BergmannLab/MONET

R1 method using default parameters fail with error 'problem too large'

Opened this issue · 10 comments

cristian931 commented

The K1 and M1 method with the same input gave no problem.
I'm working on a Centos7 machine with 82GB of RAM, so the memory should not be the issue. I'm using singularity as container.

This is the command line:
~/MONET/monet --input=network_retinal_toxicity_BIANA.txt --method=R1 --container=singularity

The log file reports as follow
2020-02-19-101559__R1__console-output__network_retinal_toxicity_BIANA.txt

This is the input file for reproducing:
It's an undirected network file formatted as explained in the readme file, since it's not weighted the weights have been set equal to 1 for every edge (don't know if this may be the problem, but again with the other two methods there were no problems). The nodes are identified by a numerical code. The total number of edges is around 400.
network_retinal_toxicity_BIANA.txt

For the moment i want to use the standard parameters for later try to tune it based on the results.

Thanks for the help

mattiat commented

Thank you so much, Cristian!
I reproduced today.
The input seems well formatted.

mattiat commented

I added a system test to reproduce this: MONET/.test/system_test/retinal_toxicity_test.sh

WeijiaZhang24 commented

Hi all,
This was caused by converting sparse matrix into matrix.
It has been addressed now and passed the test.

mattiat commented

I confirm the test passes.
image

mattiat commented

I am re-running, but there seems to be something weird with the number of edges.

  • Cristian931 says "number od edges around 400" (indeed input has 393 lines)
  • R1 debugging text indicates around 40000

@WeijiaZhang24: am I getting this wrong?
image

WeijiaZhang24 commented

I think this is caused by how the underlying C code (which is kinda difficult to address in a short time) handles input where nodes with no edge connected. It doesn't affect the result.

mattiat commented

PROBLEM: this fix causes system tests to fail. Reverting changes.
To be fixed.

image

mattiat commented

@WeijiaZhang24 Please continue to work here (and sorry for merging too early , my bad!) https://github.com/BergmannLab/MONET/commits/issues_15.

Make sure the following pass:

  • MONET/.test/system_test/retinal_toxicity_test.sh
  • MONET/.test/system_test/zachary_karate_club_test.sh
  • MONET/.test/system_test/reproduce_challenge/reproduce_challenge.sh
WeijiaZhang24 commented

@mattiat I pushed a new branch "issues_15_2", which used exception handling in R to fix the problem. Tested with the 3 scripts it seems fine.
Sorry for this messy patch, I will try to find a more elegant solution when I can squeeze more time to work on this.

mattiat commented

@WeijiaZhang24 Thank you! The last system test still fails for me, I attach the error file
2020-03-10-132648__R1__console-output__6_homology_anonym_v2.txt