Threading updates

scripts/gromacs/gromacs.py

@@ -18,7 +18,6 @@ import logging
 import shlex
 import subprocess
 import shutil
-import multiprocessing as mp
 
 GRO_FILE_DIR = os.path.join(os.path.dirname(__file__), "mdp")
 
@@ -28,6 +27,7 @@ def run_gromacs(
     outdir: str = os.getcwd(),
     gmx: str = "gmx",
     gro_file_dir: str = GRO_FILE_DIR,
+    n_threads: int = 8,
 ) -> float:
     """
     Run GROMACS on a PDB file
@@ -86,9 +86,7 @@ def run_gromacs(
     # come to "room temperature"
     grompp_cmd = f"{gmx} grompp -f {gro_file_dir}nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr"
     subprocess.call(shlex.split(grompp_cmd))
-    nvt_cmd = (
-        f"{gmx} mdrun -ntmpi 1 -ntomp {mp.cpu_count() - 1} -nb gpu -pin on -deffnm nvt"
-    )
+    nvt_cmd = f"{gmx} mdrun -ntmpi 1 -ntomp {n_threads - 1} -nb gpu -pin on -deffnm nvt"
     subprocess.call(shlex.split(nvt_cmd))
 
     # NPT
@@ -96,16 +94,14 @@ def run_gromacs(
         f"{gmx} grompp -f {gro_file_dir}npt.mdp -c nvt.gro -o npt.tpr -p topol.top"
     )
     subprocess.call(shlex.split(grompp_cmd))
-    npt_cmd = (
-        f"{gmx} mdrun -ntmpi 1 -ntomp {mp.cpu_count() - 1} -nb gpu -pin on -deffnm npt"
-    )
+    npt_cmd = f"{gmx} mdrun -ntmpi 1 -ntomp {n_threads - 1} -nb gpu -pin on -deffnm npt"
     subprocess.call(shlex.split(npt_cmd))
 
     # Production run
     grompp_cmd = f"{gmx} grompp -f {gro_file_dir}md.mdp -c npt.gro -t npt.cpt -p topol.top -o prod.tpr"
     subprocess.call(shlex.split(grompp_cmd))
     prod_cmd = (
-        f"{gmx} mdrun -ntmpi 1 -ntomp {mp.cpu_count() - 1} -nb gpu -pin on -deffnm prod"
+        f"{gmx} mdrun -ntmpi 1 -ntomp {n_threads - 1} -nb gpu -pin on -deffnm prod"
     )
     subprocess.call(shlex.split(prod_cmd))
 
@@ -156,6 +152,9 @@ def build_parser():
     parser.add_argument(
         "--mdp", type=str, default=GRO_FILE_DIR, help="MDP file directory"
     )
+    parser.add_argument(
+        "--threads", type=int, default=8, help="Threads (minimum 2)"
+    )
     return parser
 
 
@@ -170,7 +169,11 @@ def main():
     with tempfile.TemporaryDirectory() as tmpdir:
         os.chdir(tmpdir)
         energy = run_gromacs(
-            args.pdb_file, tmpdir, gmx=args.gmxbin, gro_file_dir=args.mdp
+            args.pdb_file,
+            tmpdir,
+            gmx=args.gmxbin,
+            gro_file_dir=args.mdp,
+            n_threads=args.threads,
         )
         for file in os.listdir(tmpdir):
             logging.debug(f"GROMACS file: {file}")