[CP2K:4701] How many cores can CP2K utilize in parallel computing.

Huan Wang huan... at mail.huji.ac.il
Mon Oct 7 10:19:44 CEST 2013


Dear Iain,
Thanks for your reply.
So, the memory requirement depends on the system to be studied. Is that
means if I purchased larger memory, such as 64 GB than 32 GB, calculation
performance will faster and more stable with the same number of cores?

Huan


On Mon, Oct 7, 2013 at 9:45 AM, Iain Bethune <ibet... at epcc.ed.ac.uk> wrote:

> Hi Huan,
>
> I can't comment on NAMD (except to give the same general responses as for
> CP2K).  The amount of memory needed per core depends on the size of the
> system and also the number of cores, since in CP2K the large data
> structures are distributed.  What happens when you fill your memory depends
> on the system - on many HPC systems, CP2K will stop since attempts to
> allocate more memory will fail, but on a cluster system there may be
> virtual memory so performance will reduce.
>
> There is no substitute for benchmarking with your own system to understand
> the performance and memory requirements properly.
>
> - Iain
>
> --
>
> Iain Bethune
> Project Manager, EPCC
>
> Email: ibet... at epcc.ed.ac.uk
> Twitter: @IainBethune
> Web: http://www2.epcc.ed.ac.uk/~ibethune
> Tel/Fax: +44 (0)131 650 5201/6555
> Mob: +44 (0)7598317015
> Addr: 2404 JCMB, The King's Buildings, Mayfield Road, Edinburgh, EH9 3JZ
>
>
>
>
>
>
>
>
> On 6 Oct 2013, at 14:21, Huan Wang wrote:
>
> > Dear Iain,
> >
> > Do you know what is the recommended memory per core for NAMD & CP2K?
> > Is that possible/often happened when the speed of computations slowed
> down due to the memory was insufficient?
> >
> > Best wishes,
> > Huan
> >
> >
> >
> >
> >
> > On Thu, Oct 3, 2013 at 2:45 PM, Iain Bethune <ibet... at epcc.ed.ac.uk>
> wrote:
> > Dear Huan,
> >
> > Like other parallel programs which make use of MPI, CP2K does not know
> or care exactly where each MPI process is running.  Allocation and
> placement of MPI processes onto physical nodes is up to the MPI library you
> have installed on your cluster.  We regularly run CP2K on several thousands
> of CPU cores on large-scale HPC machines, so depending on the size of
> system you wish to study you will find CP2K to be very scalable.  Without
> knowing more, I would suggest that you benchmark CP2K with your existing
> system to better understand the performance and scalability.
> >
> > How to run a parallel job across multiple compute nodes across depends
> exactly on which MPI library (e.g. OpenMPI, MPICH2, Intel MPI...) you use
> and if you use any batch job submission system (e.g. SLURM, PBS, Sun Grid
> Engine...).  Typically, one needs to have the mpi deamon running on each
> node and all the nodes added to a node-list file or similar, then the
> 'mpirun' command will launch MPI ranks across your two nodes.  Best thing
> is to speak to your local systems administrators who may be able to help
> more specifically.
> >
> > Also, you might consider upgrading to a more recent release of CP2K as
> 2.3 is over a year old and there have been many improvements, new features
> and performance improvements since.
> >
> > Cheers
> >
> > - Iain
> >
> > --
> >
> > Iain Bethune
> > Project Manager, EPCC
> >
> > Email: ibet... at epcc.ed.ac.uk
> > Twitter: @IainBethune
> > Web: http://www2.epcc.ed.ac.uk/~ibethune
> > Tel/Fax: +44 (0)131 650 5201/6555
> > Mob: +44 (0)7598317015
> > Addr: 2404 JCMB, The King's Buildings, Mayfield Road, Edinburgh, EH9 3JZ
> >
> >
> >
> >
> >
> >
> >
> >
> > On 3 Oct 2013, at 13:30, huan... at mail.huji.ac.il wrote:
> >
> > > Dear All,
> > >
> > > I would like to know is there an up-limit number of cores for CP2K
> parallel computing. My supervisor want to purchase some new computers for
> running CP2K/QuickStep. So we need to make sure that is it possible to run
> parallel computing with, such as, 40 or more cores?
> > >
> > > Another question is that Is it possible for sharing the CPU in
> different nodes for parallel computing? For example, if it is possible to
> use 2 nodes (each node has 40 processors) for one MD simulation? If it
> available, how to do it? Do I need to write some special codes in
> submitting script?   The version of CP2K I used is 2.3.
> > >
> > > I appreciated it very much if someone could answer my questions.
> Thanks in advance.
> > >
> > > Best regards,
> > > Huan
> > >
> > > --
> > > You received this message because you are subscribed to the Google
> Groups "cp2k" group.
> > > To unsubscribe from this group and stop receiving emails from it, send
> an email to cp2k+uns... at googlegroups.com.
> > > To post to this group, send email to cp... at googlegroups.com.
> > > Visit this group at http://groups.google.com/group/cp2k.
> > > For more options, visit https://groups.google.com/groups/opt_out.
> >
> >
> > --
> > The University of Edinburgh is a charitable body, registered in
> > Scotland, with registration number SC005336.
> >
> > --
> > You received this message because you are subscribed to a topic in the
> Google Groups "cp2k" group.
> > To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/cp2k/WbfiDAZTdgg/unsubscribe.
> > To unsubscribe from this group and all its topics, send an email to
> cp2k+uns... at googlegroups.com.
> > To post to this group, send email to cp... at googlegroups.com.
> > Visit this group at http://groups.google.com/group/cp2k.
> > For more options, visit https://groups.google.com/groups/opt_out.
> >
> >
> > --
> > You received this message because you are subscribed to the Google
> Groups "cp2k" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to cp2k+uns... at googlegroups.com.
> > To post to this group, send email to cp... at googlegroups.com.
> > Visit this group at http://groups.google.com/group/cp2k.
> > For more options, visit https://groups.google.com/groups/opt_out.
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
> --
> You received this message because you are subscribed to a topic in the
> Google Groups "cp2k" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/cp2k/WbfiDAZTdgg/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> cp2k+uns... at googlegroups.com.
> To post to this group, send email to cp... at googlegroups.com.
> Visit this group at http://groups.google.com/group/cp2k.
> For more options, visit https://groups.google.com/groups/opt_out.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20131007/6385797e/attachment.html>


More information about the CP2K-user mailing list