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
[2] https://wiki.umiacs.umd.edu/umiacs/index.php/SLURM/JobSubmission
[3] https://wiki.umiacs.umd.edu/umiacs/index.php/Modules
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/
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/wien@zeus.theochem.tuwien.ac.at/msg08315.html
[5]
https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17052.html
[6]
https://stackoverflow.com/questions/10056898/how-do-you-check-the-version-of-openmpi
[7] https://www.open-mpi.org/faq/?category=mpi-apps#general-build
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
[9] https://gcc.gnu.org/onlinedocs/
[10]
https://www.usgs.gov/core-science-systems/sas/arc/about/what-high-performance-computing
[11] https://en.wikipedia.org/wiki/Supercomputer
[12]
https://www.oreilly.com/library/view/running-linux-third/156592469X/ch04s14.html
[13] https://en.wikipedia.org/wiki/Desktop_sharing
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 $PATH
Run this interactively as well as in a batch job and compare. You will
find that there are something which are not present when you are
launching your slurm job that are present interactively. You need to
repair these with relevant PATH/LD_LIBRARY_PATH etc
Your problems are not Wien2k problems, they are due to incorrect
modules/script/environment or similar. Have you asked your sysadmin
for help? I am certain that someone local who is experienced with
standard linux can tell you very quickly what to do.
N.B., there is an error in your path setting.
On Tue, May 4, 2021 at 3:38 PM leila mollabashi
<le.mollaba...@gmail.com <mailto:le.mollaba...@gmail.com>> wrote:
Dear all WIEN2k users,
Thank you for your guides.
>take care on the correct location ...
It is the /usr/share/Modules/init
After adding the “source /usr/share/Modules/init/tcsh” line in to
the script the same error appeared:
mpirun: command not found
In fact, with and without “source /usr/share/Modules/init/tcsh” it
is written in slurm.out file that “ module load complete ”.
I noticed that “export” is also the bash command so I used these
commands to path the openmpi and fftw:
setenv LD_LIBRARY_PATH
{$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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