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 […]

Update GlusterFS 3.3.1 -> 3.4.0 on CentOS 6.4 cluster

Notes from the GlusterFS 3.3.1 -> 3.4.0 upgrade on my storage / compute cluster at ILRI, Kenya. I referenced Vijay Bellur’s blog post about upgrading to 3.4, then added my own bits using Ansible for my infrastructure (I gave an overview of my Ansible setup here). Our cluster is comprised of: Three “storage” nodes (gluster […]

“interactive” script for 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, […]

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, […]

Erroneous XMLUI Caching on DSpace 1.7+

We’ve been using DSpace as an outputs repository at ILRI since 2009, and since then we’ve gone through six major versions of DSpace. Starting with version 1.7 we switched our repository to the newer XML-based user interface (XMLUI), which was much easier to customize than the previous JSPUI and allowed us to have different themes […]