[Pw_forum] Memory distribution problem
Paolo Giannozzi
paolo.giannozzi at uniud.it
Sun Mar 2 15:58:27 CET 2014
On Sat, 2014-03-01 at 21:13 -0600, Peng Chen wrote:
> And I still couldn't find where this large array comes from.
the code prints the size of largest arrays at the beginning
of the calculation
P.
>
> On Sat, Mar 1, 2014 at 3:49 PM, Paolo Giannozzi
> <paolo.giannozzi at uniud.it> wrote:
> On Sat, 2014-03-01 at 14:27 -0600, Peng Chen wrote:
> >
> > And the system is not that large(32 atoms, 400 nband, 8*8*8
> kpoints)
> > which is run in 128 cores. I think you are probably right
> that QE is
> > trying to allocate a large array somehow.
>
>
> ... and ?
>
> > On Fri, Feb 28, 2014 at 10:35 AM, Paolo Giannozzi
> > <paolo.giannozzi at uniud.it> wrote:
> > On Fri, 2014-02-28 at 09:12 -0600, Peng Chen wrote:
> >
> > > I think it is memory, because the error message is
> like:
> > > : 02/27/2014 14:06:20| main|zeta27|W|job 221982
> exceeds job
> > hard
> > > limit "h_vmem" of queue (2871259136.00000 >
> > limit:2147483648.00000) -
> > > sending SIGKILL
> >
> >
> > there are a few hints on how to reduce memory usage
> to the
> > strict
> > minimum here:
> >
> http://www.quantum-espresso.org/wp-content/uploads/Doc/pw_user_guide/node19.html#SECTION000600100000000000000
> > If the FFT grid is large, reduce mixing_ndim from
> its default
> > value (8)
> > to 4 or so. If the number of bands is large,
> distribute
> > nbnd*nbnd
> > matrices using "-ndiag". If you have many k-points,
> save to
> > disk with
> > disk_io='medium'. The message you get: "2871259136 >
> > limit:2147483648"
> > makes me think that you crash when trying to
> allocate an array
> > whose
> > size is at least 2871259136-2147483648=a lot. It
> shouldn' be
> > difficult
> > to figure out where such a large array comes from
> >
> > Paolo
> >
> >
> > >
> > > I normally used h_stak=128M, it is working fine.
> > >
> > >
> > >
> > >
> > >
> > >
> > > On Fri, Feb 28, 2014 at 7:30 AM, Paolo Giannozzi
> > > <paolo.giannozzi at uniud.it> wrote:
> > > On Thu, 2014-02-27 at 17:30 -0600, Peng
> Chen wrote:
> > > > P.S. Most of the jobs failed at the
> beginning of
> > scf
> > > calculation, and
> > > > the length of output scf file is zero.
> > >
> > >
> > > are you sure the problem is the size of
> the RAM and
> > not the
> > > size of
> > > the stack?
> > >
> > > P.
> > >
> > >
> > > >
> > > >
> > > > On Thu, Feb 27, 2014 at 5:09 PM, Peng
> Chen
> > > <pchen229 at illinois.edu>
> > > > wrote:
> > > > Dear QE users,
> > > >
> > > >
> > > > Recently, our workstation is
> updated and
> > there is a
> > > hard limit
> > > > on memory (2G per core). Some of
> QE jobs
> > are
> > > constantly failed
> > > > (not always) because one of the
> MPI
> > processes
> > > exceeded the RAM
> > > > limit and was killed. I am
> wondering if
> > there is a
> > > way to
> > > > distribute using memory more
> evenly in
> > every core.
> > > >
> > > >
> > >
> > > >
> _______________________________________________
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> > > > Pw_forum at pwscf.org
> > > >
> http://pwscf.org/mailman/listinfo/pw_forum
> > >
> > >
> > > --
> > > Paolo Giannozzi, Dept.
> > Chemistry&Physics&Environment,
> > > Univ. Udine, via delle Scienze 208, 33100
> Udine,
> > Italy
> > > Phone +39-0432-558216, fax
> +39-0432-558222
> > >
> > >
> _______________________________________________
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> > >
> > >
> > >
> > > _______________________________________________
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> >
> > --
> > Paolo Giannozzi, Dept.
> Chemistry&Physics&Environment,
> > Univ. Udine, via delle Scienze 208, 33100 Udine,
> Italy
> > Phone +39-0432-558216, fax +39-0432-558222
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
> >
> >
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>
> --
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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--
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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