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 <pbl...@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> > > > > 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>> > > /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>> > > /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> > > > > *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.mollaba...@gmail.com <mailto:le.mollaba...@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 > > > > > > _______________________________________________ > > Wien mailing list > > Wien@zeus.theochem.tuwien.ac.at > > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > > > > -- > -------------------------------------------------------------------------- > Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna > Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 > Email: bl...@theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at > WWW: http://www.imc.tuwien.ac.at > ------------------------------------------------------------------------- > _______________________________________________ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html >
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