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ashkurti / gist:99cffb63f2b22bda0a8a
Created January 21, 2016 17:31
2016-01-21 14:23:37,444: radical.pilot : MainProcess : MainThread : INFO : python.interpreter version: 2.7.8 (default, Nov 6 2014, 13:37:40) [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)]
2016-01-21 14:23:37,444: radical.pilot : MainProcess : MainThread : INFO : pid: 1497721
2016-01-21 14:23:37,445: radical.pilot : MainProcess : MainThread : INFO : tid: MainThread
2016-01-21 14:23:37,445: radical.pilot : MainProcess : MainThread : INFO : radical.pilot version: 0.38
2016-01-21 14:23:38,478: radical.enmd.SingleClusterEnvironment: MainProcess : MainThread : INFO : python.interpreter version: 2.7.8 (default, Nov 6 2014, 13:37:40) [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)]
2016-01-21 14:23:38,478: radical.enmd.SingleClusterEnvironment: MainProcess : MainThread : INFO :
@ashkurti
ashkurti / gist:40dc628e211e9002f583
Created January 21, 2016 16:01
TITLE MDANALYSIS FRAMES FROM 0, SKIP 1: Created by PrimitivePDBWriter
REMARK Cpptraj Generated trajectory
CRYST1 68.936 68.936 68.936 109.47 109.47 109.47 P 1 1
MODEL 1
ATOM 1 CA ALA 1 38.039 8.843 48.075 1.00 0.00 SYST C 0
ATOM 2 CA PRO 2 34.569 9.609 49.713 1.00 0.00 SYST C 0
ATOM 3 CA ALA 3 31.716 8.041 47.782 1.00 0.00 SYST C 0
ATOM 4 CA ALA 4 29.441 11.168 47.839 1.00 0.00 SYST C 0
ATOM 5 CA VAL 5 30.675 14.714 47.472 1.00 0.00 SYST C 0
ATOM 6 CA ASP 6 28.434 17.799 46.785 1.00 0.00 SYST C 0
@ashkurti
ashkurti / gist:0ba635c8230ed8a82efa
Created January 21, 2016 15:21
2016-01-21 14:23:37,444: radical.pilot : MainProcess : MainThread : INFO : python.interpreter version: 2.7.8 (default, Nov 6 2014, 13:37:40) [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)]
2016-01-21 14:23:37,444: radical.pilot : MainProcess : MainThread : INFO : pid: 1497721
2016-01-21 14:23:37,445: radical.pilot : MainProcess : MainThread : INFO : tid: MainThread
2016-01-21 14:23:37,445: radical.pilot : MainProcess : MainThread : INFO : radical.pilot version: 0.38
2016-01-21 14:23:38,478: radical.enmd.SingleClusterEnvironment: MainProcess : MainThread : INFO : python.interpreter version: 2.7.8 (default, Nov 6 2014, 13:37:40) [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)]
2016-01-21 14:23:38,478: radical.enmd.SingleClusterEnvironment: MainProcess : MainThread : INFO :
@ashkurti
ashkurti / gist:0c09f3d245c917321707
Created January 21, 2016 13:37
[ExTASY-tools-21Jan16] ardita@moriarty 160% python extasy_amber_coco.py --RPconfig archer.rcfg --Kconfig cocoamber.wcfg
================================================================================
EnsembleMD (0.3.14)
================================================================================
Starting Allocation ok
Verifying pattern ok
Starting pattern execution ok
--------------------------------------------------------------------------------
@ashkurti
ashkurti / gist:30fae1a847a8ef05414d
Created January 21, 2016 11:24
[ExTASY-tools-21Jan16] ardita@moriarty 143% python extasy_amber_coco.py --RPconfig archer.rcfg --Kconfig cocoamber.wcfg
================================================================================
EnsembleMD (0.3.14)
================================================================================
Starting Allocation ok
Verifying pattern ok
Starting pattern execution ok
--------------------------------------------------------------------------------
@ashkurti
ashkurti / gist:1703148a679da045f48f
Created December 7, 2015 16:59
======================================================================
ERROR: test_coordinates (MDAnalysisTests.coordinates.test_dcd.TestNCDF2DCD)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysisTests-0.13.0_dev0-py2.7.egg/MDAnalysisTests/coordinates/test_dcd.py", line 373, in setUp
self.u = mda.Universe(PRMncdf, NCDF)
File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py", line 3801, in __init__
self.load_new(coordinatefile, **kwargs)
File "/users/ardita/MDAPCAvenv2/lib/python2.7/site-packages/MDAnalysis-0.13.0_dev0-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py", line 4341, in load_new
self.trajectory = reader(filename, **kwargs) # unified trajectory API
@ashkurti
ashkurti / gist:0be0b4946d0b4a34d653
Created December 7, 2015 12:12
fail to import MDAnalysis
Failure: ImportError (dynamic module does not define init function (init_distances)) ... ERROR
Failure: ImportError (cannot import name log) ... ERROR
Failure: ImportError (cannot import name log) ... ERROR
Failure: ImportError (cannot import name log) ... ERROR
Failure: ImportError (cannot import name log) ... ERROR
Failure: ImportError (cannot import name log) ... ERROR
Failure: ImportError (cannot import name log) ... ERROR
Failure: ImportError (cannot import name log) ... ERROR
Failure: ImportError (cannot import name log) ... ERROR
Failure: ImportError (cannot import name log) ... ERROR
@ashkurti
ashkurti / mda_tests3.log
Created December 3, 2015 11:14
Third MDAnalysis test with develop version including all commits up to December 3rd 2015, 10:30 am British time.
This file has been truncated, but you can view the full file.
test_box_numpy (MDAnalysisTests.analysis.test_distances.TestContactMatrix) ... ok
test_box_sparse (MDAnalysisTests.analysis.test_distances.TestContactMatrix) ... ok
test_np (MDAnalysisTests.analysis.test_distances.TestContactMatrix) ... ok
test_sparse (MDAnalysisTests.analysis.test_distances.TestContactMatrix) ... ok
MDAnalysis.analysis.align: test fasta2select() with calling ClustalW (Issue 113) ... SKIP: Skipping test: test_fasta2select_ClustalW: Test skipped because clustalw2 executable not found
test align.fasta2select() on aligned FASTA (Issue 112) ... ok
test_count_by_time (MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic) ... ok
test_count_by_type (MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic) ... ok
test_generate_table (MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic) ... ok
test_helix_backbone (MDAnalysisTests.analysis.test_hbonds.TestHydrogenBondAnalysisHeuristic) ... ok
@ashkurti
ashkurti / mda_tests.log
Created December 3, 2015 11:02
MDAnalysis test with develop version including all commits up to December 3rd 2015, 10:30 am British time.
======================================================================
ERROR: Check that get_parser returns the intended parser
----------------------------------------------------------------------
Traceback (most recent call last):
File "/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/nose/plugins/multiprocess.py", line 812, in run
test(orig)
File "/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/nose/case.py", line 45, in __call__
return self.run(*arg, **kwarg)
File "/users/ardita/MDAPCAvenv/lib/python2.7/site-packages/nose/case.py", line 133, in run
self.runTest(result)
@ashkurti
ashkurti / gist:faa44cd8647d5dc691f7
Created October 21, 2015 14:43
================================================================================
EnsembleMD (0.3.6)
================================================================================
Starting Allocation ok
Verifying pattern ok
Starting pattern execution ok
--------------------------------------------------------------------------------
Executing simulation-analysis loop with 2 iterations on 16 allocated core(s) on 'xsede.stampede'