Propagate singularity bind points from initial docker command?

[thomshaw92]

Trying to run a simg within neurodesktop but it seems the bind points from my initial Docker call (for an external drive) in Windows to neurodesktop don't propagate to singularity containers inside.
Would be a nice feature to add to a startup script (i.e., bind all external drives in Docker call (if user wants)- propogate these bindpoints to transparent singularity or wherever the code is now?)

[stebo85]

This already works. We should quickly look at this together why it doesn't work in your case :)

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On Wed, Nov 24, 2021, 8:30 AM Thom Shaw ***@***.***> wrote: Trying to run a simg within neurodesktop but it seems the bind points from my initial Docker call (for an external drive) in Windows to neurodesktop don't propagate to singularity containers inside. Would be a nice feature to add to a startup script (i.e., bind all external drives in Docker call (if user wants)- propogate these bindpoints to transparent singularity or wherever the code is now?) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#67>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA6V2WZICXC2IZ3PLRDRXRTUNQIZFANCNFSM5IUTTUAQ> .

[thomshaw92]

running

PS C:\Users\thoma> docker run --shm-size=1gb -it --privileged --name neurodesktop -v C:/neurodesktop-storage:/neurodesktop-storage -v E:/STIMMRI_DATA/:/STIMMRI -p 8080:8080 -h neurodesktop-20211028 vnmd/neurodesktop:20211028  

Then inside neurodesktop in the fMRIPrep container:

Singularity> ls /STIMMRI
ls: cannot access '/STIMMRI': No such file or directory

[stebo85]

Dear Tom,

can you try to mount the external drive to the mountpoint that we created for this use-case :/data ?

PS C:\Users\thoma> docker run --shm-size=1gb -it --privileged --name neurodesktop -v C:/neurodesktop-storage:/neurodesktop-storage -v E:/STIMMRI_DATA/:/data -p 8080:8080 -h neurodesktop-20211028 vnmd/neurodesktop:20211028

The problem is that we need to create the mountpoints at buildtime, so we cannot easily add these at runtime.

[thomshaw92]

Ah yes that works... Does it cost us anything to automatically mount all drives and do this in an automatic way at startup? e.g., My external drives in E:/ and F:/ to /mnt/e and /mnt/f/ in neurodesktop?

[stebo85]

the problem is that the docker container doesn't know that E: and F: exists, so the startup script proposed in #64 needs to do this. It shouldn't be very difficult, but will need a bit of Powershell / bat magic by @thomshaw92

[stebo85]

Dear @thomshaw92 - did you get a chance to look at this already?