Parallelism

This page comes mainly from the LMD Generic GCM user manual (https://trac.lmd.jussieu.fr/Planeto/browser/trunk/LMDZ.GENERIC/ManualGCM_GENERIC.pdf). It is still in development and needs further improvements

What is parallelism?

Parallel computing is a type of computation in which many calculations or processes are carried out simultaneously. Large problems can often be divided into smaller ones, which can then be solved at the same time.

In short : Parallelism can help you save time.

Indeed, as the problem is cut into smaller part that are solved simultaneously, the waiting time for the user is reduced. However this usually comes with a counterpart, it can increase the total computation time.

How parallelism is implemented in the model

• MPI tiling

• OMP

How to compile in parallel

To compile the model in parallel use the same command as in sequential (CITE HOW TO COMPILE) and add the following option :

 -parallel

Then there is three choices for parallelism MPI, OMP and mix MPI_OMP:

 -parallel mpi
 -parallel omp
 -parallel mpi_omp

So the command line to run in mix MPI_OMP will be for example :

./makelmdz_fcm -s XX -t XX -d LONxLATxALT -b IRxVI -p physicSuffix -arch archFile -parallel mpi_omp gcm

How to run in parallel

• Run interactively
  • MPI only :

mpirun -np N gcm.e > gcm.out 2>&1

-np N specifies the number of procs to run on.

IMPORTANT: one MUST use the mpirun command corresponding to the mpif90 compiler specified in the arch file.

Output files (restart.nc, diagfi.nc ,etc.) are just as when running in serial. But standard output messages are written by each process. If using chained simulations (run mcd/run0 scripts), then the command line to run the gcm in run0 must be adapted for local settings. NB: LMDZ.COMMON dynamics set to run in double precision, so keep NC_DOUBLE declaration (and real to double precision promotion) in the arch files.

** Mix MPI_OMP :

export OMP_NUM_THREADS=2
export OMP_STACKSIZE=2500MB
mpirun -np 2 gcm.e > gcm.out 2>&1

In this exemple, each of the 2 process MPI have 2 OpenMP tasks with a 2500MB memor.

• Run with a job scheduler

This will be different for each machine. Some example are provided here but will need to be adapted for each configuration and machine.

• • MPI only :

PBS example (on Ciclad):
#PBS -S /bin/bash
#PBS -N job_mpi08
#PBS -q short
#PBS -j eo
#PBS -l "nodes=1:ppn=8"
# go to directory where the job was launched
cd $PBS_O_WORKDIR
mpirun gcm_64x48x29_phymars_para.e > gcm.out 2>&1

LoadLeveler example (on Gnome):
# @ job_name = job_mip8
# standard output file
# @ output = job_mpi8.out.$(jobid)
# standard error file
# @ error = job_mpi8.err.$(jobid)
# job type
# @ job_type = mpich
# @ blocking = unlimited
# time
# @ class = AP
# Number of procs
# @ total_tasks = 8
# @ resources=ConsumableCpus(1) ConsumableMemory(2500 mb)
# @ queue
set -vx
mpirun gcm_32x24x11_phymars_para.e > gcm.out 2>&1

LoadLeveler example (on Ada):
module load intel/2012.0
# @ output = output.$(jobid)
# @ error = $(output)
# @ job_type = parallel
## Number of MPI process
# @ total_tasks = 8
## Memory used by each MPI process
# @ as_limit = 2500mb
# @ wall_clock_limit=01:00:00
# @ core_limit = 0
# @ queue
set -x
poe ./gcm.e -labelio yes > LOG 2>&1

• • Mix MPI_OMP :

LoadLeveler example (on Gnome):
# @ job_name = job_mip8
# standard output file
# @ output = job_mpi8.out.$(jobid)
# standard error file
# @ error = job_mpi8.err.$(jobid)
# job type
# @ job_type = mpich
# @ blocking = unlimited
# time
# @ class = AP
# Number of procs
# @ total_tasks = 8
# @ resources=ConsumableCpus(1) ConsumableMemory(5000 mb)
# @ queue
set -vx
export OMP_NUM_THREADS=2 #sinon par defaut, lance 8 threads OpenMP
export OMP_STACKSIZE=2500MB
mpirun gcm_32x24x11_phymars_para.e > gcm.out 2>&1

IMPORTANT: ConsumableMemory must be equal to OMP NUM THREADSxOMP STACKSIZE. In this case, we are using 8x2 cores.

LoadLeveler example (on Ada):
module load intel/2012.0
# @ output = output.$(jobid)
# @ error = $(output)
# @ job_type = parallel
## Number of MPI process
# @ total_tasks = 8
## Number of OpenMP tasks attached to each MPI process
# @ parallel_threads = 2
## Memory used by each MPI process
# @ as_limit = 5gb
# @ wall_clock_limit=01:00:00
# @ core_limit = 0
# @ queue
set -x
export OMP_STACKSIZE=2500MB
poe ./gcm.e -labelio yes > LOG 2>&1

IMPORTANT: In this case, each core needs 2.5gb and we are using 2 OpenMP tasks for each MPI process so as_limit = 2 × 2.5.