<div dir="ltr"><div dir="ltr">Dear all WIEN2k users,<br>Thank you for your guides.<div>>take care on the correct location ...<br>It is the /usr/share/Modules/init<br>After adding the “source /usr/share/Modules/init/tcsh” line in to the script the same error appeared:<br>mpirun: command not found</div><div><br>In fact, with and without “source /usr/share/Modules/init/tcsh” it is written in slurm.out file that
“
module load complete
”.</div><div><br></div><div>I noticed that “export” is also the bash command so I used these commands to path the openmpi and fftw:<br>setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib<br>set path = ($path /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin)</div><div>But result is the same:<br>bash: mpirun: command not found<br></div><div><br>By using this line in the script:<br>/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpiexec /home/users/mollabashi/codes/v21.1/run_lapw -p<br>The calculation stopped with the following error:<br>mpirun does not support recursive calls</div><div><br>> I wonder that you have only single modules…<br>There are different versions of ifort and mkl: ifort/15.0.0, ifort/15.0.3, ifort/17.0.1, ifort/19.1.3.304(default) mkl/11.2, mkl/<a href="http://11.2.3.187">11.2.3.187</a> mkl/2017.1.132, mkl/2019.2.187, mkl/2020.0.4(default). I used the defaults<br>> you may also wish to make a single module file to be loaded…<br>That is a good idea.<br>> On our cluster we have different W2k modules ….<br>As you know WIEN2k is not a free code and the users of the cluster that I am using are not registered WIEN2k users. Thus, according to my moral commitment to the WIEN2k developers, I cannot ask the administrator to install it on the cluster. I should install it on my user account.</div><div><br></div><div>Sincerely yours,<br>Leila<br>>PS.: maybe one should mention this tcsh "problem" in the slurm.job example on the FAQ page by adding (or similar)…<br>That is a good idea. Thank you for your suggestion.<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 3, 2021 at 4:18 PM 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">Dear Leila<br>
In your first mail you mentioned that you use<br>
slurm.job<br>
with the added lines <br>
module load openmpi/4.1.0_gcc620<br>
module load ifort<br>
module load mkl<br>
<br>
Sorry that my Sunday evening answer was too short, here a little more detail:<br>
I guess your login shell is bash, and you run the command <br>
sbatch slurm.job <br>
that is written for tcsh, but tcsh does not know where the module command is, therfore the job file should tell it where it is, <br>
e.g.: the beginning of slurm.job should look like <br>
<br>
#!/bin/tcsh<br>
#<br>
# Load the respective software module you intend to use, here for tcsh shell<br>
# NOTE: you may need to edit the source line !<br>
source /usr/share/lmod/lmod/init/tcsh<br>
module load openmpi/4.1.0_gcc620<br>
module load ifort<br>
module load mkl <br>
<br>
take care on the correct location it may be in: /usr/share/modules/init/csh<br>
if you do not find its correct location then ask your administrator<br>
<br>
I wonder that you have only single modules for ifort and mkl and not different version, <br>
I guess that are defaults, but which ? ask your administrator;<br>
you may also wish to make a single module file to be loaded, and<br>
you may also whish to send the output to the data nirvana by using >& /dev/null<br>
in that case you may have only the lines (as an example)<br>
source /usr/share/lmod/lmod/init/tcsh<br>
module load Wien2k/wien2k_21_intel19 >& /dev/null<br>
echo -n "Running Wien2k" $WienVersion<br>
<br>
<br>
PS.: maybe one should mention this tcsh "problem" in the slurm.job example on the FAQ page by adding (or similar)<br>
# NOTE: you may need to edit the following line !<br>
# source /usr/share/lmod/lmod/init/tcsh<br>
as modules are frequently used on clusters and allow easily to change between different versions.<br>
On our cluster we have different W2k modules that have been compiled with different libraries, compilers, and/or settings.<br>
<br>
PSS.: I am not aware of typos ;-)<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 leila mollabashi [<a href="mailto:le.mollabashi@gmail.com" target="_blank">le.mollabashi@gmail.com</a>]<br>
Gesendet: Montag, 3. Mai 2021 00:35<br>
An: A Mailing list for WIEN2k users<br>
Betreff: Re: [Wien] MPI error<br>
<br>
Thank you.<br>
<br>
On Mon, May 3, 2021, 3:04 AM Laurence Marks <<a href="mailto:laurence.marks@gmail.com" target="_blank">laurence.marks@gmail.com</a><mailto:<a href="mailto:laurence.marks@gmail.com" target="_blank">laurence.marks@gmail.com</a>>> wrote:<br>
You have to solve the "mpirun not found". That is due to your path/nfs/module -- we do not know.<br>
<br>
---<br>
Prof Laurence Marks<br>
"Research is to see what everyone else has seen, and to think what nobody else has thought", Albert Szent-Györgyi<br>
<a href="http://www.numis.northwestern.edu" rel="noreferrer" target="_blank">www.numis.northwestern.edu</a><<a href="http://www.numis.northwestern.edu" rel="noreferrer" target="_blank">http://www.numis.northwestern.edu</a>><br>
<br>
On Sun, May 2, 2021, 17:12 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>
>You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be "...:$LD_LIB..."<br>
Thank you. I have corrected it but I still have error in x lapw1 “mpirun: command not found”<br>
>Why not load the modules in the script to run a job? I have loaded but this error happened “bash: mpirun: command not found”.<br>
<br>
On Mon, May 3, 2021 at 2:23 AM Laurence Marks <<a href="mailto:laurence.marks@gmail.com" target="_blank">laurence.marks@gmail.com</a><mailto:<a href="mailto:laurence.marks@gmail.com" target="_blank">laurence.marks@gmail.com</a>>> wrote:<br>
You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be "...:$LD_LIB...".<br>
<br>
Why not load the modules in the script to run a job?<br>
<br>
---<br>
Prof Laurence Marks<br>
"Research is to see what everyone else has seen, and to think what nobody else has thought", Albert Szent-Györgyi<br>
<a href="http://www.numis.northwestern.edu" rel="noreferrer" target="_blank">www.numis.northwestern.edu</a><<a href="http://www.numis.northwestern.edu" rel="noreferrer" target="_blank">http://www.numis.northwestern.edu</a>><br>
<br>
On Sun, May 2, 2021, 16:35 leila mollabashi <<a href="mailto:le.mollabashi@gmail.com" target="_blank">le.mollabashi@gmail.com</a><mailto:<a href="mailto:le.mollabashi@gmail.com" target="_blank">le.mollabashi@gmail.com</a>>> wrote:<br>
Dear all WIEN2k users,<br>
Thank you for your reply.<br>
>The error is exactly what it says -- mpirun not found. This has something to do with the modules, almost certainly the openmpi one. You need to find where mpirun is on your system, and ensure that it is in your PATH. This is an issue with your OS, not Wien2k. However...<br>
which mpirun:<br>
/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun<br>
I have installed WIEN2k by loading ifort, mkl, openmpi/4.1.0_gcc620, fftw/3.3.8_gcc620 modules. when I added the path in my .bashrc file as followes:<br>
export LD_LIBRARY_PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/lib:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/lib:LD_LIBRARY_PATH<br>
export PATH=/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin:$PATH<br>
wien2k does not run:<br>
error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory<br>
0.000u 0.000s 0:00.00 0.0% 0+0k 0+0io 0pf+0w<br>
but without the path and by loading the modules it runs.<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>
.machines:<br>
lapw0:e0183:4<br>
1:e0183:4<br>
1:e0183:4<br>
Almost end of *output0000:<br>
TOTAL VALUE = -10433.492442 (H)<br>
:DEN : DENSITY INTEGRAL = -20866.98488444 (Ry)<br>
Almost end of *output0001<br>
TOTAL VALUE = -10433.492442 (H)<br>
>Assuming that you used gcc<br>
Yes.<br>
>For certain you cannot run lapw2 without first running lapw1.<br>
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.<br>
>How? Do you mean that there are no error messages?<br>
Yes and I also checked compile.msg in SRC_lapw1<br>
<br>
Sincerely yours,<br>
<br>
Leila<br>
<br>
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><mailto:<a href="mailto:fecher@uni-mainz.de" target="_blank">fecher@uni-mainz.de</a>>> wrote:<br>
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><mailto:<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><mailto:<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>><mailto:<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!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5s6X8cPOw$" rel="noreferrer" target="_blank">https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5s6X8cPOw$</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>
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