Docker images by singularity

General Discussion
1

Dear all,

Did someone run FreeFEM using singularity?
I tried:

singularity build --sandbox freefem docker://freefem/freefem
singularity run freefem

and came across the following error:

ls: cannot access ‘/data/*.edp’: No such file or directory

So what’s the right steps to run a docker image? Unfortunately my ARC system only has singularity installed (not docker engine).

Best,
Yongxing.

2

I think it’s working, you just don’t have any .edp file in the container folder /data.

3

Thank you prj.
I tried the following to specify the .edp file explicitly:

./ff.sif ./test.edp
FATAL: permission denied

Andy idea about this error?

Best,
Yongxing.

4

No, sorry, I don’t use singularity containers.

5

You have to look closely to docker image you are about to run.
Dockerfile at the very end has this commands:

# Default command
ENV GLOB *.edp
CMD ["bash", "-c", "ls /data/$GLOB | xargs -I {} /usr/freefem/bin/ff-mpirun -n 1 {}"]

So it means, that if you run freefem container without any arguments it will automatically look for *.edp files in /data/ folder.

Example provided with docker mounts local directory to /data/ folder inside container

docker run -v $(pwd):/data freefem

So you have to do the same with singularity

6

Thank you very much! This works perfect for me. Can I ask one more question:

In the FreeFem container, can I run a parallel FreeFEM code directly? All the dependent libraries have already been configured in the container?

Best,
Yongxing.

7

Yes, you should be able to. Let me know if this is not the case.

8

Dear LiudasD,

It seems I cannot pull the latest version v4.9 using the following command:

singularity pull ff.sif docker://freefem/freefem

I tried v4.9 for Windows and it worked well. How can I pull the docker image of v4.9?

Best,
Yongxing.

9

Good morning,

It seems I cannot pull the latest version v4.9 using the following command:

singularity pull ff.sif docker://freefem/freefem

I tried v4.9 for Windows and it worked well. Howe can I pull the docker image of v4.9?

Best,
Yongxing.