Issue with parallelization of get_ligand_activities_targets_DEgenes on some systems

[browaeysrobin]

Parellelization seems stalled @maartenciers

in case you encounter this issue: run the function with one core only in serial way

[browaeysrobin]

get_ligand_activities_targets_DEgenes_beta, currently in dev-branch, but soon in main branch, enables parallelization.

[browaeysrobin]

get_ligand_activities_targets_DEgenes_beta is on the main branch now.

[Huangy57]

I have tried to run both get_ligand_activities_targets_DEgenes and get_ligand_activities_targets_DEgenes_beta on RStudio Server on the gizmo compute cluster, but I still experience issues with parallelization. I had to manually remove the parallelization part to run the function in a serial way. I am not sure if this is a specific issue with the settings of RStudio Server on the cluster or with the function itself.

Could you please provide guidance on how to troubleshoot or resolve this issue? Any insights into potential configuration adjustments or code modifications that might be necessary would be greatly appreciated.

Thank you!

[browaeysrobin]

Hi @Huangy57

Unfortunately, we don't have concrete ideas for the reasons behind these issues on some systems, and currently no manpower/bandwidth to look into this.

For other people having this issue; please use n_cores = 1 as argument in the function, you don't need to code to have it run.