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radical-collaboration / extasy-grlsd

Repository to hold the input data and scripts for the ExTASY gromacs-lsdmap work
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memory option entk #107

Closed euhruska closed 5 years ago

euhruska commented 6 years ago

running out of memory on xk nodes, is there a entk option which allows me to request more memory?

re.session.leonardo.rice.edu.eh22.017852.0000/pilot.0000> vi unit.000403/STDERR
 files = md.load(traj_select[idx], top=args.path+'/iter0_input0.pdb')
  File "/mnt/b/projects/sciteam/bamm/hruska/vpy8/lib/python3.5/site-packages/mdtraj/core/trajectory.py", line 430, in load
    value = loader(filename, **kwargs)
  File "mdtraj/formats/dcd/dcd.pyx", line 134, in mdtraj.formats.dcd.load_dcd
  File "mdtraj/formats/dcd/dcd.pyx", line 140, in mdtraj.formats.dcd.load_dcd
  File "mdtraj/formats/dcd/dcd.pyx", line 382, in mdtraj.formats.dcd.DCDTrajectoryFile.read_as_traj
  File "mdtraj/formats/dcd/dcd.pyx", line 460, in mdtraj.formats.dcd.DCDTrajectoryFile.read
MemoryError