Gromacs backups

[Ardita Shkurti]

While trying out the gromacs example with wrappers the following occurs:

(coco_env) [xxx@scarf gromacs]$ python ala12_coco.py 
setting up...
Starting grompp runs...
Starting MD jobs 1...
Starting grompp runs...
Starting MD jobs 2...
Starting grompp runs...
Starting MD jobs 3...
Cycle 0: running CoCo...
Starting grompp runs...
Starting MD jobs 1...
Starting grompp runs...
Starting MD jobs 2...
Starting grompp runs...
Starting MD jobs 3...
Cycle 1: running CoCo...
Starting grompp runs...
Starting MD jobs 1...
Starting grompp runs...
Starting MD jobs 2...
Starting grompp runs...
Starting MD jobs 3...
Cycle 2: running CoCo...
Starting grompp runs...
Starting MD jobs 1...
Starting grompp runs...
Starting MD jobs 2...
Starting grompp runs...
Starting MD jobs 3...
Cycle 3: running CoCo...
Starting grompp runs...
GROMACS:    gmx grompp, VERSION 5.0.5

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Emile Apol         Rossen Apostolov   Herman J.C. Berendsen Par Bjelkmar       
Aldert van Buuren  Rudi van Drunen    Anton Feenstra     Sebastian Fritsch  
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Per Larsson        Justin A. Lemkul   Magnus Lundborg    Pieter Meulenhoff  
Erik Marklund      Teemu Murtola      Szilard Pall       Sander Pronk       
Roland Schulz      Alexey Shvetsov    Michael Shirts     Alfons Sijbers     
Peter Tieleman     Christian Wennberg Maarten Wolf       
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

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Copyright (c) 2001-2014, The GROMACS development team at
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check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
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GROMACS:      gmx grompp, VERSION 5.0.5
Executable:   /apps/gromacs/5.0.5/bin/gmx
Library dir:  /apps/gromacs/5.0.5/share/gromacs/top
Command line:
  gmx grompp -f grompp-em1.mdp -c helix.gro -o /home/cseg/scarf580/wrappers/copy_examples/CoCo-MD/gromacs/cocofiles/tmpb_OEH2.tpr -p topol.top -r /home/cseg/scarf580/wrappers/copy_examples/CoCo-MD/gromacs/cocofiles/tmpR49NQ43.gro


-------------------------------------------------------
Program gmx, VERSION 5.0.5
Source code file: /apps/src/gromacs/gromacs-5.0.5/src/gromacs/fileio/futil.cpp, line: 415

Fatal error:
Won't make more than 99 backups of mdout.mdp for you.
The env.var. GMX_MAXBACKUP controls this maximum, -1 disables backups.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------


Traceback (most recent call last):
  File "ala12_coco.py", line 65, in <module>
    gouts = b.compute()
  File "/home/cseg/scarf580/miniconda2/envs/coco_env/lib/python2.7/site-packages/dask/base.py", line 96, in compute
    (result,) = compute(self, traverse=False, **kwargs)
  File "/home/cseg/scarf580/miniconda2/envs/coco_env/lib/python2.7/site-packages/dask/base.py", line 203, in compute
    results = get(dsk, keys, **kwargs)
  File "/home/cseg/scarf580/miniconda2/envs/coco_env/lib/python2.7/site-packages/dask/multiprocessing.py", line 87, in get
    dumps=dumps, loads=loads, **kwargs)
  File "/home/cseg/scarf580/miniconda2/envs/coco_env/lib/python2.7/site-packages/dask/async.py", line 525, in get_async
    raise(remote_exception(res, tb))
dask.async.RuntimeError: Error running gmx grompp job,

Traceback
---------
  File "/home/cseg/scarf580/miniconda2/envs/coco_env/lib/python2.7/site-packages/dask/async.py", line 291, in execute_task
    result = _execute_task(task, data)
  File "/home/cseg/scarf580/miniconda2/envs/coco_env/lib/python2.7/site-packages/dask/async.py", line 272, in _execute_task
    return func(*args2)
  File "/home/cseg/scarf580/miniconda2/envs/coco_env/lib/python2.7/site-packages/dask/bag/core.py", line 1369, in reify
    seq = list(seq)
  File "/home/cseg/scarf580/.local/lib/python2.7/site-packages/extasy.wrappers-0.0.1-py2.7.egg/wrappers/grompp.py", line 76, in run
    raise RuntimeError('Error running {} job,'.format(inputs[0]))

[Charlie Laughton]

This can be fixed by preventing Gromacs from creating backups. Before running Gromacs, set the environment variable GMX_MAXBACKUP to -1 to do this.

[Ardita Shkurti]

Thanks Charlie for the suggestion, this is exactly what I was looking for in order not to have to modify the workflow.

[Ardita Shkurti]

At the end by setting GMX_MAXBACKUP to -1, everything runs fine, until the first cycle is complete! Then, a failure occurs, with the following message: "Cannot rename checkpoint file; maybe you are out of disk space?" - although there have been no issues with the disk space. So, I have been setting GMX_MAXBACKUP to a very large number, so as to account for all backups of all cycles and not to fail after doing 99 backups (that is the default). In this way, the issue I was having has no longer been verified.

[zbenta]

Ardita, did it solve your problem? I’m facing the same issue, I’ve checked the available disk space and it is more than enough for the simulation.

[Ardita Shkurti]

Yes, I remember it solved my problem at the time. Despite having enough disk space just set the GMX_MAXBACKUP parameter to a very large number. It depends on your simulation and number of cycles but if you are sure you have enough disk space for everything then just set it to a very very high value (eg. 1000000). Hope this helps.

[zbenta]

Thanks @Ardita Shkurti , I’ve added the parameter -cpt -1 on the batch and the environment variable GMX_MAXBACKUP to -1 as you’ve sugested on a previous post and it worked.