Troubleshooting machine issues

• Storage
  • Full system volume
  • Full data volumes
  • Accidentally deleted or overwritten files
• HUNT Workbench
• Software
  • Permission denied during installation
  • MATLAB
  • R and RStudio
  • Stata
  • GUI Applications
• General configuration
  • Setting locales failed

Storage

Full system volume

Lab machines becomes unresponsive if system volumes get filled up. Click here to learn how to check the size and utilization of your volumes.

Your system disk is full if /dev/vda1 states 100 percent use:

Filesystem   Size Used Avail Use% Mounted on
/dev/vda1    9.7G 9.7G   0 100% /

We recommend that you run ncdu to get an overview over what's taking up space in your volume. For example, you may consider to move your tmp folder away from your system disk

Full data volumes

Data volumes are unable to store data when they fill up. Click here to learn how to check the size and utilization of your volumes.

TIP

We recommend that you expand your volumes, or compress and/or clean up your data when your volume utilization reach 85% (Use%). Above this threshold it will become increasingly complex to do work and data cleanups.

Accidentally deleted or overwritten files

It's frustrating to accidentally delete or overwrite data that you care about. For files on /mnt/work and /mnt/archive you have nightly copies stored in 30 days. Click here to see how you can find your restore copies and how your can restore a file.

HUNT Workbench

See our Workbench troubleshooting section.

Software

Permission denied during installation

You will need to use the sudo command when you install software with the sudo apt install <package> command. If forgotten, apt will return an error message like this:

E: Could not open lock file /var/lib/dpkg/lock-frontend - open (13: Permission denied)

Rerun your command with sudo. Contact us if this doesn't solve your issue.

MATLAB

See our MATLAB troubleshooting section.

R and RStudio

See our R and RStudio troubleshooting section.

Stata

See our Stata troubleshooting section.

GUI Applications

No X11 display variable was set

Make sure you are connected into a graphical environment such as:

• Remote desktop in Workbench - recommended
• X2Go
• VNC

Alternatives:

• MobaXterm - make sure X Forwarding is enabled to allow GUI applications to run.

General configuration

Setting locales failed

In Ubuntu 18.04 and earlier may encounter the setting locales failed message when updating your packages. Example of such an error message may look like:

During startup - Warning message:Setting LC_CTYPE failed, using "C"

Solution

1. Check if locale settings are missing

locale

Example of output of missing locale:

LANG=
LC_COLLATE="C"
LC_CTYPE="UTF-8"
LC_MESSAGES="C"
LC_MONETARY="C"
LC_NUMERIC="C"
LC_TIME="C"
LC_ALL=

2. Edit ~/.profile or ~/.bashrc:

export LANG=en_US.UTF-8
export LC_ALL=en_US.UTF-8

3. Run . ~/.profile or . ~/.bashrc to read from the file.

. ~/.profile
. ~/.bashrc

4. Open a new terminal window and check that the locales are properly set:

locale

Example of output with locale set:

LANG="en_US.UTF-8"
LC_COLLATE="en_US.UTF-8"
LC_CTYPE="en_US.UTF-8"
LC_MESSAGES="en_US.UTF-8"
LC_MONETARY="en_US.UTF-8"
LC_NUMERIC="en_US.UTF-8"
LC_TIME="en_US.UTF-8"
LC_ALL="en_US.UTF-8"