HPC Support - advanced

anaconda

Anonymous (anonymous@undisclosed.example.com) — 2026-02-19T15:02:11+00:00

Anaconda Help Anaconda is a software installation and management toolset, designed to exist alongside Python and other software made available by the operating system or other software provision methods. It largely replicates the same functionality available from system tools such as

ansys_cfd_post

Anonymous (anonymous@undisclosed.example.com) — 2026-04-29T20:02:52+00:00

Ansys CFD-Post / CFX Help * See CFD-Post: * See CFX: CFD-Post / CFX is included with ANSYS as part of our Newcastle University licensing agreement to all users of the HPC facilities. ---------- Running To use ANSYS CFD-Post on Comet, please read the main

ansys_fluent

Anonymous (anonymous@undisclosed.example.com) — 2026-04-30T13:21:24+00:00

Ansys Fluent/Aero/Icing Help " Ansys Fluent is the industry-leading fluid simulation software known for its advanced physics modeling capabilities and industry leading accuracy." * See: * Fluent users guide: ---------- Running To use ANSYS Fluent on Comet, please read the main

ansys_forte

Anonymous (anonymous@undisclosed.example.com) — 2026-04-29T10:31:44+00:00

Ansys Forte Help Deprecated Content This example was written for a previous version of ANSYS on Comet. Newer versions (>= 2025 R2) will differ. This page will be replaced once 2025 R2 is fully tested. ANSYS Forte is included in the University ANSYS license package, it is normally installed as part of the larger ANSYS software module. e.g:

ansys_workbench

Anonymous (anonymous@undisclosed.example.com) — 2026-05-11T13:55:50+00:00

ANSYS Workbench " Ansys Workbench combines access to ANSYS applications with utilities that manage the product workflow. Workbench allows you to construct projects composed of multiple dependent systems that can be updated sequentially based on a workflow defined by the project schematic.

apptainer

Anonymous (anonymous@undisclosed.example.com) — 2026-03-12T16:27:42+00:00

Apptainer Help If you have used Singularity previously, then Apptainer is a 100%, like-for-like replacement. To quote the Apptainer website: " Apptainer is a secure, portable, and easy-to-use container system that provides absolute trust and security. It is widely used across industry and academia.

aws_cli

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T17:13:02+00:00

Amazon Web Services Help - aws-cli " The AWS Command Line Interface (AWS CLI) is a unified tool to manage your AWS services. With just one tool to download and configure, you can control multiple AWS services from the command line and automate them through scripts.

bede_add_proj_member

Anonymous (anonymous@undisclosed.example.com) — 2025-06-12T09:43:28+00:00

Adding New Users to your Bede Project A new user can join your project as follows: * Setup an account at SAFE: using an @newcastle.ac.uk email address * Request access to a project (Project : Request access) * Choose your project name (starting bdncl)

bede_logging_in

Anonymous (anonymous@undisclosed.example.com) — 2025-10-16T11:42:38+00:00

Logging in to Bede (see for details) The SAFE website provides authentication services to a large number of HPC facilities so has options which are not relevant to Bede. * Register with your @newcastle.ac.uk email address * Ignore options to 'Login with institutional credentials' and 'upload ssh key' - neither of these is valid for Bede.

cellranger

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T17:13:12+00:00

Cell Ranger Help Installation

comet_alpha_testers

Anonymous (anonymous@undisclosed.example.com) — 2025-10-08T08:38:58+00:00

Comet early-access users What is this page for? This page contains documentation aimed at Alpha testers and other early access users of Comet. If you have been contacted and asked if you would like to have early access to Comet in advance of the roll out to the wider University research community, then this page will detail the process of getting access to the facility as well as describing the limitations and restrictions which are in place during this early access period.

comfyui

Anonymous (anonymous@undisclosed.example.com) — 2025-11-18T21:04:33+00:00

ComfyUI " ComfyUI is a node-based interface and inference engine for generative AI. Users can combine various AI models and operations through nodes to achieve highly customizable and controllable content generation. ComfyUI - The most powerful open source node-based application for generative AI

containers

Anonymous (anonymous@undisclosed.example.com) — 2026-02-03T11:59:46+00:00

Container Technology Building more complex processing and analysis pipelines within a container can offer several advantages: * The container fully encapsulates the job and all software dependencies * Software dependencies do not need to be installed on the HPC facility

dbcan

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T17:13:29+00:00

Dbcan Help dbCAN is the standalone version of the dbCAN3 annotation tool for automated CAZyme annotation. This tool, known as run_dbcan, incorporates HMMER, Diamond, and dbCAN_sub for annotating CAZyme families, and integrates Cazyme Gene Clusters (CGCs) and substrate predictions.

dnascent

Anonymous (anonymous@undisclosed.example.com) — 2026-02-27T11:32:28+00:00

DNAscent Help DNAscent is software designed to detect the base analogues BrdU and EdU in single molecules of DNA sequenced on the Oxford Nanopore platform. In an experimental setup where BrdU and EdU are incorporated into nascent DNA by replication forks, this software can be used to answer questions that were traditionally answered by DNA fibre analysis. DNAscent can also call the genomic positions of stalled and stressed replication forks for use as a replication stress assay.

external_facilities

Anonymous (anonymous@undisclosed.example.com) — 2026-01-15T20:08:31+00:00

External HPC Facilities UK researchers are eligible to apply for access to EuroHPC JU supercomputers and facilities listed at . The comparison table below is a work in progress and currently lists only some of these facilities. Facility Name Facility Type Link

flower

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T17:13:50+00:00

Flower Help * Installation Conda is not needed to install Flower and just loads additional complexity - it works quite happily with the standard pip command including in later versions of the Python 3 modules installed on our HPC facilities. The easiest approach is to load one of our Python software modules, and then create a new python venv area to hold it. In the example below we create the

fmriprep

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T17:14:02+00:00

fMRIPrep Help Development Paused - resource required is too high for limited time of usefulness on Rocket " fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application (www.nipreps.org) for the preprocessing of task-based and resting-state functional MRI (fMRI).

genoscores

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T17:14:24+00:00

Genoscores Help " Genoscores is a database of filtered summary results of genome-wide association studies in humans together with a package of analysis tools." * Installation This is a simple install script for building a standalone version of

index

Anonymous (anonymous@undisclosed.example.com) — 2025-10-02T09:43:31+00:00

Advanced Topics This section of the documentation contains information and guides on subjects which are more useful to users who are already using the HPC facilities to run jobs. Here you can find information gathered from real-world examples of problems and use-cases the HPC community at Newcastle has encountered.

interactive

Anonymous (anonymous@undisclosed.example.com) — 2025-11-29T12:15:43+00:00

Open On-Demand and Interactive Applications Whilst most use of the HPC facilities is traditionally undertaken by logging in with SSH to a login node and then submitting Slurm SBATCH job files, it is becoming increasingly common to need graphical output - either from data generated on one or more compute nodes, or to run interactive, heavy applications directly on the compute nodes themselves.

jupyter

Anonymous (anonymous@undisclosed.example.com) — 2025-09-01T14:07:44+00:00

Jupyter Lab Help Jupyter Lab is available on our HPC facilities to all users. The only supported route to running Jupyter is: * - recommended for the desktop Matlab application Previous Workarounds Whilst Jupyter was never supported on Rocket, several users tried a number of workarounds to get it running, including setting up port forwards, starting long-running processes on one or more login nodes or similar. These are no longer supported and are against the acceptable use policies.

matlab

Anonymous (anonymous@undisclosed.example.com) — 2026-05-06T12:01:10+00:00

Matlab Help Mathworks Matlab is available on our HPC facilities as part of our University licensing agreement. It is available to all users. You can run Matlab in several ways on our HPC: * - recommended for the desktop Matlab application *

mozaik

Anonymous (anonymous@undisclosed.example.com) — 2025-11-18T10:11:35+00:00

Mozaik " Mozaik is a workflow system for spiking neuronal network simulations written in Python that integrates model, experiment and stimulation specification, simulation execution, data storage, data analysis and visualization into a single automated workflow. This way, Mozaik increases the productivity of running virtual experiments on complex heterogenous spiking neuronal networks.

nextflow

Anonymous (anonymous@undisclosed.example.com) — 2026-05-11T12:16:08+00:00

This page is under development Owain is going to fill in this page Start with install in home dir Look at recommended config file * use scratch for job files? * use Apptainer don't allow Docker discuss with existing users look at making a module

podman

Anonymous (anonymous@undisclosed.example.com) — 2025-09-22T08:31:56+00:00

Podman Help Links to the official Podman documentation material: * Podman getting started guide * Podman full documentation and API guide We recommend Podman is used by more experienced users. If you are just starting out with containers then Apptainer has a lower level of complexity for first time users. Unlike Apptainer, workflow with Podman is much more similar to

python_modules

Anonymous (anonymous@undisclosed.example.com) — 2026-04-09T14:37:46+00:00

Python Module Installation * See Python help page: Python module on Comet Using pip Using Virtual Environments ---------- Back to software

rclone

Anonymous (anonymous@undisclosed.example.com) — 2026-03-12T12:48:58+00:00

Rclone " Rclone is a command-line program to manage files on cloud storage. It is a feature-rich alternative to cloud vendors' web storage interfaces. Over 70 cloud storage products support rclone including S3 object stores, business & consumer file storage services, as well as standard transfer protocols.

rocket_comet_cheats

Anonymous (anonymous@undisclosed.example.com) — 2026-03-02T13:36:26+00:00

Comet, for existing Rocket users Key Changes For existing Rocket users, there are some major differences in how Comet operates and the features it has available - almost every aspect has been improved upon in some way, but there are some key items you need to know before you log on and start accessing the facility.

samplecontainers

Anonymous (anonymous@undisclosed.example.com) — 2026-03-12T16:58:14+00:00

Sample Container Definitions This page provides a number of sample Apptainer definition files which you may wish to make use of when developing your own container solutions for Comet if an option is not already in our software pages or directly named in our software and existing containers list. Please ensure that you read the

scrinvex

Anonymous (anonymous@undisclosed.example.com) — 2025-08-07T17:14:47+00:00

Scrinvex Help * Single Cell RNA Intron-Exon Counting " scrinvex counts intronic, exonic, and junction-spanning reads for each unique barcode encountered in the input bam. Each mapped read is checked against the input gtf to determine if the read lies entirely on introns, exons, or crosses at least one intron/exon junction. Reads with the same UMI are only checked against any given gene once. Subsequent reads with the same UMI will not be checked again…

slurm_checkpoints

Anonymous (anonymous@undisclosed.example.com) — 2025-09-04T10:37:15+00:00

Slurm Job Checkpointing & Restarting Jobs Job checkpointing is supported for most types of single-node jobs on Comet using DMTCP. This allows a job to be suspended or stopped and then resume from that point in the future without the loss of data - this may be especially useful for jobs which run for many days. Enabling checkpoints allows you to resume your job if it crashes, or if the compute resources it is using become unavailable for some reason.

slurm

Anonymous (anonymous@undisclosed.example.com) — 2025-04-09T15:03:07+00:00

Advanced Slurm Job Optimisation This section is incomplete This documentation section is still being written. Multi Node Job Multi Node Task Array Job Parallel Jobs Using MPI ---------- Back to Advanced Topics

software_list

Anonymous (anonymous@undisclosed.example.com) — 2026-05-11T14:05:45+00:00

Software List This page documents the list of centrally provisioned software on Comet. * - Types of software and levels of support available * - All of the software now installed on Comet * - All of the pre-built container images available for use on Comet

software

Anonymous (anonymous@undisclosed.example.com) — 2026-05-11T11:42:28+00:00

Advanced Software Topics Types of Software Software List Link to list of all centrally installed software on our HPC facilities: * Software list - a list of all the software modules provided on Comet, and software requests which have been made * Containers list - a list of all the pre-built container environments we provide on Comet

ssh_keys

Anonymous (anonymous@undisclosed.example.com) — 2025-04-09T15:03:27+00:00

Password-Less Authentication Using SSH Keys This section is incomplete This documentation section is still being written. ---------- Back to Advanced Topics

sshuttle

Anonymous (anonymous@undisclosed.example.com) — 2025-05-21T11:15:44+00:00

Tunneling using SSHuttle This document explains how to connect to Comet, Rocket, or any other Unix-like server from off-campus using the SSHuttle software. Intended audience: * Comet, Rocket HPC users * Other on-Campus, unix-like, server users sshuttle

star-ccm

Anonymous (anonymous@undisclosed.example.com) — 2026-04-23T12:02:52+00:00

Siemens Simcenter STAR-CCM+ Work in Progress License STAR-CCM+ is licensed software and only authorised users will be able to run the software by checking out their allocated license from the Siemens license server. STAR-CCM+ versions on Comet and Windows Software Center

statamp

Anonymous (anonymous@undisclosed.example.com) — 2026-03-12T19:50:28+00:00

Stata MP Help Stata/MP is the multiprocessor version of Stata, used for modelling and analysis of large datasets, predominantly in social sciences. Stata/MP is available as the 2-core version on our HPC facilities as part of our University licensing agreement. It is available to all users.

vs_code

Anonymous (anonymous@undisclosed.example.com) — 2026-02-19T16:46:55+00:00

Visual Studio Code (VS Code) Help It is not supported to connect Visual Studio Code to our HPC. This is because VS Code works by launching processes on the target machine (the HPC login nodes), which takes up resource and are often left running after a broken connection or just by accident.