Rebuild NEMO output and transfer from ARCHER2 to Livljobs

[ocgabs]

On the tools folder of the NEMO tree build the rebuild_nemo tool with the following command:

./maketools -m X86_ARCHER2-Cray -n REBUILD_NEMO

Inside the tools/REBUILD_NEMO folder rebuild_nemo.exe will be generated. This executable takes as input the nam_rebuild file where you specify filebase =the full path to the files you want to rebuilt and the basename of the files, and ndomain= the number of files

Then to run just:
./rebuild_nemo.exe

Because we are currently doing this in an interactive terminal of ARCHER2. Eventually we will want to do this on a serial processor.

To transfer hopefully you can pull from livljobs, to push out of ARCHER2 we have to go through livgen2 and we can only put stuff into /work on livljobs.

When you connect to livljobs you have to do ssh -X -A livljobs# (the -A passes the public keys onwards, without it you will get Permission Denied when trying to pull from ARCHER2).

From livljobs
/projectsa/CME/3DCaribbeanNEMO/OUTPUT

rsync -zav $user@login.archer2.ac.uk:/path/to/files/to/transfer ./

This will ask for your ARCHER2 password and upon authentication the transfer should begin.

[mpayopayo]

without modules loaded and unloaded 58 errors and it doesn't compile.

to build the rebuild tool needs modules:
module unload craype-network-ofi
module unload cray-mpich
module load craype-network-ucx
module load cray-mpich-ucx
module load libfabric
module load cray-hdf5-parallel
module load cray-netcdf-hdf5parallel
module load gcc

[mpayopayo]

• files frequency <5d fine with rebuild_nemo.exe on command line
• files frequency >=5d need to be rebuilt with batch script (runscript.slurm) otherwise process is killed and faulty rebuilt