Rendeiro group

Lab manual

Lab infrastructure

This document describes the infrastructure used in the lab, including CeMM-provided or our own infrastructure. So far it details only computational infrastructure.

Lab infrastructure

Hardware

  • Hilde workstation: setting up and maintaining the hilde workstation: hilde_workstation.md
    • Usage can be booked through its dedicated calendar:
      • HTML: https://outlook.office365.com/owa/calendar/92e5463911e04b688330fbd26c75faab@cemm.oeaw.ac.at/7dce5f2f61f84753bca69c49a309581114314229400116418487/calendar.html
      • ICS: https://outlook.office365.com/owa/calendar/92e5463911e04b688330fbd26c75faab@cemm.oeaw.ac.at/7dce5f2f61f84753bca69c49a309581114314229400116418487/calendar.ics

VMs

Cloud resources

Read the documentation on using Azure web services here: azure.md

CeMM infrastructure

Refer to the CeMM Intranet documentation for updated information. Below are a few notes on things which are not covered there:

Cluster containers (Podman)

On the CeMM cluster, use Podman for directory isolation (not speed): mount project data read-only, write only under /nobackup/.../results, and do not mount $HOME. The job script loads Podman (module load podman). For partitions, QoS, and GPUs, use the CeMM cluster documentation; tinyq in the examples is CPU-only.

Scripts: examples/podman/01_bash.sbatch (python:3.12-slim), examples/podman/02_lazyslide.sbatch (ghcr.io/rendeirolab/lazyslide:v0.12.0). Keep extract.py next to 02_lazyslide.sbatch. Submit from that directory so Slurm finds the files (#SBATCH --output and extract.py use the submit dir). DATA must already exist; OUT is created.

cd source/examples/podman   # or copy the three files somewhere on the cluster

PROJECT=my_project
DATA=/research/lab_rendeiro/projects/${PROJECT}/data
OUT=/nobackup/lab_rendeiro/projects/${PROJECT}/results/container-demo

sbatch --export=ALL,DATA="$DATA",OUT="$OUT" 01_bash.sbatch
sbatch --export=ALL,DATA="$DATA",OUT="$OUT" 02_lazyslide.sbatch

# Optional: a slide under DATA (path inside the container is /data/...)
# sbatch --export=ALL,DATA="$DATA",OUT="$OUT",SLIDE=/data/slide.svs 02_lazyslide.sbatch

Without SLIDE, LazySlide runs zs.datasets.sample() and writes sample.zarr in OUT. Logs: podman-bash-<jobid>.out and podman-lazyslide-<jobid>.out in the submit directory.

Printing from Linux

CeMM has Canon iR-ADV C5735/5740 printers. They support IPP printing through CUPS.

Install CUPS:

sudo apt-get install cups

Add printers:

sudo lpadmin -p CeMM_level_2 -E -v ipp://193.171.185.37/ipp -m everywhere
sudo lpadmin -p CeMM_level_3 -E -v ipp://193.171.185.212/ipp -m everywhere
sudo lpadmin -p CeMM_level_4 -E -v ipp://193.171.185.39/ipp -m everywhere
sudo lpadmin -p CeMM_level_5 -E -v ipp://193.171.185.40/ipp -m everywhere
sudo lpadmin -p CeMM_level_6 -E -v ipp://193.171.185.38/ipp -m everywhere
sudo lpadmin -p CeMM_level_7 -E -v ipp://193.171.185.41/ipp -m everywhere

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