[Wien] MPI error

Mon May 3 00:35:20 CEST 2021

Thank you.

On Mon, May 3, 2021, 3:04 AM Laurence Marks <laurence.marks at gmail.com>
wrote:

> 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$
>>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20210503/1109221a/attachment.htm>