HPC cheat sheet – Climate Dynamics and Modeling

The following is a loose collection of helpful and in some cases essential tipps and tricks for supercomputing with climate models.

MobaXterm allows graphical forwarding from the Linux HPC system to Windows. This is helpful for GUIs such as ncview, ddd and others.

Running MPI or MPI/OpenMP programs:

ulimit -s unlimited
fi_info
export I_MPI_DEBUG=3
export FI_PROVIDER=psm3
export OMP_NUM_THREADS=4
export OMP_STACKSIZE=500M

Using IMG private nodes on VSC4:

#SBATCH --account=p71386                  # use img private nodes
#SBATCH --partition=skylake_0384          # use img private nodes
#SBATCH --qos=p71386_0384                 # use img private nodes

Debugging:

mpirun --gdb -np 24 MPIPROGRAM
ddd SERIALPROGRAMM

Tipps for Vienna Scientific Cluster from Lukas Winkler: https://guides.lw1.at/vsc-slurm-spack-tips-and-tricks/

Intel MPI on VSC4/5:

export I_MPI_PIN_RESPECT_CPUSET=0

Quarto in VSC, enable screenshot pasting into qmd file: ctrl+k m, set file association of qmd file to markdown