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