[Pw_forum] time for calculation of el-ph interactions of graphene supercell

[L.F.Huang]

Dear prof. Kohlmeyer and Giannozzi:
  Thank both of you for your kindly help!
  Frankly, I have not taken serious tests. When I found the calculations
of frequencies(99 modes) for one wave vector of phonon in the 4*4*1
graphene supercell with one H atom on it took about 20 days, then I took
it for granted that the calculation of el-ph interaction would accomplish
for several hours or a little more. But nearly 3 days having passed, it is
still doing the calculation......I realy need some serious tests to let
it clear in my mind.

  Thank you for your advices for testing! Thank you very much!
Best Wishes!
                                    Yours Sincerely!
                                      L.F.Huang
PostScript:
  Amount of memory: 2GB per node
  kind of interconnect: myrinet 2000
  No. of reduced k points: 52
  No. of nodes: 13 (with npool by default 1)
  Parallel environment: MPI 1.2
  Math library: NAG ACML 1.5、ATLAS 3.6
  No. of cpus per node: 4



> Date: Fri, 5 Sep 2008 10:33:27 -0400 (EDT)
> From: Axel Kohlmeyer <akohlmey at cmm.chem.upenn.edu>
> Subject: Re: [Pw_forum] time for calculation of el-ph interactions of
> 	graphene supercell
> To: "L.F.Huang" <lfhuang at theory.issp.ac.cn>
> Cc: pw_forum at pwscf.org
> Message-ID: <Pine.LNX.4.64.0809051023550.26272 at localhost.localdomain>
> Content-Type: text/plain; charset="gb2312"
>
> On Fri, 5 Sep 2008, L.F.Huang wrote:
>
> LFH> Dear PWSCF developers and users:
> LFH>   I am calculating a graphene supercell with one H atom one it, and
> I LFH> take 4*4*1 size of supercell now, and there are 33 atoms with 32
> C atoms LFH> and 1 H atom. I calculate its phonon dispersions with 13
> nodes with 2G LFH> random memory for each node. When frequencies of one
> phonon mode are
>
> dear l.f. huang,
>
> more important that the amount of memory in your nodes would
> be know what kind of interconnect (gigabit, infiniband, myrinet, ...)
> you have and how you run in parallel (g-space parallelization only,
> g-space+k-points, ...) and what type and how many cpus/cores per node
> you have and even what kind of parallel library and math library you
> use. all of that can have a serious impact on performance.
>
> have you done a scaling test for the first part of the calculation?
> unless you are smart about it, adding more nodes does not necessarily
> speed up your calculations, specifically, if you have only a gigabit
> ethernet interconnect.
>
> please see, e.g.,
> http://www.democritos.it/pipermail/pw_forum/2008-June/009293.html
> for a demonstration of how one can affect performance through the
> way the QE codes are run.
>
> LFH> calculated, the program enter into calculation of electron-phonon
> LFH> interactions. But it has passed nearly 30 hours, and the
> calculation of LFH> el-ph interaction still not completed! And for
> graphene unit cell with LFH> 2 C atoms, this process just costs about 10
> seconds.
>
> you should be aware of the fact, that this kind of calculation does not
> scale linearly; the cost of an scf caclculation alone generally goes up
> by about an order magnitude when doubling the system size.
>
> cheers,
>    axel.
>
> LFH>   I don't know it is normal that the calculation of el-ph
> interaction LFH> of my graphene supercell costs so much or so much more
> time? Any one LFH> has the experiences in the el-ph calculation of
> supercells? Could anyone LFH> tell me how can I do or how much time I
> would expect to wait? LFH>
> LFH> Thanks very much!
> LFH> Best Wishes!
> LFH>
> LFH> Yours Sincerely
> LFH> L.F.Huang
> LFH>
> LFH>
> ======================================================================
> LFH> L.F.Huang(???) lfhuang at theory.issp.ac.cn
> LFH>
> ======================================================================
> LFH>  Add: Research Laboratory for Computational Materials Sciences,
> LFH>       Instutue of Solid State Physics,the Chinese Academy of
> Sciences, LFH>       P.O.Box 1129, Hefei 230031, P.R.China
> LFH>  Tel: 86-551-5591464-328(office)
> LFH>  Fax: 86-551-5591434
> LFH>  Web: http://theory.issp.ac.cn (website of our theory group)
> LFH>       http://www.issp.ac.cn    (website of our institute)
> LFH>
> ======================================================================
> LFH>
> LFH>
> LFH> _______________________________________________
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> LFH> Pw_forum at pwscf.org
> LFH> http://www.democritos.it/mailman/listinfo/pw_forum
> LFH>
>
> --
> =======================================================================
> Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>    Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
> ------------------------------
>
> Date: Fri, 05 Sep 2008 16:44:09 +0200
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] time for calculation of el-ph interactions of
> 	graphene supercell
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <48C145B9.9080705 at democritos.it>
> Content-Type: text/plain; charset=GB2312
>
> L.F.Huang wrote:
>
>> Could anyone tell me how can I do or how much time I would expect to
>> wait?
>
> nobody can tell you anything like this. You should try to have an
> idea of the needed time by trying first with the smaller cell, then with
> a small  supercell, etc..
>
> Paolo
> --
> Paolo Giannozzi, Democritos and University of Udine, Italy
>
>
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