Docker转Singularity部署Julia应用Whippet遇只读文件系统错误求助

我正在为Julia工具Whippet制作可同时在Docker和Singularity（singularity-ce 3.9.5）中运行的镜像。Docker镜像运行正常，但Singularity中执行时会报错无法写入/depot/logs/manifest_usage.toml，原因是Singularity以普通用户身份运行，而非Docker默认的root。

当前使用的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"]

已尝试的无效操作 #

• 更换JULIA_DEPOT_PATH到不同位置（包括默认的~/.julia）
• 创建新用户

运行对比 #

• Docker正常运行命令：docker run cloxd/whippet:1.6.1 -h
• Singularity报错信息：

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

解决建议 #

1. 禁用Julia的manifest使用日志 #

在Dockerfile中添加环境变量，直接阻止Julia生成manifest_usage.toml文件：

ENV JULIA_PKG_NO_MANIFEST_USAGE=true

也可以在Whippet的启动脚本（如whippet-quant.jl）开头添加Julia代码：

ENV["JULIA_PKG_NO_MANIFEST_USAGE"] = "true"

2. 调整Singularity运行时挂载可写目录 #

运行Singularity时，将本地可写目录挂载到Julia需要写入的路径：

# 仅挂载日志目录
singularity run -B $HOME/.julia/logs:/depot/logs docker://cloxd/whippet:1.6.1

# 或挂载整个depot目录
singularity run -B $HOME/.julia:/depot docker://cloxd/whippet:1.6.1

3. 将可写目录指向Singularity允许的临时路径 #

在Dockerfile中修改JULIA_DEPOT_PATH，把可写部分指向/tmp（Singularity默认允许写入该目录）：

RUN mkdir -p /tmp/julia_depot/logs
RUN chmod 777 -R /tmp/julia_depot/
ENV JULIA_DEPOT_PATH="/depot:/tmp/julia_depot"

4. 预编译时提前禁用写入操作 #

修改Dockerfile中的预编译命令，提前设置环境变量避免生成日志：

RUN julia --project=/whippet -e 'ENV["JULIA_PKG_NO_MANIFEST_USAGE"] = "true"; using Pkg; Pkg.instantiate(); Pkg.precompile();'

内容的提问来源于stack exchange，提问作者Claudio Lorenzi