PyMol_ray_pipeline
Ray-trace a PyMol session on cheaha
WARNING: PyMol licensing issues have not been addressed.
Sample session to render can be found in test_1aon_struct_spectrum.pse which comes from the "Huge Surfaces" PyMolWiki page
This project provides 2 different ways to run a pymol ray job:
- bash shell script that can be submitted with sbatch
- Snakemake pipeline script (coming soon)
sbatch usage
By default, it loads the session "test_1aon_struct_spectrum.pse" and creates the image "test_1aon_struct_spectrum.ray.1200x900.300dpi.png", which takes about 90 minutes to run.
module load Anaconda3/5.3.0
git clone git@gitlab.rc.uab.edu:CCTS-Informatics-Pipelines/pymol_ray_pipeline.git
cd pymol_ray_pipeline
sbatch job.80s_ray_1200x900_dpi300.shthis should launch a cluster job, which will wait in the queue. You should get 2 emails:
- when the job comes off the queue and start running
From: slurm@cheaha.rc.uab.edu [mailto:slurm@cheaha.rc.uab.edu]
Subject: SLURM Job_id=2107497 Name=pymol_24c_draw_3572x2400 Began, Queued time 01:40:38- when the jobs finishes successfully (COMPLETED, ExitCode 0)
From: slurm@cheaha.rc.uab.edu [mailto:slurm@cheaha.rc.uab.edu]
Subject: SLURM Job_id=2107403 Name=pymol_24c_ray_3572x2400 Ended, Run time 01:49:52, COMPLETED, ExitCode 0- or when if it fails (FAILED, ExitCode 1)
From: slurm@cheaha.rc.uab.edu [mailto:slurm@cheaha.rc.uab.edu]
Subject: SLURM Job_id=2107403 Name=pymol_24c_ray_3572x2400 Failed, Run time 01:49:52, FAILED, ExitCode 1Snakemake usage (not complete)
module load snakemakeslurm/4.8.0/1 Anaconda3/5.3.0 dvctools/0.9
git clone git@gitlab.rc.uab.edu:CCTS-Informatics-Pipelines/pymol_ray_pipeline.git
cd pymol_ray_pipeline
snakemakeslurm test_ray