[Wien] MPI error

Sun May 2 23:53:20 CEST 2021

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
>>
>>
>>
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>>
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