[gmx-users] "Cannot allocate memory" by grompp

[Sandeep Somani]

It is ok now. I found from the sys admin here that they are having some
memory issues with the cluster. The node I was running on has 2GB. 

Thnx 
sandeep


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of David van der Spoel
Sent: Friday, March 03, 2006 1:14 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] "Cannot allocate memory" by grompp

Sandeep Somani wrote:
> Hi 
> 
> I am testing a fresh gmx3.3 installation on a new dual opteron cluster
> running redhat linux. 
> 
> Did the standard pdb2gmx -> energy minimization -> position restrained
(PR)
> MD and everything was fine. 
> 
> But next when I did grompp for production run, got the following: 
> "
> -------------------------------------------------------
> Program grompp_d, VERSION 3.3
> Source code file: smalloc.c, line: 113
> 
> Fatal error:
> calloc for pairs->param (nelem=664225, elsize=152, file topio.c, line 125)
this corresponds to 100 Mb . How much does your computer have?


> -------------------------------------------------------
> 
> "Is This the Right Room for an Argument ?" (Monty Python)
> : Cannot allocate memory
> "
> 
> To trouble shoot I tried repeating the successful PR run and strangely
> enough got the same error with grompp. 
> 
> Suddenly grompp broke down or something went wrong with the cluster here. 
> 
> I am clueless. Looking fwd to some pointers .. 
> 
> Regards
> Sandeep
> 
> 
> ---
> Graduate Student
> Gilson Laboratory 
> Center for Advanced Research in Biotechnology
> University of Maryland Biotechnology Institute
> 9600 Gudelsky Drive
> Rockville, MD 20850
> 
> www.chemicalphysics.umd.edu/~ssomani
> 
> 
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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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