fail to precompile / install on jupyterhub

[gaelforget]

I have been trying to use GMT.jl within a containerized environment but get the error below.

To reproduce this error :

• docker run -p 8888:8888 jupyter/datascience-notebook:latest
• once browser window is open, start terminal, Julia, and using GMT

...

[gaelforget]

I tried a couple more things with this Dockerfile :

FROM jupyter/datascience-notebook:latest

USER root

RUN apt-get install -y --no-install-recommends gmt
RUN apt-get install -y --no-install-recommends gmt-dcw gmt-gshhg
RUN apt-get install -y --no-install-recommends ghostscript

USER ${NB_USER}

RUN julia -e "import Pkg; Pkg.add(\"GMT\"); Pkg.precompile()"

which follows directions from the GMT docs for the apt-get part.

This errors as

which I think indicates that apt-get does not carry gmt. Is that right?

[gaelforget]

Could be related to #1052 and #1049

[joa-quim]

Hi,

First I thought Ui, can't help. Know nothing about containers but than I saw that infamous libstdc++ error that gave so many headaches during half an year. The problem is on the Linux side that is so light on dependency breaking. GCC12 introduced a new libstdc++ lib that is incompatible with Julia versions up until 1.8.3. So you need to have at at least Julia 1.8.4

EDIT: Or install GMT independently in the container so to avoid the automatic installation done via Conda (this is the one that uses a GMT GCC12 build)

[gaelforget]

Thanks for getting back so quickly!

Know nothing about containers

You likely use containers for your CI on github and various other things like binder or jupyterlab. I am no expert either but it's really useful to learn basics imho. In case that's of interest, we made this video as prep for the JuliaEO workshop.

https://youtu.be/daNrJhPPgWg

GCC12 introduced a new libstdc++ lib that is incompatible with Julia versions up until 1.8.3. So you need to have at at least Julia 1.8.4

Too bad. I was just taking a look in context of a workshop taking place next week where we are using Docker & 1.8.3 -- https://aircentre.github.io/JuliaEO/

EDIT: Or install GMT independently in the container so to avoid the automatic installation done via Conda (this is the one that uses a GMT GCC12 build)

This failed for me too though. See #1095 (comment)

[joa-quim]

which I think indicates that apt-get does not carry gmt. Is that right?

A quick answer to this. Those VMs are often based on Ubuntu and this distro is, by default, incredibly dumb on providing updated versions. The GMT site has info on how to install/build GMT

[joa-quim]

Another possibility. The CI tests always build GMT from source. Could chunks of that GH-Action be extracted into your build env?

[gaelforget]

Another possibility. The CI tests always build GMT from source. Could chunks of that GH-Action be extracted into your build env?

Could work. Thanks for the pointers

[joa-quim]

GMT_jll artifact is now used, so these problems should have gone.