Re: shared memory in computational chemistry
Disregard the message, please. It was a mistake in the
setup.
Thanks
francesco
--- Francesco Pietra <chiendarret@yahoo.com> wrote:
> That OK below for a job in which I had made six
> fragments from the molecule. Because the partial
> charge calculation was unsatisfactory as to the
> dipole moment value, I tried again by making two
> fragments only. Although this can hardly be clear,
> what should perhaps suggest a remedy is the final
> warning below (beteen two lines) at the incomplete
> calculation. No more an issue as to the size of
> memory
> segments to allocate (I did the "echo .." as below).
> Now the issue is "inappropriate ioctl for device".
> No
> hope for suggestions from the computational software
> part. The only hope is from debian people, I
> believe.
> ___________________________
>
> Recovery file deleted
>
> 1 **********
> * 0: Singular matrix in esp_fit 2
> **********
> 0:0::: 2
> 0:0::: 2
> Last System Error Message from Task 0::
> Inappropriate
> ioctl for device
> 0: ARMCI aborting 2 (0x2).
> 0: ARMCI aborting 2 (0x2).
> system error message: Inappropriate ioctl for device
> Creating: host=deb64, user=francesco,
>
>
file=/home/francesco/application/bin/application_executable,
> port=35756
> 4: interrupt(1)
> WaitAll: No children or error in wait?]
> ______________________________
>
> Thanks
> francesco
>
> _________________________________________
> --- Francesco Pietra <chiendarret@yahoo.com> wrote:
>
> > Hi Peter:
> >
> > Thanks. I set
> >
> > echo "60000000" >/proc/sys/kernel/shmmax
> >
> > because the segment to allocate was ca 39mb. In
> > between the rows reporting the steady approach to
> > scf
> > energy, a row appeared:
> >
> > 1 warning: armci set_mem_offset: offset changed 0
> to
> > 8192
> >
> > and the calculation of partial charges completed
> > successfully.
> >
> > As to a permanent solution, is any drawback in
> > setting
> > shmmax as above (or even to a higher value)
> > permanently? Probably this issue of allocating big
> > fragments will become routine, though I can't
> > predict
> > their size.
> >
> > francesco
> >
> > --- Peter Schueller <ps@brumma.com> wrote:
> >
> > > Francesco Pietra wrote:
> > > > QUESTIONS:
> > > > 1) How to set shmmax in debian?
> > >
> > > for experiments i suggest:
> > >
> > > echo "10000000" >/proc/sys/kernel/shmmax
> > >
> > > for a permanent solution you have to edit
> > > /etc/sysctl.conf where you will be able to put a
> > > line like
> > >
> > > kernel.shmmax = 1000000
> > >
> > > (have a look at man sysctl.conf)
> > >
> > > But I don't know if this will work in your
> cluster
> > > ...
> > >
> > > Best Regards,
> > >
> > > Peter
> > >
> > >
> > > --
> > > To UNSUBSCRIBE, email to
> > > debian-science-request@lists.debian.org
> > > with a subject of "unsubscribe". Trouble?
> Contact
> > > listmaster@lists.debian.org
> > >
> > >
> >
> >
> >
> >
> >
>
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