From 9a9029ad5cc7ad4cbbeff4a71b5ab0187f6ba7a7 Mon Sep 17 00:00:00 2001 From: Theodore Fobe Date: Tue, 17 Sep 2024 12:17:14 -0600 Subject: [PATCH] updated submission scripts for ascent allocation, and changed submission using remd_workflow --- terphenyl_simulations/analysis_workflows/remd.py | 8 ++++++-- .../simulation_templates/remd/submit.berendsen_npt.slurm | 2 +- .../simulation_templates/remd/submit.berendsen_nvt.slurm | 2 +- .../simulation_templates/remd/submit_remd.continue.slurm | 2 +- .../simulation_templates/remd/submit_remd.finish.slurm | 2 +- .../remd/submit_remd.production.slurm | 2 +- 6 files changed, 11 insertions(+), 7 deletions(-) diff --git a/terphenyl_simulations/analysis_workflows/remd.py b/terphenyl_simulations/analysis_workflows/remd.py index 266213ba..c9fead2e 100644 --- a/terphenyl_simulations/analysis_workflows/remd.py +++ b/terphenyl_simulations/analysis_workflows/remd.py @@ -161,6 +161,7 @@ def apply_hmr_to_topology(job): @FlowProject.pre.after(apply_hmr_to_topology) +@FlowProject.post(lambda job: os.path.isdir(job.fn("sim0"))) @FlowProject.operation(directives={"fork" : True}) @cd_to_job_dir def setup_remd_simulations(job): @@ -177,10 +178,13 @@ def setup_remd_simulations(job): # if slurm is an executable @FlowProject.pre.after(setup_remd_simulations) -@FlowProject.pre(lambda job: shutil.which("slurm")) +@FlowProject.pre(lambda job: shutil.which("sbatch")) @FlowProject.operation(directives={"fork": True}) +@cd_to_job_dir def submit_simulations(job): - pass + subprocess.run(["bash", "submit_all.slurm"], shell = True) + subprocess.wait() + # if slurm isn't an executable diff --git a/terphenyl_simulations/data/simulation_templates/remd/submit.berendsen_npt.slurm b/terphenyl_simulations/data/simulation_templates/remd/submit.berendsen_npt.slurm index d3561181..9e2cbe40 100644 --- a/terphenyl_simulations/data/simulation_templates/remd/submit.berendsen_npt.slurm +++ b/terphenyl_simulations/data/simulation_templates/remd/submit.berendsen_npt.slurm @@ -3,7 +3,7 @@ #SBATCH -t 4:00:00 #SBATCH -p amilan #SBATCH -J 'mop-octamer-npt-equilibration' -#SBATCH --account=ucb368_asc1 +#SBATCH --account=ucb469_asc1 #SBATCH --mail-user=theodore.fobe@colorado.edu #SBATCH --mail-type=BEGIN #SBATCH --mail-type=END diff --git a/terphenyl_simulations/data/simulation_templates/remd/submit.berendsen_nvt.slurm b/terphenyl_simulations/data/simulation_templates/remd/submit.berendsen_nvt.slurm index 60ec6158..39b5f5d4 100644 --- a/terphenyl_simulations/data/simulation_templates/remd/submit.berendsen_nvt.slurm +++ b/terphenyl_simulations/data/simulation_templates/remd/submit.berendsen_nvt.slurm @@ -3,7 +3,7 @@ #SBATCH -t 4:00:00 #SBATCH -p amilan #SBATCH -J 'mop-octamer-nvt-equilibration' -#SBATCH --account=ucb368_asc1 +#SBATCH --account=ucb469_asc1 #SBATCH --mail-user=theodore.fobe@colorado.edu #SBATCH --mail-type=BEGIN #SBATCH --mail-type=END diff --git a/terphenyl_simulations/data/simulation_templates/remd/submit_remd.continue.slurm b/terphenyl_simulations/data/simulation_templates/remd/submit_remd.continue.slurm index c6661b78..b49dc130 100644 --- a/terphenyl_simulations/data/simulation_templates/remd/submit_remd.continue.slurm +++ b/terphenyl_simulations/data/simulation_templates/remd/submit_remd.continue.slurm @@ -3,7 +3,7 @@ #SBATCH -t 20:00:00 #SBATCH -p amilan #SBATCH -J 'mop-octamer-remd-continue' -#SBATCH --account=ucb368_asc1 +#SBATCH --account=ucb469_asc1 #SBATCH --mail-user=theodore.fobe@colorado.edu #SBATCH --mail-type=BEGIN #SBATCH --mail-type=END diff --git a/terphenyl_simulations/data/simulation_templates/remd/submit_remd.finish.slurm b/terphenyl_simulations/data/simulation_templates/remd/submit_remd.finish.slurm index 025b895b..f16915c6 100644 --- a/terphenyl_simulations/data/simulation_templates/remd/submit_remd.finish.slurm +++ b/terphenyl_simulations/data/simulation_templates/remd/submit_remd.finish.slurm @@ -3,7 +3,7 @@ #SBATCH -t 20:00:00 #SBATCH -p amilan #SBATCH -J 'mop-octamer-remd-finish' -#SBATCH --account=ucb368_asc1 +#SBATCH --account=ucb469_asc1 #SBATCH --mail-user=theodore.fobe@colorado.edu #SBATCH --mail-type=BEGIN #SBATCH --mail-type=END diff --git a/terphenyl_simulations/data/simulation_templates/remd/submit_remd.production.slurm b/terphenyl_simulations/data/simulation_templates/remd/submit_remd.production.slurm index 3262b5da..54846fb1 100644 --- a/terphenyl_simulations/data/simulation_templates/remd/submit_remd.production.slurm +++ b/terphenyl_simulations/data/simulation_templates/remd/submit_remd.production.slurm @@ -3,7 +3,7 @@ #SBATCH -t 20:00:00 #SBATCH -p amilan #SBATCH -J 'mop-octamer-remd' -#SBATCH --account=ucb368_asc1 +#SBATCH --account=ucb469_asc1 #SBATCH --mail-user=theodore.fobe@colorado.edu #SBATCH --mail-type=BEGIN #SBATCH --mail-type=END