[gmx-users] 'not allocate memory'

[Justin A. Lemkul]

saly jackson wrote:
> Hi
> 
> I think the error is not a reason of less memory of my computer. Because 
> in a supercomputer I see the hollowing error too.
> 

genbox is not parallelized, and thus cannot make use of multiple processors and 
the memory on them.

> Genbox could be run if I choose the number of atoms less than 5000.
> 

The fact that you can add 5000 molecules but not 80000 suggests that 
insufficient memory is precisely the problem.  Gromacs is even telling you that 
in the fatal error below.

Please refer to the solution I proposed earlier.  It is a more robust approach 
than what you're trying to do.

-Justin

> Thanks
> 
> Saly
> 
> Try 824box_margin = 0.45 overlap:
> Neighborsearching with a cut-off of 0.45
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
> System total charge: 0.000
> Grid: 33 x 33 x 33 cells
> nri = 3633, nrj = 8848
> Try 825box_margin = 0.45 overlap: success (now 4320 atoms)!
> Neighborsearching with a cut-off of 0.45
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
> System total charge: 0.000
> Grid: 33 x 33 x 33 cells
> nri = 3638, nrj = 8860
> Try 826box_margin = 0.45 overlap: success (now 4326 atoms)!
> Neighborsearching with a cut-off of 0.45
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
> System total charge: 0.000
> Grid: 33 x 33 x 33 cells
> nri = 3644, nrj = 8872
> Try 827box_margin = 0.45 overlap: success (now 4332 atoms)!
> Neighborsearching with a cut-off of 0.45
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
> System total charge: 0.000
> Grid: 33 x 33 x 33 cells
> nri = 3649, nrj = 8908
> Try 829box_margin = 0.45 overlap:
> Neighborsearching with a cut-off of 0.45
> Table routines are used for coulomb: FALSE
> Table routines are used for vdw:     FALSE
> Cut-off's:   NS: 0.45   Coulomb: 0.45   LJ: 0.45
> System total charge: 0.000
> 
> -------------------------------------------------------
> Program genbox, VERSION 4.5.4
> Source code file: smalloc.c, line: 214
> 
> Fatal error:
> Not enough memory. Failed to realloc 69408 bytes for nl->gid, nl->gid=0x0
> (called from file ns.c, line 104)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> 
> "Act like Prometheus would" (Gogol Bordello)
> : Cannot allocate memory
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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