Computations

You can either use your office PC or one of our computing servers (accessible with SSH):

We especially recommend using the computing servers if your program can benefit from multiple cores (Parallel Toolbox in MATLAB, OpenMP in C/C++, etc.)

All computations should be started by adding the special command compute before the command that starts the computation. (You may also use the special command beregning, these are equivalent. The example below uses beregning).

Examples:

syvert0:~$ beregning matlab
syvert0:~$ beregning ./a.out
syvert0:~$ beregning matlab -nojvm mysim.m
syvert0:~$ beregning ./ns -N 8 -T 10 init.dat > sim.out

and so on. The compute/beregning command makes sure that your computation is run with the right priority, so that you don't have to worry about using more than your share of CPU.

If you're running your own C/C++/Fortran code (as opposed to code written in R or Matlab), it is highly recommended to turn on optimizing in the compiler. This will increase the speed of your program. The following compilers are available:

Please do not store large data sets and results in your home directory. Files in your home directory are backed up by a central backup system to prevent data loss. Large datasets and easily reproducable result files from computations put an unneccessarily large load on the servers and backup systems, not to mention financial cost on the department as backup is quite expensive.

Data sets and computation results should be stored in your scratch directory /global/work/<username> (replace <username> with your login name). This directory is accessible from all our Unix computers, and also accessible from Windows as \\mamba.math.ntnu.no\work\<username>.

If your program is disk-intensive, please use the local /work scratch directory. While /work is local to the computer you're using and not shared (not accessible from Windows or from other Unix hosts), it is noticeably faster than /global/work, so for disk-intensive processes, /work is preferred and will make your program run much faster.

Beware that these directories are not backed up, but on the other hand, there's more space and no restrictions on usage (as long as the space you occupy is related to your computations).

However: If the computation produces results you are going to publish, or data you for other reasons can't risk to lose, you may of course save the data to your home directory. In this case, move the data to your home directory when the computation is finished. Computations should never use your home directory as working directory - please use /work or /global/work for that.

• GDB som debugger i C (norwegian)
• Gdb tutorial and another gdb tutorial
• OpenMP tutorials from kallipolis.com, nersc.gov, and llnl.gov
• MPI documentation