Virtual machine has a limited partition for /, /root, and /tmp. When building Singularity images, this error can occur: No space left on device

There are two proposed ways to fix the problem:

(1) Redirect temporary directory and disable cache when building image

using --tmpdir tag with absolute dir path to redirect temporary to use for buid (where there is more space) rather than the default /tmp. Additionally, caches also consume space, we can disable it by --disable-cache. (ref)

(2) Increase partition size for vagrant and vagrant-root.

• Install vagrant-disksize plugin

  vagrant plugin install vagrant-disksize

• Modify Vagrantfile to the size we expect (and of course in our capacity)

Vagrant.configure("2") do |config|
  config.vm.box = "sylabs/singularity-3.5-ubuntu-bionic64"
  config.disksize.size='150GB'

• vagrant hault;vagrant up

In case, it doesn’t work. We can destroy the box in Virtual Box and re-create the box, then vagrant up (ref)

• vagrant ssh and then see the disk size with df -h:

  Filesystem                    Size  Used Avail Use% Mounted on
  udev                          1.9G     0  1.9G   0% /dev
  tmpfs                         390M  548K  390M   1% /run
  /dev/mapper/vagrant--vg-root   19G  7.5G   11G  43% /
  tmpfs                         2.0G     0  2.0G   0% /dev/shm
  tmpfs                         5.0M     0  5.0M   0% /run/lock
  tmpfs                         2.0G     0  2.0G   0% /sys/fs/cgroup
  vagrant                       1.9T   20G  1.8T   2% /vagrant
  tmpfs                         390M     0  390M   0% /run/user/900
  

  Here the vagrant-root is still 20GB. To change this size (ref):

• sudo cfdisk /dev/sda
• use arrows to select your disk /dev/sda[X]
• Select Resize, enter the number you want, then select write –> Quit
• sudo resize2fs -p -F /dev/sda[X] However, in my case resize2fs didn’t work. Debug (ref):
  • sudo pvresize /dev/sda[X] (resize the Physical Volume)
  • sudo lvextend -r -l +100%FREE /dev/mapper/ubuntu--vg-root (expand logical volume)

And here is the result:

vagrant@vagrant:/vagrant$ df -h
Filesystem                    Size  Used Avail Use% Mounted on
udev                          1.9G     0  1.9G   0% /dev
tmpfs                         390M  540K  390M   1% /run
/dev/mapper/vagrant--vg-root  118G  6.8G  106G   7% /
tmpfs                         2.0G     0  2.0G   0% /dev/shm
tmpfs                         5.0M     0  5.0M   0% /run/lock
tmpfs                         2.0G     0  2.0G   0% /sys/fs/cgroup
vagrant                       1.9T   45G  1.8T   3% /vagrant
tmpfs                         390M     0  390M   0% /run/user/900