[Wien] [Wien2k Users] SGE Queuing System

[Laurence Marks]

What is the specific format in $TMPDIR/machines ? I have an
experimental code to generate a machines file which works for
qsub/msub and the sgimpi format, and if you (or someone else) can
provide this I can probably add it. The idea is to have a "x
Machines2W -opt" or similar command where "opt" would be qsub/msub/sgi
or other.

N.B., if anyone knows of other formats, please email to my personal email.

On Sat, Feb 6, 2010 at 10:09 AM, Duy Le <ttduyle at gmail.com> wrote:
> I have some notes, hope those help you:
>
> 1. W2web looks simple but it is complicated than command mode. So if
> you want to use it, use it for initializing the calculation only. You
> should not rely on w2web.
>
> 2. mpi or k-parallel or hybrid mod is defined by a file name
> .machines. Depend on this .machines file, wien2k will do mpi,
> k-parallel, or hybrid mod.
> User the wien2k guide to learn the structure of .machines file.
> Of course, you have to use also option -p
>
> 3. If you use queue system, you have to be able to parse the .machines
> file on the fly because you don't know which nodes (cores) you jobs
> will use. For this reason, w2web is very complicated.
>
> 4. Here is a sample of job file for sge engine
> http://www.wien2k.at/reg_user/faq/sge.job
> Hope you can get a idea of making job file.
>
>
> --------------------------------------------------
> Duy Le
> PhD Student
> Department of Physics
> University of Central Florida.
>
> "Men don't need hand to do things"
>
>
>
> On Fri, Feb 5, 2010 at 10:05 PM, Ghosh SUDDHASATTWA
> <ssghosh at igcar.gov.in> wrote:
>> Dear Sir,
>> My question was on the procedure of running jobs in Wien2k and not
>> submitting jobs in Wien.
>> In case, we have configured Wien2k both by mpi parallel and k-point
>> parallel, how do we tell through w2web that we want to run the job in mpi
>> parallel (and not k-point parallel) or for that matter k-point parallel.
>> The website http://wiki.cse.ucdavis.edu/support:hpc:software:wien2k gives
>> some details on how to run jobs in Wien2k by hybrid mode etc.
>> What I want to know is how do we specifically tell Wien2k to run by mpi
>> parallel by w2web.
>>
>> Suddhasattwa Ghosh
>>
>>
>> -----Original Message-----
>> From: wien-bounces at zeus.theochem.tuwien.ac.at
>> [mailto:wien-bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Peter Blaha
>> Sent: Wednesday, February 03, 2010 7:52 PM
>> To: A Mailing list for WIEN2k users
>> Subject: Re: [Wien] [Wien2k Users] SGE Queuing System
>>
>> If you really want to "click" (means use w2web), you have to configure
>> YOURSELF an "execution type", which submits a job to your queuing system
>> (SGE).
>> How to do this is briefly sketched in the UG (section 11.3). Together
>> with the provided templates (also on the faq section on www.wien2k.at)
>> it should be possible to do this, but it requires some (advanced)
>> knowledge on scripting.
>>
>> Personally, I think this is rather useless anyway, because using a
>> computer with queuing system requires anyway that you learn and use some
>> commands specific for this queing system and thus you can also submit the
>> job
>> by typing    "qsub job"  (instead of "clicking".
>>
>> Use w2web for    initialization and for analysis (tasks), but run the scf
>> cycle
>> (or min_lapw) from the command line.
>>
>>
>>
>> Ghosh SUDDHASATTWA schrieb:
>>> Thanks Marks for the reply.
>>> That means if we configure Wien2k by mpi parallel, then by clicking the
>>> parallel option in w2web, it is most likely (if our machines file is
>>> correct) that it will run mpi_lapw! and not lapw.
>>>
>>> Suddhasattwa Ghosh
>>>
>>>
>>> -----Original Message-----
>>> From: wien-bounces at zeus.theochem.tuwien.ac.at
>>> [mailto:wien-bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Laurence
>> Marks
>>> Sent: Wednesday, February 03, 2010 7:28 PM
>>> To: A Mailing list for WIEN2k users
>>> Subject: Re: [Wien] [Wien2k Users] SGE Queuing System
>>>
>>> I think the answer to your question is that Wien2k does not know, you
>>> as the user are responsible for this, an appropriate submission script
>>> as well as having the right form of the .machines file. You should do
>>> some google searching of documents on SGE, and you will almost
>>> certainly have to submit jobs outside of w2web.
>>>
>>> 2010/2/3 Ghosh SUDDHASATTWA <ssghosh at igcar.gov.in>:
>>>> Dear Prof. Blaha,
>>>>
>>>> I have posted this mail before. Unfortunately, I have not got any
>> response
>>>> so far. Since I am fairly a new user of Wien2k, I would kindly request
>> you
>>>> to help me in this regard.
>>>>
>>>> I would like to configure Wien2k in mpi parallel and k-point mode.
>>>>
>>>> My system is SGE.
>>>>
>>>> I would like to know as to how by w2web we can ask Wien2k to work by mpi
>>>> parallel or through by k-point parallel. How Wien2k knows that my job
>>>> submission system is SGE and not PBS.
>>>>
>>>>
>>>>
>>>> Kindly reply.
>>>>
>>>> Suddhasattwa Ghosh
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Wien mailing list
>>>> Wien at zeus.theochem.tuwien.ac.at
>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>>
>>>>
>>>
>>>
>>>
>>
>> --
>>
>>                                       P.Blaha
>> --------------------------------------------------------------------------
>> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
>> Phone: +43-1-58801-15671             FAX: +43-1-58801-15698
>> Email: blaha at theochem.tuwien.ac.at    WWW:
>> http://info.tuwien.ac.at/theochem/
>> --------------------------------------------------------------------------
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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.