linux: To do
liezeltamon opened this issue · 1 comments
liezeltamon commented
- Questions
- Configure FileZilla to use ssh tunnels?
- Move to SSH key talk to day 1? to make sure they can easily log into the odds server for the rest of the week (see Kevin's notes)? No, the ssh key is too much on day 1, so just keep it on day 2
- No job profiling on obds server? - Yes there won't be but can keep the slides (and make it shorter and less jade-specific)
- Defaults and limits of resources on OBDS serverr? - there is a program summing usage (non-interactive, interactive, etc.) per user and tries to limit usage, atm a user cannot exceed 5% of resources so 20 users can log in at 1 time
- Will OBDS resources in on CCB cluster be moved to OBDS server? - Yes
- Decide with group whether to edit .bashrc or keep .bashrc untouched and then use .bash_alias instead - Solution: Source central bashrc from /etc/bashrc in /home//.bashrc
- Jade / obds server not sending an email when job finishes or fails - waiting reply from IT
- Day 1: Welcome
- Add reception signup to welcome slides
- Update instructor slide
- Day 1: Remote connection to server and SSH key
- Test ssh config written by Kevin - Works like a charm!
- Change to recommended type instead of type in slide
- Update remote connection slides
- Update ssh config file template (in datashare)
- Add prompt for file name and password / passphrase when generating key
- Insert sentence to check for existing ssh config in ~/.ssh
- Test on windows
- Day 2: .bashrc
- Update .bashrc slides based on decision
- Update own .bashrc on obds server for demo - wait for and source central .bashrc - just show .bashrc in resources
- Day 3: HPC
- Update slides to refer to obds server instead of jade (or both)
- Update slurm template to be compatible with obds server (see Kevin's template) (in datashare)
- Slide on job profiling
- Slide on components of HPC system
- Update partition slide once time limits are changed
- Transferring files (important for transferring multiqc html output)
- Install FileZilla
- Add note to demo connection to OBDS server and copying files
- Try if possible to double ssh with FileZilla - yes with port forwarding as in RStudio
- Transfer FileZilla slide right after ssh remote connection so they can easily transfer files including ssh config - just find another way to share config template because normally they make the config anyway, not copy it from somewhere
- Put on one drive folder shared with participants - Add to exercise downloading of multiqc output using FileZilla and rsync
- Figure out important paths for exercises - have to specify this before first exercise (especially important for Day 2 - data management)
- Participant's HOME directory
- Participant's COURSE WORKING directory - scratch (will be renamed)
- RESOURCES for exercises
- Finalise exercises
- Day 1
- Day 2 - do together the ssh key section?
- Day 3
- Move data for exercises on obds server - read-only data on obds/shared, modified data on obds/datashare/ltamon
- Run exercises on obds server
- Review slides and exercises again once all changes are done - Friday
- Work on remaining bonus topics
- Day 1 Talk 1 - Bonus: Genomic file formats bonus topics
- Day 1 Talk 1 - Bonus: Key concepts and considerations - do not include
- Day 2 Talk 2 - Bonus: Advanced shell and SSH client configuration
- Day 2 Talk 3 - Bonus: Downloading remote files using the command line
- Day 2 Talk 3 - Bonus: Transferring files using
rsync- Moved to Day 2 Talk 2 lecture - General
- Work on formatting of slides
- Add reminder slide to Day 1 to download FileZilla for Day 2
- Mark breaks on slides
- Go through slides and exercises chronologically - Sunday
- Render html with solutions
liezeltamon commented
- On the day
- Participants one drive link put on welcome slides
- Put latest lecture on one drive
- Slack invites
- Open terminals - local (tmp/obds_demo), obds server
- Give paths to resources and course working directory