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General exercise instructions

For most of the exercises, skeleton codes are provided both for Fortran and C in the corresponding subdirectory. Some exercise skeletons have sections marked with “TODO” for completing the exercises. In addition, all of the exercises have exemplary full codes (that can be compiled and run) in the solutions folder. Note that these are seldom the only or even the best way to solve the problem.

Computing servers

We will use CSC’s Cray XC40 supercomputer Sisu for the exercises. Log onto Sisu using the provided username and password, for example

ssh -X [email protected]

For editing program source files you can use e.g. Emacs editor with or without (the option -nw) X-Windows:

emacs -nw prog.f90
emacs prog.f90

Also other popular editors (vim, nano) are available. In case you have working parallel program development environment in your laptop (Fortran or C compiler, MPI development library, etc.) you may also use that.

Compilation and execution

Compilation of the source codes is performed with the ftn and cc wrapper commands:

ftn -o my_mpi_exe test.f90

or

cc -o my mpi_exe test.c

The wrapper commands include automatically all the flags needed for building MPI programs. Typically we will use the default Cray compiling environment. There are also other compilers (GNU and Intel) available on Sisu, which can be changed via (for example)

module swap PrgEnv-cray PrgEnv-gnu

Use the commands module list and module avail to see the currently loaded and available modules, respectively.

Batch jobs

You can run small (short parallel or serial) jobs interactively using the aprun application placement utility:

aprun -n 4 ./my_mpi_exe

where -n specifies the number of MPI tasks.

Larger and/or longer runs should be submitted via the batch system. An example batch job script (a text file, let’s call it sisu_job.sh) for a MPI job could look like

#!/bin/bash
#SBATCH -t 00:10:00
#SBATCH -J MPI_job
#SBATCH -o out.%j
#SBATCH -e err.%j
#SBATCH -p test
#SBATCH --nodes=2
aprun -n 48 ./my_mpi_exe

The batch script is then submitted with the sbatch command as

sbatch sisu_job.sh

We have a special reservation Summerschool for the summer school which can be utilized with the --reservation flag:

sbatch --reservation=Summerschool sisu_job.sh

See the Sisu User’s Guide at http://research.csc.fi/sisu-user-guide for more details.