[gmx-users] How to check memoryuse limit?

Berk Hess gmx3 at hotmail.com
Tue May 22 16:06:01 CEST 2007

>From: Stéphane Téletchéa <steletch at jouy.inra.fr>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] How to check memoryuse limit?
>Date: Tue, 22 May 2007 15:09:37 +0200
>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.

Using the double version will only makes things worse, since it uses
double the amount of memory.

But are you sure you want to make a box with 30 million water molecules?
Maybe you mixed up Angstroms and nanometers?


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