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

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 3 19:14:28 CET 2006


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
> 
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++



More information about the gromacs.org_gmx-users mailing list