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