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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| --- | ||
| title: "Admin resources" | ||
| title: "Troubleshooting" | ||
| description: "Utility commands/scripts, troubleshooting, tips and suggestions." | ||
| date: "" | ||
| toc: false | ||
| number-sections: false | ||
|
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@@ -21,15 +22,11 @@ upres5 <- y$uppmax_res_5 | |
| rm(y) | ||
| ``` | ||
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| ::: {.alert .alert-primary} | ||
| Useful utility commands/scripts and troubleshooting for course managers. | ||
| ::: | ||
|
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| # Status | ||
| ## Status | ||
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| Useful commands for monitoring status and user activity on UPPMAX. | ||
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| ## List jobs | ||
| ### List jobs | ||
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| List all jobs running an a project | ||
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@@ -53,7 +50,7 @@ Sample output | |
| 23185119 core (null) wingf R 2:53:40 1 r479 | ||
| ``` | ||
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| ## Jobs per user | ||
| ### Jobs per user | ||
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| Sorted list of jobs per user | ||
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@@ -79,7 +76,7 @@ Sample output | |
| ``` | ||
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| ## Core usage | ||
| ### Core usage | ||
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| Total number of cores used on a project | ||
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@@ -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}'")) | ||
| ``` | ||
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| ## Space usage | ||
| ### Space usage | ||
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| Amount of storage space used per project | ||
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@@ -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 | ||
| ``` | ||
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| ## Reservation use | ||
| ### Reservation use | ||
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| List users by reservation ID | ||
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@@ -134,7 +131,7 @@ Sample output | |
| ``` | ||
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| ## User activity | ||
| ### User activity | ||
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| List last activity in a directory for all users | ||
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@@ -156,7 +153,7 @@ analopez 2021-11-22 14:56:16 (/proj/snic2021-22-644/nobackup/analopez | |
| private Not available () | ||
| ``` | ||
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| ## List reservations for a project | ||
| ### List reservations for a project | ||
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| ```{r} | ||
| #| echo: false | ||
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@@ -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 | ||
| ``` | ||
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| ## List project members | ||
| ### List project members | ||
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| ```{r} | ||
| #| echo: false | ||
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@@ -193,19 +190,19 @@ snic2022-22-123 berka Berkay Paylar | |
| snic2022-22-123 btleren Betül Eren Keskin | ||
| ``` | ||
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| ## User identity | ||
| ### User identity | ||
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| Fetch user information from username | ||
|
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| ``` | ||
| finger username | ||
| ``` | ||
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| # Troubleshooting | ||
| ## Troubleshooting | ||
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| ## X-forwarding | ||
| ### X-forwarding | ||
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| ### Setup | ||
| #### Setup | ||
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| **Mac users** | ||
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@@ -223,41 +220,49 @@ Also use this when logging in to the compute node! | |
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| In MobaXTerm, go to settings and make sure that X-forwarding is checked. | ||
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| ### Testing X-forwarding | ||
| #### Testing X-forwarding | ||
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| Type `xeyes` in the terminal. | ||
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| ### Open .html documents on Rackham | ||
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| First ensure X-forwarding works, then run `firefox --no-remote filename.html` | ||
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| ## Data transfer | ||
| ### Data transfer | ||
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| ### SCP fails with * | ||
| #### SCP fails with * | ||
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| Sometimes students have problems to download files with SCP when there is a `*` in the end of the line. For example; `scp [email protected]:/proj/bla/HG00097.bam* .`. It needs to be changed to `scp [email protected]:/proj/bla/HG00097.bam\* .`. | ||
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| ## Thinlinc | ||
| ### Thinlinc | ||
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| ### Login | ||
| #### Login | ||
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| When logging in through an installed client, **username/password** seems to work. When logging in through the browser, **username/password+2FA** may be required. | ||
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| ### Minimize the ThinLinc window | ||
| #### Minimize the ThinLinc window | ||
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| On a Mac, press <kbd>Fn+F8</kbd>, then select: Minimize window. | ||
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| ### Gedit opening issues | ||
| #### Gedit opening issues | ||
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| 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. | ||
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| ## Set persistent home directory in MobaXTerm | ||
| ### Set persistent home directory in MobaXTerm | ||
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| 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. | ||
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| ## Typing `$` on a Swedish keyboard | ||
| ### Typing `$` on a Swedish keyboard | ||
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| Press <kbd>AltGr+4</kbd>. | ||
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| ### Transparent or black background for XQuartz windows on M1 Mac | ||
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| As documented [here](https://github.com/XQuartz/XQuartz/issues/31), run: | ||
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| ``` | ||
| defaults write org.xquartz.X11 enable_render_extension 0 | ||
| ``` | ||
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| *** | ||