MX-HPC online interactive training on Zoom

This online training introduce MX software in an HPC environment intended for structural biologists new to HPC. The ideal number of participants is one to five and PReSTO membership is obligatory prior to the event.

PReSTO membership

Please join PReSTO by following the steps under Academic PReSTO access open to academic structural biologists with Swedish research projects.

Session duration

Multiple 1-2 hours online sessions until curriculum is covered

Request training

Send an email to Martin Moche and ask for a 2 hour startup session

Training procedures

Participants are encouraged to bring their own data and then we perform screen sharing at EuroHPC resource Arrhenius (or LUNARC resource Cosmos/MAXIV offline cluster) and demonstrate.

Curriculum - what to demo and discuss:

We demo and get trainee started with MX software listed below. Structural biology software in PReSTO.

1. xds, xdsapp, dials, xdsgui, autoPROC (compute node)
2. high-resolution xdsapp prior to staraniso web server (compute node)
3. ccp4i, ccp4i2 (login node except phaser/buccaneer)
4. pymol (login node) how to make 
    a. videos and images
    b. display electron density maps
    c. label atoms and residues
    d. display symmetry molecules
5. phenix-GUI at login node launches jobs to compute nodes. SLURM settings for long/short jobs
6. sharp, buster (compute node)
7. hkl2map (compute node)
8. adxv och albula (login node)
9. uppsala software factory (login node)
10. Issues and workarounds
  a. Workarounds for DIALS omptbx and out-of-memory error messages
11. Structural biology software NOT included in demo 
  a. chimera, chimeraX, ccp4mg (login node & PReSTO menu)
  b. relion with gpu support (cryo-EM software)
  c. cryo-EM software
  d. NMR or SAXS software
  e. XFEL software (nxds, crystfel)

Managing the HPC environment:

A) Compute and login nodes
B) Launch of default/latest version from terminal window or presto menu
C) Handling the SLURM queue with sbatch, squeue, etc
D) Interactive command and development nodes
E) EuroHPC resource Arrhenius "home-made" commands such as lastjobs, jobsh, storagequota
F) /home/user vs /nobackup/proj/disk/xray/personal/ vs /nobackup/proj/disk/xray/shared at EuroHPC resource Arrhenius
G) Snapshot file recovery
H) Pros and Cons of EuroHPC/NAISS resource Arrhenius, NSC resource Berzelius, LUNARC resource Cosmos and the MAXIV offline cluster
I) Basic job monitoring "top -u user"

User Area

User support

Guides, documentation and FAQ.

Getting access

Applying for projects and login accounts.

System status

Everything OK!

No reported problems

Self-service

SUPR
NSC Express