[Wien] .machines files and pbs system

[Bin Shao]

Dear Prof. Peter Blaha,

Thank your for your reply!

Best,

On Wed, Nov 9, 2011 at 12:23 AM, Peter Blaha
<pblaha at theochem.tuwien.ac.at>wrote:

> The problem is the following:
>
> When doing a scf calculation (run_lapw -p), the
> x lapw1 -p step will use the    .machines   file
> for parallelization (usually created on the fly by the PBS job),
> but at the same time it will create automatically a
> .processes  file, which will be used for parallelization
> of the later steps of an scf (lapwso, lapw2).
>
> This scheme allows to modify the .machines file DURING a running
> scf calculation.
>
> Thus what you have to do is modify your PBS script and create instead of
> the .machines file the   .processes file.
>
> Just examine an existing file, its content should be clear from that.
>
> Am 08.11.2011 12:07, schrieb Bin Shao:
>
>> Dear all,
>>
>> I use PBS system to submit jobs to a cluster with the K-point
>> parallelization mode. I intend to do a nos-scf calculation (soc) after a
>> scf calculation. In the scf
>> calculation, the .machines files were created by the script in the wien2k
>> website. Then, I copy the directory including the old .machines files of
>> scf to a new directory to
>> do the nonscf calculation with the same submitting script, just replacing
>> the scf wien2k command with nonscf one. When I submit the new job, the pbs
>> system shows that the
>> new job run in the new nodes, but it actually run in the old nodes.
>>
>> The following is the script to submit jobs:
>>
>> # setting up local SCRATCH
>> #setenv SCRATCH /tmp/$PBS_JOBID
>>
>> # creating .machines
>> cat $PBS_NODEFILE > .machines_current
>> set aa=`wc .machines_current`
>> echo '#' > .machines
>>
>> # run lapw1/2 using k-point parallel
>> set i=1
>> while ($i <= $aa[1])
>>   echo -n '1:' >> .machines
>> #  head -$i .machines_current |tail -1 >> .machines
>>   set nn = `head -$i .machines_current |tail -1`
>>   echo $nn >> .machines
>> #  echo -n '1:' >> .machines
>> #  echo $nn >> .machines
>> #  rsh $nn mkdir -p $SCRATCH
>>   @ i++
>> end
>> echo 'granularity:1' >>.machines
>> echo 'extrafine:1' >>.machines
>>
>> # setup $delay and $sleepy
>> setenv LAPW_DELAY  1
>> setenv LAPW_SLEEPY  1
>>
>> # Wien2k command
>> runsp_lapw -p -i 100 -ec 0.000001 -NI (scf)
>> ------------------------------**------------------------------**
>> -----------------
>> # Wien2k command
>> x lapwso -up -p -c              (nonscf)
>> x lapw2 -up -p -so -c
>> x lapw2 -dn -p -so -c
>>
>> So how can I submit the new job (nonscf) to a different nodes?
>>
>> Thank you in advanced. Any suggestion will be appreciated!
>>
>> Best regards,
>>
>> --
>> Bin Shao, Ph.D. Candidate
>> College of Information Technical Science, Nankai University
>> 94 Weijin Rd. Nankai Dist. Tianjin 300071, China
>> Email: bshao at mail.nankai.edu.cn <mailto:bshao at mail.nankai.edu.**cn<bshao at mail.nankai.edu.cn>
>> >
>>
>>
>>
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>>
>
> --
> ------------------------------**-----------
> Peter Blaha
> Inst. Materials Chemistry, TU Vienna
> Getreidemarkt 9, A-1060 Vienna, Austria
> Tel: +43-1-5880115671
> Fax: +43-1-5880115698
> email: pblaha at theochem.tuwien.ac.at
> ------------------------------**-----------
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>



-- 
Bin Shao, Ph.D. Candidate
College of Information Technical Science, Nankai University
94 Weijin Rd. Nankai Dist. Tianjin 300071, China
Email: bshao at mail.nankai.edu.cn
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