[gmx-users] 答复: Can't allocate memory problem

[Yunlong Liu]

Hi,

Thank you for your reply.
I am actually not doing anything unusual, just common MD simulation of a protein. My system contains ~250000 atoms, more or less depend on how many water molecules I put in it.

The way I called mdrun is 
ibrun mdrun_mpi_gpu -pin on -ntomp 8 -deffnm pi3k-wt-1 -gpu_id 00

I pinned 8 threads on 1 MPI task (this is the optimal way to run simulation on Stampede). It has been problem with other systems like lysosome. But my system is a little unusual and I don't really understand where is unusual. 

The systems are doing fine if I use CPU to run the simulation but as soon as I turned on the GPU, the simulation sucks frequently. One of the guesses is that GPU is more sensitvie in dealing with the non-bonded interactions.

Thank you.
Yunlong

________________________________________
发件人: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> 代表 Mark Abraham <mark.j.abraham at gmail.com>
发送时间: 2014年7月18日 23:52
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] Can't allocate memory problem

Hi,

That's highly unusual, and suggests you are doing something highly unusual,
like trying to run on huge numbers of threads, or very large numbers of
bonded interactions. How are you setting up to call mdrun, and what is in
your tpr?

Mark
On Jul 17, 2014 10:13 PM, "Yunlong Liu" <yliu120 at jhmi.edu> wrote:

> Hi,
>
>
> I am currently experiencing a "Can't allocate memory" problem on Gromacs
> 4.6.5 with GPU acceleration.
>
> Actually, I am running my simulations on Stampede/TACC supercomputers with
> their GPU queue. My first experience is when the simulation length longer
> than 10 ns, the system starts to throw out the "Can't allocate memory"
> problem as follows:
>
>
> Fatal error:
> Not enough memory. Failed to realloc 1403808 bytes for f_t->f,
> f_t->f=0xa912a010
> (called from file
> /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c,
> line 3840)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "These Gromacs Guys Really Rock" (P.J. Meulenhoff)
> : Cannot allocate memory
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun_mpi_gpu on CPU 0 out of 4
>
> -------------------------------------------------------
> Program mdrun_mpi_gpu, VERSION 4.6.5
> Source code file:
> /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/smalloc.c,
> line: 241
>
> Fatal error:
> Not enough memory. Failed to realloc 1403808 bytes for f_t->f,
> f_t->f=0xaa516e90
> (called from file
> /admin/build/admin/rpms/stampede/BUILD/gromacs-4.6.5/src/gmxlib/bondfree.c,
> line 3840)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Recently, this error occurs even I run a short NVT equilibrium. This
> problem also exists when I use Gromacs 5.0 with GPU acceleration. I looked
> up the Gromacs errors website to check the reasons for this. But it seems
> that none of those reasons will fit in this situation. I use a very good
> computer, the Stampede and I run short simulations. And I know gromacs use
> nanometers as unit. I tried all the solutions that I can figure out but the
> problem becomes more severe.
>
> Is there anybody that has an idea on solving this issue?
>
> Thank you.
>
> Yunlong
>
>
>
>
>
>
>
>
> Davis Yunlong Liu
>
> BCMB - Second Year PhD Candidate
>
> School of Medicine
>
> The Johns Hopkins University
>
> E-mail: yliu120 at jhmi.edu<mailto:yliu120 at jhmi.edu>
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