[gmx-users] trjcat error

Mark Abraham Mark.Abraham at anu.edu.au
Fri Dec 18 10:46:43 CET 2009


Anirban Ghosh wrote:
> Thanks Mark for the reply.
> The simulation ran fine and at the end of the .log file I got the 
> following line:
> 
> ---------------------------------------------------------------------------------------------------------------------------------
>         Parallel run - timing based on wallclock.
> 
>                NODE (s)   Real (s)      (%)
>        Time: 125029.000 125029.000    100.0
>                        1d10h43:49
>                (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
> Performance:    932.867     46.259      3.729      6.436
> Finished mdrun on node 0 Fri Dec 11 22:58:06 2009
> ----------------------------------------------------------------------------------------------------------------------------------
> 
> There was no error and I did not ran out of disk space. What should I do 
> now? Can I repair this .trr file anyway?
> Any suggestion is welcome.

Well if you haven't broken the file since (check its size), it was not 
written properly during the calculation. This sort of thing can happen 
with remote-mounted disks, etc. if the underlying filesystem is not solid.

Mark

> On Fri, Dec 18, 2009 at 2:02 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     Anirban Ghosh wrote:
> 
>         Thanx Tsjerk for the reply.
>         I checked the .trr files with gmxcheck and one of the .trr files
>         is giving the error:
> 
>         ---------------------------------------------------------------------------------------------------------------------------
>         Checking file PRO_DAH_10_NS.part0004.trr
>         trn version: GMX_trn_file (single precision)
>         Reading frame       0 time 10000.000  # Atoms  135496
>         Reading frame    1400 time 12800.001
>          -------------------------------------------------------
>         Program gmxcheck, VERSION 4.0.5
>         Source code file: trnio.c, line: 66
> 
>         File input/output error:
>         Can not determine precision of trn file
>         ----------------------------------------------------------------------------------------------------------------------------
> 
>         Is there any way to recover this .trr file? Or do I need to
>         re-run the simulation again?
> 
> 
>     Probably. Did the simulation end correctly? Did you run out of disk
>     space?
> 
>     Mark
>     -- 
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