[gmx-users] Gromacs on IBM cluster

[Marius Retegan]

I have aprox. 81000 atoms. The system worked on a Itanium 2 cluster.
On the IBM machine I've used the IBM compilers.
I'm going to give it a try with gcc.
Thank you
Marius Retegan

On 10/31/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Marius Retegan wrote:
> > 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
> It could still be too little, since this is the additional memory. What
> kind of system are you using, how many atoms? Does a small water box
> work? There have been problems with compilation on IBM machines as well,
> in particular when using IBM compilers. Recompiling with gcc resolves that.
>
> >
> > 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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>
> --
> 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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