Training Background Materials
Information useful for training courses on research computing provided by IT Services
CSF and Course Materials
For CSF-based courses we have provided a Quick Start Guide (pdf) (v1.5)
You may also follow the links from the current list of courses for the particular course you want.
Getting the exercises and solutions
On the CSF: To get the course examples on the day of the course (inc. solutions): on the CSF, run the following command to download all course exercises. This will create a directory named training in your home directory. Do this each time your attend a course to get any updates:
module load training/training_material
When asked for a password, please note this is your central username password.
Moving files from CSF to your file space
Most courses are run on the Computation Shared Facility (CSF). Course attendees have access to the CSF (and help using it) until the end of the course session. At which point you may wish to move your files from the CSF to your local machine eg
UNIX/Linux/MacOS: from a terminal window, use either rsync or scp. Presuming you logged in to your local machine and are in the required destination directory on your local machine:
rsync -rt firstname.lastname@example.org:~/training ./
scp -pr email@example.com:~/training ./
- Windows: install winscp, connect to the CSF, then drag the training directory from the CSF pane to the local pane
Info on how to copy to your P:drive and to your Isilon storage (RDS) will follow shortly
CSF: Getting Started
The below links give further information to back up the Quick Start Guide (pdf)
- Accessing CSF:
- Using Linux
- Using modules:
- Accessing Compilers on CSF
See CSF Software, in particular
Programming Techniques for Research Computing course includes a fews slides & an example on using the Intel compiler and comparing its optimisation values for -O
- Compiling and Running Parallel Codes on CSF
MPI (1 or more nodes). Nodes may be connected by gigEthernet (1Gb/sec) or InfiniBand (4xQDR on CSF which equates to 32Gb/sec). The MPI module required depends on the compiler you wish to use (eg Intel or GCC) and the interconnect between nodes. For the courses, we have 2 non-InfiniBand connected nodes and ask people to use the Intel compilers (v12.0 is current) and the only MPI implementation is v1.6 of OpenMPI, therefore the relevant MPI module to load is mpi/intel-12.0/openmpi/1.6. This gives access to the compilers (mpif90/mpicc) and the MPI launcher mpirun. The number of MPI processes is controlled by the -np flag to mpirun.
OpenMP (max of 1 node). The Intel compiler supports OpenMP by use of the -openmp flag. No additional commands are required to run a threaded executable. The number of threads is controlled, essentially, by the OMP_NUM_THREADS environment variable.
- Makefiles (to follow)
Programming Techniques for Research Computing course includes a fews slides & an example
- Submitting Jobs on CSF:
- Editors available on Linux Desktop and CSF: