Rendeiro group

Lab manual

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

VMs

Cloud resources

Documentation on using Azure web services (private repository, lab members only).

Finished projects are archived in the lab's Azure storage account: see data archiving.

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 imageFORCE C5140/5150 printers (upgraded from the iR-ADV C5735/5740 series in 2026). They support printing from Linux via CUPS.

Since the upgrade the devices no longer expose IPP (port 631 is closed and they are not advertised over mDNS/Bonjour), so CUPS's driverless -m everywhere no longer works. Plain PostScript over the raw socket port (9100) still prints without authentication, so add the queues with a PostScript PPD instead. Install CUPS first:

sudo apt-get install cups

Then add the queues:

PPD=foomatic:Canon-iR-ADV_C5235_5240-Postscript.ppd
sudo lpadmin -p CeMM_level_2 -E -v socket://193.171.185.37:9100  -m "$PPD" -o PageSize=A4 -o sides=two-sided-long-edge
sudo lpadmin -p CeMM_level_4 -E -v socket://193.171.185.39:9100  -m "$PPD" -o PageSize=A4 -o sides=two-sided-long-edge
sudo lpadmin -p CeMM_level_6 -E -v socket://193.171.185.38:9100  -m "$PPD" -o PageSize=A4 -o sides=two-sided-long-edge
sudo lpadmin -p CeMM_level_7 -E -v socket://193.171.185.41:9100  -m "$PPD" -o PageSize=A4 -o sides=two-sided-long-edge

Any PostScript PPD works — the model in the foomatic: name is irrelevant (the imageFORCE series has PostScript 3 as standard); on distributions without foomatic-db-ppds, use any generic PostScript PPD.

IPs are as observed in 2026-09. Levels 3 (193.171.185.212) and 5 (193.171.185.40) did not respond — ask CeMM IT if you need them, or if the printers move again. Test with:

lp -d CeMM_level_2 -o sides=two-sided-long-edge document.pdf

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