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Welcome to the CoNES wiki!

Brain dump:

How to:

submit containerised runs using:

srun

mpirun

Outline consenter build process:

etc etc

Notes

• Some changes to the NEMO SVN repo mean that https://github.com/NOC-MSM/singularity-nemo/blob/gyre_singularity/scripts/nemo_setup_gyre doesn't work anymore. I got round it by downloading revision r12073 instead

Compiling using cray-mpich (not yet working...)

• test 1: compile NEMO using cray-mpich and AndrewC's fcm file inside a sandboxed container

  1. create a normal ubuntu singularity container, including gcc + gfortran (I think both are necessary) where you have root access (I also downloaded NEMO in this step, but I think you could do it as a Step 4b)
  2. copy to Archer2
  3. convert to sandbox: singularity build --sandbox nemo.simg nemo.sif
  4. shell in: singularity shell -B /work/n01/shared,/work/y07/shared,/opt/cray,/usr/lib64:/usr/lib64/host,/usr/lib64/tcl --writable -c nemo.simg
  5. add cray compilers to path: PATH=/opt/cray/pe/craype/2.7.2/bin:$PATH
  6. compile NEMO using AndrewC's fcm file (copying at appropriate time) and xios install
  7. ./makenemo -m X86_ARCHER2-Cray -r GYRE_PISCES -j 8

      module load cray-netcdf-hdf5parallel/
      module load cray-hdf5-parallel/

      singularity build --sandbox nemo.simg nemo.sif
      singularity shell -B /work/y07/shared,/work/n01/shared,/opt/cray,/usr/lib64:/usr/lib64/host,/usr/lib64/tcl -wc nemo.simg/