Various instructions for using the 'quark' cluster from Subatomic Physics
In case of questions, feel free to ask me (Marco van Leeuwen)
The quark cluster is a small computing cluster that is available for students and staff of the Institute for Subatomic Physics. You can reach it via ssh:
from any computer at the university network (including wireless). To access the cluster from outside the university, you need to first ssh to the gateway machine gemini.science.uu.nl (or use VPN). Use your solis-id as username (no capital letter at the start) and your solis password to log in. Your account has to be activated for access to quark; if this is not the case, ask your project supervisor, or ask me directly.
There is a graphical interface to see the main parameters of the cluser and find a user manual.
Some basic information:
ROOT and aliroot are installed on the system in directories under /data1/software/alisoft, with the standard aliBuild/alienv scheme To use root and aliroot, you need to set some environment variables: After these, you should be able to use:
Using ROOT and AliRoot
module load python/2.7
alienv enter --shellrc AliPhysics/latest-master-root6
to set up the ALICE software and run aliroot and root.
ROOT and aliroot are installed on the system in directories under /data1/software/alisoft, with the standard aliBuild/alienv scheme
To use root and aliroot, you need to set some environment variables:
After these, you should be able to use:
These steps can be done automatically at log in, by adding the correspoding lines to your '.bashrc' file. You can download the file here and copy it to quark using 'scp'; don't forget to add the dot back in the file name after downloading (most browsers will store the file as 'bashrc', i.e. omitting the dot at the start).
The command to submit jobs is 'qsub'. You need to write a bash script to submit to the batch queue.Use 'qsub -V -cwd' after loading the AliRoot environment (see above) to use root/aliroot in a batch job. This template provides an example; it sets the -V and -cwd options from within the script.