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