The PReSTO menu

We created a Linux Desktop menu for my own Linux computer feeling. Using the PReSTO menu launch software either at the login node or at the compute nodes. Importantly for graphics software (ccp4mg, coot, pymol, chimera, etc) the PReSTO menu launch graphics software in gl accelerated mode by default.

PReSTO menu

Figure 1. The PReSTO menu is available at the thinlinc desktop

The PReSTO menu use a dialogue box for SLURM scheduling of XDSAPP/XDSGUI/hkl2map because these softwares should be run at a compute node and the dialogue box make this happen. The dialogue box is used to schedule 1-32 cores at Tetralith (or 1-20 cores at Lunarc Aurora) for a certain amount of time and SNIC project.

Figure 2. This dialogue box corresponds to the interactive command and set project, compute time and number of cores at a single node before launching compute intensive software with GUIs such as xdsapp, xdsgui or hkl2map

When launching MX software from the PReSTO menu, the menu itself selects between either login or compute node according to the list below. If you for instance want to run phaser in parallel mode using ccp4i2 use and interactive compute node

  1. interactive --nodes=1 --exclusive -t 01:00:00 -A snic2020-5-368

  2. module load CCP4

  3. ccp4i2

Software available in PReSTO menu

Essentially only MX software with GUIs are available from the PReSTO menu, while MX software that does not have a GUI such as xds, autoPROC, pipedream etc. cannot be launched from the menu but should be executed using a sbatch script. In the future we could perhaps enable multi-node executions of xdsapp and xdsgui could from the PReSTO menu however right now we limit ourselves to using a single node when launching software from the PReSTO menu.

hkl2map     - Compute node (single-node only)
xdsapp      - Compute node (single-node only)
xdsgui      - Compute node (single-node only)
phenix      - Login node
ccp4i2      - Login node, gl accelerated mode
ccp4i       - Login node, gl accelerated mode
coot        - Login node, gl accelerated mode
ccp4mg      - Login node, gl accelerated mode
adxv        - Login node, gl accelerated mode
albula      - Login node, gl accelerated mode
xds-viewer  - Login node
pymol       - Login node, gl accelerated mode
Chimera     - Login node, gl accelerated mode

How the PReSTO menu launch MX software

User Area

User support

Guides, documentation and FAQ.

Getting access

Applying for projects and login accounts.

System status

Everything OK!

No reported problems


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