Cluster Software
We have currently got thousands of pieces of software already installed on the cluster. They are installed in the directory /share/apps.
Within this directory are domain specific sub-directories (for example: genomics and econ). These contain commonly used softwares within the relevant academic domains.
If you want a shared set of software for a research group, we can create a directory for this under /share/apps. Permissions can be set on this directory to restrict access to only group members.
/share/apps/source_files
/share/apps/source_files contains source scripts and example scripts. Source scripts are used to help you configure your environment.
For example, if you wanted to use python v3.6.5, you can easily set up your environment to use this version by typing the following:
source /share/apps/source_files/python/python-3.6.4.source
New Software
If you require software that is not already installed, please send an email to our support team. Please keep in mind that not all software is compatible with our cluster.
Python Packages and Managing Environments
Please see the Python Software page for more info.
JAX
To run JAX use something like
#usual SGE flags
source /share/apps/examples/source_files/python/python-3.7.2.source
source /share/apps/examples/source_files/cuda/cuda-10.0.source
export XLA_FLAGS="--xla_gpu_cuda_data_dir=/share/apps/cuda-10.0"
LD_LIBRARY_PATH="/share/apps/glibc-2.28/lib:/share/apps/gcc-5.5/lib64:${LD_LIBRARY_PATH}" /share/apps/glibc-2.28/lib/ld-2.28.so $(command -v /share/apps/python-3.7.2-shared/bin/python3) ~/test_jax.py
Visual Studio Code Config
In order to connect a local Visual Studio Code session to the cluster, you should modify your ssh config to include the following:
Host tails
HostName tails.cs.ucl.ac.uk
User <username>
Host beaker
HostName beaker.cs.ucl.ac.uk
User <username>
ProxyCommand ssh -W %h:%p tails
Then, from Visual Studio Code, add a new host called ‘beaker’, and select the relevant ssh config file. You should then be able to connect to the ‘beaker’ host, and be prompted for your password.
You can replace the lines ‘beaker’ and ‘beaker.cs.ucl.ac.uk’ with whichever login node you usually use, for example, if you usually log into pchuckle:
Host pchuckle
HostName pchuckle.cs.ucl.ac.uk
User <username>
ProxyCommand ssh -W %h:%p tails