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.

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 use d to schedule 1-32 cores at Tetralith for a certain amount of time and 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 x dsapp, xdsgui or hkl2map

When launching 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 cc p4i2 use and interactive compute node

1. _interactive –nodes=1 –exclusive -t 01:00:00 -A naiss2023-22-811

2. module load CCP4

3. ccp4i2

MX software with GUI available from the PReSTO menu

Right now we limit ourselves to use the login node for graphics or a single compute node when launching parallell MX 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
chimerax    - Login node, gl accelerated mode
nanopeakcell- Login node, gl accelerated mode
o           - Login node, gl accelerated mode
shelxle     - Login node, gl accelerated mode _How the PReSTO menu launch software_

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. Phenix is unique among MX software having its GUI running at the login node but being able to submit parallel compute jobs to the compute nodes via slurm. Adapting Phenix to slurm schuduling