[Wien] MPI error
Peter Blaha
pblaha at theochem.tuwien.ac.at
Thu May 6 17:38:35 CEST 2021
Once the blacs problem has been fixed, the next step is to run lapw0 in
sequential and parallel mode.
Add:
x lapw0 and check the case.output0 and case.scf0 files (copy them to
a different name) as well as the message from the queuing system.
add: mpirun -np 4 $WIENROOT/lapw0_mpi lapw0.def
and check the messages and compare the results with the previous
sequential run.
And finally:
create a .machines file with:
lapw0:localhost:4
and execute
x lapw0 -p
-------------
The same thing could be made with lapw1
Am 06.05.2021 um 15:09 schrieb leila mollabashi:
> 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 <https://files.fm/u/m2qak574g>. The
> compile.msg_lapw0 and compile.msg_lapw0 are in the
> https://files.fm/u/pvdn52zpw <https://files.fm/u/pvdn52zpw> .
>
> Sincerely yours,
>
> Leila
>
>
> On Wed, May 5, 2021 at 5:14 PM Laurence Marks <laurence.marks at gmail.com
> <mailto:laurence.marks at gmail.com>> 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 $WIENROOT/lapw0_mpi
>
> Please focus just of the PATH first. If you have problems, find a
> way (DropBox/Drive etc) to post the script and result.
>
> _____
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what
> nobody else has thought", Albert Szent-Györgyi
> www.numis.northwestern.edu <http://www.numis.northwestern.edu>
>
> On Tue, May 4, 2021, 22:24 Gavin Abo <gsabo at crimson.ua.edu
> <mailto:gsabo at crimson.ua.edu>> wrote:
>
> Three additional comments:
>
> 1) If you are running the slurm.job script as Non-Interactive
> [1,2], you might need a "source /etc/profile.d/ummodules.csh"
> line like that at [3].
>
> [1] https://slurm.schedmd.com/faq.html#sbatch_srun
> <https://urldefense.com/v3/__https://slurm.schedmd.com/faq.html*sbatch_srun__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdoCMq2-Yw$>
> [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 at 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$>
> username at computername:~/Desktop$ mpicc --showme:version
> mpicc: Open MPI 4.1.1 (Language: C)
> username at computername:~/Desktop$ mpifort --showme:version
> mpifort: Open MPI 4.1.1 (Language: Fortran)
> username at 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 at 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/wien@zeus.theochem.tuwien.ac.at/msg08315.html
> <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08315.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4Tfdqey1lHyg$>
> [5]
> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17052.html
> <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17052.html__;!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdraaFQRnw$>
> [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 $PATH
>>
>> Run this interactively as well as in a batch job and compare.
>> You will find that there are something which are not present
>> when you are launching your slurm job that are present
>> interactively. You need to repair these with relevant
>> PATH/LD_LIBRARY_PATH etc
>>
>> Your problems are not Wien2k problems, they are due to
>> incorrect modules/script/environment or similar. Have you
>> asked your sysadmin for help? I am certain that someone local
>> who is experienced with standard linux can tell you very
>> quickly what to do.
>>
>> N.B., there is an error in your path setting.
>>
>> On Tue, May 4, 2021 at 3:38 PM leila mollabashi
>> <le.mollabashi at gmail.com <mailto:le.mollabashi at gmail.com>> wrote:
>>
>> Dear all WIEN2k users,
>> Thank you for your guides.
>> >take care on the correct location ...
>> It is the /usr/share/Modules/init
>> After adding the “source /usr/share/Modules/init/tcsh”
>> line in to the script the same error appeared:
>> mpirun: command not found
>>
>> In fact, with and without “source
>> /usr/share/Modules/init/tcsh” it is written in slurm.out
>> file that “ module load complete ”.
>>
>> I noticed that “export” is also the bash command so I used
>> these commands to path the openmpi and fftw:
>> setenv LD_LIBRARY_PATH
>> {$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 <http://www.numis.northwestern.edu/>
>> "Research is to see what everybody else has seen, and to think
>> what nobody else has thought" Albert Szent-Györgyi
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--
--------------------------------------------------------------------------
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: blaha at theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at
WWW: http://www.imc.tuwien.ac.at
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