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bigginlab / ABFE_workflow

This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
GNU General Public License v3.0
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Using the ABFE_workflow with PBS scheduler #27

Open prateekrai18 opened 3 months ago

prateekrai18 commented 3 months ago

I am currently working on a high-performance cluster at my university where we utilize the PBS scheduler. I've encountered an issue with my workflow as it was originally designed for use with the Slurm scheduler. Is there a method to adapt or extend the workflow to be compatible with a PBS script?

RiesBen commented 3 months ago

@prateekrai18 hi, so if you look into this file and adapted to your needs, you might be able to get it running! :) https://github.com/bigginlab/ABFE_workflow/blob/5619e0c2d735569725e9e39e7c565eacbd681cfd/src/abfe/template/cluster_configs/default_slurm_template.json

prateekrai18 commented 3 months ago

Hi @RiesBen,

Thank you for your response. Do we need to make any changes to the Python scripts in ABFE_workflow/src/abfe/orchestration or elsewhere? Additionally, I want to ensure that I am following the correct steps:

  1. I installed ABFE_workflow on the HPC cluster as described.
  2. In the examples directory, I ran the command: cli-abfe -p ./data/CyclophilinD_min/receptor.pdb -l ./data/CyclophilinD_min/ligands -nr 3 -njr 8 -njl 40 -o output This generated a folder called output, which contains various folders for the ligands along with scheduler.sh, job.sh, Snakefile.smk, and snake_conf.json. I am unsure how to proceed from here.

Also, I noticed two files: example_execution.sh and example_execution.py. I am not certain how to use these files to run ABFE on the HPC cluster, which uses the PBS scheduler. Could you please provide guidance on this?

RiesBen commented 3 months ago

Hej @prateekrai18 your steps 1 and 2 sound perfect! :) in theory running the scheduler.sh should do the trick for you :) this submits the job.sh to your cluster. (depending on the template file I sent above)

the example_execution.py file is a variant, that could be used from the python level. but right now, you don't need it.

right now I'm not aware of required changes in ABFE_workflow/src/abfe/orchestration :)