Login to vsc4
Please open a terminal and connect to vsc4:
(see email for password & details, the ## has to be replaced by your ID)
(Windows users can connect via Power Shell or via PuTTY - see email)
• ssh -t trainee##@vmos.vsc.ac.at vsc4
If your terminal becomes unresponsive, please hit the Return key, then type ~.
(if it does not help, open a new terminal and connect again)!
Editors: vi, vim, nano, emacs, nedit --> editors cheat sheets: nano, vi(m)
Setup your user (needs to be done only once):
During the course, we provide a node reservation to avoid queuing times.
Activate the node reservation!
• ~training/setup.sh
• source ~/.bashrc
Copy the exercises (needs to be done only once):
Hands-on labs are prepared for the course participants directly on the vsc4 cluster.
(A link to download the exercise material outside of the course is provided on the Moodle.)
• cd ~; cp -a ~training/HY-VSC .
• cd ~/HY-VSC
~/HY-VSC holds subdirectories for all exercises:
• he-hy - MPI+OpenMP: compiling, starting, pinning
• jacobi - MPI+OpenMP: hybrid through OpenMP parallelization
• data-rep - MPI: how to avoid replicated data
Load the required modules:
• module load intel intel-mpi
We'll use the Intel software stack on vsc4, since vsc4 is an entirely Intel system.
The Intel compilers are called icc (for C), icpc (for C++) and ifort (for Fortran).
For reasonable optimization including SIMD vectorization, use options -O3 -xAVX -fno-alias
(sometimes you might get better performance with -O2 ...)
By default, OpenMP directives in your code are ignored. Use the -qopenmp option to activate OpenMP.
Compile @login node:
• mpiicc -o my-program.exe my-program.c # C (example is for pure MPI; note the double ii)
• mpiifort -o my-program.exe my-program.f90 # Fortran (example is for pure MPI; note the double ii)
Submit to queuing system:
• sbatch job.sh # submit a job
• sq # check own jobs, sq is an alias for: squeue -u $USER
• scancel JOB_ID # cancel a job
• output will be written to: slurm-*.out # output