Dear all wien2k users, >I suggest that you focus on the PATH first, using I followed your suggestion. The script and results are in the https://files.fm/u/m2qak574g. The compile.msg_lapw0 and compile.msg_lapw0 are in the https://files.fm/u/pvdn52zpw .
Sincerely yours, Leila On Wed, May 5, 2021 at 5:14 PM Laurence Marks <[email protected]> wrote: > I think we (collectively) may be confusing things by offering too much > advice! > > Let's keep it simple, and focus on one thing at a time. The "mpirun not > found" has nothing to do with compilers. It is 100% due to your not having > the PATH variable set right. This is not fftw, but probably in the general > options and mpi module. (It is not in the compiler.) > > The library not being found is similarly due to LD_LIBRARY_PATH not being > right, or perhaps nfs mounting issues. This may be from the compiler > variables (mpiifort for Intel), which may not be correctly set by the > module. > > I suggest that you focus on the PATH first, using > which mpirun > which lapw1 > echo $PATH > echo $WIENROOT > > When this is correct in the script that runs your job we can move forward > and solve the library issue using > echo $LD_LIBRARY_PATH > ldd $WIENROOT/lapw1_mpi > ldd $WIENROOT/lapw0_mpi > > Please focus just of the PATH first. If you have problems, find a way > (DropBox/Drive etc) to post the script and result. > > _____ > Professor Laurence Marks > "Research is to see what everybody else has seen, and to think what nobody > else has thought", Albert Szent-Györgyi > www.numis.northwestern.edu > > On Tue, May 4, 2021, 22:24 Gavin Abo <[email protected]> wrote: > >> Three additional comments: >> >> 1) If you are running the slurm.job script as Non-Interactive [1,2], you >> might need a "source /etc/profile.d/ummodules.csh" line like that at [3]. >> [1] https://slurm.schedmd.com/faq.html#sbatch_srun >> <https://urldefense.com/v3/__https://slurm.schedmd.com/faq.html*sbatch_srun__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdoCMq2-Yw$> >> [2] https://wiki.umiacs.umd.edu/umiacs/index.php/SLURM/JobSubmission >> <https://urldefense.com/v3/__https://wiki.umiacs.umd.edu/umiacs/index.php/SLURM/JobSubmission__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdqwsBiRag$> >> [3] https://wiki.umiacs.umd.edu/umiacs/index.php/Modules >> <https://urldefense.com/v3/__https://wiki.umiacs.umd.edu/umiacs/index.php/Modules__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdrUX-bsYA$> >> >> 2) To eliminate any possible conflicts between Intel compilers (ifort, >> icc) and GNU compilers (gfortran, gcc) such as those mentioned in posts >> [4,5]. I suggest compiling of WIEN2k using the same C compiler and Fortran >> compiler that Open MPI was compiled with. >> >> The commands [6] below might help you check that the Linux environment is >> using the intended Open MPI and mpi parallel compilers [7]: >> >> username@computername:~/Desktop$ mpirun -V >> mpirun (Open MPI) 4.1.1 >> >> Report bugs to http://www.open-mpi.org/community/help/ >> <https://urldefense.com/v3/__http://www.open-mpi.org/community/help/__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdpyptJ4aw$> >> username@computername:~/Desktop$ mpicc --showme:version >> mpicc: Open MPI 4.1.1 (Language: C) >> username@computername:~/Desktop$ mpifort --showme:version >> mpifort: Open MPI 4.1.1 (Language: Fortran) >> username@computername:~/Desktop$ mpicc --version >> gcc (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 >> Copyright (C) 2019 Free Software Foundation, Inc. >> This is free software; see the source for copying conditions. There is NO >> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >> PURPOSE. >> >> username@computername:~/Desktop$ mpifort --version >> GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0 >> Copyright (C) 2019 Free Software Foundation, Inc. >> This is free software; see the source for copying conditions. There is NO >> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >> PURPOSE. >> [4] >> https://www.mail-archive.com/[email protected]/msg08315.html >> <https://urldefense.com/v3/__https://www.mail-archive.com/[email protected]/msg08315.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4Tfdqey1lHyg$> >> [5] >> https://www.mail-archive.com/[email protected]/msg17052.html >> <https://urldefense.com/v3/__https://www.mail-archive.com/[email protected]/msg17052.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdraaFQRnw$> >> [6] >> https://stackoverflow.com/questions/10056898/how-do-you-check-the-version-of-openmpi >> <https://urldefense.com/v3/__https://stackoverflow.com/questions/10056898/how-do-you-check-the-version-of-openmpi__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4Tfdph7KJdew$> >> [7] https://www.open-mpi.org/faq/?category=mpi-apps#general-build >> <https://urldefense.com/v3/__https://www.open-mpi.org/faq/?category=mpi-apps*general-build__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdosQiVCzQ$> >> >> 3) Those cluster administrators are usually more savvy than I am with >> installation and optimization of software (using compiler documentation, >> e.g. [8,9]) on a high performance computing (hpc) supercomputer [10,11]. >> They would know your situation better. For example, they could login to >> their administrator account on the cluster to install WIEN2k only in your >> user account directory (/home/users/mollabashi), and they would know how to >> set the appropriate access permissions [12]. Alternatively, if your not >> using a personal laptop but a computer at the organization to remotely >> connect to the cluster then they might use remote desktop access [13] to >> help you with the installation within only your account. Or they might use >> another method. >> [8] >> https://software.intel.com/content/www/us/en/develop/articles/download-documentation-intel-compiler-current-and-previous.html >> <https://urldefense.com/v3/__https://software.intel.com/content/www/us/en/develop/articles/download-documentation-intel-compiler-current-and-previous.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdqQX1Yugg$> >> [9] https://gcc.gnu.org/onlinedocs/ >> <https://urldefense.com/v3/__https://gcc.gnu.org/onlinedocs/__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdobQb5a1g$> >> [10] >> https://www.usgs.gov/core-science-systems/sas/arc/about/what-high-performance-computing >> <https://urldefense.com/v3/__https://www.usgs.gov/core-science-systems/sas/arc/about/what-high-performance-computing__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdqNzk9j6g$> >> [11] https://en.wikipedia.org/wiki/Supercomputer >> <https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Supercomputer__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4Tfdr6pni8Lw$> >> [12] >> https://www.oreilly.com/library/view/running-linux-third/156592469X/ch04s14.html >> <https://urldefense.com/v3/__https://www.oreilly.com/library/view/running-linux-third/156592469X/ch04s14.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdroF-ZgDw$> >> [13] https://en.wikipedia.org/wiki/Desktop_sharing >> <https://urldefense.com/v3/__https://en.wikipedia.org/wiki/Desktop_sharing__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4Tfdr-07_1qQ$> >> >> On 5/4/2021 3:40 PM, Laurence Marks wrote: >> >> For certain, "/opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpiexec >> /home/users/mollabashi/codes/v21.1/run_lapw -p" is completely wrong. You >> do not, repear do not use mpirun or mpiexec to start run_lapw. It has to be >> started by simply "run_lapw -p ..." by itself. >> >> I suggest that you create a very simple job which has the commands: >> >> which mpirun >> which lapw1_mpi >> echo $WIENROOT >> ldd $WIENROOT/lapw1_mpi >> ldd $WIENROOT/lapw1 >> echo env >> echo $PATH >> >> Run this interactively as well as in a batch job and compare. You will >> find that there are something which are not present when you are launching >> your slurm job that are present interactively. You need to repair these >> with relevant PATH/LD_LIBRARY_PATH etc >> >> Your problems are not Wien2k problems, they are due to incorrect >> modules/script/environment or similar. Have you asked your sysadmin for >> help? I am certain that someone local who is experienced with standard >> linux can tell you very quickly what to do. >> >> N.B., there is an error in your path setting. >> >> On Tue, May 4, 2021 at 3:38 PM leila mollabashi <[email protected]> >> wrote: >> >>> Dear all WIEN2k users, >>> Thank you for your guides. >>> >take care on the correct location ... >>> It is the /usr/share/Modules/init >>> After adding the “source /usr/share/Modules/init/tcsh” line in to the >>> script the same error appeared: >>> mpirun: command not found >>> >>> In fact, with and without “source /usr/share/Modules/init/tcsh” it is >>> written in slurm.out file that “ module load complete ”. >>> >>> I noticed that “export” is also the bash command so I used these >>> commands to path the openmpi and fftw: >>> setenv LD_LIBRARY_PATH >>> {$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 >>> set path = ($path >>> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin:/opt/exp_soft/local/generic/fftw/3.3.8_gcc620/bin) >>> But result is the same: >>> bash: mpirun: command not found >>> >>> By using this line in the script: >>> /opt/exp_soft/local/generic/openmpi/4.1.0_gcc620/bin/mpiexec >>> /home/users/mollabashi/codes/v21.1/run_lapw -p >>> The calculation stopped with the following error: >>> mpirun does not support recursive calls >>> >>> > I wonder that you have only single modules… >>> There are different versions of ifort and mkl: ifort/15.0.0, >>> ifort/15.0.3, ifort/17.0.1, ifort/19.1.3.304(default) mkl/11.2, mkl/ >>> 11.2.3.187 >>> <https://urldefense.com/v3/__http://11.2.3.187__;!!Dq0X2DkFhyF93HkjWTBQKhk!BD88XA2ujgG8Gel0NZaSOKaSrtPN7kq75O9hkG-dnIZQJRbsnQE-ArEqbFqA6XVu7qQFcg$> >>> mkl/2017.1.132, >>> mkl/2019.2.187, mkl/2020.0.4(default). I used the defaults >>> > you may also wish to make a single module file to be loaded… >>> That is a good idea. >>> > On our cluster we have different W2k modules …. >>> As you know WIEN2k is not a free code and the users of the cluster that >>> I am using are not registered WIEN2k users. Thus, according to my moral >>> commitment to the WIEN2k developers, I cannot ask the administrator to >>> install it on the cluster. I should install it on my user account. >>> >>> Sincerely yours, >>> Leila >>> >PS.: maybe one should mention this tcsh "problem" in the slurm.job >>> example on the FAQ page by adding (or similar)… >>> That is a good idea. Thank you for your suggestion. >>> >>> -- >> Professor Laurence Marks >> Department of Materials Science and Engineering >> Northwestern University >> www.numis.northwestern.edu >> "Research is to see what everybody else has seen, and to think what >> nobody else has thought" Albert Szent-Györgyi >> >> _______________________________________________ >> Wien mailing list >> [email protected] >> >> https://urldefense.com/v3/__http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4Tfdoe8NT97g$ >> SEARCH the MAILING-LIST at: >> https://urldefense.com/v3/__http://www.mail-archive.com/[email protected]/index.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdrbLIpdvQ$ >> > _______________________________________________ > 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 >
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