[gmx-users] -append on jugene overwrites trr

[Mark Abraham]

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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