search

sylabs / singularity

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.
https://sylabs.io/docs/
Other
772 stars 98 forks source link

Fail to create Container, Fail to mount tmpfs exit status 255 running --sandbox build on definition file #2676

Closed gregorex333 closed 8 months ago

gregorex333 commented 8 months ago

Version of Singularity

4.1.1

Describe the bug

Fail to establish mount using -- sandbox on a definition file

To Reproduce Followed install instructions listed below. Attempted to build sif using --sandbox with "https://github.com/yilewang/tvbdemos/blob/master/container/tvb_ukbb_gpu/tvb-ukbb-gpu.def" that definition file (replacing %files with my own folders). It uses a Library bootstrap for ubuntu 20.04 as base. sudo singularity -d build --sandbox siftobemade.sif definitionfile.def gave error shown in attached debug files. Tried again using "--remote --sandbox" & it mounted and ran, but did not finish within 1hr so was terminated. Tried again setting an "export SINGULARITY_TMPDIR=" path on HOME, then changing mount tmp to "no" in config. Almost same result (failed to mount).

Expected behavior

I expected the mount to be successful & to at least start the process of creating a large sif file. I expected to maybe have a heavy RAM /memory demand on tmpfs and perhaps fail that way, but not to not be able to mount at all.

OS / Linux Distribution

Ubuntu Focal Fossa 20.04.6 LTS kernel version 5.15.0-94-generic

Installation Method

Followed instructions on https://docs.sylabs.io/guides/latest/admin-guide/installation.html#installation-on-linux using singularity-ce-4.1.1.tar.gz download from sylab releases github Compiled / make installed with sudo & with Source bash completion file step

Additional context

Key Errors: FATAL [U=0,P=141410] Master() "Container creation failed: mount tmpfs->/usr/local/var/singularity/mnt/session error: while mounting tmpfs: can't mount tmpfs filesystem to /usr/local/var/singularity/mnt/session: read unix @->@: read: connection reset by peer : exit status 255"

""Could not keep file descriptor for user bind path /lib/x86_64-linux-gnu/[various.so]"

"Could not keep file descriptor for user bind path /lib/x86_64-linux-gnu/lib" [...] No mount point

debug log

edit: i have a suspicion I made a mistake related to libfuse installation or symbolic links? that wont be easy to reproduce or sort out, if so. ill update if i make any progress or can more clearly describe my installation steps in restarting 4.1.1 install. sorry for mess. havent used issues before.

gregorex333 commented 8 months ago

nevermind. i will reset this drive linux is dual boot installed on & start over from a completely base state. libfuse is too complicated to deal with after too much tinkering / installing /reinstalling / apt-ing all over the place. thank you. if there are future issues (hopefully no) repro instructions will be very clear and straight forward.

gregorex333 commented 8 months ago

created a more detailed issue report when i tried again on fresh install. closing this one to focus on the other newer issue report

dtrudg commented 8 months ago

Closing in favour of #2677