[Wien] MPI error

Mon May 3 00:33:54 CEST 2021

You have to solve the "mpirun not found". That is due to your
path/nfs/module -- we do not know.

---
Prof Laurence Marks
"Research is to see what everyone else has seen, and to think what nobody
else has thought", Albert Szent-Györgyi
www.numis.northwestern.edu

On Sun, May 2, 2021, 17:12 leila mollabashi <le.mollabashi at gmail.com> wrote:

> >You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be
> "...:$LD_LIB..."
>
> Thank you. I have corrected it but I still have error in x lapw1 “mpirun:
> command not found”
>
> >Why not load the modules in the script to run a job? I have loaded but
> this error happened “bash: mpirun: command not found”.
>
> On Mon, May 3, 2021 at 2:23 AM Laurence Marks <laurence.marks at gmail.com>
> wrote:
>
>> You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be
>> "...:$LD_LIB...".
>>
>> Why not load the modules in the script to run a job?
>>
>> ---
>> Prof Laurence Marks
>> "Research is to see what everyone else has seen, and to think what nobody
>> else has thought", Albert Szent-Györgyi
>> www.numis.northwestern.edu
>>
>> On Sun, May 2, 2021, 16:35 leila mollabashi <le.mollabashi at gmail.com>
>> wrote:
>>
>>> Dear all WIEN2k users,
>>>
>>> Thank you for your reply.
>>>
>>> >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...
>>>
>>> which mpirun:
>>>
>>> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpirun
>>>
>>> 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:
>>>
>>> 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
>>>
>>> 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
>>>
>>> wien2k does not run:
>>>
>>> error while loading shared libraries: libiomp5.so: cannot open shared
>>> object file: No such file or directory
>>>
>>> 0.000u 0.000s 0:00.00 0.0%      0+0k 0+0io 0pf+0w
>>>
>>> but without the path and by loading the modules it runs.
>>>
>>> > 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.
>>>
>>> .machines:
>>>
>>> lapw0:e0183:4
>>>
>>> 1:e0183:4
>>>
>>> 1:e0183:4
>>>
>>> Almost end of *output0000:
>>>
>>> TOTAL VALUE = -10433.492442     (H)
>>>
>>> :DEN  : DENSITY INTEGRAL  =        -20866.98488444   (Ry)
>>>
>>> Almost end of *output0001
>>>
>>> TOTAL VALUE = -10433.492442     (H)
>>>
>>> >Assuming that you used gcc
>>>
>>> Yes.
>>>
>>> >For certain you cannot run lapw2 without first running lapw1.
>>>
>>> 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.
>>>
>>> >How? Do you mean that there are no error messages?
>>>
>>> Yes and I also checked compile.msg in SRC_lapw1
>>>
>>> Sincerely yours,
>>>
>>> Leila
>>>
>>>
>>> On Mon, May 3, 2021 at 12:42 AM Fecher, Gerhard <fecher at uni-mainz.de>
>>> wrote:
>>>
>>>> I guess that module does not work with tcsh
>>>>
>>>> Ciao
>>>> Gerhard
>>>>
>>>> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
>>>> "I think the problem, to be quite honest with you,
>>>> is that you have never actually known what the question is."
>>>>
>>>> ====================================
>>>> Dr. Gerhard H. Fecher
>>>> Institut of Physics
>>>> Johannes Gutenberg - University
>>>> 55099 Mainz
>>>> ________________________________________
>>>> Von: Wien [wien-bounces at zeus.theochem.tuwien.ac.at] im Auftrag von
>>>> Laurence Marks [laurence.marks at gmail.com]
>>>> Gesendet: Sonntag, 2. Mai 2021 21:32
>>>> An: A Mailing list for WIEN2k users
>>>> Betreff: Re: [Wien] MPI error
>>>>
>>>> Inlined response and questions
>>>>
>>>> On Sun, May 2, 2021 at 2:19 PM leila mollabashi <
>>>> le.mollabashi at gmail.com<mailto:le.mollabashi at gmail.com>> wrote:
>>>> Dear Prof. Peter Blaha and WIEN2k users,
>>>> Now I have loaded the openmpi/4.1.0 and compiled Wine2k. The admin told
>>>> me that I can use your script in >
>>>> http://www.wien2k.at/reg_user/faq/slurm.job
>>>> <https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5s6X8cPOw$>
>>>> <
>>>> https://urldefense.com/v3/__http://www.wien2k.at/reg_user/faq/slurm.job__;!!Dq0X2DkFhyF93HkjWTBQKhk!G_67ZheBzKx4rn9SJ-7AOPNV2M9DFC6mHQ4b1S_sPZITO1RwQsLYLGNWwENJJwPKlowiXQ$>
>>>> . I added this lines to it too:
>>>> module load openmpi/4.1.0_gcc620
>>>> module load ifort
>>>> module load mkl
>>>> but this error happened “bash: mpirun: command not found”.
>>>> 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...
>>>>
>>>> In an interactive mode “x lapw0 –p” and “x lapw2 –p” are executed MPI
>>>> but “x lapw1 –p” is stoped with following error:
>>>> w2k_dispatch_signal(): received: Segmentation fault
>>>> 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).
>>>>
>>>> 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.
>>>>
>>>>
>>>> --------------------------------------------------------------------------
>>>> 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.
>>>> 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.
>>>>
>>>> I have checked that lapw1 has compiled correctly.
>>>> How? Do you mean that there are no error messages?
>>>>
>>>>
>>>> Sincerely yours,
>>>>
>>>> Leila
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Wien mailing list
>>>> Wien at zeus.theochem.tuwien.ac.at
>>>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>>>> <https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5uDU05KOQ$>
>>>> SEARCH the MAILING-LIST at:
>>>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>>> <https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5swXEtm0g$>
>>>>
>>> _______________________________________________
>>> Wien mailing list
>>> Wien at zeus.theochem.tuwien.ac.at
>>>
>>> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5uDU05KOQ$
>>> SEARCH the MAILING-LIST at:
>>> https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5swXEtm0g$
>>>
>> _______________________________________________
>> Wien mailing list
>> Wien at zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> <https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!CZnbK8WwpYpOc2mUYWb9cTAiCvhVrGX09mpZmoHtNgKXf6RoG5gXEtluuJ63EqfuT1QoPw$>
>> SEARCH the MAILING-LIST at:
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>> <https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!CZnbK8WwpYpOc2mUYWb9cTAiCvhVrGX09mpZmoHtNgKXf6RoG5gXEtluuJ63Eqdv4aqpLg$>
>>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
>
> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!CZnbK8WwpYpOc2mUYWb9cTAiCvhVrGX09mpZmoHtNgKXf6RoG5gXEtluuJ63EqfuT1QoPw$
> SEARCH the MAILING-LIST at:
> https://urldefense.com/v3/__http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!CZnbK8WwpYpOc2mUYWb9cTAiCvhVrGX09mpZmoHtNgKXf6RoG5gXEtluuJ63Eqdv4aqpLg$
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20210502/29358be9/attachment.htm>