<div dir="ltr"><p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">Dear Prof.
Peter Blaha and WIEN2k users,</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">Thank you
for your assistances.</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">Here it is
the admin reply:</span></p>
<ul style="margin-top:0cm;margin-bottom:0cm" type="square">
<li class="MsoNormal" style="color:rgb(31,73,125);line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">mpirun/mpiexec
command is supported after loadin propper module ( I suggest openmpi/4.1.0
with gcc 6.2.0 or icc )</span></li>
<li class="MsoNormal" style="color:rgb(31,73,125);line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">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)</span></li>
<li class="MsoNormal" style="color:rgb(31,73,125);line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">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</span></li>
</ul>
<ul style="margin-top:0cm;margin-bottom:0cm" type="square">
<li class="MsoNormal" style="color:rgb(31,73,125);line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">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</span></li>
</ul>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">Now should I
compile WIEN2k with SL or LI?</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">Sincerely
yours,</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">Leila
Mollabashi</span></p></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Apr 14, 2021 at 10:34 AM Peter Blaha <<a href="mailto:pblaha@theochem.tuwien.ac.at">pblaha@theochem.tuwien.ac.at</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">It cannot initialize an mpi job, because it is missing the interface <br>
software.<br>
<br>
You need to ask the computing center / system administrators how one <br>
executes a mpi job on this computer.<br>
<br>
It could be, that "mpirun" is not supported on this machine. You may try <br>
a wien2k installation with system "LS" in siteconfig. This will <br>
configure the parallel environment/commands using "slurm" commands like <br>
srun -K -N_nodes_ -n_NP_ ..., replacing mpirun.<br>
We used it once on our hpc machine, since it was recommended by the <br>
computing center people. However, it turned out that the standard mpirun <br>
installation was more stable because the "slurm controller" died too <br>
often leading to many random crashes. Anyway, if your system has what is <br>
called "tight integration of mpi", it might be necessary.<br>
<br>
Am 13.04.2021 um 21:47 schrieb leila mollabashi:<br>
> Dear Prof. Peter Blaha and WIEN2k users,<br>
> <br>
> Then by run x lapw1 –p:<br>
> <br>
> starting parallel lapw1 at Tue Apr 13 21:04:15 CEST 2021<br>
> <br>
> -> starting parallel LAPW1 jobs at Tue Apr 13 21:04:15 CEST 2021<br>
> <br>
> running LAPW1 in parallel mode (using .machines)<br>
> <br>
> 2 number_of_parallel_jobs<br>
> <br>
> [1] 14530<br>
> <br>
> [e0467:14538] mca_base_component_repository_open: unable to open <br>
> mca_btl_uct: libucp.so.0: cannot open shared object file: No such file <br>
> or directory (ignored)<br>
> <br>
> WARNING: There was an error initializing an OpenFabrics device.<br>
> <br>
> Local host: e0467<br>
> <br>
> Local device: mlx4_0<br>
> <br>
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD<br>
> <br>
> with errorcode 0.<br>
> <br>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>
> <br>
> You may or may not see output from other processes, depending on<br>
> <br>
> exactly when Open MPI kills them.<br>
> <br>
> --------------------------------------------------------------------------<br>
> <br>
> [e0467:14567] 1 more process has sent help message <br>
> help-mpi-btl-openib.txt / error in device init<br>
> <br>
> [e0467:14567] 1 more process has sent help message <br>
> help-mpi-btl-openib.txt / error in device init<br>
> <br>
> [e0467:14567] Set MCA parameter "orte_base_help_aggregate" to 0 to see <br>
> all help / error messages<br>
> <br>
> [warn] Epoll MOD(1) on fd 27 failed. Old events were 6; read change was <br>
> 0 (none); write change was 2 (del): Bad file descriptor<br>
> <br>
>>Somewhere there should be some documentation how one runs an mpi job on<br>
> your system.<br>
> <br>
> Only I found this:<br>
> <br>
> Before ordering a task, it should be encapsulated in an appropriate <br>
> script understandable for the queue system, e.g .:<br>
> <br>
> /home/users/user/<a href="http://submit_script.sl" rel="noreferrer" target="_blank">submit_script.sl</a> <<a href="http://submit_script.sl" rel="noreferrer" target="_blank">http://submit_script.sl</a>><br>
> <br>
> Sample SLURM script:<br>
> <br>
> #! / bin / bash -l<br>
> <br>
> #SBATCH -N 1<br>
> <br>
> #SBATCH --mem 5000<br>
> <br>
> #SBATCH --time = 20:00:00<br>
> <br>
> /sciezka/do/pliku/binarnego/<a href="http://plik_binarny.in" rel="noreferrer" target="_blank">plik_binarny.in</a> <<a href="http://plik_binarny.in" rel="noreferrer" target="_blank">http://plik_binarny.in</a>>> <br>
> /sciezka/do/pliku/wyjsciowego.out<br>
> <br>
> To order a task to a specific queue, use the #SBATCH -p parameter, e.g.<br>
> <br>
> #! / bin / bash -l<br>
> <br>
> #SBATCH -N 1<br>
> <br>
> #SBATCH --mem 5000<br>
> <br>
> #SBATCH --time = 20:00:00<br>
> <br>
> #SBATCH -p standard<br>
> <br>
> /sciezka/do/pliku/binarnego/<a href="http://plik_binarny.in" rel="noreferrer" target="_blank">plik_binarny.in</a> <<a href="http://plik_binarny.in" rel="noreferrer" target="_blank">http://plik_binarny.in</a>>> <br>
> /siezka/do/pliku/wyjsciowego.out<br>
> <br>
> The task must then be ordered using the *sbatch* command<br>
> <br>
> sbatch /home/users/user/<a href="http://submit_script.sl" rel="noreferrer" target="_blank">submit_script.sl</a> <<a href="http://submit_script.sl" rel="noreferrer" target="_blank">http://submit_script.sl</a>><br>
> <br>
> *Ordering interactive tasks***<br>
> <br>
> <br>
> Interactive tasks can be divided into two groups:<br>
> <br>
> ·interactive task (working in text mode)<br>
> <br>
> ·interactive task<br>
> <br>
> *Interactive task (working in text mode)***<br>
> <br>
> <br>
> Ordering interactive tasks is very simple and in the simplest case it <br>
> comes down to issuing the command below.<br>
> <br>
> srun --pty / bin / bash<br>
> <br>
> Sincerely yours,<br>
> <br>
> Leila Mollabashi<br>
> <br>
> <br>
> On Wed, Apr 14, 2021 at 12:03 AM leila mollabashi <br>
> <<a href="mailto:le.mollabashi@gmail.com" target="_blank">le.mollabashi@gmail.com</a> <mailto:<a href="mailto:le.mollabashi@gmail.com" target="_blank">le.mollabashi@gmail.com</a>>> wrote:<br>
> <br>
> Dear Prof. Peter Blaha and WIEN2k users,<br>
> <br>
> Thank you for your assistances.<br>
> <br>
> > At least now the error: "lapw0 not found" is gone. Do you<br>
> understand why ??<br>
> <br>
> Yes, I think that because now the path is clearly known.<br>
> <br>
> >How many slots do you get by this srun command ?<br>
> <br>
> Usually I went to node with 28 CPUs.<br>
> <br>
> >Is this the node with the name e0591 ???<br>
> <br>
> Yes, it is.<br>
> <br>
> >Of course the .machines file must be consistent (dynamically adapted)<br>
> <br>
> with the actual nodename.<br>
> <br>
> Yes, to do this I use my script.<br>
> <br>
> >When I use “srun --pty -n 8 /bin/bash” that goes to the node with 8 free<br>
> cores, and run x lapw0 –p then this happens:<br>
> <br>
> starting parallel lapw0 at Tue Apr 13 20:50:49 CEST 2021<br>
> <br>
> -------- .machine0 : 4 processors<br>
> <br>
> [1] 12852<br>
> <br>
> [e0467:12859] mca_base_component_repository_open: unable to open<br>
> mca_btl_uct: libucp.so.0: cannot open shared object file: No such<br>
> file or directory (ignored)<br>
> <br>
> [e0467][[56319,1],1][btl_openib_component.c:1699:init_one_device]<br>
> error obtaining device attributes for mlx4_0 errno says Protocol not<br>
> supported<br>
> <br>
> [e0467:12859] mca_base_component_repository_open: unable to open<br>
> mca_pml_ucx: libucp.so.0: cannot open shared object file: No such<br>
> file or directory (ignored)<br>
> <br>
> LAPW0 END<br>
> <br>
> [1] Done mpirun -np 4 -machinefile<br>
> .machine0 /home/users/mollabashi/v19.2/lapw0_mpi lapw0.def >> .time00<br>
> <br>
> Sincerely yours,<br>
> <br>
> Leila Mollabashi<br>
> <br>
> <br>
> _______________________________________________<br>
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> <br>
<br>
-- <br>
--------------------------------------------------------------------------<br>
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna<br>
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982<br>
Email: <a href="mailto:blaha@theochem.tuwien.ac.at" target="_blank">blaha@theochem.tuwien.ac.at</a> WIEN2k: <a href="http://www.wien2k.at" rel="noreferrer" target="_blank">http://www.wien2k.at</a><br>
WWW: <a href="http://www.imc.tuwien.ac.at" rel="noreferrer" target="_blank">http://www.imc.tuwien.ac.at</a><br>
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</blockquote></div>