[gmx-users] How to check memoryuse limit?

[Stéphane Téletchéa]

Alif M Latif a écrit :
> Dear GROMACS users,
> 
> I'm having problem using genbox while trying to solvate my micelle 
> structure. The program produced error "cannot allocate memory". I 
> checked the mailing list archive, and found that Dr. David once told to 
> check the limit command. I tried to type "limit" but the command was not 
> found. Do I need to move to specific directory to use this command? I'm 
> using OS Kernel: Linux version 2.6.9-34.ELsmp (Red Hat 3.4.5-2). Or 
> Maybe something wrong anywhere else?.. I've include the error message 
> (just in case).
> 
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Opening library file /usr/local/gromacs/share/gromacs/top/atommass.dat
> Opening library file /usr/local/gromacs/share/gromacs/top/vdwradii.dat
> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
> #Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
> Reading solute configuration
> Built with Packmol
> Containing 787 atoms in 21 residues
> Initialising van der waals distances...
> Reading solvent configuration
> "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
> solvent configuration contains 648 atoms in 216 residues
> 
> Initialising van der waals distances...
> Will generate new solvent configuration of 54x54x54 boxes
> -------------------------------------------------------
> Program genbox, VERSION 3.3
> Source code file: smalloc.c, line: 137
> 
> Fatal error:
> realloc for atoms_solvt->atom (-213500416 bytes, file gmx_genbox.c, line 
> 399, at oms_solvt->atom=0x0x 81f07a0)
> -------------------------------------------------------
> "We Don't Bother Anyone" (LIVE)
> : Cannot allocate memory
> 
> 

You don't have enough memory available.
See the command: ulimit -a

You can try also to use the double version of the program (genbox_d 
instead of genbox), allocate swap on the machine (man mkswap), or use a 
computer having more memory to create your input file.

Cheers,
Stéphane

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901