[gmx-users] -append on jugene overwrites trr

Dr. Leonid Yelash yelash at uni-mainz.de
Wed Jul 29 15:42:30 CEST 2009

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.
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

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!

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