[Users] Issue with Multiple Node Simulation on cluster

[Steven R. Brandt]

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
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>
>