[gmx-users] Gromacs on IBM cluster

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 30 19:19:26 CET 2007

Marius Retegan wrote:
> Dear Gromacs users
> I'm having some troubles running grompp on a IBM cluster P575 with AIX
> 5.3 installed.
> This is the error message that I'm getting:
> ====================================================
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> -------------------------------------------------------
> Program grompp_d, VERSION 3.3.1
> Source code file: smalloc.c, line: 113
> Fatal error:
> calloc for nbsnew (nelem=677329, elsize=148, file grompp.c, line 723)
This says it wants one Gb of RAM. How much do you have?
You can run grompp on a machine with a lot of memory and the mdrun on 
your cluster.
> -------------------------------------------------------
> "I'm An Oakman" (Pulp Fiction)
> : Not enough space
> ====================================================
> While digging into the archive I've managed to find this post
> http://www.gromacs.org/pipermail/gmx-users/2006-February/020066.html,
> which basically says that there is not enough memory for the job. My
> job is lunched with LoadLeveler where I can define the @resources =
> ConsumableMemory (value), but if this is not defined in the
> LoadLeveler script, I think that the program should thake as much
> memory as it requires.
> So my question is why does Gromacs, a program renowned for low memory
> requirements, give this error message?
> Thank you
> Marius Retegan
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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