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troubleshooting.qmd
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troubleshooting.qmd
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---
title: "Status & Troubleshooting"
description: "Utility commands/scripts, troubleshooting, tips and suggestions."
date: ""
sidebar: false
format: html
---
```{r}
#| echo: false
library(yaml)
library(here)
y <- yaml::read_yaml(here("_quarto.yml"))
upid <- y$uppmax_project
rm(y)
```
## Status
Useful commands for monitoring status and user activity on UPPMAX.
### List jobs
List all jobs running an a project
```{r}
#| echo: false
#| class-output: bash
cat(paste0("squeue -A ",upid," | sort -k 4"))
```
Sample output
```
23186770 core _interac analopez R 2:15:00 1 r55
23175660 core (null) anitav R 6:52:28 1 r480
23188713 core (null) annha R 1:42:59 1 r480
23185442 core (null) annha R 2:47:11 1 r480
23185433 core (null) inene424 R 2:47:42 1 r479
23185391 core (null) inene424 R 2:50:04 1 r479
23185540 core (null) shengyz R 2:46:20 1 r480
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
23185119 core (null) wingf R 2:53:40 1 r479
```
### Jobs per user
Sorted list of jobs per user
```{r}
#| echo: false
#| class-output: bash
cat(paste0("squeue -A ",upid," | tr -s ' ' | cut -d' ' -f5 | sort | uniq -c | sort -k1"))
```
Sample output
```
1 tami
1 tommal
1 USER
1 valeriia
1 vioww
1 vishnupk
1 ylvafr
2 mehran96
2 miika
3 mariasve
```
### Core usage
Total number of cores used on a project
```{r}
#| echo: false
#| class-output: bash
cat(paste0("squeue -A ",upid," -o %C | awk '{total += $0} END{print total}'"))
```
### Space usage
Amount of storage space used per project
```{r}
#| echo: false
#| class-output: bash
cat(paste0("uquota | grep ",upid))
```
Sample output
```
Your project Your File Area Unit Usage Quota Limit Over Quota
--------------- --------------------- -------- ------ ----------- ----------
snic2022-22-123 /proj/snic2022-22-123 GBytes 4.6 128
```
### User activity
List last activity in a directory for all users
```{r}
#| echo: false
#| class-output: bash
cat(paste0("bash /sw/courses/utils/list_modification_times.sh /proj/",upid,"/nobackup/"))
```
Sample output
```
hkyle 2021-11-22 13:59:59 (/proj/snic2021-22-644/nobackup/hkyle/uppmax_tutorial/job_template)
malinh 2021-11-22 14:12:10 (/proj/snic2021-22-644/nobackup/malinh/slurm-23182638.out)
aliraz 2021-11-22 14:23:16 (/proj/snic2021-22-644/nobackup/aliraz/slurm-23184022.out)
kristaps 2021-11-22 14:25:08 (/proj/snic2021-22-644/nobackup/kristaps/uppmax_tutorial/jobData.sam)
anapin 2021-11-22 14:56:14 (/proj/snic2021-22-644/nobackup/anapin/uppmax_tutorial/uppmax_tutorial/jobData.sam)
analopez 2021-11-22 14:56:16 (/proj/snic2021-22-644/nobackup/analopez/uppmax_tutorial/jobData.sam)
private Not available ()
```
### List reservations for a project
```{r}
#| echo: false
#| class-output: bash
cat(paste0("scontrol show res | grep ",upid))
```
Sample output
```
ReservationName=snic2021-22-644_wed StartTime=2021-11-24T12:00:00 EndTime=2021-11-24T18:00:00 Duration=06:00:00
Users=(null) Accounts=snic2021-22-644 Licenses=(null) State=INACTIVE BurstBuffer=(null) Watts=n/a
ReservationName=snic2021-22-644_thu StartTime=2021-11-25T08:30:00 EndTime=2021-11-25T17:30:00 Duration=09:00:00
Users=(null) Accounts=snic2021-22-644 Licenses=(null) State=INACTIVE BurstBuffer=(null) Watts=n/a
ReservationName=snic2021-22-644_fri StartTime=2021-11-26T08:30:00 EndTime=2021-11-26T13:30:00 Duration=05:00:00
Users=(null) Accounts=snic2021-22-644 Licenses=(null) State=INACTIVE BurstBuffer=(null) Watts=n/a
```
### List project members
```{r}
#| echo: false
#| class-output: bash
cat(paste0("projmembers ",upid))
```
Sample output
```
snic2022-22-123 abusiddi Abu Bakar Siddique
snic2022-22-123 afifac Afifa Enam Chowdhury
snic2022-22-123 asve0014 Ashish Verma
snic2022-22-123 berka Berkay Paylar
snic2022-22-123 btleren Betül Eren Keskin
```
### User identity
Fetch user information from username
```{bash}
#| eval: false
finger username
```
## Troubleshooting
### X-forwarding
#### Setup
**Mac users**
- Install Xquartz and restart computer
- Open the Xquartz terminal and connect to Uppmax
- In my recent macos (10.xxx) , x-forwarding only works if I explicitly run the Xquartz terminal
`ssh -XY username@rackham.uppmax.uu.se`
Also use this when logging in to the compute node!
`ssh -XY username@node`
**Windows users**
In MobaXTerm, go to settings and make sure that X-forwarding is checked.
#### Testing X-forwarding
Type `xeyes` in the terminal.
### Open .html documents on Rackham
First ensure X-forwarding works, then run `firefox --no-remote filename.html`
### 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
#### 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
On a Mac, press <kbd>Fn + F8</kbd>, then select: Minimize window.
#### 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
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
Press <kbd>AltGr + 4</kbd>.
### Black background for XQuartz windows on M1 Mac
As documented [here](https://github.com/XQuartz/XQuartz/issues/31), run:
```{bash}
#| eval: false
defaults write org.xquartz.X11 enable_render_extension 0
```
***