From: Martin Höfling <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: Discussion list for GROMACS users <[email protected]>
Subject: Re: [gmx-users] fatal error
Date: Wed, 23 May 2007 13:20:42 +0200
Am Mittwoch, 23. Mai 2007 schrieb Sonali:
> Program g_covar, VERSION 3.3
> Source code file: smalloc.c, line: 113
>
> Fatal error:
> calloc for mat (nelem=997170084, elsize=4, file gmx_covar.c, line 219)
> -------------------------------------------------------
>
> "Whatever Happened to Pong ?" (F. Black)
>
> : Cannot allocate memory
If i read the above correct, it's trying to allocate 1G * 4 * 4 or 8
(depending on single or double prec.)
That's at least 16G of memory and might be to much depending on available
mem
and/or architecture.
Cheers
Martin
Your group apparently has sqrt(997170084)=31578 atoms.
You could use backbone only, or maybe protein-h.
Also one should normally use the same group for fitting and covariance.
Berk.
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