Launching simultaneous parabricks jobs fail

I have installed Parabricks version 3.0 and I am testing it with singularity. I can run a job at a time successfully, both on a single GPU and on multiple GPUs.

However, I am unable to unable to run two simultaneous jobs of parabricks, getting the following error:

FATAL:   error while locking ext3 overlay partition from /sw/csgv/parabricks/ can't open /sw/csgv/parabricks/ for writing, currently in use by another process


Could not run fq2bam

Exiting pbrun ...

The intent is to install Parabricks as a module in a shared space on a cluster for easy of access for multiple user.

Hello Mohsin,

Thanks for your interest in Parabricks and apologies for the troubles/inconvenience. There’s a limitation with Parabricks at the moment which will require you to copy the installation directory for each run and install with the --disable-fakeroot flag. That way you should be able to do multiple runs without any issue using singularity.

Hope this helps.