.py", line 51, in wrap_function
return sync_function (self, *args, **kwargs)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/adaptors/slurm/slurm_job.py", line 287, in init_instance
self._open ()
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/adaptors/slurm/slurm_job.py", line 358, in _open
self._logger)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_shell.py", line 228, in __init__
self.pty_shell = self.factory.run_shell (self.pty_info)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_shell_factory.py", line 418, in run_shell
self._initialize_pty (sh_slave, info, is_shell=True)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_shell_factory.py", line 384, in _initialize_pty
raise ptye.translate_exception (e)
NoSuccess: Insufficient system resources: Insufficient system resources: read from process failed '[Errno 5] Input/output error' : (Shared connection to stampede.tacc.utexas.edu closed.
) ((Shared connection to stampede.tacc.utexas.edu closed.
)) (/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/saga/utils/pty_exceptions.py +59 (translate_exception) : e = se.NoSuccess ("Insufficient system resources: %s" % cmsg))
2014:10:06 11:05:46 radical.pilot.MainProcess: [INFO ] ComputePilot '5432696554737d58ea7cdc15' state changed from 'Launching' to 'Failed'.
[Callback]: ComputePilot '5432696554737d58ea7cdc15' state changed to Failed.
pilot manager controller thread caught system exit -- forcing application shutdown
Traceback (most recent call last):
File "/users/ardita/ExTASY-toolsOct2/bin/extasy", line 9, in <module>
load_entry_point('radical.ensemblemd.extasy==0.1', 'console_scripts', 'extasy')()
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/extasy/bin/runme.py", line 130, in main
Simulator(umgr,RPconfig,Kconfig,i)
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/ensemblemd/extasy/bin/Simulator/Gromacs/simulator.py", line 56, in Simulator
umgr.wait_units()
File "/users/ardita/ExTASY-toolsOct2/lib/python2.6/site-packages/radical/pilot/unit_manager.py", line 669, in wait_units
time.sleep (0.1)
KeyboardInterrupt
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