DMDMD gromacs workflow fails with the extasy wrappers
Issue #3
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I launched the python rundmd.py command from wrappers/examples/DMDMD/dmdmd_gromacs and it has been running from at least 2 and a half hours. Could @claughton @cclementi @ehruska or any others familiar with lsdmap performance have a look at this please.
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The lsdmap instances have been running for 4 hours now, so I have killed their related PIDs. Any suggestions?
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@claughton how long does this workflow take for you?
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On tirith I can run this job in about six minutes, so clearly something is going wrong for you. Does it hang the first time it runs LSDMap, or at a later cycle? For reference, this is the output you should see on the screen:
charlie@tirith 211% python rundmd.py Starting grompp runs... Starting MD jobs... Running LSDMap... Running selection... Running reweighting... Starting grompp runs... Starting MD jobs... Running LSDMap... Running selection... Running reweighting... Starting grompp runs... Starting MD jobs... Running LSDMap... Running selection... Running reweighting... Starting grompp runs... Starting MD jobs... Running LSDMap... Running selection... Running reweighting... Starting grompp runs... Starting MD jobs... Running LSDMap... Running selection... Running reweighting... charlie@tirith 212% -
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Ok, I did a fresh pull today and rerun the workflow, but now I have an error:
ardita@moriarty 136% python rundmd.py Starting grompp runs... Starting MD jobs... Running LSDMap... /users/ardita/.local/lib/python2.7/site-packages/dask/array/numpy_compat.py:29: DeprecationWarning: Implicitly casting between incompatible kinds. In a future numpy release, this will raise an error. Use casting="unsafe" if this is intentional. or not np.allclose(np.divide(1, .5, dtype='i8'), 2) /users/ardita/.local/lib/python2.7/site-packages/dask/array/numpy_compat.py:29: DeprecationWarning: Implicitly casting between incompatible kinds. In a future numpy release, this will raise an error. Use casting="unsafe" if this is intentional. or not np.allclose(np.divide(1, .5, dtype='i8'), 2) Traceback (most recent call last): File "/users/ardita/.local/bin/lsdmap", line 5, in <module> lsdm.LSDMap().run() File "/users/ardita/.local/lib/python2.7/site-packages/lsdmap/lsdm.py", line 408, in run self.initialize(comm, config, args) Traceback (most recent call last): File "/users/ardita/.local/bin/lsdmap", line 5, in <module> File "/users/ardita/.local/lib/python2.7/site-packages/lsdmap/lsdm.py", line 36, in initialize lsdm.LSDMap().run() c = x2h.Cofasu(f) File "/users/ardita/.local/lib/python2.7/site-packages/lsdmap/lsdm.py", line 408, in run File "/users/ardita/.local/lib/python2.7/site-packages/lsdmap/rw/x2h.py", line 166, in __init__ self.initialize(comm, config, args) File "/users/ardita/.local/lib/python2.7/site-packages/lsdmap/lsdm.py", line 36, in initialize c = x2h.Cofasu(f) File "/users/ardita/.local/lib/python2.7/site-packages/lsdmap/rw/x2h.py", line 166, in __init__ b = db.from_sequence([f._process(hdfdir=hdfdir) for f in fasulist]) b = db.from_sequence([f._process(hdfdir=hdfdir) for f in fasulist]) File "/users/ardita/.local/lib/python2.7/site-packages/lsdmap/rw/x2h.py", line 105, in _process File "/users/ardita/.local/lib/python2.7/site-packages/lsdmap/rw/x2h.py", line 105, in _process u = mdt.load(self.trajectory, atom_indices=sel) u = mdt.load(self.trajectory, atom_indices=sel) File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/core/trajectory.py", line 331, in load File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/core/trajectory.py", line 331, in load t = [load(f, **kwargs) for f in filename_or_filenames] t = [load(f, **kwargs) for f in filename_or_filenames] File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/core/trajectory.py", line 362, in load File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/core/trajectory.py", line 362, in load value = loader(filename, **kwargs) value = loader(filename, **kwargs) File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/formats/gro.py", line 101, in load_gro File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/formats/gro.py", line 101, in load_gro traj = Trajectory(xyz=coordinates, topology=topology, time=time) traj = Trajectory(xyz=coordinates, topology=topology, time=time) File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/core/trajectory.py", line 1062, in __init__ File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/core/trajectory.py", line 1062, in __init__ self.xyz = xyz self.xyz = xyz File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/core/trajectory.py", line 811, in xyz File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/core/trajectory.py", line 811, in xyz warn_on_cast=False, add_newaxis_on_deficient_ndim=True) warn_on_cast=False, add_newaxis_on_deficient_ndim=True) File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/utils/validation.py", line 148, in ensure_type File "/users/ardita/.local/lib/python2.7/site-packages/mdtraj/utils/validation.py", line 148, in ensure_type raise error ValueError: xyz must be shape (Any, 132, 3). You supplied (1, 65, 3) raise error ValueError: xyz must be shape (Any, 132, 3). You supplied (1, 65, 3) Traceback (most recent call last): File "rundmd.py", line 57, in <module> lout = lsdmap.run(linp) File "/users/ardita/.local/lib/python2.7/site-packages/extasy.wrappers-0.0.1-py2.7.egg/wrappers/lsdmap.py", line 62, in run raise RuntimeError('LSDMap job failed.') RuntimeError: LSDMap job failed. -
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- changed title to DMDMD gromacs workflow fails with the extasy wrappers
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Hi Ardita, I have just pulled the very latest versions of a) the mdt branch of pyPcazip, b) the devel branch of pyCoCo, and c) the master branch of wrappers, and for me the job works fine. One thing just to check - did you: setenv GMX_MAXBACKUP -1
as otherwise your directory fills up with gromacs backup files, and then an error can be generated.
Please could you try again and see if you still get the same problem?
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