Cluster Cosmology

h1. New computing cluster in Koeniginstrasse

h2. Introduction

Since January 2022 we have a new computing cluster which is installed int he server room of the physiscs department at Koeniginstrasse.

h2. Hardware

* there are in total 9 compute nodes available;

* eight nodes are named "usm-cl-bt01n[1-4]" and "usm-cl-bt02n[1-4]";

* there is one new node (Nov. 2022) named "usm-cl-1024us01";

* each node usm-cl-bt[01, 02]n[1-4] has 128 logical cores (64 physical cores) and 512GB RAM available;

* the node "usm-cl-1024us01" has 256 logical (126 physical cores) and 1024GB RAM available;

* one storage for our group has 686Tb (/project/ls-mohr);

h2. Login

* public login server (for non-graphic, e.g. ssh): login.physik.uni-muenchen.de;

* Jupyterhub: https://jupyter.physik.uni-muenchen.de;

* both the server and the Jupyterhub require a two-factor-authentication;

* for the second factor you need to register with a smartphone app such as Google Authenticator (or any other app that generates time-based one-time-passwords) here: https://otp.physik.uni-muenchen.de. You need to create a so called "soft-token".

* for all logins you need to provide:

** the user name of your *physics account*;

** the pwd of your *physics account*;

** the 6 digit number (soft-token) you read from the smartphone app;

h2. Graphic Remote Login

A graphical remote login from outside the LMU network require a VPN connection. From June 2022 the only VPN connection  is provided by "eduVPN":https://doku.lrz.de/display/PUBLIC/VPN+-+eduVPN+-+Installation+und+Konfiguration. After establishing a VPN connection the login is then done with X2GO as explained "here":https://www.en.it.physik.uni-muenchen.de/dienste/netzwerk/rechnerzugriff/zugriff3/remote_login/index.html. I was pointed to using the following logins:

* cip-sv-login01.cip.physik.uni-muenchen.de

* cip-sv-login02.cip.physik.uni-muenchen.de

but I am assuming the connections for Garching work as well. X2GO opens a KDE desktop, and of course the machine can connect to our cluster.

h2. Processing

* as on our local cluster "slurm" is being used as the job scheduling system. Access to the computing nodes and running jobs requires starting a corresponding slurm job;

* the partition of our cluster is "usm-cl";

* from the login node you can start an interactive job via "intjob --partition=usm-cl" (additional slurm arguments are accepted as well);

* I created a "python script":https://cosmofs3.kosmo.physik.uni-muenchen.de/attachments/download/285/scontrol.py which provides information on our partition (which jobs are running on which node, the owner of the job and so on);

* I have also put together a rather silly "slurm script":https://cosmofs3.kosmo.physik.uni-muenchen.de/attachments/download/283/test.slurm which can be used as a starting point;

* note that it is possible to directly "ssh" to all nodes on which one of your batch jobs is running. This can help to supervise the processing;

h2. Disk space

* users can create their own disk space under "/project/ls-mohr/users/" such as "/project/ls-mohr/users/martin.kuemmel";

h2. Installed software

We use a package manager called spack to download and install software that is not directly available from the linux distribution. To see what is already installed, do the following on a computing node:

* "module load spack"

* "module avail"

Adding more software is not a problem.

h2. Euclid processing on the cluster

While OS, libraries and setup is different from EDEN-?.?, it is possible to load and run in an EDEN-3.0 environment using a container solution. The cluster offers "singularity":https://sylabs.io/guides/3.0/user-guide/quick_start.html as a container solution. While singularity is not officially supported in Euclid, it is being used in a limited role, and singularity is able to run docker images, which is the supported container format in Euclid. To work in an EDEN-3.0 on the new cluster you need to get the docker image doing:

* load singularity via:

  <pre>

  $ module load spack

  $ module load singularity</pre> Note that the singularity version which is directly available on the computing nodes at "/usr/bin/singularity" does *not* work. The correct version loaded via the modules is at "/software/opt/focal/x86_64/singularity/v3.8.1/bin/singularity".

* it is *recommended* to move the singularity cache to somewhere under "/scratch-local", e.g. via:<pre>$ mkdir -p /scratch-local/$USER/singularity

$ export SINGULARITY_CACHEDIR=/scratch-local/$USER/singularity</pre> On the default cache location "/home/$HOME/.cache/singularity" there are problems deleting the entire cache when leaving singularity.

* pull the Euclid docker image via: <pre>singularity pull --docker-login docker://gitlab.euclid-sgs.uk:4567/st-tools/ct_xodeen_builder/dockeen</pre> With the gitlab credentials the docker image is stored in the file "dockeen_latest.sif"

The docker image can be run interactively:

 <pre>$ singularity run --bind /cvmfs/euclid.in2p3.fr:/cvmfs/euclid.in2p3.fr --bind /cvmfs/euclid-dev.in2p3.fr:/cvmfs/euclid-dev.in2p3.fr <path_to>dockeen_latest.sif</pre>

It is also possible to directly issue a command in EDEN-3.0:

 <pre>$ singularity exec --bind /cvmfs/euclid.in2p3.fr:/cvmfs/euclid.in2p3.fr --bind /cvmfs/euclid-dev.in2p3.fr:/cvmfs/euclid-dev.in2p3.fr <path_to>dockeen_latest.sif  <command_name></pre>

In both cases the relevant EDEN environment must first be loaded with:

<pre>

$ source /cvmfs/euclid-dev.in2p3.fr/CentOS7/EDEN-3.0/bin/activate

</pre>

Information on the usage of singularity in Euclid is available at the "Euclid Redmine":https://euclid.roe.ac.uk/projects/codeen-users/wiki/EDEN_SINGULARITY.

h3. Problems with the cvmfs

All Euclid related software is centrally installed and deployed via cvmfs. This means that on the host machine the two directories:

<pre>

martin.kuemmel@usm-cl-bt02n4:~$ ls -ltr /cvmfs/

drwxr-xr-x 2 cvmfs cvmfs 0 Feb 13 16:09 euclid-dev.in2p3.fr

drwxr-xr-x 2 cvmfs cvmfs 0 Feb 13 17:22 euclid.in2p3.fr

</pre>

*must* exist on the host machine such that they can be mounted in singularity as indicated above. It looks like cvmfs "sometimes get stuck" and needs to be re-installed or re-mounted. I there are problem mounting cvmfs in singularity and the above directories do not exist on the host, please write a ticket to the sysadmins below and they will fix it.

h2. Support

Support is provided by the IT support (Rechnerbetriebsgruppe) of the LMU faculty of physics with the helpdesk email: helpdesk@physik.uni-muenchen.de. Please keep Joe Mohr and me (Martin Kuemmel: mkuemmel@usm.lmu.de) in the loop such that we can maintain an overview on the cluster performance.