[gmx-users] Gromacs on IBM cluster

[Marius Retegan]

32 Gb on each node of the cluster.
Maybe I should add that I've also ran CPMD and cp2k jobs on the
cluster but I've never had memory problems.
Marius Retegan

On 10/30/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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.
> ________________________________________________________________________
> 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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