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Christopher Bull

Aspiring Oceanographer at the British Antarctic Survey. Big data python enthusiast. Outdoor adventurer.

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Running an idealised test case configuration with NEMO

Testing NEMO

We will now test NEMO by running a double gyre test case. cd into NEMOGCM/CONFIG and run ./makenemo -n GYRE_XIOS -m XC_ARCHER_INTEL -j 8 (took 121 seconds).

If you have loaded netCDF, HDF5 and installed XIOS correctly this should work. Go into NEMOGCM/CONFIG/GYRE_XIOS/EXP00. Make a link to XIOS by: ln -sf /path/to/xios/bin/xios_server.exe xios_server.exe

This particular branch needs the following namelist tweak (/fs2/n02/n02/chbull/nemo/models/dev_r5518_GO6_package/NEMOGCM/CONFIG/GYRE_XIOS/EXP00/namelist_cfg):

&nameos        !   ocean physical parameters
!-----------------------------------------------------------------------
   nn_eos      =   0       !  type of equation of state and Brunt-Vaisala frequency
   ln_useCT    = .false.   ! use of Conservative Temp. ==> surface CT converted in Pot. Temp. in sbcssm

Make a runscript named “run_gyre.pbs” like this:

#!/bin/bash 
#!
#PBS -N PC-eos80
#PBS -l walltime=1:00:00
#PBS -l select=7
#PBS -j oe
#PBS -A n02-bas

  export PBS_O_WORKDIR=$(readlink -f $PBS_O_WORKDIR)               
  export OMP_NUM_THREADS=1
  cd $PBS_O_WORKDIR

  echo " ";
  OCEANCORES=144
  XIOCORES=3
###############################################################

ulimit -c unlimited
ulimit -s unlimited
        aprun -b -n $XIOCORES -N 3 ./xios_server.exe : -n $OCEANCORES -N 24 ./opa

Run qsub run_gyre.pbs

NEMO will now run on 144 cores (6 nodes) and pass all output to XIOS on 3 cores (1 node) which will glue data from all processors into one file. You’re output should be in: GYRE_5d_0001010100011230_grid*.nc

(Hopefully!) congratulations, you’ve just run NEMO!

In category: nemo