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 <[EMAIL PROTECTED]> 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 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
[EMAIL PROTECTED] [EMAIL PROTECTED] 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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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