On 27/09/2011 10:42 PM, A Taqia wrote:
Dear Gromacs experts,
I ran a Gromacs simulation (with Gromacs 4.5.4) on a BlueGene/P system
and generated a trajectory file. However, when I performed analysis
on this file (traj.trr) (for example using g_clustsize), the following
error was encountered:
-------------------------------------------------------
Program trjconv_d, VERSION 4.5.1
Source code file: trnio.c, line: 68
Fatal error:
Float size 164738970. Maybe different CPU?
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I used the post processing tool (g_clustsize) from different versions
of Gromacs (4.5.4, 4.5.1, 4.0.x) on both the front end and back end
nodes of the BlueGene. I even tried using g_clustsize built on a
Linux, but encountered the same error. I was wondering if anyone can
shed me some lights on how to resolve this problem. Your assistance
is greatly appreciated.
The simplest explanation for the symptoms is that your trajectory file
is corrupt somehow - most likely because of something someone did to the
file, or to the file system. The size of a .trr file is linear in the
number of frames, so if you can run a short version of the simulation
separately, you can estimate how big this file should have been.
gmxcheck is available to probe the integrity of the file, but I expect
it will also simply tell you something is catastrophically wrong.
Mark
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