[Wien] MPI error

Thu May 6 15:09:52 CEST 2021

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 <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 $WIENROOT/lapw0_mpi
>
> Please focus just of the PATH first. If you have problems, find a way
> (DropBox/Drive etc) to post the script and result.
>
> _____
> Professor Laurence Marks
> "Research is to see what everybody else has seen, and to think what nobody
> else has thought", Albert Szent-Györgyi
> www.numis.northwestern.edu
>
> On Tue, May 4, 2021, 22:24 Gavin Abo <gsabo at crimson.ua.edu> wrote:
>
>> Three additional comments:
>>
>> 1)  If you are running the slurm.job script as Non-Interactive [1,2], you
>> might need a "source /etc/profile.d/ummodules.csh" line like that at [3].
>> [1] https://slurm.schedmd.com/faq.html#sbatch_srun
>> <https://urldefense.com/v3/__https://slurm.schedmd.com/faq.html*sbatch_srun__;Iw!!Dq0X2DkFhyF93HkjWTBQKhk!C5RwGaeHepJtMl42xVZlEAUWtk2DM4zXGp3jfTPI5NJGAplXozUMwOc-7I4TfdoCMq2-Yw$>
>> [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 $PATH
>>
>> Run this interactively as well as in a batch job and compare. You will
>> find that there are something which are not present when you are launching
>> your slurm job that are present interactively. You need to repair these
>> with relevant PATH/LD_LIBRARY_PATH etc
>>
>> Your problems are not Wien2k problems, they are due to incorrect
>> modules/script/environment or similar. Have you asked your sysadmin for
>> help? I am certain that someone local who is experienced with standard
>> linux can tell you very quickly what to do.
>>
>> N.B., there is an error in your path setting.
>>
>> On Tue, May 4, 2021 at 3:38 PM leila mollabashi <le.mollabashi at gmail.com>
>> wrote:
>>
>>> Dear all WIEN2k users,
>>> Thank you for your guides.
>>> >take care on the correct location ...
>>> It is the /usr/share/Modules/init
>>> After adding the “source /usr/share/Modules/init/tcsh” line in to the
>>> script the same error appeared:
>>> mpirun: command not found
>>>
>>> In fact, with and without “source /usr/share/Modules/init/tcsh” it is
>>> written in slurm.out file that “ module load complete ”.
>>>
>>> I noticed that “export” is also the bash command so I used these
>>> commands to path the openmpi and fftw:
>>> setenv LD_LIBRARY_PATH
>>> {$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
>>
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