Wiki DIFA

Some useful links:

• Recording of the meeting with betatesters (ITA)
• A tutorial (skip to “Building Singularity Containers” and remember you don't have 'sudo' access on the cluster!)
• Another tutorial, more in-depth

By Amalie Louise Stokholm

apptainer build --sandbox rockylinux8/ docker://rockylinux:8 
find rockylinux8 -type d -not -writable -exec chmod +w {} +
apptainer run -f --writable rockylinux8/ yum groupinstall -y "Development Tools"
apptainer run -f --writable rockylinux8/ yum install -y zlib-devel libffi-devel openssl-devel bzip2-devel readline-devel sqlite-devel xz-devel
mv .pyenv/versions/3.9.12{,_old4}
apptainer run rockylinux8/ ~/.pyenv/bin/pyenv install 3.9.12
.pyenv/versions/3.9.12/bin/python3 -c 'import ctypes'

By Vsevolod Chestnov

How to setup `X11` forwarding on `compute_node` via `apptainer`

1. Create a file `config` with the following content:

   Bootstrap: docker
   From: ubuntu:16.04
   
   %post
       apt-get update -y
       apt-get install -y openssh-server
       # some tools, remove if not needed
       apt-get install -y vim firefox
   
   %startscript
       echo 'root:12345' | chpasswd
       sed -i 's/Port.*/Port 12121/'                                      /etc/ssh/sshd_config
       sed -i 's/PermitRootLogin prohibit-password/PermitRootLogin yes/'  /etc/ssh/sshd_config
       sed -i 's/UsePrivilegeSeparation yes/UsePrivilegeSeparation no/'   /etc/ssh/sshd_config
       sed -i 's/#PasswordAuthentication yes/PasswordAuthentication yes/' /etc/ssh/sshd_config
       mkdir /var/run/sshd
       chmod 700 /var/run/sshd
       # /usr/sbin/sshd

2. Then build the container, here we call it `ubuntu16`

   apptainer build --sandbox --force ubuntu16 config

3. Next go to the `compute_node` (say `mtx27` – you need to have an active reservation)

   ssh compute_node

4. Create an instance of the `ubuntu16` container and call it `test`

   apptainer instance start -f -w ubuntu16 test

5. Jump into the `test` instance

   apptainer shell instance://test

6. Once inside, run the `sshd` daemon

   /usr/sbin/sshd

   which will listen to the `Port 12121`, as prescribed by the file `config` file above.

7. In a new shell to test things connect to the running instance use `root` as the username

   ssh -X -p 12121 root@localhost

   after which you'll be prompted for `root`'s password, which was set to `12345` in the `config` file above. Now you may run some GUI application, for example:

   firefox

   At this stage `X11` forwarding will allow the application to use your machine's display to show the GUI.

8. To connect from the outside one possibility is to setup port forwarding from `2010` on your machine to `12121` on the `compute_node` (where the instance is running) via the frontend node:

   ssh -L2010:compute_node_id:12121 your_unibo_username@137.204.50.71

9. And then access via

   ssh -X -p 2010 root@localhost

   from your machine

10. Done! Now you may run GUI applications on `compute_node` (like `firefox` and `Mathematica` frontend) and their graphical output will be forwarded to your machine's display.