Docker to Apptainer/Singularity image for Julia application: manifest_usage.toml Read-only file system - docker

Question

I'm trying to create a docker image that could work also in singularity for the software Whippet ( https://github.com/timbitz/Whippet.jl ).
The docker image works fine, but when I try to use it with singularity (singularity-ce version 3.9.5), It's not able to write the manifest_usage.toml ( that is comprehensible, since in singularity the command is executed by the user and not by the root as in docker).
Here's my Dockerfile:
FROM julia:bullseye
LABEL version=v1.6.1
RUN apt-get update && apt-get install -y git
RUN mkdir /depot
ENV JULIA_PATH=/usr/local/julia
ENV JULIA_DEPOT_PATH=/depot
ENV JULIA_PROJECT=/whippet
RUN mkdir /whippet/ && cd /whippet && \
git clone --depth 1 --branch v1.6.1 https://github.com/timbitz/Whippet.jl.git . && \
julia --project=/whippet -e 'using Pkg; Pkg.instantiate(); Pkg.precompile();'
RUN chmod 777 -R /depot/
ENV PATH="/whippet/bin/:${PATH}"
RUN whippet-quant.jl -h || echo "Done"
RUN whippet-index.jl -h || echo "Done"
RUN whippet-delta.jl -h || echo "Done"
ENTRYPOINT ["whippet-quant.jl"]
Any suggestions?
I tried using diffrent locations for the JULIA_DEPOT_PATH ( also the default ~/.julia ) creating a new user, but I got the same issue.
the command
docker run cloxd/whippet:1.6.1 -h
works nicely, meanwhile the same command with singularity raise the following error
singularity run docker://cloxd/whippet:1.6.1
INFO: Using cached SIF image
Whippet v1.6.1 loading...
Activating project at `/whippet`
ERROR: LoadError: SystemError: opening file "/depot/logs/manifest_usage.toml": Read-only file system
Stacktrace:
[1] systemerror(p::String, errno::Int32; extrainfo::Nothing)
# Base ./error.jl:176
[2] #systemerror#80
# ./error.jl:175 [inlined]
[3] systemerror
# ./error.jl:175 [inlined]
[4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Bool)
# Base ./iostream.jl:293
[5] open(f::Pkg.Types.var"#44#46"{String}, args::String; kwargs::Base.Pairs{Symbol, Bool, Tuple{Symbol}, NamedTuple{(:append,), Tuple{Bool}}})
# Base ./io.jl:382
[6] write_env_usage(source_file::String, usage_filepath::String)
# Pkg.Types /usr/local/julia/share/julia/stdlib/v1.8/Pkg/src/Types.jl:487
[7] Pkg.Types.EnvCache(env::Nothing)
# Pkg.Types /usr/local/julia/share/julia/stdlib/v1.8/Pkg/src/Types.jl:345
[8] EnvCache
# /usr/local/julia/share/julia/stdlib/v1.8/Pkg/src/Types.jl:325 [inlined]
[9] add_snapshot_to_undo(env::Nothing)
# Pkg.API /usr/local/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1862
[10] add_snapshot_to_undo
# /usr/local/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1858 [inlined]
[11] activate(path::String; shared::Bool, temp::Bool, io::Base.TTY)
# Pkg.API /usr/local/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1700
[12] activate(path::String)
# Pkg.API /usr/local/julia/share/julia/stdlib/v1.8/Pkg/src/API.jl:1659
[13] top-level scope
# /whippet/bin/whippet-quant.jl:12
in expression starting at /whippet/bin/whippet-quant.jl:12

Answer 1

Finally I found a working solution: after the initialization, it's enough to add /tmp/ to the JULIA_DEPO_PATH and Julia is using /tmp/logs/manifest_usage.toml instead of the protected /depot/logs/manifest_usage.toml.
For clarity, here's the Dockerfile
FROM julia:bullseye
LABEL version=v1.6.1
RUN apt-get update && apt-get install -y git
RUN mkdir /depot
ENV JULIA_PATH=/usr/local/julia
ENV JULIA_DEPOT_PATH=/depot
ENV JULIA_PROJECT=/whippet
RUN mkdir /whippet/ && cd /whippet && \
git clone --depth 1 --branch v1.6.1 https://github.com/timbitz/Whippet.jl.git . && \
julia --project=/whippet -e 'using Pkg; Pkg.instantiate(); Pkg.precompile();'
RUN chmod 777 -R /depot/
ENV PATH="/whippet/bin/:${PATH}"
RUN whippet-quant.jl -h || echo "Done"
RUN whippet-index.jl -h || echo "Done"
RUN whippet-delta.jl -h || echo "Done"
ENV JULIA_DEPOT_PATH="/tmp/:${JULIA_DEPOT_PATH}"
ENTRYPOINT ["whippet-quant.jl"]