Biotin4.hpc.uio.no
biotin4.hpc.uio.no
biotin4 is a server that is available for every UiO account associated with NCMM. To connect, an ssh client is required. MacOS, Linux and Windows all come with a pre-installed ssh client.
First, start your terminal:
- MacOS: Start Terminal.app
- Windows: Start PowerShell or Command
- Linux: Start terminal
Then, enter the command ssh uio-username@biotin4.hpc.uio.no (replace
uio-username with your UiO username). When asked for your password, enter your
UiO username.
If connecting from outside of the UiO network, you will need to use the
following command ssh -J uio-username@login.uio.no uio-username@biotin4.hpc.uio.no, and enter your password twice. This will
force all traffic to pass through the "jumphost" login.uio.no.
You are strongly encouraged to read more about this: Ssh at ncmm
There is no submission- or queue-system on biotin4, which means that you should
have a general idea of how busy the server is before starting jobs. Use the
commands uptime or htop for this. Also free -h to check memory usage.
Generally: Be nice! Think twice before starting a job requiring more than 50 CPUs. Remember, this is a shared resource. If you would like to start larger jobs, please head over to Educloud and register a new account.
Hardware
biotin4 is our most recent server.
- CPU: AMD EPYC 7643, 96 cores/192 threads
- Memory: 2 TB
- Storage: ~500 TB
- Super fast storage (NVMe): 7 TB
- GPUs: None
Software
On biotin4, all software is installed as modules. To view installed modules, use
the command module avail.
Modules can be loaded with the command module load BWA/0.7.17-GCC-11.3.0. By
doing that, the command bwa will be available.
It's possible to load multiple software modules. However, loading a different version of the same tool will replace the previously loaded version of that tool.
To unload a module, use the command module unload BWA/0.7.17-GCC-11.3.0.
To unload all modules, use the command module purge.
For further information, have a look at the documentation for the Fox cluster in Educloud: Available Software on Fox.
Local storage
Group storage volumes can be found in the /storage/ folder. You should already have access according to the research group you belong to.
For temporary storage for your pipellines, you have two options:
-
/storage/scratch/: A 15 TB volume on spinning drives. This is the primary scratch area. -
/scratch/: A 7 TB very fast flash storage (NVMe) volume. Use this if your software requires very fast disk access.
Please create your own subfolder under these volumes. After running your pipeline, move the end-results back to your home- or group folder, and remove the scratch files.
