Lightweight HPC (freebio[1-4], bioint0[1-4]) is a resource for all UiO users interested in testing out scientific applications, simulation software, parallel code etc. This service is free of charge for all UiO users.
These are stand-alone machines for low-threshold use, and with best-effort user support.
Note that there is no batch system, i.e you can not run jobs that span over two machines (like on a typical HPC system). There is therefore no queue system, so use the machines in a solidaric way!
Alternatives:
There is also Fox in Educloud. Fox has a job submission queueing system and has a somewhat more streamlined setup, in addition to interactive nodes similar to the ML-nodes.
Looking for some other computing service? This page may help you.
What are Freebio[1-4] ?
- These are ARM based servers running Linux (RHEL/Ubuntu) and the very few ARM based HPC servers in production in Norway. The processors all run a large set of software and are popular with Julia and R.
- Freebio1 + Freebio2 have 64 cores (Cortex A72), 256 GiB RAM and a 36 TiB of local disk and run RHEL.
- Freebio[3-4] have 96 cores (Neoverse N1), 512 GiB RAM and a 3.5 TiB scratch area (/scratch) on local NVME disk and run Ubuntu.
How to use
Freebio[2-4] and Bioint0[1-4] are available to all UiO users and partners that are granted an UiO account.
Get access by filling in this nettskjema.
What are bioint0[1-4]?
- These are AMD/Intel based servers running Linux (RHEL) and a selection of software. Common software is installed as modules and yet other per demand.
- bioint01 has AMD EPYC 7501 CPUs, 128 cores and 128 GB RAM and a 7.3 TB scratch area (/work) on local disk.
- bioint0[2-4] have Intel Xeon E5-2690 CPUs, 32 cores and 512 GB RAM each.
What can I store in Light-HPC system ?
Access
First, request access by filling in this nettskjema. Once access has been granted, you log into the machine using Secure Shell (SSH) in a terminal. SSH login is available natively to Linux or Mac OSX (or any UNIX-based systems). On Windows machines you might use the ssh client in a PowerShell session, or for example, PuTTY.
If you are on the UiO network you can:
ssh <username>@<server>.hpc.uio.no
Replace <username> with your registered username, and <server> with the server name, e.g. freebio1.
However, if you are outside the UiO network you must go via an UiO machine first:
ssh <username>@login.uio.no ssh <server>.hpc.uio.no
Or combined into a single command:
ssh -J <username>@login.uio.no <username>@<server>.hpc.uio.no
Copying files to and from machines at UiO with SCP
The scp command to copy files works similarly to SSH. If you are on UiO network:
scp local_file <username>@<server>hpc.uio.no:<destination-directory>/<filename>
If you are outside UiO network:
scp -J <username>@login.uio.no local_file <username>@<server>hpc.uio.no:<destination-directory>/<filename>
Shared home directory
Users of the Lightweight HPC machines get a home directory that is shared between all Lightweight HPC machines but that is separate from their regular UiO home directory allowing for easy data transfer between the machines.
What amount of resources can I use?
Please note that the nodes are a shared resource and in high demand. You should be considerate of available resources of each machine (the machines are not the same). The following commands are useful to know the limits and what's available.
To list the number of processor cores.
[ ~]# nproc 192
You should not use more than 1/4 of the value shown. So the maximum you should use should in this example is less than 48 cores or threads.
To list the amount of available memory:
[~]# free -h
total used free shared buff/cache available
Mem: 1,0Ti 103Gi 837Gi 6,6Gi 66Gi 891Gi
Here you should not try to use no more than 1/4 of the "total" value and less than the "free" limit.
If you violate above limits then the machine may crash and you and the fellow users will loose all ongoing work. If we can save others jobs, we might consider killing the jobs that violates the conditions.
Software
We install software on lightHPC using the EasyBuild framework. The module system allows you to see what software is available and load it for use.
To see available software, please run the following command:
module avail
To load a module, use name and full version of the module:
module load <some-package-listed-in-module-avail>
For example:
module load R-bundle-Bioconductor/3.12-foss-2020b-R-4.0.3
To get a clean environment and unload all modules:
module purge
Installed software
- Python, R, Bioconductor, Julia, Singularity (installed on all six servers)
- MATLAB, Gaussian, Molpro (only for x86_64, i.e. bioint0[1-4]
- GATK, Keras, Tensorflow (only aarch64, i.e. freebio1 and freebio2 at the moment)
- Qiime (only at bioint01 at the moment)
Software requests
If you need additional software or want us to upgrade an existing software package, we are happy to do this for you (or help you to install it yourself if you prefer that).
Request software by filling in this nettskjema.
It provides us with the relevant information needed for installation. After filling in the nettskjema a ticket will be created in RT and we will get back to you with the installation progress.
Contact
Do you need help or support for the Lightweight-HPC resources?
- The fastest way to get support is to fill in this form
- You can also email us at hpc-drift@usit.uio.no