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.
Welcome to the QMUL HPC blog¶
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 Fortran. To run the examples we'll learn about interactive sessions on compute nodes, modules and compiling source code. We'll also look at examples in MATLAB, Python and R. For these we'll see how to use modules to select suitable interpreters.
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 this post we look at common forms of compiler bug, with examples, and what we can do when our work is affected by such an issue.
Modules Update December 2019
Since the last module update in August, we have added 22 modules to dev, added 22 modules to production and removed 4 modules.
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 the ITS Research team, we spend quite a bit of time monitoring the Apocrita cluster and checking jobs are running correctly, to ensure that this valuable resource is being used effectively. If we notice a problem with your job, and think we can help, we might send you an email with some recommendations on how your job can run more effectively. If you receive such an email, please don't be offended! We realise there are users with a range of experience, and the purpose of this post is to point out some ways to ensure you get your results as quickly and correctly as possible, and to ease the learning curve a little bit.
Comparing common compression tools using real-world data
Compression tools can significantly reduce the amount of disk space consumed by your data. In this article, we will look at the effectiveness of some compression tools on real-world data sets, make some recommendations, and perhaps persuade you that compression is worth the effort.
Modules Update August 2019
Since the last update in April, we have updated the following module files:
Simplification of parallel queues on Apocrita
We are simplifying the way that the multi-node parallel jobs are run on the cluster.
Currently, users wishing to run multi-node MPI jobs on the public queues must choose beforehand whether to run on the nxv parallel nodes or the sdv parallel nodes, and to configure the job accordingly for the number of cores on each type of node.
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:
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 work.