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Differences between JADE and the older CentOS 7 cluster

  • JADE does not support graphical logins such as XRDP or X2go; this is deliberate, maximising resources available for other purposes. This can cause issues when making graphical plots in R.

  • The JADE login nodes are provided for file management, light work, and job submission to cluster. Not for running demanding analysis or pipelines, so all user logins have limited access to CPU and memory. For more resources you probably want to submit jobs to cluster.

  • Multiple Python-based packages have been moved into module python-cbrg, both to improve our ability to update them and to reduce duplication. Please check whether packages part of python-cbrg before requesting we install them.

  • The Slurm scheduler is configured with multiple queues to enable a fairer share of the resources.

  • Conda is not installed centrally and we are only able to offer the most basic support for Conda related issues. Note that Conda was also not supported on CentOS, but was installed centrally for some time.

  • JADE uses a modern version of Ubuntu Linux, and work started on JADE should not be moved back onto CentOS as it may not be fully backwards compatible. Equally, if you have old workflows constructed on CentOS that do not run on JADE, and cannot be rebuilt, then consider creating a container that replicates the old CentOS environment.

  • JADE correctly differentiates between the Bash and Sh command shells, so you must specify Bash directly in your shell scripts. Ensure your scripts have line #!/bin/bash at top, especially in Slurm scripts.

  • JADE uses a different setup for the Bash initialisation scripts, so you may find your command-line colours for directories are missing. To fix simply reset your Bash configuration on JADE - if your configuration is custom, you will need to manually add it back after.

    cp ~/.bashrc ~/.bashrc.backup
cp /etc/skel/.bashrc ~/

  • JADE does not have the folder /Filers, which on Centos 7 just contains 3 symlinks to other folders. The destination folders still exist. If your workflows depend on filepaths containing /Filers, then just remove/modify this prefix.

    $ ls -l /Filers
        home -> /ceph/home      package -> /ceph/package/c7     scratch -> /var/scratch