[Wien] MPI error

Mon May 3 00:12:18 CEST 2021

>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
>>>
>>>
>>>
>>> _______________________________________________
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>>>
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>>
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