Genome assembly likes RAM!

This is what it looks like when you do a genome assembly and run out of memory… The machine in question actually has 384GB of RAM (not much, as far as machines which do genome assembly go!). Assembling a genome is like doing a massive puzzle; you need to have all the “pieces” in contiguous […]

Sysadmin is happy when users use SLURM

I recently rolled out a new distributed model for our research computing cluster at work. We’re using GlusterFS for networked home directories and SLURM for job/resource scheduling. GlusterFS allows us to scale storage with minimal downtime or service disruption, and SLURM allows us to treat compute nodes as generic resources for running users’ jobs (ie, […]

This server should be on fire

Sometimes users run scripts without checking the parameters first, often recycling scripts they’ve used elsewhere, at former jobs or at other institutes. Sometimes this works out, sometimes it doesn’t… With a load of ~75 and 32 physical cores, the CPU usage on this server is oversubscribed 2.3 times a “normal” 100% load (where 100% of […]

A match made in heaven

Strong Swedish coffee and a full-screen, white-on-black terminal: a match made in heaven. There’s no better way to hack than with a cup of strong Swedish coffee. I’ve got about five kilograms of the stuff on my desk at work: We have a Swedish guy in the office and whenever he goes home he brings […]

What keeps me busy at work

I work as a Systems Analyst at the International Livestock Research Institute (ILRI) in Nairobi, Kenya. In the name of alleviating poverty in the developing world, our scientists generate a lot of data about diseases, weather, markets, etc. Lots of data means lots of servers, routers, switches, etc and, because most science types aren’t tech […]