No space left on device with 'singularity build --sandbox'

[Kaur Alasoo]

Hi,

I am running Singularity in an Ubuntu virtual machine:

vagrant@ubuntu-bionic:~$ singularity --version

2.5.2-master.b258b651

I managed to create and start a Singularity container using the following commands:

sudo singularity build --sandbox ubuntu shub://singularityhub/ubuntu

sudo singularity shell ubuntu/

Within the container, I can see that there is 2GB of free space:

Singularity ubuntu:~> df -h

Filesystem      Size  Used Avail Use% Mounted on

singularity     2.0G     0  2.0G   0% /

I then installed a number of software packages:

apt-get update

apt-get install wget bzip2 -y

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh

bash Miniconda3-latest-Linux-x86_64.sh -b -p /software/minconda3

rm Miniconda3-latest-Linux-x86_64.sh

PATH="/software/minconda3/bin:$PATH"

conda update -y conda

conda config --add channels defaults

conda config --add channels conda-forge

conda config --add channels bioconda

conda install -y salmon

All of these steps succeeded, but they used up almost all of the available space:

Singularity ubuntu:~> df -h

Filesystem      Size  Used Avail Use% Mounted on

singularity     2.0G     1.96G  2.0G   98% /

I then tried to install hisat2 (conda install -y hisat2), but this failed with the "No space left on device" error. The same error also occurred when I tried to copy large files exceeding the 2GB limit to the / filesystem. Is it possible to increase the size of the / filesystem or am I doing something obviously wrong?

Best,

Kaur

[Dave Godlove]

Hiya Kaur,

For your second command, try this:

sudo singularity shell --writable ubuntu/

Does that work?

Dave

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[Kaur Alasoo]

Thanks, Dave!

This solved the issue.

Best,

Kaur

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