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

[Szilárd Páll]

On Fri, Jul 18, 2014 at 7:31 PM, Yunlong Liu <yliu120 at jhmi.edu> wrote:
> 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).

FYI: That can't be universally true. The best run configuration will
always depend on at least the machine characteristics  parallelization
capabilities and behavior of the software/algorithms used as well as
often the  setting/size of input too (especially as different type of
runs may use different algorithms).

More concretely, GROMACS will not always perform best with 8
threads/rank - even though that's the number of cores/socket on
Stampede. My guess is that you'll be better off with 2-4 threads per
rank.

One thing you may have noticed is that a single K20 that Stampede's
visualization nodes seem to have (based on http://goo.gl/9fG7Vd), will
probably not be enough to keep up with two Xeon E5 2680-s and a
considerable amount of runtime will be lost as the CPU will be idling
while waiting for the GPU to complete the non-bonded calculation. You
may want to give a try to the "-nb gpu_cpu" option.

Cheers,
--
Szilárd

> 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>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.