Dear colleagues,
In a cluster where I run my Lammps simulations, there is a queue (pbs queue system) with 96 processors available (8 nodes and 12 processors per node). The directives suggested in the .pbs file are:
#PBS -q queue96
#PBS -l nodes = 8: ppn = 12
mpirun -np 96 lmp_intelmpi < lammps.inp
Is there a possibility that I can use the 96 processors to simultaneously perform 16 simulations with 6 processors (a reasonable number of processors for my system)? I would like to optimize the computational time spent.
Checking the Lammps manual (https://lammps.sandia.gov/doc/Howto_multiple.html), I noticed that there is the -partition command-line switch. In this way, could I simultaneously start 16 simulations with 6 processors each one at the same time?
In the Lammps manual (https://lammps.sandia.gov/doc/Howto_multiple.html) , the last example says:
"if LAMMPS were run on 3 partitions, the same scripts could be used if the“ index ”and“ loop ”variables were replaced with universe-style variables, as described in the variable command. Also, the“ next t ”and“ next a ”commands would need to be replaced with a single“ next a t ”command. With these modifications, the 8 simulations of each script would run on the 3 partitions one after the other until all were finished. Initially, 3 simulations would be started simultaneously , one on each partition. When one finished, that partition would then start the fourth simulation, and so forth, until all 8 were completed. "
From those comments, I made the modifications below. Could someone tell me if they are correct?
Going back to my example (16 simulations with 6 processors each), with the command -p (-partition) I should change my .pbs file as follows:
#PBS -q queue96
#PBS -l nodes = 8: ppn = 12
mpirun -p 16x6 lmp_intelmpi < lammps.inp
Or am I mistaken? Sorry but I don’t understand the -partition command very well.
Any suggestions are welcome, as I don’t know anything about parallel computing.
Thank you very much in advance and sorry for the long email.
Best regards,
Emerson Parazzi Lyra
PhD candidate
School of Chemical Engineering
University of Campinas
500 Albert Einstein Ave, Campinas, SP, 13083-852, Brazil
Email: [email protected]
Orcid ID: https://orcid.org/0000-0002-7969-3764