During the service window 23/08-26/08/2024, the cluster’s operating system has been migrated from Scientific Linux 7.9 to Alma Linux 9.4.
Despite our efforts in making the transition frictionless for the users, the cluster users can be affected at different degrees. Users will most likely need to actively make some changes in their own environments, in order to be able to use the cluster as they are used to, hopefully even better.
Here we want to collect information and advice, that should help users to take the actions needed to be able to start as soon as possible their work on the new operating system.
This page will be updated with new hints before and after the update, so please consider coming back to check this page.
Overview of the main changes
There are no significant structural changes in the way the cluster can be accessed and used. However, under the hood, a lot of things have changed, and some of these changes require actions from the user side. More specifically:
Minor or no changes
- Access with thinlinc and ssh via the same login nodes. (RSA/SHA1 has been disabled on all our systems, so if you have problems to connect via ssh (‘no mutual signature algorithm’), just update your ssh-client to a “modern” version)
- The Thinlinc interface remains the same, but there has been some cleanup in the menu structure.
- No change in the scheduler/scheduling limits.
- The software structure remains the same: most of the software is available as modules, and there still will be two main alternative software stacks.
- The HOME directory remains the same.
- The /work3 scratch directory will remain available (remember this is NOT backed up).
Significant changes
- ThinLinc client version >= 4.16 is required, because the server side has enhanced security requirements.
- The system software and libraries have been updated.
- Most of the modules have new names. Just check for available modules with for example
module avail R - Very old versions of some programs and libraries will not be available any longer.
- Programs installed by the users in their
HOMEdirectory will most likely need to be re-installed by re-compiling them in the new setup. - The /work1 scratch directory has been retired and is not available any longer (see details below). Users of /work1 have been informed beforehand.
- References to environment variables like
PATH,LD_LIBRARY_PATH,PYTHONPATH, modules in scripts, in configuration files (e.g..bashrc), need to be checked and eventually changed.
More details
ThinLinc client
Due to enhanced security requirements on the server side, access via thinlinc requires version >=4.16.
Symptom:
You cannot connect to the ThinLinc server at all, or you get an connection error with the message
“Couldn’t set up secure tunnel to ThinLinc agent. (Couldn’t establish SSH tunnel, SSH terminated)”
Actions to take:
If the ThinLinc client you have is older than 4.16, then go to the Cendio website and download a recent version to be able to access the cluster. No special configuration should be needed.
If you are using a Windows PC installed by a DTU IT department, you can install ThinLinc version 4.17 from DTU Software Center.
Symptom:
Your ThinLinc client is up to date, but you get the error message
“No agent server was available”.
Actions to take:
You have used up your disk quota, and therefore ThinLinc cannot establish a new connection to the desktop (agent) servers. Please free up some disk space, either logging in via SSH, or connecting to your home folder via WinSCP, FileZilla.
ThinLinc desktop
There can be issues with the ThinLinc desktop, e.g. if you had a customized desktop on the old setup.
Symptom: the Terminal (and other applications) won’t start, and you see an error message like
Failed to execute command "/apps/dcc/thinlinc/bin/...“.
Action to take:
You need to reset your panel to the new defaults. From the ‘Applications’ menu at the top, go to ‘DTU’, then ‘Utilities’ and click on the ‘XFCE4 Panel reset (system defaults)’ icon. This will reset all your settings to match the new setup.
If you don’t like the new ‘dark mode’ of the setup, then right-click on the panel at the top of the desktop, ‘Panel’ and then ‘Panel Preferences’. In the ‘Appearance’ pane, you can toggle the ‘Dark mode’ setting.
Symptom: some applications, e.g. ParaView, are transparent and you can see the background
Action to take:
This can happen, when the transparency features of the window manager are enabled. You can fix this problem, by changing the settings: from the ‘Applications’ menu at the top, go to ‘Settings’, and then ‘Window Manager Tweaks’. Activate the last tab, ‘Compositor’, and untick the ‘Enable display compositing’ check box at the top. Close the window, and the settings are saved.
Scratch storage
The /work1 scratch directory is going to be retired.
Actions to take:
A new directory under /work3 has been created for all users who had a directory under /work1. If you have data under /work1, you should select which data you want to save, and and move them to your new /work3 folder. Please follow this short guide.
After August 26 the data will be available readonly on transfer.gbar.dtu.dk until December 1st 2024, and then will be permanently deleted.
If you have any doubt or issues, write to support@hpc.dtu.dk.
Modules
The module system does not change, but you have to assume that:
- all modules get a new name;
- modules for very old versions of programs/libraries are not be available any longer.
Actions to take:
- If you have scripts that load specific modules, you have to change the scripts so that they reference the new modules.
- If you have compiled a program using a module, you are encouraged to recompile it using the corresponding new module.
- Check if you are referencing modules in the system configuration files (e.g.
.bashrc).
Compilers, tools and libraries
All compilers (GCC, Intel,…) and libraries (MPI, OpenBLAS, PETSc, …) have been updated, and are available as modules.
The oldest versions have not been migrated, but we still keep some old versions for reproducibility reasons.
Actions to take:
It is recommended to recompile programs with the new compilers and libraries.
Commercial programs
Commercial programs (like MATLAB, COMSOL, ANSYS, …) and libraries (Gurobi, CPLEX, …) should just work as under the previous operating system.
Very old versions are not migrated to the new system, but we keep some of the older versions for reproducibility purpose.
Actions to take:
- Make sure that the you are using the new module or the correct
PATH.
Python
python 2 has been deprecated for a long time, and it is not available any longer.
Several python 3 versions are available, as one can check with the command
module avail python
Old versions of python 3 are not migrated to the new system. Also the most commonly used libraries (numpy, matplotlib, pandas,…) are available, but only the recent versions.
Actions to take:
- In your script, make sure to select one of the new modules for each of the python packages you need.
- If you have virtual environments, they could work, but it is likely that they will not work as expected. It is recommended to re-create the environment with the new modules.
R
Several versions of R are available, but not the oldest ones.
Actions to take:
Due to the way R manages packages, it is very likely that all the packages you have previously installed needs to be reinstalled. The procedure should be straightforward, without the need for complex recipes as on the old system. Just move away the old modules first with: mv ~/R ~/R.old and also rename and/or check your .R/Makevars file. In case of troubles write us at support@hpc.dtu.dk, explaining what packages you need to install, for which R version, and what issues you are encountering.
julia
We have several version of julia installed as modules, for reproducibility reasons.
Actions to take:
- Make sure to use one of the new modules in your scripts.
- It may be necessary to reinstall the packages in julia, and it is recommended anyway.