singularity shell exclude some directories

[Tong Qiu]

Hi all,

singularity -B is used to mount some directories so that those directories can be used inside the singularity container. However, there are some directories that I would like to exclude. For example, I would like to use

singularity shell -B /foo/ bar.simg to have access to /foo

But I would like to exclude /foo/foo1/ in the container. Is there any way to work around this?

Best,

Tong

[Robert Lugg]

I don't believe this is possible.

[Thomas Hartmann]

Hi Tong,

unfortunately no 'nested' bind mount seem to be possible

I.e., with a structure as
> ls /tmp/foo/
baz nope

my idea was just to bind another dir/file over one of the subdirs, e.g.,

--bind /tmp/foo:/tmp/foo --bind /dev/null:/tmp/foo/nope

but unfortunately that fails

It seems to be a general thing, as also stacking manual binds into each
other is not well received

> mount --bind /tmp/foo /tmp/bindfoo

> mount --bind /dev/null /tmp/bindfoo/nope/
mount: /tmp/bindfoo/nope: mount(2) system call failed: Not a directory.

> stat /tmp/bindfoo/nope/
File: /tmp/bindfoo/nope/
Size: 40 Blocks: 0 IO Block: 4096 directory
Device: 2ch/44d Inode: 12988919 Links: 2
Access: (0755/drwxr-xr-x) Uid: ( 1000/hartlocal) Gid: ( 1000/hartlocal)
Context: unconfined_u:object_r:user_tmp_t:s0
Access: 2019-05-13 09:46:57.473719869 +0200
Modify: 2019-05-13 09:37:20.746773623 +0200
Change: 2019-05-13 09:37:20.746773623 +0200
Birth: -


Cheers,
Thomas

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[David Godlove]

I think you could do this creatively by only binding the exact directories and files you need.  The argument to the --bind option can be a very long comma separated list if you want it to be.  

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[David Godlove]

For instance:

vagrant@vagrant:~$ tree /data

/data

├── bindme

│   └── foo

├── dontbindme

│   └── bar

├── that

└── this

2 directories, 4 files

vagrant@vagrant:~$ singularity exec --bind /data/bindme,/data/this,/data/that my-container.sif tree /data

/data

|-- bindme

|   `-- foo

|-- that

`-- this