Writing this here, since it caused some issues at the Day Job, and took a little bit of work to debug. Hopefully this will save some of you some time, and will jog my memory should something like this happen again.

Anyway, last week, one of my team wanted to deploy a new release of our Access Management System (ARIA), which involved deploying a bunch of containers. The release procedure worked fine, however after the deploy, the main web app container was entirely unable to talk to our API layer.

My team did a little bit of debug, but it was at this point that it got escalated to me. I rolled the live environment back, and began debugging the problem.

On the face of it, it seemed that networking, or at least name resolution, was no longer working from within the container. A curl call from the command line produced:

curl: (6) getaddrinfo() thread failed to start

However, a connection to an IP address would work. So, I began looking at networking / name resolution. The next step was to see what the name servers were doing… however, nslookup gave me:

isc_thread_create(): fatal error: pthread_create(): Operation not permitted

Interesting… so something was blocking creating new threads within the container. Likely the security model that docker was running… not sure why this would change, but I confirmed this by redeploying with SECCOMP turned off:

      - "apparmor:unconfined"
      - "seccomp:unconfined"

Confirmed, networking was working.

Not sure what’s changed, but it would appear that somewhere down the line the base Apache Linux image has updated, and is now using a different system call for starting threads. Likely a new version of GLIBC has been rolled into the container somewhere.

The final fix was to update the various containers to make sure they were all running on the newer base image, and then to redeploy docker on our estate so that it was running the latest version.


Everything back to normal, hope this saves you some time!

Molgenis is an open-source platform for scientific data management and research. The name “Molgenis” is derived from “Molecular Genetics Information Systems.” It provides tools for researchers to design, capture, and share data in the field of molecular genetics and other related areas.

Molgenis is designed to facilitate the handling of large-scale, complex datasets in genomics and other biomedical research domains. It offers features such as data integration, data modeling, and data management. Researchers can use Molgenis to create databases, design forms for data entry, and perform data analysis.

At The Day Job, we’re using it as part of our oncology research infrastructure project to act as a source of truth for certain system information as we build out a distributed access platform to help scientists and doctors conduct their research.

Anyway, at time of writing, there wasn’t a PHP client library for it, so I quickly put one together. Have fun!

» Visit the project on Gitlab...

In Linux, it is possible to expand an existing filesystem over multiple disk drives. I recently had to do this for a few VPS as part of my day job, since they were running out of disk space and causing some instability with one of our core services.

Here’s how to do it, mainly for my own benefit, for when I inevitably have to do it again and have forgotten how…

  1. First, after you have connected your new drive (either physically or virtually), you need to create a new logical partition on that drive using cfdisk. You can use fdisk -l to find out the drive’s name (e.g. /dev/sdc)
  2. Create a new physical volume for this partition using pvcreate, e.g. pvcreate /dev/sdc5
  3. Extend the existing volume group to include this, e.g. vgextend VOLUMEGROUP /dev/sdc5, where VOLUMEGROUP is the name of the volume group. You can find out what the volume group is called by using the command vgdisplay.
  4. Extend the logical volume to include this extra space, e.g. lvextend -l +100%FREE /dev/VOLUMEGROUP/root
  5. Resize the filesystem. The command for this varies depending on what filesystem is currently installed, so for ext4 this would be resize2fs, and in my case for xfs this is xfs_growfs. E.g. xfs_growfs /dev/VOLUMEGROUP/root

After which, you should be able to type df -h and see increased disk space available to you.