Request to install Sage

HPC Support HPC Wish list
1

Dear HPC Team,

Is it possible to install Sage (the SageMaths9.4 kernel) for jupyter notebooks computations?

Thanks a lot in advance,
Dani

2

Hi,

are you talking about this software? S.A.G.E. - Statistical Analysis for Genetic Epidemiology | S.A.G.E. - Statistical Analysis for Genetic Epidemiology

It seems version 6.4.2 is available, not 9.4?

3

Thank you for looking into this. It is SageMaths https://www.sagemath.org/ (no epidemiology involved)

4

Hi,

I tried hard to build this software from source, but I give up. This soft has too many dependencies and is trying to build itself the missing dependencies.

I found it is possible to run it inside a docker container: docker-images/README.md at master · sagemath/docker-images · GitHub

Can you give a try with Singularity?

5

Hi,

Thank you for trying! I cannot make it work with Singularity and I don’t know if it is possible, I’m sorry. There is no way to get Sagemaths installed on the HPC? I thought it is quite a popular software in pure mathematics, with more than 30k active users on CoCalc, and I have been using it on several clusters before (it is installed at the Max Planck in Bonn, at the University of Padova in Italy, and at Paris Saclay). I could try to put you in contact with one of these teams if that helps, or maybe we can set up a call for the docker container method? Have you tried? I have never done it before. I got my files in ready, and I can open a Jupyter-notebook in CoCalc in the HPC through Firefox browser, but without Sage it cannot be interpreted and executed.

6

Hi,

this singularity pipeline seems to work.
Best
Julien

Command line

# Get an interactive bash into a Baobab worker node:
salloc --partition=shared-cpu --time=1:00:00

# Load singularity module
ml GCC/9.3.0 Singularity/3.7.3-Go-1.14

# Build a Sagemath image from a docker repository
singularity build --sandbox /scratch/sagemath_9.5/ docker://sagemath/sagemath:9.5

# Run Sagemath
singularity run /scratch/sagemath_9.5/

In the web browser:

# Run sage-jupyter
singularity run /scratch/sagemath_9.5/ sage-jupyter

# Follow guideline
# https://hpc-community.unige.ch/t/tutorial-ssh-tunneling-and-socks-proxy/1795
7

Hi, thanks, this is what I wanted to try just before noticing we had storage issue and then I couldn’t finished my tests!

@Danilo.Lewanski is this a working solution for you?