[Users] Issue with Multiple Node Simulation on cluster

[Erik Schnetter]

Steve

Code that runs as part of the Cactus executable is running too late
for this. At that time, OpenMP has already been initialized.

There is the environment variable "CACTUS_NUM_THREADS" which is
checked at run time, but only if it is set (for backward
compatibility). Most people do not bother setting it, leaving this
error undetected. There is a warning output, but these are generally
ignored.

-erik

On Thu, Dec 8, 2022 at 3:48 PM Steven R. Brandt <sbrandt at cct.lsu.edu> wrote:
>
> We could probably add some startup code in which MPI broadcasts the
> OMP_NUM_THREADS setting to all the other processes and either checks the
> value of the environment variable or calls omp_set_num_threads() or some
> such.
>
> --Steve
>
> On 12/8/2022 9:03 AM, Erik Schnetter wrote:
> > Spandan
> >
> > The problem is likely that MPI does not automatically forward your
> > OpenMP setting to the other nodes. You are setting the environment
> > variable OMP_NUM_THREADS in the run script, and it is likely necessary
> > to forward this environment variable to the other processes as well.
> > Your MPI documentation will tell you how to do this. This is likely an
> > additional option you need to pass when calling "mpirun".
> >
> > -erik
> >
> > On Thu, Dec 8, 2022 at 2:50 AM Spandan Sarma 19306
> > <spandan19 at iiserb.ac.in> wrote:
> >> Hello,
> >>
> >>
> >> This mail is in continuation to the ticket, “Issue with compiling ET on cluster”, by Shamim.
> >>
> >>
> >> So after Roland’s suggestion, we found that using the –prefix <openmpi-directory> command along with hostfile worked successfully in simulating a multiple node simulation in our HPC.
> >>
> >>
> >> Now we find that the BNSM gallery simulation evolves for only 240 iterations on 2 nodes (16+16 procs, 24 hr walltime), which is very slow with respect to, simulation on 1 node (16 procs, 24 hr walltime) evolved for 120988 iterations. The parallelization process goes well within 1 node, we received iterations - 120988, 67756, 40008 for procs - 16, 8, 4 (24 hr walltime) respectively. We are unable to understand what is causing this issue when openmpi is given 2 nodes (16+16 procs).
> >>
> >>
> >> In the output files we found the following, which may be an indication towards the issue:
> >>
> >> IINFO (Carpet): MPI is enabled
> >>
> >> INFO (Carpet): Carpet is running on 32 processes
> >>
> >> INFO (Carpet): This is process 0
> >>
> >> INFO (Carpet): OpenMP is enabled
> >>
> >> INFO (Carpet): This process contains 1 threads, this is thread 0
> >>
> >> INFO (Carpet): There are 144 threads in total
> >>
> >> INFO (Carpet): There are 4.5 threads per process
> >>
> >> INFO (Carpet): This process runs on host n129, pid=20823
> >>
> >> INFO (Carpet): This process runs on 1 core: 0
> >>
> >> INFO (Carpet): Thread 0 runs on 1 core: 0
> >>
> >> INFO (Carpet): This simulation is running in 3 dimensions
> >>
> >> INFO (Carpet): Boundary specification for map 0:
> >>
> >>     nboundaryzones: [[3,3,3],[3,3,3]]
> >>
> >>     is_internal   : [[0,0,0],[0,0,0]]
> >>
> >>     is_staggered  : [[0,0,0],[0,0,0]]
> >>
> >>     shiftout      : [[1,0,1],[0,0,0]]
> >>
> >> WARNING level 1 from host n131 process 21
> >>
> >>    in thorn Carpet, file /home2/mallick/ET9/Cactus/arrangements/Carpet/Carpet/src/SetupGH.cc:426:
> >>
> >>    -> The number of threads for this process is larger its number of cores. This may indicate a performance problem.
> >>
> >>
> >> This is something that we couldn’t understand as we asked for only 32 procs, with num-threads set to 1. The command that we used to submit our job was:
> >>
> >>   ./simfactory/bin/sim create-submit p32_mpin_npn --procs=32 --ppn=16 --num-threads=1 --ppn-used=16 --num-smt=1 --parfile=par/nsnstohmns1.par --walltime=24:10:00
> >>
> >>
> >> I have attached the out file, runscript, submitscript, optionlist, machine file for reference. Thanks in advance for help.
> >>
> >>
> >> Sincerely,
> >>
> >> --
> >> Spandan Sarma
> >> BS-MS' 19
> >> Department of Physics (4th Year),
> >> IISER Bhopal
> >> _______________________________________________
> >> Users mailing list
> >> Users at einsteintoolkit.org
> >> http://lists.einsteintoolkit.org/mailman/listinfo/users
> >
> >
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-- 
Erik Schnetter <schnetter at gmail.com>
http://www.perimeterinstitute.ca/personal/eschnetter/