Rocky 9 benefits
The majority of the cluster has now been upgraded to Rocky 9 and the remaining CentOS 7 nodes will be updated in due course. There may be some users that are still hesitant to move over, but there are a few reasons why you should.
Welcome to the QMUL HPC blog¶
R on Rocky 9
With the major operating system upgrade from Centos 7 to Rocky 9, we want to ensure that using R, RStudio, and Open OnDemand (OOD) is as seamless as possible. This post will include new tips for a better experience, as well as a reiteration of the important or frequently forgotten old tips.
Using Python inside of R with reticulate
A previous blog post covered
Using R inside of Conda, but what about
if you want to use Python packages inside an existing
R or
RStudio via OnDemand session?
This is where the
reticulate R Interface to Python
comes in.
Using uv for Python package management
Traditionally we have recommend that users use a
Python virtualenv
or Conda environment
to manage personal package installations via pip install and mamba install
commands. But a new contender has entered the fray:
uv, an extremely fast Python package and
project manager, written in Rust.
Moving from CentOS 7 to Rocky 9 for Python users
The Apocrita cluster has been upgraded from CentOS 7 to Rocky 9 recently. There are some important things Python users need to know, such as how to migrate your existing environments to Rocky 9, as well as how to tackle some common problems during the process.
The next era for Apocrita is here
For much of the year we have been working on a major project to upgrade Apocrita to a new operating system, (Rocky Linux 9, hereafter known as Rocky 9). As part of the project, we have deployed a new package building tool to help us recompile all of the research applications to work on the new system.
The majority of the cluster has now been upgraded to Rocky 9. The remaining CentOS 7 nodes will be updated in due course.
A PyTorch DDP Case Study With ImageNet
In this blog post, we will play about with neural networks, on a dataset called
ImageNet, to give some intuition on how these neural networks work. We will
train them on Apocrita with
DistributedDataParallel
and show benchmarks to give you a guide on how many GPUs to use. This is a
follow on from a previous blog post where we explained how to
use DistributedDataParallel to speed up your neural network training with
multiple GPUs.
High Performance Computing (HPC) events from late 2024
2024 has been productive year in the outreach and education of HPC to different schools at Queen Mary University of London. We have formed alliances with different managers and PIs from various schools within the University who understand the value that HPC can add to their scientific research. We are pleased to share our latest event in 2024:
Unification of Memory on the Grace Hopper Nodes
The delivery of new GPUs for research is continuing, most notable is the new Isambard-AI cluster at Bristol. As new cutting-edge GPUs are released, software engineers are tasked with being made aware of the new architectures and features these new GPUs offer.
The new Grace-Hopper GH200 nodes, as announced in a previous blog post, consist of a 72-core NVIDIA Grace CPU and an H100 Tensor Core GPU. One of the key innovations is the NVIDIA NVLink Chip-2-Chip (C2C) and unified memory, which allows fast and seamless automation of transferring data from CPU to GPU. It also allows the GPU to be oversubscribed, allowing it to handle data much larger than it can host, potentially tackling out-of-GPU memory problems. This allows software engineers to focus on implementing algorithms without having to think too much about memory management.
This blog post will demonstrate manual GPU memory management and introduce
managed and unified memory with simple examples to illustrate its benefits.
We'll try and keep this to an introductory level but the blog does assume basic
knowledge of C++, CUDA and compiling with nvcc.
Beginner’s Guide to Regular Expressions with Examples
Regular expressions, or regex, are patterns used to match strings of text. They can be very useful for searching, validating, or manipulating text efficiently. This guide will introduce the basics of regex with easy-to-follow examples.