[gmx-users] Re: : Extending run append

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 20 11:36:29 CEST 2012

On 20/04/2012 7:21 PM, lloyd riggs wrote:
> Dear Dr. Abrahams,
> I tried to re-create the issue per another e-mail and someone has since fixed the problem as it gives no errors now?  I wish I could say what the problem was, but as I dint fix it I have no clue.
> The origional command was:
>   qsub -M stephan.watkins at insel.ch -cwd -V -l h_cpu=200:00:00 -l h_vmem=6G -pe mpi 24 -r yes -R yes -b yes mpirun mdrun_mpi_d -s $HOME/21a_20/traj_7/traj_7.tpr -cpi state_prev.cpt -append -compact
> And the error message: (trying from memory)
> 5 of seven files not found
> --When I looked at the log, it looked for the varied files such as energy.edr, .xtc , .trr but could not find them.

As I suggested last time, the simplest explanation is that you (or your 
system admins) have not correctly managed to allow the execution host to 
see the files you need it to see. In the absence of fully-qualified 
filenames, GROMACS can only look in the working directory in which it is 
finally run (which need not be the same as the directory from which you 
ran qsub, and may or may not be affected by arguments to qsub). Using a 
fully-qualified -s filename and allowing other filenames to be found in 
the working directory is a recipe for exactly the problem you observe.

Notice how giving the command line you used allows someone to suggest 
what is wrong. Speculating that it is a compile-time problem does not.


> Thats about it.
> Gutten Tag,
> Stephan Watkins
> -------- Original-Nachricht --------
>> Datum: Fri, 20 Apr 2012 12:44:13 +1000
>> Von: Mark Abraham<Mark.Abraham at anu.edu.au>
>> An: Discussion list for GROMACS users<gmx-users at gromacs.org>
>> Betreff: Re: [gmx-users] Re: : Extending run append
>> On 20/04/2012 1:45 AM, lloyd riggs wrote:
>>> Dear All,
>>> Another error here with Gromacs
>>> The append from continuing runs does not work.  It complains that
>> several files are missing.  When I try to give it the files in the working DIR or
>> direct paths, it still gives the same complaint.
>>> I woundered if such a thing could also be a compilation time error, or
>> something else.
>> Not likely. User error or file system issue are the most likely
>> explanations, but we have nowhere near enough information to help.
>> Mark
>> -- 
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