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2_input.gro is not a multiple of natoms+3 #114

Closed oleweidner closed 9 years ago

oleweidner commented 9 years ago

Jenkins tests fail for GROMACS/LSDMap on stampede. The full log is here:

http://ci.radical-project.org/job/ExTASY/EXTASY_HOST=stampede,EXTASY_WORKFLOW=gromacslsdmap,PYTHON=System-CPython-2.7/22/consoleFull

The failing compute unit prints the following to STDERR:

Traceback (most recent call last):
  File "spliter.py", line 15, in <module>
    grofile_obj = gro.GroFile(os.path.dirname(os.path.realpath(__file__)) + '/' + grofile_name)
  File "/work/00988/tg802352/radical.pilot.sandbox/pilot-547f38e1cec86a162b43ece8/unit-547f3e77cec86a162b43ed10/gro.py", line 14, in __init__
    self.nruns=self.get_nruns()
  File "/work/00988/tg802352/radical.pilot.sandbox/pilot-547f38e1cec86a162b43ece8/unit-547f3e77cec86a162b43ed10/gro.py", line 29, in get_nruns
    assert self.nlines%(self.nlines_per_run)==0, "number of lines in %s is not a multiple of natoms+3" %self.filename
AssertionError: number of lines in /work/00988/tg802352/radical.pilot.sandbox/pilot-547f38e1cec86a162b43ece8/unit-547f3e77cec86a162b43ed10/2_input.gro is not a multiple of natoms+3
vivek-bala commented 9 years ago

Same as #113

oleweidner commented 9 years ago

@vivek-bala: you said that there's a fix for that in master. Why can't this be applied to devel as well for the Extasy 0.1 release?

vivek-bala commented 9 years ago

added a temporary fix for this. Needs to be revisited.

oleweidner commented 9 years ago

Opened a separate ticket #122

marksantcroos commented 9 years ago

Hi Vivek, What was (roughly) the size of this 1_input.gro file? (Trying to reproduce this ...) Thanks!

vivek-bala commented 9 years ago

About 1-2 Mbytes in size .. for the example in the documentation (https://raw.githubusercontent.com/radical-cybertools/ExTASY/devel/gromacs_lsdmap_example/input.gro)

marksantcroos commented 9 years ago

Thanks.

I had tested with 1 MB files also for what it matters.

On 22 Dec 2014, at 17:59 , Vivekanandan (Vivek) Balasubramanian notifications@github.com wrote:

About 1-2 Mbytes in size .. for the example in the documentation (https://raw.githubusercontent.com/radical-cybertools/ExTASY/devel/gromacs_lsdmap_example/input.gro)

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