# UPPMAX website - userguide

- Web page:
- https://uppmax.github.io/UPPMAX-documentation/
- http://docs.uppmax.uu.se
- Source code:
- https://github.com/UPPMAX/UPPMAX-documentation

## Recurring meetings Fridays at 13.15
- https://uu-se.zoom.us/j/68615105731
Meeting ID: 686 1510 5731
Passcode: 798243

## Meeting

### Issues

## To determine SiteVision vs MkDocs

### General rule

- Suggestion for overall rule 1
- Most **info** on SiteVision

- All **HowTos** on MkDocs, example:
- SiteVision: overview of what we can offer
- links to project information
- MkDocs: applying for NIASS projects in
- YES: BC, RB, ML
- No: PL
- PL: I would prefer something like this, clearly defined what category of pages go where. But think many howtos about especially apply for project should be on SV.

What is the guiding premise:

- Until applying on SiteVision (proj application on MkDocs) - All instructions:
- [VOTED] BC, DI, ML, RB
- Until using (including applying) on SiteVision:
- ?PL

Applying for an account:
- On SiteVision: ?PL
- On MkDocs: BC, DI, ML, RB

Applying for NAISS projects:
- On SiteVision: ?PL
- On MkDocs: BC, DI, ML, RB

Applying for a local project:
- On SiteVision: ?PL
- On MkDocs: BC, DI, ML, RB

PUBA:
- On SiteVision:
- On MkDocs: BC, DI, ML, RB, ?PL

Hardware:
- On SiteVision:
- On MkDocs:

Instructions about (howto) Services offered through UIT (if a page is needed):
- On SiteVision:
- On MkDocs: RB, DI, ML

- Suggestion for overall rule 2
- [VOTED]: try hard for minimal duplication
- Minimize double info
- [VOTED] Yes: **BC**, RB, PL
- No
- 2b: absolutely no double (no pragmatism)
- Yes: PL
- No: **BC**, RB, PL
- PL: I vote for both... "no pragmatism" sounds a bit harsh, but we should really minimize hard. The end user experience gets confusing when info are in two places - "am I reading in the correct place?" One page would be best. If we need two pages it is good if they are clearly defined to cover different parts, this will also minimize the times you have to jump between the two pages.

- Suggestion for other alternative rule(s)
- **Extreme MkDocs**:
- everything except links to mkdocs on SiteVision
- no subpages
- **Almost Extreme MkDocs**:
- keep subpages but only put links here
- **Like today**
- on cluster on MkDocs
- Project management on SiteVision
- More SiteVision: PL
- Some MkDocs content --> SiteVision
- As much as possible on SiteVision
- Only use mkdocs when we can motivate it
- dynamic pages (sw list)
- frequently updates pages - easier on mkdocs(?)
- lots of code - easier with markdown

### Specific topics

- Log in to each cluster, now at SiteVision And MkDocs
- SiteVision only:
- Cons/pros??
- MkDocs only: **BC**, RB, PL (if other howtos/userguides are on mkdocs)
- Both

- General description of hardware, now at SiteVision and MkDocs
- [VOTED] SiteVision only: DI, ML, BC
- MkDocs only: RB
- Both:

- Detailed Hardware (how to access), now at SiteVision and MkDocs
- SiteVision only:
- [VOTED] MkDocs only: DI, BC, RB, ML
https://github.com/UPPMAX/UPPMAX-documentation/blob/main/docs/hardware/clusters/rackham.md

- System usage, **now a link from SiteVision** to mkdocs
- Link from SiteVision
- Link from MkDocs (move):
- [VOTED] Link from Both: RB, BC, ML, DI
- PL: this might become problematic on SV in the future if we want to add more, and more dynamic content. job dashbords and such. But we can move to mkdocs later if necessary.

- Applying for a projects and accounts, now SiteVision
- Problem today: can be much more pedagocigal in MkDocs
- PL: "can be much more pedagogical" - how?
- SiteVision (keep): PL
- MkDocs (move): RB
- Both: **BC**
- Example:
- Info about projects in SiteVision
- How to: in MkDocs, of course with links from SiteVision

- Our Courses, Now SiteVision
- https://www.uu.se/en/centre/uppmax/study/courses-and-workshops
- SiteVision (keep): **BC**, PL
- Pro: we can keep the existing formatting
- MkDocs (move):
- Pro: Everyone can easily modify their courses. Don't have to bother about swedish + english versions that have to be in phase
- Example: Singularity was just updated in Eng version
- However: important to make the existence of courses visible on SV
- Both: listing courses on SV, course pages on MkDocs
- [VOTED] BC, RB, DI, ML,

Course registrations:
- Use SiteVision form for future course registrations:
- Yes: ML, DI
- No:
- Neutral: RB
- [VOTED] Investigate first, then move to future meeting

SiteVision additions:
- SV calender/news (courses instance?)
- Move to later meeting

- Support on SiteVision (consists of links), now duplicated
- [VOTED] Keep: PL, BC, ML, DI (and keep what we have on MkDocs)
- Mkdocs (move): RB

- Links back?
- Can links in the mkdocs menu redirect to SiteVision?
- For example, the Support link at the top could go to [support in sitevision](https://www.uu.se/centrum/uppmax/support)
- Keep things as they are!

- [x] Björn changes the UPPMAX link name in the menu from "main page"

## Meeting 27 Sep 13:15

### Status

- For next week: [What is the rule for SiteVision versus MkDocs](https://github.com/UPPMAX/UPPMAX-documentation/issues/128)
- Advantage SiteVision: inbuilt text-to-speed
- R: but there are also programs for that ...?
- Advantage MkDocs: all the checks
- Rule 1: before on the cluster (e.g. apply), on SiteVision
- Rule 2: before having decided to be a user, on SiteVision. Or: on MkdDocs if possible

- SiteVision
- More and more evident that SiteVision needs revision

- Follow-up
- Gitlab account for Richel
- [ ] R asks GitLab account to Marcus Lundberg

- GH-pages

### Discussions

- SiteVision
- More and more evident that SiteVision needs revision
- Issues needed, where to put
- "alias GH repo"?
- Text to speech
- [ ] R: [#117](https://github.com/UPPMAX/UPPMAX-documentation/issues/117): How important is text-to-speech, contact Marcus Lundberg

### Prioritizations

## Meeting 13 Sep 13:15

### Status

- Go through https://github.com/UPPMAX/UPPMAX-documentation/issues
- RB: [#91](https://github.com/UPPMAX/UPPMAX-documentation/issues/91) about GitLab? Anyone knows?
- BC: It is at https://gitlab.uppmax.uu.se
- RB: will take a look before next meeting, due to setting up proxy
- BC: RB needs to ask Marcus Lundberg to get access
- [ ] RB needs to ask Marcus Lundberg to get access

### Coming changes

- Software table update from
- first: Rocky9 Rackham
- 2025: Pelle
- New clusters
- when time approaches
- make a branch for the new systems Pelle/Maja?
- or develop to main: RB (and volunteers)
- Pelle = new Rackham
- Maja = new Bianca, re-uses Cygnus storage
- Gorilla = new storage system, mainly for Pelle

### Prioritizations
- not right now

## Meeting 14 June 13.00

- Status SiteVision
- Has access
- Björn
- Pavlin
- Marcus
- See issue [#85](https://github.com/UPPMAX/UPPMAX-documentation/issues/85) how to apply
- Contact is up-to-date
- https://www.uu.se/en/centre/uppmax/contact

**Focus on Docs**
- Status
- https is working thanks to Erik
- https links are automatically re-directed

- Issues to discuss
- [Running first job #8](https://github.com/UPPMAX/UPPMAX-documentation/issues/8)
- probably after summer
- [Software table backend: rm irma, milou etcera #94](https://github.com/UPPMAX/UPPMAX-documentation/issues/94)
- [Use case of module avail #98](https://github.com/UPPMAX/UPPMAX-documentation/issues/98)

- Special issues
- [Software table searchable #93](https://github.com/UPPMAX/UPPMAX-documentation/issues/93)
- SiteVision [#85](https://github.com/UPPMAX/UPPMAX-documentation/issues/85)
- YOU apply!
- Do not forget mentioning UPPMAX in free text

- Close?
- put in cluster_guides and what in software folder [#62](https://github.com/UPPMAX/UPPMAX-documentation/issues/62)
- anything left?

## Meeting May 31

**Focus on Docs**

- Status
- Where are we?
- What is left?
- see below about issues and table and list
- project related things may need some overview again
- https (JIRA): Bjorn talked to Erik and it should not take long time from now (hopefully)
-

- Issues to be removed?
- [Write content "Courses and workshops"](https://github.com/UPPMAX/UPPMAX-documentation/issues/9)
- yes
- [white logo and text for the menu](https://github.com/UPPMAX/UPPMAX-documentation/issues/10)
- yes
- Discuss issues
- [Running your first job](https://github.com/UPPMAX/UPPMAX-documentation/issues/8)
- June, someone takes!
- postpone
- [What to put in cluster_guides and what in software?](https://github.com/UPPMAX/UPPMAX-documentation/issues/62)
- everything to s
- [Link back to uppmax.uu.se](https://github.com/UPPMAX/UPPMAX-documentation/issues/72)
- [Suggest: add CODE_OF_CONDUCT.md](https://github.com/UPPMAX/UPPMAX-documentation/issues/75)
- [Suggest: add LICENSE.md](https://github.com/UPPMAX/UPPMAX-documentation/issues/76)
- Issues with missing owner
- [Add screenshots to docs/cluster_guides/transfer_dardel.md](https://github.com/UPPMAX/UPPMAX-documentation/issues/70)
- also some update for before the Tuesday Rackham2Dardel zoom-in
- like, file management?

### Status 31 May

Heading 1| Heading 2 | Name | Content to start from | Responsible
---------|------|---------|--|--
Cluster user guide|Install|install own software| in IG so far (integrate) |BC
||Snowy portal/slurm|gpu snowy|in IG so far|DI
||Bianca portal/slurm|gpu bianca|no deep docs yet|DI
||Running jobs|display disk quota|cluster_guides/old|RB (BC solution OK?) :heavy_check_mark:
||Running jobs|Managing module dependencies| in IG so far but really old|BC
||Running jobs|Conflicting modules (in runtime tips)| in IG so far| BC

### Still needing formatting on Software May 31 ?

- allinea ddt F+WebTree,
- Installing and development/debuggers
- debuggers and profile gdb F+WT- RB, put under misc
- Installing and development/debuggers
- thinlinc - RB, put under misc
- done?

### ToDo:s in June
- investigate local GitLab

## Meeting May 17

**Focus on Docs**

- Status
- Where are we?
- What is left?
- see below about issues and table and list
- project related things may need some overview again
- https (JIRA): Bjorn requested a month ago, no progress yet. Bjorn will ask again
- Port to GitLab to host server at UPPMAX: will do in future
- **SiteVision**
- new web tree (fixes)
- google crawl
- redirects
- solve both or prioritize one? Or wait :-)
- status pages
- host locally all pages
- or ask for html modules producing figures
- Discuss issues
- [Running you first job](https://github.com/UPPMAX/UPPMAX-documentation/issues/8)
- June, someone takes!
- [Some pages have no side menu](https://github.com/UPPMAX/UPPMAX-documentation/issues/26)
- close
- [What to put in cluster_guides and what in software?](https://github.com/UPPMAX/UPPMAX-documentation/issues/62)
- halfways
- [Add CONTRIBUTE.md?](https://github.com/UPPMAX/UPPMAX-documentation/issues/68)
- [Branch deletion policy](https://github.com/UPPMAX/UPPMAX-documentation/issues/67)
- [Link back to uppmax.uu.se](https://github.com/UPPMAX/UPPMAX-documentation/issues/72)
- Issues with missing owner
- [Talk to PDC about Dardel documentation](https://github.com/UPPMAX/UPPMAX-documentation/issues/23)
- [Conda: merge InfoGlue wisdom](https://github.com/UPPMAX/UPPMAX-documentation/issues/54)
- [Allinea](https://github.com/UPPMAX/UPPMAX-documentation/issues/57)
- [Swedish Science Cloud EAST/Dis Portal](https://github.com/UPPMAX/UPPMAX-documentation/issues/59)
- [Add screenshots to docs/cluster_guides/transfer_dardel.md](https://github.com/UPPMAX/UPPMAX-documentation/issues/70)
- Issues to be removed?
- [Write content "Courses and workshops"](https://github.com/UPPMAX/UPPMAX-documentation/issues/9)
- [white logo and text for the menu](https://github.com/UPPMAX/UPPMAX-documentation/issues/10)
-
### Status 17 May

Heading 1| Heading 2 | Name | Content to start from | Responsible
---------|------|---------|--|--
Cluster user guide|Bianca|git on Bianca | in IG so far| BC:heavy_check_mark:
||Misc|webexport| cluster_guides/old| BC:heavy_check_mark:
||Install|install own software| in IG so far (integrate) |BC
||Snowy portal/slurm|gpu snowy|in IG so far|DI
||Bianca portal/slurm|gpu bianca|no deep docs yet|DI
||Running jobs|display disk quota|cluster_guides/old|RB (BC solution OK?) :heavy_check_mark:
||Running jobs|much time left on project| in IG so far| BC :heavy_check_mark:
||Running jobs|Managing module dependencies| in IG so far but really old|BC
||Running jobs|Locale settings (in Runtime tips)| in IG so far| BC :heavy_check_mark:
||Running jobs|Conflicting modules (in runtime tips)| in IG so far| BC
||Managing your project| New page with sub files| move some from IG |BC :heavy_check_mark:
||Managing your project| some of the above may go here || :heavy_check_mark:

## Still needing formatting on Software May 17 ?

- allinea ddt F+WebTree,
- Installing and development/debuggers
- debuggers and profile gdb F+WT- RB, put under misc
- Installing and development/debuggers
- thinlinc - RB, put under misc
- done?
- perl needs formatting - Doug
- conda needs formatting (issue) :heavy_check_mark:
done?

## Status 3 May and afterwards

- Check links: [RB, #36](https://github.com/UPPMAX/UPPMAX-documentation/issues/36)

Heading 1| Heading 2 | Name | Content to start from | Responsible
---------|------|---------|--|--
Cluster user guide|Misc??|UPPMAX in a can| in IG so far | Remove
||Integrate to Bianca sub-pages|Bianca more info | in IG so far (software)| Diana (not needed)
||Bianca|git on Bianca | in IG so far| BC:heavy_check_mark:
||Misc|webexport| cluster_guides/old| Dahlö
||Install|singularity| in IG so far|PM :heavy_check_mark:
||Install|spack| in IG so far |BC :heavy_check_mark:
||Install|install own software| in IG so far (integrate) |BC
||Snowy portal/slurm|gpu snowy|in IG so far|DI
||Bianca portal/slurm|gpu bianca|no deep docs yet|Diana
||Running jobs|disk storage guide|cluster_guides/old | BC:heavy_check_mark:
||Running jobs|display disk quota|cluster_guides/old|RB
||Running jobs|much time left on project| in IG so far| BC
||Running jobs|Managing module dependencies| in IG so far but really old|BC
||Running jobs|Locale settings (in Runtime tips)| in IG so far| BC
||Running jobs|Conflicting modules (in runtime tips)| in IG so far| BC
||Managing your project| New page with sub files| move some from IG |BC
||Managing your project| some of the above may go here || BC

### Still needing formatting on Software

gamess-us needs formatting part of web tree - PM :heavy_check_mark:
allinea ddt F+WebTree,
- Installing and development/debuggers
debuggers and profile gdb F+WT- RB, put under misc
- Installing and development/debuggers
gaussian - PM :heavy_check_mark:
molcas - PM :heavy_check_mark:
thinlinc - RB, put under misc

detachable screen - PM - from IG, to "running jobs" :heavy_check_mark:
perl needs formatting - Doug
conda needs formatting (issue) :heavy_check_mark:
wrf -BC :heavy_check_mark:
nvidia deep learning - PM :heavy_check_mark:
spack BC :heavy_check_mark:

- machine learning + AI
- created :heavy_check_mark:
- whisper goes here :heavy_check_mark:

## Status 2 May

- Prios in docs to be added by tomorrow Friday:
- slurm things
- Queue
- running jobs
- Checking and optimizing jobs
- needs subpages
- Runtime tips
- Björn adds some :heavy_check_mark:
-

## Status 29 April

- Björn's suggestion for web tree :heavy_check_mark:

- Old:

- Cluster user guide:
- The UPPMAX clusters: cluster_guides/uppmax_cluster.md
- General cluster tools:
- Start an interactive node: cluster_guides/start_interactive_node.md
- Modules: cluster_guides/modules.md
- Slurm: cluster_guides/slurm.md
- Optimizing jobs: cluster_guides/optimizing_jobs.md

- Proposal:

- Cluster user guide:
- The UPPMAX clusters: cluster_guides/uppmax_cluster.md
- Cluster portals:
- Bianca portal: cluster_guides/bianca_portal.md
- Dardel portal: cluster_guides/dardel_portal.md
- Rackham portal: cluster_guides/rackham_portal.md
- Snowy portal: cluster_guides/snowy_portal.md
- General cluster tools:
- Start an interactive node: cluster_guides/start_interactive_node.md
- Modules: cluster_guides/modules.md
- Slurm: cluster_guides/slurm.md
- Optimizing jobs: cluster_guides/optimizing_jobs.md
- Running jobs
- Running jobs tips (all could be gathered as sub-sections)
- much time left on project
- https://www.uppmax.uu.se/support/faq/projects-and-accounts-faq/how-can-i-see-how-much-time-there-is-left-on-my-project/
- https://www.uppmax.uu.se/support/faq/projects-and-accounts-faq/how-do-i-specify-which-project-i-am-running-my-job-on/
-
- mv basically all relevant FAQs Running jobs in InfoGlue here
- https://www.uppmax.uu.se/support/faq/running-jobs-faq/
- plus some more spread out in InfoGlue
- Storage and compression (all could be gathered as sub-sections)
- mv https://www.uppmax.uu.se/support/faq/projects-and-accounts-faq/how-can-i-display-my-disk-quota/
- mv FAQs Resources in InfoGlue here
- https://www.uppmax.uu.se/support/faq/resources-faq/
- plus some more spread out in InfoGlue https://www.uppmax.uu.se/support/faq

## Status 16 April

- Missing in documentation from Info Glue. Heading below are from the InfoGlue Tree

### Needs formatting!

- http://docs.uppmax.uu.se/getting_started/get_started/#getting-started-first-login-to-uppmax
- Who takes?

### User guides Cluster
- https://www.uppmax.uu.se/support/user-guides/
#### Slurm user guide
- Needs to be expanded
- Who takes? Diana
- https://www.uppmax.uu.se/support/user-guides/slurm-user-guide/
- [ ] content
- [ ] formatting
#### Plotting core hours
- Who takes? Dahlö
- Place? Link from Slurm
- https://www.uppmax.uu.se/support/user-guides/plotting-your-core-hour-usage/
- [ ] content
- [ ] formatting
#### Compute time policy
- Who takes? Björn
- Place? Link from Slurm
- https://www.uppmax.uu.se/support/user-guides/compute-time-policy/
- [ ] content
- [ ] formatting
#### Disk storage
- Who takes? Björn
- Place?
- https://www.uppmax.uu.se/support/user-guides/disk-storage-guide/
- [ ] content
- [ ] formatting
#### Web export
- Who takes? ???
- Place?
- [ ] content
- [ ] formatting
#### Jobstats
- Who takes? Diana
- https://www.uppmax.uu.se/support/user-guides/jobstats-user-guide/
- [ ] content
- [ ] formatting
#### detachable screen
- Who takes? Pavlin
- Place?
- https://www.uppmax.uu.se/support/user-guides/running-a-detachable-screen-process-in-a-job/
- [ ] content
- [ ] formatting
#### transferring files with 2-factor
- Who takes? Pavlin
- [x] done
#### node's own disk
- Who takes? Björn
- [ ] content
- [ ] formatting
#### singularity
- Who takes? Pavlin
- [ ] HTML+md file is in software/ and ready to be formatted
- Place? Installation section
- https://www.uppmax.uu.se/support/user-guides/singularity-user-guide/
- [ ] content
- [ ] formatting
#### spack
- Who takes? Björn
- Place? Link from "Installing"
- https://www.uppmax.uu.se/support/user-guides/spack-on-uppmax/
- [ ] content
- [ ] formatting
#### gpu snowy
- Who takes? Diana
- Place?
- https://www.uppmax.uu.se/support/user-guides/using-the-gpu-nodes-on-snowy/
- [ ] content
- [ ] formatting
#### (gpu bianca)
- Who takes? Diana
- Place?
- [ ] content
- [ ] formatting

### User guides software
#### GAMESS-US
- Who takes? Lars
- [x] HTML+md file is in software/directly-from-IG/ and ready to be formatted
- [ ] integrated in formatted
#### ALLINEA DDT
- Who takes? Diana
- [x] HTML+md file is in software/directly-from-IG/ and ready to be formatted
- [x] images
- [ ] integrated in formatted
#### Gaussian
- Who takes? Pavlin
- [x] HTML+md file is in software/directly-from-IG/ and ready to be formatted
- [ ] integrated in formatted

#### OpenMolcas
- Who takes? Lars/Diana
- [x] HTML+md file is in software/directly-from-IG/ and ready to be formatted
- [ ] integrated in formatted

#### debuggers and profile gdb
- Who takes? Björn
- [x] HTML+md file is in software/directly-from-IG/ and ready to be formatted
- [ ] integrated in formatted
- Place?
#### wrf
- Who takes? Björn
- [x] HTML+md file is in software/directly-from-IG/ and ready to be formatted
- [x] integrated in formatted

#### nvidia deep learning
- Who takes? Diana
- [x] HTML+md file is in software/directly-from-IG/ and ready to be formatted
- Place?
- [ ] integrated in formatted

### Decomissioned
#### deliver
- decomissioned
#### grus
- Decomissioned

### FAQ
- Some can be merged with existing docs
- Check here: https://www.uppmax.uu.se/support/faq/
- Do we want some as quick answers?
- Which ones in such case
- Vote with :+1:

#### Login problems THIS IS DONE
- https://www.uppmax.uu.se/support/faq/
- See files under Login Problems FAQs
#### Running jobs (common problems)
- https://www.uppmax.uu.se/support/faq/
- See files under: Running jobs FAQs
-

#### Login problems with sub pages
- [x] Site vision Björn
- [ ] docs
- Make link from docs

#### Projects and accounts with sub pages
- [x] Site vision Björn
- [ ] docs
#### Resources with sub pages
- [x] Site vision Björn
- [ ] docs
#### Software
##### Table
- [ ] Site vision
- [x] docs Dahlö

## Meeting Fri 15 March
- We postponed and last meetings

- Status:
- Links to docs from **main** documentation documentation pages in infoglue ready
- Individual pages not ready
- Missing pages in docs
- deeper slurm, like jobstats , queue
- who takes?
- spack installation
- who takes?
- NVIDIA Deep Learnings Framework
- https://www.uppmax.uu.se/support/user-guides/nvidia-deep-learning-frameworks/
- how to repoduce this?
- we have Tensorflow part http://docs.uppmax.uu.se/software/tensorflow/#tensorflow-as-a-python-package-for-gpu
- this one refers back to infoglue!
- [x] Björn includes how-to in the docs page
- pytorch??

- [Richel] When are we done? I feel we are done when we merged all wisdom from https://www.uppmax.uu.se to http://docs.uppmax.uu.se . Could we keep track by replacing the text of the www.uppmax.uu.se pages by a link to the docs.uppmax.uu.se pages?
- When done: [answers here]
- Replace text by links: [answer here]
- [X] just landing pages are done
- shall Björn do for individual pages (started)?
- or individuals?

- [Richel] We want our users to move to Dardel. However,
- (1) the http://docs.uppmax.uu.se/cluster_guides/migrate_dardel/ is not ready yet, may be on 2024-02-27 23:59
- (2) the www.uppmax.uu.se pages never link to http://docs.uppmax.uu.se/cluster_guides/migrate_dardel
- ... would it be a good idea to start linking when the docs are ready? After that, I'll suggest to notify our users of the Dardel migration guide.
- agree to start linking when docs are ready: [answer here]
- notify users when ready: [answer here]
- [Richel] Vote on https://github.com/UPPMAX/UPPMAX-documentation/issues/21 . Richel votes yes, if his vote counts
- [vote outcome here]

- [x] Docs are linked to from InfoGLue pages /Björn C

## Meeting Fri 2 Feb 13:30

- [DONE] adding `ssh-keys` page. Some content from here https://hackmd.io/@pmitev/SSH_tips
- Content of Pavlins page has been merged with http://docs.uppmax.uu.se/software/ssh/
- FAQs from https://www.uppmax.uu.se/support/faq/? FAQ in menu or everything in the logical tree?
- Richel asked for what decision was taken
- [VOTED: `ssh -X` first] Which SSH decision tree? `ssh -X` first or `ssh -Y` first? See a tree at http://docs.uppmax.uu.se/software/ssh/#difference-between-ssh-x-and-ssh-y

## Meeting Fri 26 Jan 13:30

- Just some general discussions

## Meeting Fri 12 Jan at 13:30

No meeting.

## Meeting Tue 9 Jan at 9:15

- Björn: cluster environments in quickstart containig modules and Slurm
- There are different ideas what makes a pretty schematical picture. In an earlier meeting, the idea was that Jonas would decide upon a color scheme. Richel now thinks that that is overkill and he suggest the rule 'If you don't like the look of a schemetical picture, just edit it'. People agreed that we should use a more lightweight approach and we discussed in which way to do so:
- Freely edit
- Notify the original author after an edit
- Ask the original author for ideas what to change

- This differed between team members:
- Pavlin and Richel are in the 'freely edit' camp; hence you can freely modify their pictures
- Björn and Jonas prefer to be notified on editr

## Status December 2023
- Aim for getting site ready for 15 Jan
- New sub-domain
- docs.uppmax.uu.se :+1::+1::+1::+1:
- Informed in JIRA to use this!
- support.uppmax.uu.se :+1:
- help.uppmax.uu.se :+1:
- stjälp.uppmax.uu.se :-1::-1::-1:
- Test deploy from own GitLab server
- GitLab pages

## Meeting Fri 22 Dec at 11.00

- Status
- BC:
- databases v1 done
- most software pages formatted
- continue format "compiling pages"
- Discuss
- mermaid colors: we discussed a procedure to allow us to all agree,
instead of discussing every little hue every time.
Jonas seemed most eager to make these color decisions and Richel and
Pavlin will accept his decisions. Jdddng thongas will join the UPPMAX meeting
on Tuesday ?10 January and talk with Elisabeth.
Note that Diana also was working on a color scheme suggestion.
Jonas will contact Diana and discuss

- Bianca portal look:
- .bashrc?
- links and overview
- running-first-job --> Best practice (demo)
- .bashrc
- uquota/projinfo
- home vs proj folders
- first batch job
- develop from https://uppmax.github.io/uppmax_intro/working.html
- links to other parts
- modules
- slurm
- software
- conda
- etc...
- ToDos
- Jonas
- design
- talked to Diana and Jessica
- Björn
- pages
- pavlin
- linux tools from windows
- Richèl
- bianca
- from course

## Meeting Fri 15 Dec at 13.30

- Discuss
- Make public 15 Jan?
- What do we need to have done? Focus on
- Getting started
- Logging in to Bianca (from [course material from Bianca course](https://uppmax.github.io/bianca_workshop/intro/)): Richel
- Start an interactive node (from [course material from Bianca course](https://uppmax.github.io/bianca_workshop/intro/)): Richel
- file transfer using GUI (from [course material from Bianca course](https://uppmax.github.io/bianca_workshop/intro/)): Richel
- etc (from [course material from Bianca course](https://uppmax.github.io/bianca_workshop/intro/)): Richel
- Cluster user guides
- modules: Richel (from [course material from Bianca course](https://uppmax.github.io/bianca_workshop/intro/))
- Slurm Diana
- installing Björn
- include conda+ containers here as well, links to python PyPi in Software section
-Bianca portal
- Software (sorted alphabetically)
- GROMACS finished
- Julia Björn
- Matlab Björn
- Perl modules
- Python Björn
- R:
- RStudio: Richel (from [course material from Bianca course](https://uppmax.github.io/bianca_workshop/intro/))
- **Software table**
- VSCodium: Richel (from [course material from Bianca course](https://uppmax.github.io/bianca_workshop/intro/))

- Who's responsible?

## Meeting Fri 17 Nov at 13.30
- Overview and staff
- Site-vision [name=Björn C] & [name=Marcus]
- everything except documentaion
- also Course pages (info and dates and registrations and links to materials)
- Github pages [name=All]
- documentation
- software table
- Software table and its backend [name=?]
- frontend [name=?]
- backend [name=?]

- Status

## Needed?
- [x] Grus user guide (NGI)
- [ ] where?
- [ ] MOLCAS user guide (chem)
- [ ] Lars
- [ ] GAMESS-US user guide (quant chem)
- [ ] Lars
- [x] Introduction to VTK programming using Python
- [ ] look at infravis (discuss with Anders H?)
- [ ] passé
- [x] if q:s from user tell about infravis

## Meeting Fri 20 Oct at 13.30

### Needed?

- [x] Grus user guide (NGI)
- [ ] where?
- [ ] MOLCAS user guide (chem)
- [ ] Lars
- [x] GROMACS
- [x] menu
- [ ] What Perl modules are in the omnibus module perl_modules/5.18.4?
- [x] What Perl modules are in the omnibus module perl_modules/5.24.1?
- [X] One page only in menu
- [ ] GAMESS-US user guide (quant chem)
- [ ] Lars
- [x] Garli user guide
- [ ] not needed
- [ ] Introduction to VTK programming using Python
- [ ] look at infravis (discuss with Anders H?)
- [x] SGE vs Slurm comparison
- not needed
- [x] Starting Integrative Genomics Viewer (IGV) on Rackham/Snowy
- [x] needed
- [ ] table link or menu
- [x] Using CRAM to compress BAM files
- needed
- [x] Accessing Swegen
- link from bianca portal
- in menu for databases

### ToDos
- [ ] Look into adding dynamic width to software table. Possibly also for content (mid panel) in general.

## Meeting Fri 13 Oct at 13.30

This was a bit interesting: [LUNARC docu](https://lunarc-documentation.readthedocs.io/en/latest/)
- having buttons for different material specific for the type of user you are
- New - used before - expert user - developing software

## Meeting Fri 6 Oct at 13:30
- On-boarding Richel
- Status?
- Björn started to play with new pages in Site-vision
- Björn has started "[serial compiling page](https://uppmax.github.io/UPPMAX-documentation/running_jobs/compiling_serial)"
- include make, git etc..?
- Matias made a lighter style look red-->grey
- software table!
- Plans on structure:
- add umbrella page for user installation?
- based on [intro-course](https://uppmax.github.io/uppmax_intro/software.html)

- Plans software documentation
- overview with table
- add the keywords as a list?
- minst 2 mjukvaror per keyword
- specific software doc under software

- ToDos
- yaml-filerna [name=Jonas]
- software-tabell på GH-pages [name=Mattias]
- hämta från aktuell DB
- /sw/infrastructure/swdb_files
- kolla keywords
- https://github.com/UPPMAX/install-methods/tree/main/swcrawl
- curated_list_filtered
- curated_list
- all_curated_keywords

### Pages done or worked on (as seen under Support on old web)

- Getting started
- Slurm [name=Diana]
- First log-in to UPPMAX [name=Björn]
- rackham
- snowy
- bianca
- Disk storage guide [name=Marcus] (move to Clusters)
- Apply for a project [name=Marcus]
- Cluster user guide HPC
- compiling source code [name=Björn]
- MPI and OpenMP user guide [name=Björn]
- workshops and courses
- workshops and courses [name=Diana]

**outside the UU structure:**
- Software page [name=Matias, Jonas]
-- the link out will not work in firefox because of security interactions with linking embeded pages.
-- add {:target="_blank"} to the links that link out. To fix the embeded link security issue with frames.
- Setup `Mkdocs` insiders [name=Matias]
- Update theme [name=Matias]

## Meeting Fri 29 sep at 13:30
- Status?
- Björn started to play with new pages in Site-vision
- Matias made a lighter style look red-->grey
- software table!
-

## Meeting Fri 22 Sep at 13:30
- To discuss?
- insiders 5$/month
- ledningsgrupp next Tuesday

## On GH
- new menu
- some present pages coupled
- created files to be filled with content
- mv hardware to site vision

## Pages done or worked on (as seen under Support on old web)

- Getting started
- Slurm [name=Diana]
- First log-in to UPPMAX [name=Björn]
- Disk storage guide [name=Marcus] (move to Clusters)
- Apply for a project [name=Marcus]
- Cluster user guide HPC
- compiling source code [name=Björn]
- MPI and OpenMP user guide [name=Björn]
- workshops and courses
- workshops and courses [name=Diana]

**outside the UU structure:**
- Software page [name=Matias, Jonas]
-- the link out will not work in firefox because of security interactions with linking embeded pages.
-- add {:target="_blank"} to the links that link out. To fix the embeded link security issue with frames.
- Setup `Mkdocs` insiders [name=Matias]
- Update theme [name=Matias]

## Meeting 8 Sep
- To discuss
- who takes what?
- see list above
- where to prioritize?
- see list above

### Tree
- Getting Started:
- Applying for a Project: getting_started/project_apply.md
- Logging into Rackham: getting_started/login_rackham.md
- Logging into Snowy: getting_started/login_snowy.md
- Logging into Bianca: getting_started/login_bianca.md
- Running your first job: getting_started/first_job.md
- Hardware:
- Overview: hardware/overview.md
- Clusters:
- Rackham: hardware/clusters/rackham.md
- Snowy: hardware/clusters/snowy.md
- Bianca: hardware/clusters/bianca.md
- Storage:
- Crex: hardware/storage/crex.md
- Domus: hardware/storage/domus.md
- Castor: hardware/storage/castor.md
- Lutra: hardware/storage/lutra.md
- Running Jobs:
- Slurm: running_jobs/slurm.md
- Software/:
- Overview: software/overview.md
- Software-specific guides
- Databases
- "Courses and workshops"
- Overview of all courses

- Support: support.md

## Meeting 1 Sep
- incorporate FAQ into the userguide
- have a search button
- in-built tags for pages/sections
- SiteVision lacks some nice features, could not be suitable for code documentation
- mkdocs or else?
- menu - location to be decided

Top level categories
====
Keep in mind a user-oriented logic: welcome, get access, log in, details

- Landing page
- menus according to below top-levels
- big buttons
- Get started?
- Cluster guides?
- Software and databases
- Courses and workshop
- Lost credentials
- Site-vision link
- Footer
- links
- addresses

- "**Get Started**" - How to apply, get accounts, basic usage, etc
- for inspiration: https://docs.lxp.lu/first-steps/connecting/ or https://www.lumi-supercomputer.eu/get-started/ (DI: I like the "Select" that filters out irrelevant info)
- rackham+snowy specific?
- bianca specific?
- for PIs,
- projects
- sens...?
- for users
- SUPR
- pswd
- go to cluster guides
- for students
- needed or part of users
-
- **Cluster** user guides
- rackham+snowy
- descriptive
- puff
- bianca
- puff
- **linux**
- modules here
- incorporate basic slurm into basic cluster user guide
- disk usage guide included here
- basic installation and compiling

- **Courses and workshops**

- "**Available Software**"
- structure inherited from /sw/mf tree
- specific guides etc available here
- have a link to info about lmod, slurm
- "Databases"
- "Other articles"
- e.g. advanced slurm
- compiling tips

To be included:
- Cluster user status
- links to navigate back and forth between SiteVision and MKDocs

Articles that should be kept in SiteVision:
- technical info on the hardware
- info for press
- info on personnel?
- wait a bit