Merge branch 'workflow_parameterization' of https://github.com/shirts…

…group/terphenyl_simulations into workflow_parameterization
shirtsgroup · Sep 17, 2024 · f9e2589 · f9e2589
2 parents 9dd7323 + 11f13f0
commit f9e2589
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Showing 6 changed files with 11 additions and 7 deletions.
diff --git 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
@@ -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 [email protected]
 #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
@@ -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 [email protected]
 #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
@@ -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 [email protected]
 #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
@@ -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 [email protected]
 #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
@@ -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 [email protected]
 #SBATCH --mail-type=BEGIN
 #SBATCH --mail-type=END