[Wien] parallel under sge environment

[zhaoyh]

Thanks for your suggestion. 
It looks like that I'd better try mpi paralleling than k-points
paralleling.

yonghong
On Tue, 2010-04-20 at 07:32 -0500, Laurence Marks wrote:
> Several comments:
> 
> 1) Your sysadmin is expecting you to run single mpi jobs, rather than
> the Wien2k method of splitting up k-points to run on different
> machines. So long as you are setting up a machines file correctly,
> using mpi and are using 9.3 I think you can set MPI_REMOTE=0 and
> USE_REMOTE=0 and avoid rsh/ssh completely. If you have no rsh/ssh you
> are not going to be able to do anything except use mpi.
> 
> 2) More serious. In the submit.sh script you attached there is the line
> module load compilers/gcc/4.1.2 mpi/openmpi/1.3.4_gcc
> 
> Obviously you don't want gcc for the compilers. Very serious --
> openmpi 1.3.4 has several bugs in it which will prevent running large
> Wien2k jobs but are OK for small ones. Use version 1.4.X if available,
> otherwise request that it be compiled.
> 
> N.B., I have a small utility somewhere (it is too early in the morning
> at the moment in the US for me to find it) which will create a Wien2k
> machines file for qsub/msub and a few other cases which I can send --
> you can probably customize it for the particular format you have in
> the PE_HOSTS file.
> 
> 2010/4/20 zhaoyh <yhzhao.mail at gmail.com>:
> > Dear Prof. Blaha,
> >
> > Thanks for your reply.
> >
> > "I cannot use ssh" means that this supercomputer doesn't allow users to
> > log in to the compute node directly. I have consulted the admin already.
> > He just ask me to use sge script to submit job. The attachment is the
> > sge script used to submit a PWSCF job.
> >
> > I also have tried "ssh-keygen -t rsa", and copy the public key to
> > authorized-key. However, it still prompts me to input the password of
> > the compute node when using "ssh node1.........".
> >
> > In fact, I just want to use wien2k under the k-points paralleling, not
> > the mpi-version, because the cell contains only about forty atoms.
> >
> > Any suggestion is grateful.
> >
> > Regards,
> >
> > yonghong
> > On Tue, 2010-04-20 at 08:12 +0200, Peter Blaha wrote:
> >> What does it mean: "I cannot use ssh".
> >> You need to describe your procedure and the error message in much more
> >> detail.
> >>
> >> -----------------------------------------------------------
> >> It depends on your cases, if you want to use k-parallel or mpi-parallel
> >> versions.
> >> For small cases (less than 20-40 atoms) the mpi-version is completely
> >> useless!!! It may even run faster on one node than on 16.
> >>
> >> You have to follow the previous advise:
> >>
> >> Ask your computing center if ssh is possible and how one can do it.
> >>
> >> You may need to generate ssh-keys  (ssh-keygen -t rsa)
> >> and copy the public key into "authorized_keys".
> >>
> >> if ssh is really not possible (I doubt that!), install WIEN2k with the
> >> option "shared memory" in siteconfig.
> >> Then you can at least use all 4-8 cores of one node (if your hardware
> >> has dual quadcore nodes) for k-parallel runs.
> >>
> >> Just to be sure: Most likely you cannot ssh from the fronend (where you
> >> login) to the compute nodes, so you need to put the run_lapw -p into
> >> your script.
> >>
> >> Maybe you need some additional switches in your job script to get a
> >> proper environment.....
> >>
> >>
> >> Am 19.04.2010 21:39, schrieb zhaoyh:
> >> > Dear Blaha,
> >> >
> >> > I want to use wien2k in a supercomputer which uses sge batch submission
> >> > system. I can use sge variable $PE_HOSTFILE to get the name of the
> >> > computing nodes, and then write the correct .machines file. However, I
> >> > cannot use ssh or rsh to log in the computing nodes then I cannot
> >> > execute run_lapw which include "rsh/ssh node...." command.
> >> >
> >> > Would you please help me?
> >> >
> >> > Regards,
> >> >
> >> > Yonghong Zhao
> >> >
> >> >
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> >>
> >
> >
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> >
> 
> 
> 
> -- 
> Laurence Marks
> Department of Materials Science and Engineering
> MSE Rm 2036 Cook Hall
> 2220 N Campus Drive
> Northwestern University
> Evanston, IL 60208, USA
> Tel: (847) 491-3996 Fax: (847) 491-7820
> email: L-marks at northwestern dot edu
> Web: www.numis.northwestern.edu
> Chair, Commission on Electron Crystallography of IUCR
> www.numis.northwestern.edu/
> Electron crystallography is the branch of science that uses electron
> scattering and imaging to study the structure of matter.
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