[gmx-users] Gromacs on IBM cluster

[David van der Spoel]

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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>>
> _______________________________________________
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> www interface or send it to gmx-users-request at gromacs.org.
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++