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<p>Comments:</p>
<p>Edison does look retired [1].<br>
</p>
<p>Based on the usage of <font color="#ff0000">hostname</font> in
Bushra's job file (below), it looks like that is configured for a
shared memory super computer.</p>
<p>However, if the super computer is not a shared memory (single
node) system but a distributed memory (multiple node) system [2],
the use of <font color="#ff0000">hostname</font> is potentially
problematic.</p>
<p>That is because on a distributed memory system the head node
typical is not a compute node [3]. <br>
</p>
<p>One bad thing that can happen is that head node calculations can
break the cluster login, for example [4]:</p>
<p><i>Do NOT use the login nodes for work. If everyone does this,
the login nodes will crash keeping 700+ HPC users from being
able to login to the cluster.</i><i><br>
</i></p>
<p>It depends on local policy, but most clusters I have seen have a
policy that the system administrators can permanently take away a
user's access to the cluster if a calculation is executed on the
head node, for example [5]:</p>
<p><i>CHTC staff reserve the right to kill any long-running or
problematic processes on the head nodes and/or disable user
accounts that violate this policy, and users may not be notified
of account deactivation.</i><br>
</p>
<p>Instead of <font color="#ff0000">hostname</font>, the job file
usually needs to get a node list that it gets from the queuing
system's job scheduler. That could be a script like gen.machines
[6] or Machines2W [7]. Or it could be environment variable, which
name depends on the queuing system, for example the PBS_NODEFILE
variable for PBS [8,9].<br>
</p>
[1]
<a class="moz-txt-link-freetext" href="https://www.nersc.gov/news-publications/nersc-news/nersc-center-news/2019/edison-supercomputer-to-retire-after-five-years-of-service/">https://www.nersc.gov/news-publications/nersc-news/nersc-center-news/2019/edison-supercomputer-to-retire-after-five-years-of-service/</a><br>
[2]
<a class="moz-txt-link-freetext" href="https://www.researchgate.net/figure/Shared-vs-Distributed-memory_fig3_323108484">https://www.researchgate.net/figure/Shared-vs-Distributed-memory_fig3_323108484</a><br>
[3] <a class="moz-txt-link-freetext" href="https://zhanglab.ccmb.med.umich.edu/docs/node9.html">https://zhanglab.ccmb.med.umich.edu/docs/node9.html</a><br>
[4] <a class="moz-txt-link-freetext" href="https://hpc.oit.uci.edu/running-jobs">https://hpc.oit.uci.edu/running-jobs</a><br>
[5] <a class="moz-txt-link-freetext" href="http://chtc.cs.wisc.edu/HPCuseguide.shtml">http://chtc.cs.wisc.edu/HPCuseguide.shtml</a><br>
<font face="Times New Roman">[6]
<a class="moz-txt-link-freetext" href="https://docs.nersc.gov/applications/wien2k/">https://docs.nersc.gov/applications/wien2k/</a></font><br>
[7] SRC_mpiutil:
<a class="moz-txt-link-freetext" href="http://susi.theochem.tuwien.ac.at/reg_user/unsupported/">http://susi.theochem.tuwien.ac.at/reg_user/unsupported/</a><br>
<div class="moz-cite-prefix">[8] Script for "pbs":
<a class="moz-txt-link-freetext" href="http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html">http://susi.theochem.tuwien.ac.at/reg_user/faq/pbs.html</a></div>
<div class="moz-cite-prefix">[9]
<a class="moz-txt-link-freetext" href="http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm">http://docs.adaptivecomputing.com/torque/4-0-2/Content/topics/commands/qsub.htm</a><br>
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<div class="moz-cite-prefix"><br>
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<div class="moz-cite-prefix">On 11/4/2019 6:37 AM, Dr. K. C. Bhamu
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAJYci+RZwO2y8xhYvB5KRzctzuPfhEw_8_HqPRF4fd2kkGFYoA@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div style="font-size:large" class="gmail_default">Dear Bushra,</div>
<div style="font-size:large" class="gmail_default"><br>
</div>
<div style="font-size:large" class="gmail_default">I hope you
are using the same cluster you are using before (NERSC:
cori/edison).</div>
<div style="font-size:large" class="gmail_default">From your job
file it seems that you want to submit job on edison (28
cores).</div>
<div style="font-size:large" class="gmail_default">Please make
sure that edison is still working. My available information
says that edison has retired now. Please confirm from the
system admin.</div>
<div style="font-size:large" class="gmail_default">I would
suggest you to submit job on cori. A job file is there on
web-page of NERSC.</div>
<div style="font-size:large" class="gmail_default"><br>
</div>
<div style="font-size:large" class="gmail_default">Anyway,
please send the details as Prof. Peter has requested so that
he can help you.<br>
</div>
<div style="font-size:large" class="gmail_default"><br>
</div>
<div style="font-size:large" class="gmail_default"><br>
</div>
<div style="font-size:large" class="gmail_default">Regards</div>
<div style="font-size:large" class="gmail_default">Bhamu<br>
</div>
<div style="font-size:large" class="gmail_default"><br>
</div>
</div>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Nov 4, 2019 at 1:14 PM
Peter Blaha <<a href="mailto:pblaha@theochem.tuwien.ac.at"
moz-do-not-send="true">pblaha@theochem.tuwien.ac.at</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">What
means: " does not work" ??<br>
<br>
We need details.<br>
<br>
On 11/3/19 10:48 PM, BUSHRA SABIR wrote:<br>
> Hi experts,<br>
> I am working on super computer with WIEN2K/19.1 and using
the following <br>
> job file, but this job file is not working for parallel
run of LAPW1.<br>
> Need help to improve this job file.<br>
> #!/bin/bash<br>
> #SBATCH -N 1<br>
> #SBATCH -p RM<br>
> #SBATCH --ntasks-per-node 28<br>
> #SBATCH -t 2:0:00<br>
> # echo commands to stdout<br>
> # set -x<br>
> module load mpi<br>
> module load intel<br>
> export SCRATCH="./"<br>
> <br>
> #rm .machines<br>
> #write .machines file<br>
> echo '#' .machines<br>
> # example for an MPI parallel lapw0<br>
> #echo 'lapw0:'`hostname`' :'$nproc >> .machines<br>
> # k-point and mpi parallel lapw1/2<br>
> <br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> echo '1:'`<font color="#ff0000">hostname</font>`':1'
>> .machines<br>
> <br>
> echo 'granularity:1' >>.machines<br>
> echo 'extrafine:1' >>.machines<br>
> export SCRATCH=./<br>
> runsp_lapw -p -ec 0.000001 -cc 0.0001 -i 40 -fc 1.0<br>
> <br>
> <br>
> Bushra<br>
> <br>
> <br>
>
------------------------------------------------------------------------<br>
> <br>
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> <br>
<br>
-- <br>
<br>
P.Blaha<br>
--------------------------------------------------------------------------<br>
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060
Vienna<br>
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982<br>
Email: <a href="mailto:blaha@theochem.tuwien.ac.at"
target="_blank" moz-do-not-send="true">blaha@theochem.tuwien.ac.at</a>
WIEN2k: <a href="http://www.wien2k.at" rel="noreferrer"
target="_blank" moz-do-not-send="true">http://www.wien2k.at</a><br>
WWW: <a href="http://www.imc.tuwien.ac.at/TC_Blaha"
rel="noreferrer" target="_blank" moz-do-not-send="true">http://www.imc.tuwien.ac.at/TC_Blaha</a><br>
--------------------------------------------------------------------------<br>
</blockquote>
</div>
</blockquote>
<blockquote type="cite"
cite="mid:CAJYci+RZwO2y8xhYvB5KRzctzuPfhEw_8_HqPRF4fd2kkGFYoA@mail.gmail.com"></blockquote>
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