[lammps-users] Question about multi-partition mode

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

you can answer all of your questions yourself by just using a simple input and testing on a local machine with fewer processors.
I would also recommend to use the -in flag to tell LAMMPS the input file instead of redirecting from stdin with ‘<’.

Axel.

I thought I would need to add some different or additional commands considering the pbs queuing system. So before doing something wrong in the cluster, I decided to ask.

But I agree and now I know that I could just test on the Lammps installed on my personal computer.

I’ll do some tests.

Thanks Dr. Axel Kohlmeyer.

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