[gmx-users] -append on jugene overwrites trr

[Berk Hess]

Hi,

I don't know if you know eneconv and trjcat, these programs can merge your output.
So you can still do all your analysis.

Berk

> Date: Wed, 29 Jul 2009 23:48:36 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] -append on jugene overwrites trr
> 
> Dr. Leonid Yelash wrote:
> > Hello all together,
> > 
> > in my compilation of Gromacs 4.0.5 on JUGENE (a Blue
> > Gene/P machine in Jülich), the -append option does not
> > work properly.
> 
> Possibly that's intrinsic to the way I/O is handled on BlueGene. It 
> should be simple to create a test program that tries to append to an 
> existing file.
> 
> Mark
> 
> > When i restart a simulation from a checkpoint, the mdrun
> > recognizes the checkpoint and -append (one can see it in
> > md.log), but instead of appending to md.log, traj.trr, ener.edr,
> > it overwrites them. The file offsets in state.cpt (printed
> > by gmxdump -cp) are shown here:
> > 
> >> number of output files = 3
> >> output filename = md.log
> >> file_offset_high = 0
> >> file_offset_low = 21265
> >> output filename = traj.trr
> >> file_offset_high = 0
> >> file_offset_low = 9021240
> >> output filename = ener.edr
> >> file_offset_high = 0
> >> file_offset_low = 5872
> > 
> > The same distribution compiled for JUMP (a Power6 machine
> > running under AIX) works correctly. Details to the machines
> > can be found here
> > http://www.fz-juelich.de/jsc/service/sco_ibmBGP
> > http://www.fz-juelich.de/jsc/service/sco_ibmP6
> > 
> > Does anybody know how to solve/work around? At the
> > moment i have to store continuations of a simulation run into
> > different directories, which complicates analysing data, e.g.
> > the calculation of time-dependent properties for the whole run.
> > 
> > Many thanks in advance for any hints!
> > Leonid
> > 
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