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saeyslab / multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
GNU General Public License v3.0
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Issue with parallelization of `get_ligand_activities_targets_DEgenes` on some systems #20

Open browaeysrobin opened 1 year ago

browaeysrobin commented 1 year ago

Parellelization seems stalled @maartenciers

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

browaeysrobin commented 8 months ago

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

browaeysrobin commented 3 months ago

get_ligand_activities_targets_DEgenes_beta is on the main branch now.

Huangy57 commented 3 months ago

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 commented 2 months ago

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.