Job stopped after 40 steps

giulia palermo giulia.p... at gmail.com
Tue Jul 12 19:26:20 CEST 2011


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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