F.A.Q.
Frequently Asked Questions (most with answers!)
When I run a job on sun cluster, I see that the job progress (data) does not show in the output file promptly but it takes a while later to write out data, why?
The output files only get written to when the run completes; to get around this, redirect the output to a file. So the line in the moab script that runs a program looks like this:
mpirun -np $nproc -machinefile $PBS_NODEFILE ./elemental > output.txt
This only redirects the output, not the error messages; if you want both you'd put 2>&1 at the end of the line.
I want to run a specific software package. Can you install it for me please?
First please check whether it is not already installed. Most software is accessible via the modules system
module avail
will give you a list of most software installed on the system. If you want to search for a package named “XYZ”, the following command will do the trick:
module avail 2>&1 |grep XYZ
You can, of course, replace XYZ with any software package name. There are a few software packages that are installed but do not use the modules system. These include OpenFOAM and some commercially licensed software packages. For these, check the howto section for details. If you cannot find your software package there, then you can ask us to install it for you by sending an email to helpdesk@chpc.ac.za. But: It must run on linux If it is commercially licensed, you must contact the license holder to arrange to fulfill the licensing requirements. In most circumstances, the CHPC will not provide the license for you or pay for it. Note that if you intend to do commercial work with it, you must have a commercial license - we may not bend any licensing rules.
Also note that it is sometimes considerably more complex to install software on a supercomputer than on a laptop - you may have to be a little patient while we do this.
