[CP2K:3363] Job stopped after 40 steps

Jacopo Sgrignani sgr... at gmail.com
Tue Jul 12 22:50:59 CEST 2011


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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