<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Thank you! The ssh was, in fact, the issue. We have three workstations linked as a “cluster” via nfs mounts and set up our system to use modules that load certain elements into the PATH, so the ssh was losing the loaded modules. Everything seems to be working OK now.</div><div dir="ltr"><br></div><div dir="ltr">Matt</div><div dir="ltr"><br>On Jan 10, 2019, at 11:10 PM, Gavin Abo <<a href="mailto:gsabo@crimson.ua.edu">gsabo@crimson.ua.edu</a>> wrote:<br><br></div><blockquote type="cite"><div dir="ltr">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<p>As Prof. Marks hinted at, it looks to me that mpirun is properly
set in your PATH of your current terminal such that mpirun works.</p>
<p>However, when you run "run_lapw -p", probably when that script
executes the lapw1para_lapw script, the program is probably then
doing an ssh into the nodes you have set in your .machines file.
It is on the nodes that that mpirun command probably cannot be
found.</p>
<p>You can likely test if that is the case in the terminal by trying
commands like:</p>
ssh localhost<br>
which mpirun<br>
exit
<p>where localhost above should be replaced by the hostname (or ip
address) to one of your local (e.g.
<a class="moz-txt-link-freetext" href="https://en.wikipedia.org/wiki/Localhost">https://en.wikipedia.org/wiki/Localhost</a> ) or remote nodes that you
have used in your hand edited .machines file. Or if your
.machines file is created automatically on the fly by your job
script [ <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>
], which is usually the case for the clusters needed and used for
mpi parallel calculations, you should be able find the hostnames
in the .machines file that it tried to use for the calculation
when it failed.<br>
</p>
<p>If you set the base path to mpirun in the PATH of your .bashrc
(or .cshrc) [e.g.,
<a class="moz-txt-link-freetext" href="https://www.open-mpi.org/faq/?category=running#adding-ompi-to-path">https://www.open-mpi.org/faq/?category=running#adding-ompi-to-path</a>
] and your system pushes that out to all nodes, that might resolve
the problem. If you are using a job script, depending on your
queuing system, you might have to add an option to push the
environment to the nodes [
<a class="moz-txt-link-freetext" href="https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15985.html">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15985.html</a>
].<br>
</p>
<p>If your system doesn't access remote nodes with ssh, see section
"11.4 Environment Variables" in the WIEN2k 18.2 userguide
[<a class="moz-txt-link-freetext" href="http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf">http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf</a>]
about setting "USE_REMOTE 0" in parallel_options so that it does
not use ssh.</p>
<p>Depending on the hardware specifications of your workstation,
keep in mind as mentioned in the list before if it is a
general-purpose computer, and not a high performance computing
(HPC) cluster [ <a class="moz-txt-link-freetext" href="https://en.wikipedia.org/wiki/Supercomputer">https://en.wikipedia.org/wiki/Supercomputer</a> ],
that k-point parallel might work better than mpi parallel for
certain computer systems (or calculation cases):</p>
<a class="moz-txt-link-freetext" href="http://susi.theochem.tuwien.ac.at/reg_user/benchmark/">http://susi.theochem.tuwien.ac.at/reg_user/benchmark/</a><br>
<a class="moz-txt-link-freetext" href="https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg03793.html">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg03793.html</a><br>
<a class="moz-txt-link-freetext" href="https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08301.html">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08301.html</a><br>
<a class="moz-txt-link-freetext" href="https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13632.html">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13632.html</a><br>
<a class="moz-txt-link-freetext" href="https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09334.html">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg09334.html</a><br>
<br>
<div class="moz-cite-prefix">On 1/10/2019 12:44 PM, Laurence Marks
wrote:<br>
</div>
<blockquote type="cite" cite="mid:CANkSMZAW+Niwub7Ynd7fGWo1Stf0pFCFK1bdFHy6g+bA53kViw@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div class="gmail_default" style="font-family:verdana,sans-serif;color:#000000">Most
probably you forgot to export your PATH (e.g. from bash do
"export PATH") so the information is not making it beyond your
shell. You might have a bad csh/tcsh. Try adding "which
lapw1_mpi" to $WIENROOT/parallel_options, and check that file
has correct setenv for WIEN_MPIRUN.</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Thu, Jan 10, 2019 at 12:00 PM Matthew D Redell
<<a href="mailto:mredell1@binghamton.edu" moz-do-not-send="true">mredell1@binghamton.edu</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">
<div style="overflow-wrap: break-word;">
Hello,
<div><br>
</div>
<div>I am running WIEN2k_2018.2 on CentOs7 and have come
across the following problem that I cannot seem to
resolve.</div>
<div><br>
</div>
<div>After successfully initializing the calculation and
setting up the .machines for a single host (local
workstation), I run: run_lapw -p</div>
<div><br>
</div>
<div>lapw0 ends fine, but the lapw1 returns</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:10px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)"><span style="font-variant-ligatures:no-common-ligatures">bash:
mpirun: command not found</span></div>
<div><br>
</div>
<div>The same error occurs if I just try </div>
<div>x lapw1 -p</div>
<div><br>
</div>
<div>However, which mpirun</div>
<div>returns </div>
<div><span style="color:rgb(242,242,242);font-family:Monaco;font-size:10px;background-color:rgba(0,0,0,0.85)">/opt/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpirun</span></div>
<div><br class="gmail-m_3555412282474309645webkit-block-placeholder">
</div>
<div>I also did a little troubleshooting to see if I could
run lapw1 in parallel via</div>
<div>
<pre style="font-family:courier,"courier new",monospace;font-size:14px;white-space:pre-wrap;margin-top:0px;margin-bottom:0px">mpirun -n 4 lapw1_mpi lapw1_1.def</pre>
<div><br>
</div>
</div>
<div>which ran without any issues. Also, checking more…</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:10px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)"><span style="font-variant-ligatures:no-common-ligatures">grep
MPIRUN $WIENROOT/WIEN2k_OPTIONS</span></div>
</div>
<div>returns</div>
<div>
<div style="margin:0px;font-stretch:normal;font-size:10px;line-height:normal;font-family:Monaco;color:rgb(242,242,242);background-color:rgba(0,0,0,0.85)"><span style="font-variant-ligatures:no-common-ligatures">current:</span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(180,36,25)">MPIRUN</span><span style="font-variant-ligatures:no-common-ligatures">:mpirun
-np _NP_ -machinefile _HOSTS_ _EXEC_</span></div>
</div>
<div><br class="gmail-m_3555412282474309645webkit-block-placeholder">
</div>
<div>So, the only possibility I am able to deduce is that
either the run_lapw script or the lapw1para script is
not locating the mpirun command, but I do not know how
to begin sorting out this issue. Any help would be
greatly appreciated.</div>
<div><br>
</div>
<div>Best,</div>
<div>Matt</div>
<div><br>
</div>
<div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">------------------------</div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Matthew
D Redell<br>
<i>Graduate Student/Teaching Assistant</i>
<div><i>Department of Physics, Applied Physics,
and Astronomy</i></div>
<div><b>Binghamton University-State University of
New York</b></div>
<div><a href="mailto:mredell1@binghamton.edu" target="_blank" moz-do-not-send="true">E-mail:
mredell1@binghamton.edu</a></div>
<div>Office: SN-2011D<br>
<div><br>
</div>
</div>
</div>
<br class="gmail-m_3555412282474309645Apple-interchange-newline">
</div>
<br class="gmail-m_3555412282474309645Apple-interchange-newline">
</div>
<br class="gmail-m_3555412282474309645Apple-interchange-newline">
<br class="gmail-m_3555412282474309645Apple-interchange-newline">
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr"><span style="font-size:12.8px">Professor
Laurence Marks</span><br>
</div>
<div dir="ltr"><span style="font-size:12.8px">"Research
is to see what everybody else has seen, and
to think what nobody else has thought", </span><span style="font-size:12.8px">Albert Szent-Gyorgi</span><br>
<a href="http://www.numis.northwestern.edu" target="_blank" moz-do-not-send="true">www.numis.northwestern.edu</a> ; <span style="font-size:12.8px">Corrosion in 4D: </span><a href="http://MURI4D.numis.northwestern.edu" style="font-size:12.8px" target="_blank" moz-do-not-send="true">MURI4D.numis.northwestern.edu</a>
<div><span style="font-size:12.8px">Partner of
the CFW 100% program for gender equity, </span><a href="http://www.cfw.org/100-percent" style="font-size:12.8px" target="_blank" moz-do-not-send="true">www.cfw.org/100-percent</a></div>
<div>Co-Editor, Acta Cryst A</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<blockquote type="cite" cite="mid:CANkSMZAW+Niwub7Ynd7fGWo1Stf0pFCFK1bdFHy6g+bA53kViw@mail.gmail.com"></blockquote>
</div></blockquote><blockquote type="cite"><div dir="ltr"><span>_______________________________________________</span><br><span>Wien mailing list</span><br><span><a href="mailto:Wien@zeus.theochem.tuwien.ac.at">Wien@zeus.theochem.tuwien.ac.at</a></span><br><span><a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a></span><br><span>SEARCH the MAILING-LIST at: <a href="http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html">http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html</a></span><br></div></blockquote></body></html>