<div dir="ltr"><pre style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:Consolas"><span style="font-family:"Times New Roman",serif">Dear all</span><span lang="EN-US" style="font-family:"Times New Roman",serif"></span></pre><pre style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:Consolas"><span lang="EN-US" style="font-family:"Times New Roman",serif">The admin told me that I can use this line in the script “</span><span style="font-family:"Courier New"">/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpiexec /home/users/SOME_USER/app/my_mpi_app -o option 1 -in /home/users/SOME_USER/path/to/input1 -o ./output1”</span></pre><pre style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:Consolas"><span style="font-family:"Times New Roman",serif">Would you please guide me about this line? Should I use “run_lapw -p” insead of my_mpi_app? I don’t know what should I do instead of input1 and output1</span></pre><pre style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:Consolas"><span style="font-family:"Times New Roman",serif">Sincerely yours,</span></pre><pre style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:Consolas"><span style="font-family:"Times New Roman",serif">Leila</span></pre></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 3, 2021 at 2:04 AM leila mollabashi <<a href="mailto:le.mollabashi@gmail.com">le.mollabashi@gmail.com</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 dir="ltr"><p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">Dear all WIEN2k users,</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">Thank you for your reply.</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:rgb(31,73,125)">>The error is exactly what it says -- mpirun not found. This has
something to do with the modules, almost certainly the openmpi one. You need to
find where mpirun is on your system, and ensure that it is in your PATH. This
is an issue with your OS, not Wien2k. However...</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span lang="EN-US" style="font-family:"Times New Roman",serif">which mpirun:</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span lang="EN-US" style="font-family:"Times New Roman",serif;color:rgb(31,73,125)">/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:black">I have installed WIEN2k by loading ifort, mkl, openmpi/4.1.0_gcc620, fftw/3.3.8_gcc620 modules. when I added the
path in my .bashrc file as followes:</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:rgb(31,73,125)">export
LD_LIBRARY_PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib:LD_LIBRARY_PATH</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:rgb(31,73,125)">export PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin:$PATH</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:black">wien2k </span><span style="font-family:"Times New Roman",serif">does not</span><span style="font-family:"Times New Roman",serif;color:black"> run:</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:rgb(192,80,77)">error while loading shared libraries: libiomp5.so: cannot open shared
object file: No such file or directory</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:rgb(192,80,77)">0.000u 0.000s 0:00.00 0.0% 0+0k 0+0io
0pf+0w </span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">but without the path and by loading
the modules it runs.</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">></span><span style="font-size:12pt;font-family:Verdana,sans-serif;color:black"> </span><span style="font-family:"Times New Roman",serif">First do
"x lapw0 -p", send the .machines file and the last few lines of your
*.output0*. Then we can confirm if that worked right, did not or what.</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">.machines:</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:rgb(31,73,125)">lapw0:e0183:4</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:rgb(31,73,125)">1:e0183:4</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:rgb(31,73,125)">1:e0183:4</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">Almost end of *output0000:</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:10pt;font-family:"Times New Roman",serif;color:rgb(79,129,189)">TOTAL VALUE = -10433.492442 (H)</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:10pt;font-family:"Times New Roman",serif;color:rgb(79,129,189)">:DEN :
DENSITY INTEGRAL = -20866.98488444 (Ry)</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">Almost end of *output0001</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:10pt;font-family:"Times New Roman",serif;color:rgb(79,129,189)">TOTAL VALUE = -10433.492442 (H)</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">>Assuming that you used gcc</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">Yes.</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">>For certain you cannot run
lapw2 without first running lapw1.</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif">Yes. You are right. When x
lapw1 –p has not executed I have changed the .machines file and run in kpoint
parallel mode then changed the .machines file again and run lapw2 –p.</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:black;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">>How? Do you mean that there are no error messages?</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-family:"Times New Roman",serif;color:black;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">Yes and I also checked compile.msg in SRC_lapw1 </span><span style="font-size:10pt;font-family:"Times New Roman",serif;color:rgb(79,129,189)"></span></p>
<pre style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:Consolas"><span style="font-size:11pt;font-family:"Times New Roman",serif">Sincerely yours,</span></pre><pre style="background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 0.0001pt;font-size:10pt;font-family:Consolas"><span style="font-size:11pt;font-family:"Times New Roman",serif">Leila</span></pre></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 3, 2021 at 12:42 AM Fecher, Gerhard <<a href="mailto:fecher@uni-mainz.de" target="_blank">fecher@uni-mainz.de</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">I guess that module does not work with tcsh <br>
<br>
Ciao<br>
Gerhard<br>
<br>
DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:<br>
"I think the problem, to be quite honest with you,<br>
is that you have never actually known what the question is."<br>
<br>
====================================<br>
Dr. Gerhard H. Fecher<br>
Institut of Physics<br>
Johannes Gutenberg - University<br>
55099 Mainz<br>
________________________________________<br>
Von: Wien [<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a>] im Auftrag von Laurence Marks [<a href="mailto:laurence.marks@gmail.com" target="_blank">laurence.marks@gmail.com</a>]<br>
Gesendet: Sonntag, 2. Mai 2021 21:32<br>
An: A Mailing list for WIEN2k users<br>
Betreff: Re: [Wien] MPI error<br>
<br>
Inlined response and questions<br>
<br>
On Sun, May 2, 2021 at 2:19 PM leila mollabashi <<a href="mailto:le.mollabashi@gmail.com" target="_blank">le.mollabashi@gmail.com</a><mailto:<a href="mailto:le.mollabashi@gmail.com" target="_blank">le.mollabashi@gmail.com</a>>> wrote:<br>
Dear Prof. Peter Blaha and WIEN2k users,<br>
Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told me that I can use your script in ><a href="http://www.wien2k.at/reg_user/faq/slurm.job" rel="noreferrer" target="_blank">http://www.wien2k.at/reg_user/faq/slurm.job</a><<a href="https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!G_67ZheBzKx4rn9SJ-7AOPNV2M9DFC6mHQ4b1S_sPZITO1RwQsLYLGNWwENJJwPKlowiXQ$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!G_67ZheBzKx4rn9SJ-7AOPNV2M9DFC6mHQ4b1S_sPZITO1RwQsLYLGNWwENJJwPKlowiXQ$</a>> . I added this lines to it too:<br>
module load openmpi/4.1.0_gcc620<br>
module load ifort<br>
module load mkl<br>
but this error happened “bash: mpirun: command not found”.<br>
The error is exactly what it says -- mpirun not found. This has something to do with the modules, almost certainly the openmpi one. You need to find where mpirun is on your system, and ensure that it is in your PATH. This is an issue with your OS, not Wien2k. However...<br>
<br>
In an interactive mode “x lapw0 –p” and “x lapw2 –p” are executed MPI but “x lapw1 –p” is stoped with following error:<br>
w2k_dispatch_signal(): received: Segmentation fault<br>
Is this mpi mode? None of lapw0/1/2 can work in true parallel without mpirun, so there is something major wrong here. I doubt that anything really executed properly. For certain you cannot run lapw2 without first running lapw1. What is your .machines file? what is the content of the error files? (cat *.error).<br>
<br>
First do "x lapw0 -p", send the .machines file and the last few lines of your *.output0*. Then we can confirm if that worked right, did not or what.<br>
<br>
--------------------------------------------------------------------------<br>
I noticed that the FFTW3 and OpenMPI installed on the cluster are both compiled by gfortan. But I have compiled WIEN2k by intel ifort. I am not sure whether the problem originates from this inconsistency between gfortan and ifort.<br>
Almost everything in FFTW3 and OpenMPI is in fact c. Assuming that you used gcc there should be no problem. In general there should be no problem.<br>
<br>
I have checked that lapw1 has compiled correctly.<br>
How? Do you mean that there are no error messages?<br>
<br>
<br>
Sincerely yours,<br>
<br>
Leila<br>
<br>
<br>
<br>
_______________________________________________<br>
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SEARCH the MAILING-LIST at: <a href="http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html" rel="noreferrer" target="_blank">http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html</a><br>
</blockquote></div>
</blockquote></div>