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Troubleshooting & FAQ

If you have any issues, please create an issue.

Make sure to include:

  • include OS, Julia version
  • description of steps to reproduce
  • be concise yet complete

Can I change the singularity image ?

Yes, if you clone the repository, and are using Linux, you need to do 2 things

./buildimage.sh

This will rebuild the image, first checking out the latest version of the code.

System requirements

Expected RAM usage for images of sizes 500x500x20 ~ 5GB RAM, 2000x2000x70: ~ 50GB RAM, and so on. By default, all of JULIANUMTHREADS cores will be used to run in parallel. > 8 is overkill, so set to 4-8 at most:

export JULIA_NUM_THREADS=4

On desktops this is unlikely to be an issue, but on a cluster node with > 64 cores you will probably get a slowdown if you exceed 8-12 cores.

I cloned the repo but I get conflicts during the installation ?

First, make sure you install and clone in a clean environment:

mdkir mydir
cd mydir
julia
julia> ]
(@v1.x) pkg> activate .
(@v1.x) pkg> update

Do not use Julia < 1.7, there's no guarantee that deprecated APIs will still work, and performance and user friendliness of the e.g. the package manager alone make 1.7 the ideal baseline.

Memory usage

Current memory usage is higher than it strictly needs to be because we generate a lot of intermediate steps. In principle we could reduce usage by x2 or more, but it would come at the cost of debugging/interpretability.

Installation gives errors on MacOs

MacOS + Conda has a bug where a certificate error triggers a cascade of errors. The errors can be ignored, including the failing tests, this is an optional part of the module. When the bug in conda is resolved, this issue should be resolved as well.