Re: [AMBER] Odd coordinate writing problem in pmemd.MPI

From: Ross Walker <>
Date: Thu, 5 Apr 2012 09:42:55 -0700

Hi Thomas,

> I have just experienced a strange coordinate writing issue with a pmemd
> simulation. I ran a 1 ns standard NPT MD of a small solvated protein
> writing to disk very often (10 gig total traj size), when at a random
> point (after 418ps) the structure when viewed in vmd appears to become
> completely scrambled.
> A relevant cutout of my crd file for the first problematic snapshot
> looks
> like this:

Is this reproducible? Or does it appear to be random?

Is there anything magical about the point at which it happens as well. I.e.
if it occurs almost exactly when the trajectory reaches 2GB in size (or 4GB)
then it is almost certainly some corruption due to use of 32 bit ints in the
file handling. It would take some searching to locate this, it could be
anywhere from within the pmemd code, in the MPI library or in the operating
system I/O library (maybe even the compiler used). Can you confirm that you
are running a 64 bit OS with 64 bit compilers, and 64 bit MPI?

Also are you writing locally or to a remote file system?

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Thu Apr 05 2012 - 10:00:03 PDT
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