v3.0.1 /var mounted as read-only filesystem, even when using sudo

[PaulJ]

Hi All:

I created my own singularity "container" with the build file:

host> cat test3.script

BootStrap: yum

OSVersion: 6

MirrorURL: http;//localhost/centos/%{OSVERSION}/os/$basearch/

Include: yum

After building the image (sudo singularity build test3.sif test3.script), I can run it with:

host> sudo singularity shell test3.sif

in the image, if I attempt to write to /var (and I am the root user because I called singularity with sudo), it returns an error message:

> id

uid=0(root) gid=0(root) groups=0(root)

> touch /var/abc

touch: cannot touch '/var/abc': Read-only file system

I discovered this, since I was trying to perform yum commands in the image, and they were hanging (because it could not write to /var/lib/rpm)

thanks,

Paul

[Thomas Hartmann]

Hi Paul,

have you tried to bind /var/abc explicitly in the container?
I.e.,
--bind /var/abc

But mounting your host's /var might be not really desirable as you are
mixing your container's and hots's /var/lib etc.
Probably a sandbox-container or --writable would be safer.

Cheers,
Thomas

On 2018-11-06 20:44, PaulJ wrote:
> Hi All:
>
> I created my own singularity "container" with the build file:
>
> host> cat test3.script
>

> /BootStrap: yum/
> /OSVersion: 6/
> /MirrorURL: http;//localhost/centos/%{OSVERSION}/os/$basearch//
> /Include: yum/
> /
> /

> After building the image (sudo singularity build test3.sif
> test3.script), I can run it with:
> host> sudo singularity shell test3.sif
>
> in the image, if I attempt to write to /var (and I am the root user
> because I called singularity with sudo), it returns an error message:
>
>> id
> uid=0(root) gid=0(root) groups=0(root)
>> touch /var/abc
> touch: cannot touch '/var/abc': Read-only file system
>
> I discovered this, since I was trying to perform yum commands in the
> image, and they were hanging (because it could not write to /var/lib/rpm)
>
> thanks,
> Paul
>

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[PaulJ]

Hi Thomas:

I would not be able to use --bind, since my host is Fedora 28, while the guest is CentOS 6, and it would mess up the host if I tried to yum install anything in the guest.

I did try the --writable option, but that gives me a message: WARNING: no overlay partition found

I tried the --writable-tmpfs and this works.  It will allow me to write to /var.  But, the way the /var filesystem shows up in df, it looks like there is 0% space available on it:

> df -kh .

df: Warning: cannot read table of mounted file system: No such file or directory

Filesystem          Size     Used     Avail    Use Mounted on

-                             0           0           0       -   /

And, a "yum install" or "yum update" will fail, since it believe the filesystem is out of space so it can't download the files

thanks,

Paul

> <mailto:singularity+unsub...@lbl.gov>.

[Dave Godlove]

It sounds like you need to create a sandbox (writable container).  Try adding the --sandbox option to your build command and then invoke the container with the --writable option.  

By default Singularity creates a squashfs partition housed in a SIF file and that is read-only.  

> <mailto:singularity...@lbl.gov>.

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Dave Godlove

Engineering Coordinator, Sylabs Inc.

sylabs.io