If you're logged into one of our JADE cluster login nodes, note that you can read this information at any time using the man(1) command, e.g:
- If you plan to use a Jupyter notebook, please read https://datashare.molbiol.ox.ac.uk/public/files/Jupyter.pdf before spending time working out how to set custom sessions. This uses the same physical hardware as R-Studio.
- For direct SSH logins, there are two primary login servers for the CCB cluster. login1.molbiol.ox.ac.uk and login2.molbiol.ox.ac.uk can be used equivalently and you can connect using any SSH client and using a command such as:
ssh -l your_user_name login1.molbiol.ox.ac.ukBoth tmux(1) and screen(1) are installed for session persistence between logins. Please be aware that the CCB login nodes are provided in order to allow file managment, light development work and submission of jobs to the cluster. As such, all user logins are limited to a maximum of 2 CPU cores and 4GB memory ; if you attempt to use more than 2 cores then nothing bad will happen (it will just be no faster). On the other hand, if you attempt to use more memory your processes will be automatically terminated. In addition, to guard against the system slowing to a crawl if too many people are logged in at the same time, watchdog programs are installed as a last line of defence. See cpuwatch(7) , memwatch(7) and acceptable-use(7) for further details. If you think need more than this, see slurm-basics(7) for information on interactive Slurm sessions.
- There is no graphical login available. If you'd like to learn more about the Linux command line, please consider attending an OBDS training course as described at https://www.imm.ox.ac.uk/research/units-and-centres/mrc-wimm-centre-for-computational-biology/training/oxford-biomedical-data-science-training-programme . If you want to use programs such as Jupyter which provide graphical interfaces, please consider using our pre-provided services described above; for advanced users, you can additionally use SSH tunnels with port forwarding as described at ssh-tunnel(7). To view files installed locally, note that the -X option to SSH is enabled for X forwarding, and that the image viewer feh(1) and PDF viewer xpdf(1) are both installed.
- your password must be at least 16 characters
- it must not be a password used anywhere else
- you must never, ever share it
For more information on choosing secure passwords, please see the University's Information Security website at https://www.infosec.ox.ac.uk/create-strong-passwords
If you're confident that you know exactly what you're doing you are, of course, free to modify this in any way you wish. At the same time, please be aware that a significant percentage of issues that we're asked to help with turn out to be the result of misconfiguration of a .bashrc and that you can even block your own logins.
In particluar, we recommend that you do not add any of the following to your .bashrc :
- Any commands which load modules
- Any commands which load Python venvs
- Any commands which load Conda evironments
- Any commands which alter your LD_LIBRARY_PATH
If you find yourself in the situation where you're considering doing any of these, please consider contacting us for help before doing so. We may be able to suggest a better alternative and save you hours (or even days) of wasted time trying to figure out why something has broken.
If you need to store large files such as NGS data or to share data with other users on the cluster you can request collaboration projects, which will be set up for you in /project/. Please note that the quota for a project is for all of the data in it and not on a per-user basis. Collaboration projects are a secure way for data to be shared with specific groups of people. You just pick the logical set of data and define the people it needs to be shared with, then we create the project for you and update the list of people as time goes on so that it's always correct. They're a secure, convenient way to share data. For more information, see project(7). To join an exiting project, please ask the PI to contact us via firstname.lastname@example.org and ask for your username to be added.
You can additionally share data with other people over the internet using our public datashare service. For further details, see datashare(7).
If you are handling data that needs especially high confidentially (e.g. human patient data) or where there are specific security requirements imposed by the data source or funder (e.g. UK Biobank data), please get in touch with us before uploading it.
Username: [your CCB username]
Password: [your CCB password]
Then click the Quickconnect button to establish the connection. The files in your home directory on login1 will be displayed in the lower right panel of FileZilla. These can be dragged to the left panel in order to copy files from the cluster to your local machine. Similarly, dragging files from the left panel to the right panel will copy them from your local machine to a directory on the cluster.
On the CCB servers these files can be found at /databank/igenomes/. More information can be found in igenomes(7)
We recommend taking the time to read modules(7) , python-cbrg(7) and R-cbrg(7) before attempting to run any programs or install software which appears to be "missing".
JADE also has the singularity container solution installed (aka apptainer), and is available without loading any module. Example: singularity exec your-Singularity-container.sif ... . This is also compatible with Docker container images, example: singularity run docker://ubuntu:latest
We also recommend that you send a single question or request per email, and that you always send new requests as new emails and not as replies to old ones. Doing this makes it both more likely that your quick questions are answered quickly, and less likely that your requests are overlooked because we think that we've already done them.