Tag Archives: science

ORCA & OpenMPI: File Descriptor Limits

I’ve just been tinkering around with an interesting issue: ORCA, the computational chemistry program I’ve been using because I can’t afford Gaussian, crashes during geometry optimisation of a (moderately) complex molecule because of OpenMPI.

OpenMPI is complaining about running out of file descriptors. Eh? Seriously? OK…

Turns out that Ubuntu 16.04 (even the server version) sets the open file limit at what is frankly a little on the low side – 1024 open files. That sounds like a lot, until you think that when running something via MPI it can be crunching across¬†a lot of temporary files and so on… and it suddenly doesn’t seem so many. Interestingly, I never had this problem before because I was running Ubuntu 14.04 previously which (from what the internet says) had a limit of 4096. I checked with the latest release (14.04.5) which had a limit of 1024, so I’ll assume for now that the 4096 limit was in an older release…

I’ll be honest, since this is the first time I’ve encountered this issue, I’ve never actually checked previously…

Anyway, there appear to be two fixes that work, one on a per-user basis, one on a system-wide basis. Pick your poison.

The user-level fix is super easy, add the following to your .bashrc:

if [ $USER = "paramagnetic" ]; then
ulimit -n [pick-a-big-number, eg; 32768]
fi

Can also be added to /etc/profile

At the system level, it’s a little more difficult, but still totally doable. Edit /etc/security/limits.conf

* soft nofile 32768
* hard nofile 32768
root soft nofile32768
root hard nofile 32768

Then add:

session required pam_limits.so

To /etc/pam.d/common-sessions and /etc/pam.d/common-sessions-noninteractive

And reboot in all cases. If you have another form of system management software running, it might overrule you, which is annoying, but outside of the scope of this post.

A New Job

So, I’ve moved on to newer pastures.

I’m not involved directly with magnetic resonance any longer, although that will always be close to my (scientific) heart. Being back in a wet lab, albeit while still doing a lot of computing related work, is exciting.

This blog/site/whatever-you-want-to-call-it won’t focus on my job. I’ll post now and again regarding curiosities encountered, minor challenges overcome (particularly when in respect to a reticent bit of code) but almost anything that catches my attention may be fair game.

Books, music, computing, science… perhaps a bit of sight-seeing if I go somewhere particularly worth sharing with others than close friends or family… all are good.

But if you just come for one or two posts, that’s fine too.

Of course, the remit might expand as time passes, but on that front… we shall have to see.

In the mean time, take care all.