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BlueBrain / AstroVascPy

Vasculature blood flow computation and impact of astrocytic endfeet on vessels
https://astrovascpy.rtfd.io
Apache License 2.0
8 stars 2 forks source link

load graph using nexus #42

Open StephLisa opened 1 month ago

StephLisa commented 1 month ago

We need to be able to run the simulation from Nexus. Actually, Nexus only points to a config file stored in gpfs so far. But at least we could just change the links to the files and folders when the AWS platform will be ready.

We are able to run the code. But the output graph file is corrupted. Here is the link Nexus points to: /gpfs/bbp.cscs.ch/project/proj162/Model_Data/NGV/NGV_circuits/rat_O1

But we obtained also a corrupted file while running the code locally.

It is not corrupted when we run locally the code with this other circuit: /gpfs/bbp.cscs.ch/project/proj137/NGVCircuits/rat_O1/

Jean checked, both circuits are identical. we need to investigate while in one case we have a corrupted file, not in the other one.

Furthermore, we can not run sbatch file using Nexus. We need to set the global variables in the terminal before running the simulation.

jacquemi-bbp commented 2 weeks ago

  1. With this new version, it is no longer necessary to pass the Nexus Token, the BBP keycloak service is used with the molsys group user ID bbp-molsys-sa . Note: The keycloak secret must be defined as a KCS environment variable.

  2. The good news: when using NGV O1.v5 (Rat) or tiny_real_spine_morph NGV circuits with Nexus, the output graph files are now correct (not corrupted). The bad news is that I don't understand what's changed compared to when it was failing.