difference between working directory of docker and singularity

Question

I have a very basic question about docker and singularity. I'd like to be able to run a docker container using both docker and singularity, but I'm confused about the difference between the working directory. Here's an example: INSIDE my docker container, I have main.sh and test.sh.

Content of main.sh:

#!/bin/bash

echo "Executing main.sh"
./test.sh

Content of test.sh:

#!/bin/bash

echo "Executing test.sh"

When executing the following: sudo docker run -t myuser/mydocker:1.0 ./main.sh

I get the expected output:

Executing main.sh
Executing test.sh

But when executing singularity exec -e docker://myuser/mydocker:1.0 /main.sh

I get this error:

Executing main.sh
/main.sh: line 4: ./test.sh: No such file or directory

Why is test.sh not accessible? Is there a way to let it work through singularity without changing the content of main.sh? My singularity version is 3.6.3.

Thank you!

question from:https://stackoverflow.com/questions/65642199/difference-between-working-directory-of-docker-and-singularity

Answer 1

This is one of the big differences between docker and singularity.

In docker, the working directory is set in the Dockerfile with WORKDIR /some/path or the -w /some/path command line argument. Otherwise, it uses the default of /.

With singularity however, your home directory (or current directory, on older versions) on the host machine is mounted in and used as the working directory inside the container. You can use the --pwd flag to override this.

So given the Dockerfile:

FROM debian:buster-slim
COPY main.sh test.sh /

Running with docker:

$ docker run --rm myuser/mydocker:1.0 ./main.sh
Executing main.sh
Executing test.sh

$ docker run --rm myuser/mydocker:1.0 pwd
/

In singularity:

# note the full path of the file that isn't found
$ singularity exec -e mydocker.sif ./main.sh
FATAL:   stat /home/tsnowlan/main.sh: no such file or directory

# does NOT match the WORKDIR from the Dockerfile
$ singularity exec -e mydocker.sif pwd
/home/tsnowlan

# use full path to the script
# BUT still executing from $HOME so `./test.sh` is resolves to `$HOME/test.sh`
$ singularity exec -e mydocker.sif /main.sh
Executing main.sh
/main.sh: line 4: ./test.sh: No such file or directory

# tell singularity to run from /
$ singularity exec -e --pwd / mydocker.sif ./main.sh
Executing main.sh in
Executing test.sh