Question 167255 in Amazon Web Sevices Question posted in
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Amazon web services – Python script file missing in Singularity image

In AWS, created a docker image with a python script to print a string(basicprint.py)

docker file:

FROM python

COPY ./basicprint.py ./
CMD ["python", "basicprint.py"]

It works fine then saved docker image as .tgz file.

copy that .tgz file in to my local.

I converted docker image(.tgz) into singularity image by using

singularity build sing_image.sif docker-archive://filename.tgz

it was successfully created sing_image.sif

singularity run sing_image.sif

It throws an error : basicprint.py: No such file or directory

Any suggestions on correct method of conversion without missing the file.

Tags:

2

Answers


  1. 0

    For testing, you could use a def file, using %file instead of the Dockerfile:

    The %files section allows you to copy files into the container with greater safety than using the %setup section.

    In your case, create a Singularity.def file with:

    Bootstrap: docker
Registry: docker.io
Namespace: library
From: python

%files
    basicprint.py /opt/

%runscript
    exec python /opt/basicprint.py

    Check if that approach is working with:

    singularity build sing_image.sif Singularity.def
singularity run sing_image.sif

    Regarding your Dockerfile, try and use a different folder, again for testing:

    FROM python

COPY ./basicprint.py /app/
CMD ["python", "/app/basicprint.py"]

    Then:

    docker build -t my-python-image .
docker save my-python-image:latest | gzip > my-python-image.tgz
singularity build sing_image.sif docker-archive://my-python-image.tgz
singularity run sing_image.sif

    Check also the .sif file includes your file: singularity exec sing_image.sif ls /app.

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  2. 0

    Note that you put your file under the very root. singularity removed your file during conversion and cleaning. Similar issues have been reported and are, in general, expected when working with containers.

    This slightly modified image

    FROM python:3.11-slim
COPY ./basicprint.py ./
CMD ["ls"]

    demonstrates that the file lands under the linux root:

    (base) maciej.skorski@kaggle-cpu-maciej:~/docker-debug$ docker build . --tag test-sing
(base) maciej.skorski@kaggle-cpu-maciej:~/docker-debug$ docker run -it test-sing
root@ed8e3545a00b:/# ls
basicprint.py  bin  boot  dev  etc  home  lib  lib64  media  mnt  opt  proc  root  run  sbin  srv  sys  tmp  usr  var

    Now, let me demonstrate the working version. Importantly, follow best Docker practices and use the working dir

    # Dockerfile
FROM python:3.11-slim-bullseye

RUN mkdir -p /usr/src
WORKDIR /usr/src
COPY ./basicprint.py /usr/src/

CMD ["python", "/usr/src/basicprint.py"]

    where the sample Python script is

    # basicprint.py
print('Welcome to my Docker!')

    Then I build and test on Debian GNU/Linux 10 with Docker 20.10.17 and Singularity 3.11:

    (base) maciej.skorski@kaggle-cpu-maciej:~/docker-debug$ singularity --version
singularity-ce version 3.11.0+277-gcd6fa5c0d

(base) maciej.skorski@kaggle-cpu-maciej:~/docker-debug$ sudo docker build . --tag test-sing:latest
Successfully tagged test-sing:latest

(base) maciej.skorski@kaggle-cpu-maciej:~/docker-debug$ docker save test-sing:latest --output test-sing.tgz

(base) maciej.skorski@kaggle-cpu-maciej:~/docker-debug$ sudo singularity build test-sing.sif docker-archive:test-sing.tgz
...
INFO:    Build complete: test-sing.sif
(base) maciej.skorski@kaggle-cpu-maciej:~/docker-debug$ sudo singularity run test-sing.sif
Welcome to my Docker!

    Under the same software, I reproduced your error. So I think it has been solved! If you need any further assistance, we can set up a shared Virtual Machine with GitHub Codespace to make it fully reproducible.

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