Job stopped after 40 steps
giulia.p... at gmail.com
Wed Jul 13 09:09:59 UTC 2011
Yes, I am running on cineca SP6.
I will change the number of processors to 128 and 256 and I see what
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?
> 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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