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 <[email protected]> wrote: > >You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be > "...:$LD_LIB..." > > Thank you. I have corrected it but I still have error in x lapw1 “mpirun: > command not found” > > >Why not load the modules in the script to run a job? I have loaded but > this error happened “bash: mpirun: command not found”. > > On Mon, May 3, 2021 at 2:23 AM Laurence Marks <[email protected]> > wrote: > >> You have an error in the LD_LIBRARY_PATH def you sent -- it needs to be >> "...:$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 <[email protected]> >> 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 <[email protected]> >>> 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 [[email protected]] im Auftrag von >>>> Laurence Marks [[email protected]] >>>> 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 < >>>> [email protected]<mailto:[email protected]>> 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 >>>> [email protected] >>>> 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/[email protected]/index.html >>>> <https://urldefense.com/v3/__http://www.mail-archive.com/[email protected]/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5swXEtm0g$> >>>> >>> _______________________________________________ >>> Wien mailing list >>> [email protected] >>> >>> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5uDU05KOQ$ >>> SEARCH the MAILING-LIST at: >>> https://urldefense.com/v3/__http://www.mail-archive.com/[email protected]/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!A4zeMc6H184Nsbinv0lWLQyzxpdvRUetaqlHDTUV8sC-k8WlE7z_qcoC_7AzO5swXEtm0g$ >>> >> _______________________________________________ >> Wien mailing list >> [email protected] >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> <https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!CZnbK8WwpYpOc2mUYWb9cTAiCvhVrGX09mpZmoHtNgKXf6RoG5gXEtluuJ63EqfuT1QoPw$> >> SEARCH the MAILING-LIST at: >> http://www.mail-archive.com/[email protected]/index.html >> <https://urldefense.com/v3/__http://www.mail-archive.com/[email protected]/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!CZnbK8WwpYpOc2mUYWb9cTAiCvhVrGX09mpZmoHtNgKXf6RoG5gXEtluuJ63Eqdv4aqpLg$> >> > _______________________________________________ > Wien mailing list > [email protected] > > 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/[email protected]/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!CZnbK8WwpYpOc2mUYWb9cTAiCvhVrGX09mpZmoHtNgKXf6RoG5gXEtluuJ63Eqdv4aqpLg$ >
_______________________________________________ Wien mailing list [email protected] http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/[email protected]/index.html
