To run software on Shark you need to use a queuing system. The queuing on Shark is Open Grid Scheduler (OGS).. A queuing system divides your software in to jobs, which are scheduled on another computer (a worker node). This implies that your software does not always run straight away, but is put in a queue. There are many worker nodes, so it will not take long, before it is started.
On this page some starting hints are given for the most used software packages.
Unix Shell Scripts
It is possible to start/submit an OGS jobs manually. On this page you can find information about how to submit your first OGS job.
In order to use FSL you need to load the right module with eg:
module load fsl/5.0.11-shark
In order to use FSLeyes you need to load the fsl/FSLeyes module with:
module load fsl/FSLeyes
When you only use FSL via de graphical interface everything is set-up to use OGS.
Most FSL analyses can also be started via an Unix Shell Scripts. See above.
When running the same analyses for different subjects, it is quiet beneficial to write a script. This script can submit analyses (an OGS job) per subject.
When starting a new project using FSL you start using the latest version (5.0.10). Once you start a project you want to remain using the same version, while other users (or the same user for a different project) want to use another version. To overcome this problem you can use the command
Use the command
module avail so see which modules are available. And use
module load fsl/5.0.10-shark to load the FSL 5.0.10 module. When starting
fsl after that, the FSL 5.0.10 graphical interface will be started.
A more technical explanation about modules can be found here.
There are 2 Matlab versions available on Shark for FSW. These can be started using the full path (good practice on a cluster), by typing one of the following commands (depending on which version is needed):
For convenience there are 2 modules. Use this in the following way:
module load matlab/matlab-2018b matlab
To run the full matlab graphical interface you need a graphical connection. On Windows you can do so, by using MobaXterm. See How_to_connect_windows_direct MobaXterm.
It is also possible to start matlab in a command line only (Putty) connection by using the command:
matlab -nodisplay -nojvm
FSW users use the FSW license server, which is different as for LUMC users. They differ in the available toolboxes etc.
Using Matlab on a cluster is different than on your own workstation. Interactive development with Matlab does not work well with an queuing system. To overcome this problem you have to submit a special interactive job with OGS. Use the following command:
You will be logged into one of the worker nodes, where you can start
matlab (using the module load) and use Matlab.
As stated on the Example page from the Shark Wiki: To avoid the cluster being overloaded with idle qlogin sessions your session will automatically logout after 12 hours.
Follow the instructions on this page for using fMRI_prep with Singularity.