Failure is one of those topics that is discussed far less than it should be —It is hard to tell other people about mistakes you have made— yet failure is usually a far better teacher than success. This is why I want to share my story of how I spent the first two years of my PhD collecting useless data because of a bug in my code.
The Problem I perform computer simulations of toy molecular systems, using something simple and understandable to gain insights into more complicated chemical systems.
While there are numerous guides to installing Docker on Fedora, none of the guides leave the installation in a state that I would consider usable. This is intended to be a single complete guide for the setup and configuration of Docker, highlighting the differences that are required to get Docker running on Fedora. I will be demonstrating using Fedora 28, however, this should be the same for previous or future releases.
A common criticism about the Python programming language is that it is slow, often with reference to a benchmark comparing a range of tasks. This criticism is widely addressed with articles by Jake van der Plass and Anthony Shaw being two excellent examples. While I don’t disagree with any of the points raised in these articles, I think they miss an important aspect of performance—specificity. Python is a general purpose language, used for nearly everything from embedded devices with uPython to distributed processing of petabytes of data.
Abstract One of the key features of computational experiments is being able to run the experiment over a large variable space. However, in my experience there aren’t tools available to assist with this, particularly in the realm of High Performance Computing (HPC), where bash arrays and loops are commonplace. Using the current toolset, I made lots of errors in the specification of files, turning a ‘quick edit’ into a tedious process of find the bug.
A piece of software I have been using in my reasearch is Hoomd, a ‘relatively’ new package for running Molecular Dynamics (MD) simulations. These MD simulations have the basic premise of throwing hundreds of balls into a box and shaking it to find out what happens. The relative newness of Hoomd is in comparison to other software packages like LAMMPS and GROMACS which have been around for decades, while the initial release of Hoomd was in 2012.
Competition is a strange thing making you suddenly interested in the most unusual of problems It has become a tradition of The Lancer Band, of which I am a member, to produce a video as part of our ANZAC Day commemorations. These videos have been highly successful garnering millions of views on Facebook and with some choice communications throughout the rest of the year have resulted in a commendable social media following.
In the right (or wrong) hands ssh is a powerful tool for the remote management of a Unix system. Most desktop, or workstation distributions of Linux disable remote access over ssh by default. The simplest method to check if you have ssh server running on your machine is to run
$ ssh localhost If ssh is not installed or running this will print out a message
ssh: connect to host localhost port 22: Connection refused most likely indicating that the ssh server is not running.
Calling the current python visualisation landscape fragmented would probably be an understatement, since itself requires a visualisation to even begin to comprehend. For various reasons I have been unhappy with the tool I was using for visualisation at that time and I have been searching for the one visualisation package to rule them all (spoiler: it doesn’t exist)
About a year ago I was using Matplotlib for all my figures, which enabled me to create anything I wanted, usually with a stackoverflow answer giving me a working example to adapt.
You may have heard of a zip bomb or other decompression ‘bombs’, which have the basic premise of containing a large volume of highly redundant data that when decompressed takes up more resources than the system can handle. Within the HDF5 file format there is support for compression, an excellent tool for reducing file sizes, however also ripe for exploitation. This ‘issue’1 of a file containing far more data expected, whether accidental or malicious, is not limited to HDF5 files, any filetype supporting compression is susceptible.