[CP2K:3373] Re: Job stopped after 40 steps

giulia palermo giulia.p... at gmail.com
Wed Jul 13 12:15:24 CEST 2011


Ciao Jacopo,
Thank you for your reply,
I will try also using 1400Mb of memory.

Giulia

On Wed, Jul 13, 2011 at 11:56 AM, Jacopo Sgrignani <sgr... at gmail.com>wrote:

> Ciao Giulia
> I've run a lot of QM/MM calculations on enzimes using QM/MM on SP6,
> and it usually works fine.
> However I don't use the cp2k version available with the module
> command, but I use a version recompiled by myself.
> Your system is really very big, but the QM region seems quite small
> then, i think, you should run also with 64 procs.
>
> Did you put this line in your submission script?
> # @ resources   = ConsumableMemory(1400Mb)
>
> Jacopo
>
>
>
>
>
>
> 2011/7/13 giulia palermo <giulia.p... at gmail.com>:
> > Dear J.Sgrignani,
> > Yes, I am running on cineca SP6.
> > I will change the number of processors to 128 and 256 and I see what
> > will happens.
> >
> > Thank you,
> > Giulia
> >
> > On Jul 12, 10:50 pm, Jacopo Sgrignani <sgr... at gmail.com> wrote:
> >> Hi Giulia
> >> Maybe you can solve the memory problem increasing the number of
> processors.
> >>
> >> Are you running on the cineca SP6?
> >>
> >> Jacopo
> >>
> >> 2011/7/12, giulia palermo <giulia.p... at gmail.com>:
> >>
> >> > Dear Dr. Laino,
> >> > probably CP2K is miscompiled in the machine that I were using. This
> >> > conclusion arises from the subsequent arguments:
> >>
> >> > 1) Coping all the files to another machine the job has started, the
> >> > geometry optimization has finished properly again, and we are
> >> > currently running the MD simulation without problem for more than 100
> >> > steps.
> >>
> >> > 2) As supposed by the system managers of the IBM sp6 machine, the most
> >> > common error that I had is related to memory:
> >>
> >> > ATTENTION: 0031-408  64 tasks allocated by LoadLeveler, continuing...
> >> > ERROR: 0031-161  EOF on socket connection with node sp0025
> >>
> >> > Even if my calculation are now running on an other machine, the
> >> > problem on the IBM sp6 machine persists.
> >> > How can be possible that other users of the sp6 are running cp2k,
> >> > using the same submission file, without any problem?
> >> > I will send an e-mail to the system manager ASAP.
> >>
> >> > Thank you very much for your quick response.
> >> > Giulia Palermo
> >>
> >> > On Jul 12, 4:07 pm, Teodoro Laino <teodor... at gmail.com> wrote:
> >> >> Hi Giulia,
> >> >> it's not easy to say with these few info. Don't you get any error
> message
> >> >> from the OS?
> >> >> Neither locallog files?
> >>
> >> >> Teo
> >>
> >> >> On Jul 12, 2011, at 3:56 PM, giulia palermo wrote:
> >>
> >> >> > Dear all,
> >> >> > I am a new cp2k user and I am working with a big enzyme/inhibitor
> system
> >> >> > (~180000 atoms) in order to study the covalent inhibition of the
> enzyme.
> >> >> > I am running the calculations on an IBM sp6 machine and I asked 64
> >> >> > processors for 05.55 hours (in order to quickly enter in the
> queue).
> >>
> >> >> > I successfully did the first geometry optimization step for the QM
> part,
> >> >> > maintaining fixed the Classical enzymatic environment.
> >>
> >> >> > Now I am trying to equilibrate the system in NVT ensemble at 300K,
> >> >> > asking 1000 steps (with a timestep of 0.5 fs).
> >> >> > Unfortunately, the calculation finishes after 40 steps even if the
> >> >> > Energy values seem to be good.
> >>
> >> >> > I send an e-mail to the IBM-sp6 system managers. They reply that
> could
> >> >> > be a memory problem.
> >> >> > So, I tried several times to change the memory in the submission
> file
> >> >> > (run.ll that you will find in attachment),
> >> >> > but the problem persists.
> >>
> >> >> > Have you any suggestion about what could be the problem?
> >> >> > You will also find in attachment the input file (md01.inp)
> >>
> >> >> > Thank you
> >> >> > Giulia Palermo
> >>
> >> >> > --
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> >> >> > <md01.inp><run.ll>
> >>
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