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msmbuilder / msmbuilder-legacy

Legacy release of MSMBuilder
http://msmbuilder.org
GNU General Public License v2.0
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CalculateImpliedTimescales check input lagtimes #358

Closed mpharrigan closed 10 years ago

mpharrigan commented 10 years ago

If the range of lagtimes includes zero, it gives a cryptic AssertionError from threads.pool

We should check for valid input

lilipeng commented 10 years ago

Command: CalculateImpliedTimescales.py -l 0,50 -a OuterProductAssignments.h5 -o ImpliedTimescales_2.dat

Error: IS Haque, KA Beauchamp, VS Pande. In preparation. A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD.

{'assignments': 'OuterProductAssignments.h5', 'eigvals': 10, 'interval': 1, 'lagtime': '0,50', 'notrim': False, 'output': 'ImpliedTimescales_2.dat', 'procs': 1, 'quiet': False, 'symmetrize': 'MLE'} 19:24:07 - Getting 10 eigenvalues (timescales) for each lagtime... 19:24:07 - Building MSMs at the following lag times: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] 19:24:07 - Calculating implied timescales at lagtime 0 19:24:07 - Calculating implied timescales at lagtime 13 Traceback (most recent call last): File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/bin/CalculateImpliedTimescales.py", line 5, in pkg_resources.run_script('msmbuilder==2.8', 'CalculateImpliedTimescales.py') File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/lib/python2.7/site-packages/pkg_resources.py", line 499, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/lib/python2.7/site-packages/pkg_resources.py", line 1239, in run_script execfile(script_filename, namespace, namespace) File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/lib/python2.7/site-packages/msmbuilder-2.8-py2.7-linux-x86_64.egg/EGG-INFO/scripts/CalculateImpliedTimescales.py", line 83, in (not args.notrim), args.symmetrize, args.procs) File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/lib/python2.7/site-packages/msmbuilder-2.8-py2.7-linux-x86_64.egg/EGG-INFO/scripts/CalculateImpliedTimescales.py", line 65, in run trimming=trimming, symmetrize=symmetrize, n_procs=nProc) File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/lib/python2.7/site-packages/msmbuilder-2.8-py2.7-linux-x86_64.egg/msmbuilder/msm_analysis.py", line 185, in get_implied_timescales lags = result.get(999999) File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/lib/python2.7/multiprocessing/pool.py", line 528, in get raise self._value AssertionError

rmcgibbo commented 10 years ago

Merged the fix.