[Wien] MPI error

leila mollabashi le.mollabashi at gmail.com
Sun May 2 21:18:53 CEST 2021


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
. 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”.

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

--------------------------------------------------------------------------

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.

I have checked that lapw1 has compiled correctly.

Sincerely yours,

Leila


On Fri, Apr 23, 2021 at 7:26 PM Peter Blaha <pblaha at theochem.tuwien.ac.at>
wrote:

> Recompile with LI, since mpirun is supported (after loading the proper
> mpi).
>
> PS: Ask them if -np and -machinefile is still possible to use. Otherwise
> you cannot mix k-parallel and mpi parallel and for sure, for smaller
> cases it is a severe limitation to have only ONE mpi job with many
> k-points, small matrix size and many mpi cores.
>
> Am 23.04.2021 um 16:04 schrieb leila mollabashi:
> > Dear Prof. Peter Blaha and WIEN2k users,
> >
> > Thank you for your assistances.
> >
> > Here it is the admin reply:
> >
> >   * mpirun/mpiexec command is supported after loadin propper module ( I
> >     suggest openmpi/4.1.0 with gcc 6.2.0 or icc )
> >   * you have to describe needed resources (I suggest : --nodes and
> >     --ntasks-per-node , please use "whole node" , so ntasks-pper-node=
> >     28 or 32 or 48 , depending of partition)
> >   * Yes, our cluster have "tight integration with mpi" but the
> >     other-way-arround : our MPI libraries are compiled with SLURM
> >     support, so when you describe resources at the beginning of batch
> >     script, you do not have to use "-np" and "-machinefile" options for
> >     mpirun/mpiexec
> >
> >   * this error message " btl_openib_component.c:1699:init_one_device" is
> >     caused by "old" mpi library, so please recompile your application
> >     (WIEN2k) using openmpi/4.1.0_icc19
> >
> > Now should I compile WIEN2k with SL or LI?
> >
> > Sincerely yours,
> >
> > Leila Mollabashi
> >
> >
> > On Wed, Apr 14, 2021 at 10:34 AM Peter Blaha
> > <pblaha at theochem.tuwien.ac.at <mailto:pblaha at theochem.tuwien.ac.at>>
> wrote:
> >
> >     It cannot initialize an mpi job, because it is missing the interface
> >     software.
> >
> >     You need to ask the computing center / system administrators how one
> >     executes a mpi job on this computer.
> >
> >     It could be, that "mpirun" is not supported on this machine. You may
> >     try
> >     a wien2k installation with  system   "LS"  in siteconfig. This will
> >     configure the parallel environment/commands using "slurm" commands
> like
> >     srun -K -N_nodes_ -n_NP_  ..., replacing mpirun.
> >     We used it once on our hpc machine, since it was recommended by the
> >     computing center people. However, it turned out that the standard
> >     mpirun
> >     installation was more stable because the "slurm controller" died too
> >     often leading to many random crashes. Anyway, if your system has
> >     what is
> >     called "tight integration of mpi", it might be necessary.
> >
> >     Am 13.04.2021 um 21:47 schrieb leila mollabashi:
> >      > Dear Prof. Peter Blaha and WIEN2k users,
> >      >
> >      > Then by run x lapw1 –p:
> >      >
> >      > starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021
> >      >
> >      > ->  starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021
> >      >
> >      > running LAPW1 in parallel mode (using .machines)
> >      >
> >      > 2 number_of_parallel_jobs
> >      >
> >      > [1] 14530
> >      >
> >      > [e0467:14538] mca_base_component_repository_open: unable to open
> >      > mca_btl_uct: libucp.so.0: cannot open shared object file: No such
> >     file
> >      > or directory (ignored)
> >      >
> >      > WARNING: There was an error initializing an OpenFabrics device.
> >      >
> >      >    Local host:   e0467
> >      >
> >      >    Local device: mlx4_0
> >      >
> >      > MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> >      >
> >      > with errorcode 0.
> >      >
> >      > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
> processes.
> >      >
> >      > You may or may not see output from other processes, depending on
> >      >
> >      > exactly when Open MPI kills them.
> >      >
> >      >
> >
>  --------------------------------------------------------------------------
> >      >
> >      > [e0467:14567] 1 more process has sent help message
> >      > help-mpi-btl-openib.txt / error in device init
> >      >
> >      > [e0467:14567] 1 more process has sent help message
> >      > help-mpi-btl-openib.txt / error in device init
> >      >
> >      > [e0467:14567] Set MCA parameter "orte_base_help_aggregate" to 0
> >     to see
> >      > all help / error messages
> >      >
> >      > [warn] Epoll MOD(1) on fd 27 failed.  Old events were 6; read
> >     change was
> >      > 0 (none); write change was 2 (del): Bad file descriptor
> >      >
> >      >>Somewhere there should be some documentation how one runs an mpi
> >     job on
> >      > your system.
> >      >
> >      > Only I found this:
> >      >
> >      > Before ordering a task, it should be encapsulated in an
> appropriate
> >      > script understandable for the queue system, e.g .:
> >      >
> >      > /home/users/user/submit_script.sl <http://submit_script.sl>
> >     <http://submit_script.sl <http://submit_script.sl>>
> >      >
> >      > Sample SLURM script:
> >      >
> >      > #! / bin / bash -l
> >      >
> >      > #SBATCH -N 1
> >      >
> >      > #SBATCH --mem 5000
> >      >
> >      > #SBATCH --time = 20:00:00
> >      >
> >      > /sciezka/do/pliku/binarnego/plik_binarny.in
> >     <http://plik_binarny.in> <http://plik_binarny.in
> >     <http://plik_binarny.in>>>
> >      > /sciezka/do/pliku/wyjsciowego.out
> >      >
> >      > To order a task to a specific queue, use the #SBATCH -p
> >     parameter, e.g.
> >      >
> >      > #! / bin / bash -l
> >      >
> >      > #SBATCH -N 1
> >      >
> >      > #SBATCH --mem 5000
> >      >
> >      > #SBATCH --time = 20:00:00
> >      >
> >      > #SBATCH -p standard
> >      >
> >      > /sciezka/do/pliku/binarnego/plik_binarny.in
> >     <http://plik_binarny.in> <http://plik_binarny.in
> >     <http://plik_binarny.in>>>
> >      > /siezka/do/pliku/wyjsciowego.out
> >      >
> >      > The task must then be ordered using the *sbatch* command
> >      >
> >      > sbatch /home/users/user/submit_script.sl
> >     <http://submit_script.sl> <http://submit_script.sl
> >     <http://submit_script.sl>>
> >      >
> >      > *Ordering interactive tasks***
> >      >
> >      >
> >      > Interactive tasks can be divided into two groups:
> >      >
> >      > ·interactive task (working in text mode)
> >      >
> >      > ·interactive task
> >      >
> >      > *Interactive task (working in text mode)***
> >      >
> >      >
> >      > Ordering interactive tasks is very simple and in the simplest
> >     case it
> >      > comes down to issuing the command below.
> >      >
> >      > srun --pty / bin / bash
> >      >
> >      > Sincerely yours,
> >      >
> >      > Leila Mollabashi
> >      >
> >      >
> >      > On Wed, Apr 14, 2021 at 12:03 AM leila mollabashi
> >      > <le.mollabashi at gmail.com <mailto:le.mollabashi at gmail.com>
> >     <mailto:le.mollabashi at gmail.com <mailto:le.mollabashi at gmail.com>>>
> >     wrote:
> >      >
> >      >     Dear Prof. Peter Blaha and WIEN2k users,
> >      >
> >      >     Thank you for your assistances.
> >      >
> >      >     >  At least now the error: "lapw0 not found" is gone. Do you
> >      >     understand why ??
> >      >
> >      >     Yes, I think that because now the path is clearly known.
> >      >
> >      >     >How many slots do you get by this srun command ?
> >      >
> >      >     Usually I went to node with 28 CPUs.
> >      >
> >      >     >Is this the node with the name  e0591 ???
> >      >
> >      >     Yes, it is.
> >      >
> >      >     >Of course the .machines file must be consistent (dynamically
> >     adapted)
> >      >
> >      >     with the actual nodename.
> >      >
> >      >     Yes, to do this I use my script.
> >      >
> >      >     >When I  use “srun --pty -n 8 /bin/bash” that goes to the
> >     node with 8 free
> >      >     cores, and run x lapw0 –p then this happens:
> >      >
> >      >     starting parallel lapw0 at Tue Apr 13 20:50:49 CEST 2021
> >      >
> >      >     -------- .machine0 : 4 processors
> >      >
> >      >     [1] 12852
> >      >
> >      >     [e0467:12859] mca_base_component_repository_open: unable to
> open
> >      >     mca_btl_uct: libucp.so.0: cannot open shared object file: No
> such
> >      >     file or directory (ignored)
> >      >
> >      >
>  [e0467][[56319,1],1][btl_openib_component.c:1699:init_one_device]
> >      >     error obtaining device attributes for mlx4_0 errno says
> >     Protocol not
> >      >     supported
> >      >
> >      >     [e0467:12859] mca_base_component_repository_open: unable to
> open
> >      >     mca_pml_ucx: libucp.so.0: cannot open shared object file: No
> such
> >      >     file or directory (ignored)
> >      >
> >      >     LAPW0 END
> >      >
> >      >     [1]    Done                          mpirun -np 4 -machinefile
> >      >     .machine0 /home/users/mollabashi/v19.2/lapw0_mpi lapw0.def >>
> >     .time00
> >      >
> >      >     Sincerely yours,
> >      >
> >      >     Leila Mollabashi
> >      >
> >      >
> >      > _______________________________________________
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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
> >     <mailto:blaha at theochem.tuwien.ac.at>    WIEN2k: http://www.wien2k.at
> >     <http://www.wien2k.at>
> >     WWW: http://www.imc.tuwien.ac.at <http://www.imc.tuwien.ac.at>
> >
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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
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