diff --git a/admin.qmd b/troubleshooting.qmd similarity index 89% rename from admin.qmd rename to troubleshooting.qmd index 9d96ef64e..114fbe339 100644 --- a/admin.qmd +++ b/troubleshooting.qmd @@ -1,5 +1,6 @@ --- -title: "Admin resources" +title: "Troubleshooting" +description: "Utility commands/scripts, troubleshooting, tips and suggestions." date: "" toc: false number-sections: false @@ -21,15 +22,11 @@ upres5 <- y$uppmax_res_5 rm(y) ``` -::: {.alert .alert-primary} -Useful utility commands/scripts and troubleshooting for course managers. -::: - -# Status +## Status Useful commands for monitoring status and user activity on UPPMAX. -## List jobs +### List jobs List all jobs running an a project @@ -53,7 +50,7 @@ Sample output 23185119 core (null) wingf R 2:53:40 1 r479 ``` -## Jobs per user +### Jobs per user Sorted list of jobs per user @@ -79,7 +76,7 @@ Sample output ``` -## Core usage +### Core usage Total number of cores used on a project @@ -89,7 +86,7 @@ Total number of cores used on a project cat(paste0("squeue -A ",upid," -o %C | awk '{total += $0} END{print total}'")) ``` -## Space usage +### Space usage Amount of storage space used per project @@ -107,7 +104,7 @@ Your project Your File Area Unit Usage Quota Limit Over Quot snic2022-22-123 /proj/snic2022-22-123 GBytes 4.6 128 ``` -## Reservation use +### Reservation use List users by reservation ID @@ -134,7 +131,7 @@ Sample output ``` -## User activity +### User activity List last activity in a directory for all users @@ -156,7 +153,7 @@ analopez 2021-11-22 14:56:16 (/proj/snic2021-22-644/nobackup/analopez private Not available () ``` -## List reservations for a project +### List reservations for a project ```{r} #| echo: false @@ -175,7 +172,7 @@ ReservationName=snic2021-22-644_fri StartTime=2021-11-26T08:30:00 EndTime=2021-1 Users=(null) Accounts=snic2021-22-644 Licenses=(null) State=INACTIVE BurstBuffer=(null) Watts=n/a ``` -## List project members +### List project members ```{r} #| echo: false @@ -193,7 +190,7 @@ snic2022-22-123 berka Berkay Paylar snic2022-22-123 btleren Betül Eren Keskin ``` -## User identity +### User identity Fetch user information from username @@ -201,11 +198,11 @@ Fetch user information from username finger username ``` -# Troubleshooting +## Troubleshooting -## X-forwarding +### X-forwarding -### Setup +#### Setup **Mac users** @@ -223,7 +220,7 @@ Also use this when logging in to the compute node! In MobaXTerm, go to settings and make sure that X-forwarding is checked. -### Testing X-forwarding +#### Testing X-forwarding Type `xeyes` in the terminal. @@ -231,33 +228,41 @@ Type `xeyes` in the terminal. First ensure X-forwarding works, then run `firefox --no-remote filename.html` -## Data transfer +### Data transfer -### SCP fails with * +#### SCP fails with * Sometimes students have problems to download files with SCP when there is a `*` in the end of the line. For example; `scp user@rackham.uppmax.uu.se:/proj/bla/HG00097.bam* .`. It needs to be changed to `scp user@rackham.uppmax.uu.se:/proj/bla/HG00097.bam\* .`. -## Thinlinc +### Thinlinc -### Login +#### Login When logging in through an installed client, **username/password** seems to work. When logging in through the browser, **username/password+2FA** may be required. -### Minimize the ThinLinc window +#### Minimize the ThinLinc window On a Mac, press Fn+F8, then select: Minimize window. -### Gedit opening issues +#### Gedit opening issues When opening it from the terminal (`gedit &`), it was not able to connect to a display to show the graphics. The `DISPLAY` variable was empty. This was when using ThinLinc, so it should have worked. The issue was solved by opening gedit from the menu. Gedit could be labelled Text Editor. -## Set persistent home directory in MobaXTerm +### Set persistent home directory in MobaXTerm This is to specify where the **home directory** in MobaXTerm is located in the computer’s file system. In **Settings > Configuration**, set the persistent home directory to a suitable folder. Restart MobaXTerm. -## Typing `$` on a Swedish keyboard +### Typing `$` on a Swedish keyboard Press AltGr+4. +### Transparent or black background for XQuartz windows on M1 Mac + +As documented [here](https://github.com/XQuartz/XQuartz/issues/31), run: + +``` +defaults write org.xquartz.X11 enable_render_extension 0 +``` + ***