Christmas Closure 2021

Please note that due to college closure for Christmas, there will be minimal customer support after Tuesday 21st Dec 2021 until the college re-opens on the 4th January 2022. Please ex...

in news, Dec 07, 2021

A guide to using Apocrita's scratch storage

The Apocrita scratch storage is a high performance storage system designed for short-term file storage, such as working data. We recently replaced the hardware that provides this serv...

in news, Jun 24, 2021

ITS Research FAQ regarding use of services during COVID-19 pandemic

As a result of the large-scale shift to remote working due to the COVID-19 pandemic, we have been asked various questions relating to computational research, which we’ll try to addres...

in news, Mar 19, 2020

Apocrita newsletter - March 2020

Here is a round-up of recent QMUL HPC cluster news from the ITS Research team, including information about new compute nodes.

in news, Mar 01, 2020

Christmas Closure 2019

Please note that due to college closure for Christmas, there will be minimal customer support after Monday 23rd Dec 2019 until the college re-opens on the 2nd January 2020. Please exe...

in news, Dec 20, 2019

Simplification of parallel queues on Apocrita

We are simplifying the way that the multi-node parallel jobs are run on the cluster.

in news, Jun 27, 2019

Cluster update summary

As part of our commitment to providing stable and manageable systems, here is a round-up of some recent updates we have been working on behind the scenes:

in news, Jun 12, 2019

Storage Upgrade June 2019

Apocrita Research Data Storage: Notice of “at risk” period

in news, Jun 12, 2019

GitHub Enterprise Maintenance 02/05/2019

On Thursday 02/05/2019 at 10:00 the GitHub Enterprise instance will be taken down for maintenance to increase the disk capacity that contains user data as it is currently over 80% full.

in news, Apr 26, 2019

New high performance storage for scratch data

We are pleased to announce a new scratch storage array that is based on fast NvME based hardware. This will hopefully make I/O related tasksmuch faster

in news, Mar 20, 2019

NAG Fortran compiler available on Apocrita for SEF

We have installed the NAG Fortran compiler on Apocrita for use by researchers from the School of Economics and Finance. In this post we look at how to access the compiler, why we may...

in news, Mar 18, 2019

GitHub Enterprise Upgrade 2.16

On Wednesday 2019-02-20 at 14:00 we will be applying an upgrade to our GitHub Enterprise instance to version 2.16.2, which includes bug fixes and the latest security updates.

in news, Feb 14, 2019

Cluster Hardware Upgrades and Additions

As part of our commitment to regular upgrades to the HPC service, and to keep up with ever-growing demand, we are pleased to announce the addition of new hardware to the Apocrita HPC ...

in news, Dec 04, 2018

GitHub Enterprise Upgrade 2.15

On Wednesday 2018-11-21 at 14:00 we will be applying an upgrade to our GitHub Enterprise instance to version 2.15.2, which includes bug fixes and the latest security updates.

in news, Nov 19, 2018

AI tools

For the increasing number of Researchers working with Deep Learning technologies, we also have the existing GPU nodes attached to Apocrita. Tensorflow is available, and we are working...

in news, Sep 15, 2018

AI tools

QMUL have access to powerful Tier 2 (formerly known as Regional) HPC resources, predominantly for EPSRC researchers. If you run multi-node parallel code (using MPI, for example), you ...

in news, Sep 15, 2018

POWER servers

QMUL installed two IBM AC922 POWER 9 servers to support research into deep learning and artificial intelligence, the first of their kind in UK HE. These servers come with a suite of c...

in news, Sep 15, 2018

Home and Group Directories

During the summer, home directories were migrated to the new storage platform. This means that quotas have grown slightly as the underlying block size has increased.

in news, Sep 15, 2018

Deprecated modules

We removed some problematic module files. Please check your job scripts for use of these modules:

in news, Sep 15, 2018

Short queue

Please note that frontend/login nodes are for preparing and submitting your job scripts and running computational tasks directly on the frontend nodes is forbidden, since it can impai...

in news, Sep 15, 2018

Decommissioning of ccn nodes

The ccn nodes have been removed to make way for the new sdv nodes. The nodes were very old, had become unreliable, and were an inefficient use of space and power.

in news, Apr 05, 2018

New cluster announcement

We are pleased to announce that the new cluster is available for general use. This has been a large project, involving the following:

in news, Jul 11, 2017

Midplus Consortium

The Midlands Plus consortium have now deployed a new 14,000 core cluster, located in Loughborough. You can hear more about this from your local institution.

in news, Jul 11, 2017

1PB added storage

We recently added an additional petabyte of storage, it is necessary to move all files to the new storage to benefit from improved performance.

in news, Mar 20, 2017


Comparing common compression tools using real-world data

Compression tools can significantly reduce the amount of disk space consumed by your data. In this two-part article, we will look at the effectiveness of some compression tools on rea...

in article, Oct 10, 2019

Performance testing with NVMe storage and Spectrum Scale 5

We have recently procured 120TB of NVMe based SSD storage from E8 Storage for the Apocrita HPC Cluster. The plan is to deploy this to replace our oldest and slowest provision of scrat...

in article, Dec 19, 2018

Python performance in containers

Singularity is a container solution designed for HPC. Due to the secure and simple design, it can be easily used to provide applications for use with HPC clusters where other containe...

in article, Jul 03, 2017


Modules Update December 2021

Since the last module update in December 2019, we have:

in modules, Jan 06, 2022

Modules Update December 2019

Since the last module update in August, we have added 23 modules to dev, added 22 modules to production and removed 4 modules.

in modules, Dec 11, 2019

Modules Update August 2019

Since the last update in April, we have updated the following module files:

in modules, Aug 09, 2019

Modules Update April 2019

Since the last update in March, we have updated the following module files:

in modules, Apr 26, 2019

Modules Update March 2019

Since the last update (on 29/11/2018), we have updated the following module files:

in modules, Mar 11, 2019

Update of environment modules to version 4.2.1

We have deployed the latest version of Environment Modules (4.2.1) across the cluster on all frontend and compute nodes.

in modules, Jan 18, 2019

ppc64le own modules

You may now load private ppc64le modules after loading the use.own module on nodes with POWER9 processors. Private modules must be placed in the directory ${HOME}/privatemodules_ppc64...

in modules, Dec 12, 2018

Development modules update

We have moved the following modules from dev to deprecated:

in modules, Nov 29, 2018

Deprecated openmpi 2.0.2-gcc module

We identified a problem with the openmpi/2.0.2-gcc module and have removed it as the correct interface was not being used for the MPI communication between nodes. This resulted in pot...

in modules, Apr 05, 2018


Using compiler options to help debug programs

Once we’ve written a program more advanced than our “Hello, world!” example, we’re going to make mistakes. In this post, we’ll look at how we can use the very compilers we’re using to...

in rse, May 11, 2022

Introducing Sherman Lo, RSE

Hello! I am Sherman and I have just joined the RSE team at Queen Mary. Glad to meet you all!

in rse, Jan 26, 2022

One year of code review club with the William Harvey Research Institute

Over the past year, researchers from QMUL’s William Harvey Research Institute (WHRI) have engaged on a collaborative code review club. Through this collaborative effort the group aims...

in rse, Dec 21, 2021

Introductory computing skills for researchers: Software Carpentry with RSLondon

Research Software London is a community to support the use and development of research software in London and the South East. Since 2019, RSLondon has run a number ofSoftware Carpentr...

in rse, Dec 16, 2021

Comparison of Python Distributions on Apocrita

When it comes to picking a distribution, Python programmers are spoilt for choice. We’re going to compare two of the most popular (CPython and Anaconda) and one that promises big perf...

in rse, Dec 01, 2021

Jigsaws with GIMP and Python

Jigsaw puzzles proved wildly popular during lockdown, but they weren’t all done on the dining room table on rainy afternoons. The puzzle faced by researchers from the School of Englis...

in rse, Aug 03, 2021

Using Apocrita's GPUs with OpenMP

On Apocrita we can use OpenMP to execute code on GPU devices. This post looks at how to compile such programs and submit them to run on the GPU nodes. The post assumes that you have c...

in rse, Jul 02, 2021

Faster Fast Fourier Transforms in Python

A little while ago, we were approached by a researcher from the School of Mathematical Sciences with the classic request of “I’d like my code to run more quickly”. They were simulati...

in rse, Jun 11, 2021

Intel Parallel Studio XE 2020 update 4

The Intel Parallel Studio XE Cluster Edition 2020 update 4 suite is now installed and available on Apocrita. This release will be the last of the Parallel Studio releases we support, ...

in rse, Apr 22, 2021

Remote development on Apocrita with Visual Studio Code

Visual Studio Code (VS Code) is an open-source and lightweight text editor from Microsoft, and distinctly different from Visual Studio. In this short tutorial we aim to set up VS Code...

in rse, Feb 08, 2021

Parameterized derived types in Fortran - introduction

User-defined data types in Fortran may have parameters which control certain aspects of their definition. In this post we look at what these parameterized types are, how they are use...

in rse, Sep 10, 2020

Introducing Iain Stenson, RSE

Hello. I’m Iain, the newest recruit to the QMUL ITSR RSE team. We are the group of software engineers within ITS Research who help people at Queen Mary write readable, correct and hi...

in rse, Jul 13, 2020

Apocrita says Hello, world!: basic use of our cluster

A common first program to write in a new language is a “Hello world” example where we print a simple line of output. In this tutorial we first look at examples written in C, C++ and F...

in rse, Feb 12, 2020

When good compilers go bad

Many people rely on compilers, for languages such as C, C++ and Fortran, to create executable programs from source code. Just like our source code, compilers themselves may have bugs....

in rse, Dec 16, 2019

Getting REAL with Fortran

Fortran provides a variety of intrinsic representations of real numbers. In this post we look at what these representations are and how we choose a particular representation for our w...

in rse, Jun 12, 2019

Using Ford to document Fortran programs

Ford is a tool which can help document Fortran source code. Here we show how to use Ford and the value of automatic documentation generation.

in rse, Dec 19, 2018

What is the ITSR RSE team?

ITS Research has a Research Software Engineering team. This post introduces the team and how it supports research in Queen Mary University of London. You can also see how to contact t...

in rse, Dec 10, 2018


Visualising HEALPix results with Jupyter Notebook

In this tutorial we’ll be showing you how to visualise HEALPix results using Jupyter Notebook in our OnDemand appliance on the Apocrita HPC cluster. We’ll start with installing the re...

in tutorial, Mar 07, 2022

File Permissions

An understanding of file permissions is important to the success of computational jobs, and the security of your files.

in tutorial, Jan 10, 2022

Running Machine Learning workloads on Apocrita

In this tutorial we’ll be showing you how to run a TensorFlow job using the GPU nodes on the Apocrita HPCcluster. We will expand upon the essentials provided on the QMUL HPCdocs site,...

in tutorial, Oct 14, 2021

SSH authentication and regaining access to Apocrita

In response to a coordinated security attack on HPC sites world-wide, it has been necessary to implement some changes to enforce a higher level of authentication security. In this art...

in tutorial, Jun 12, 2020

Productivity tips for Apocrita cluster users

This article presents a selection of useful tips for running successful and well-performing jobs on the QMUL Apocrita cluster.

in tutorial, Oct 23, 2019

Sizing your Apocrita jobs for quicker results

At any one time, a typical HPC cluster is usually full. This is not such a bad thing, since it means the substantial investment is working hard for the money, rather than sitting idle...

in tutorial, Jan 28, 2019