Tags
infrastructure
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
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
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
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
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
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
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
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
storage
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
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
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
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
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
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
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
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
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
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
upgrade
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
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
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
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
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
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
containers
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
benchmarking
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
python
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
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
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
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
applications
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
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
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
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
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
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
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
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
hpc
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
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
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
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
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
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
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
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
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
tier2
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
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
nodes
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
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
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
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
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
modules
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 modules
We removed some problematic module files. Please check your job scripts for use of these modules:
in news, Sep 15, 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
deprecated
Development modules update
We have moved the following modules from dev to deprecated:
in modules, Nov 29, 2018
Deprecated modules
We removed some problematic module files. Please check your job scripts for use of these modules:
in news, Sep 15, 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
mpi
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
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
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
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
decommission
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
queues
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
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
ppc64le
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
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
ai
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
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
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
gpu
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
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
github
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
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
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
maintenance
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
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
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
dev
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
Development modules update
We have moved the following modules from dev to deprecated:
in modules, Nov 29, 2018
networking
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
featured
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
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
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
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
rse
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
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
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
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
introduction
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
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
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
scratch
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
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
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
documentation
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
fortran
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
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
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
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
tutorial
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
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
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
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
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
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
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
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
announcement
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
compilers
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
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
coding
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
compression
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
misc
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
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
beginner
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
compilation
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
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
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
faq
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
language-features
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
apocrita
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
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
visual studio code
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
news
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
openmp
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
cpu
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
scheme
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
tensorflow
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
training
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
code review
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
WHRI
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
crucible
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
ondemand
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
jupyter
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
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