Add a docker wrapper for gromacs

scripts/gromacs/gromacs.py

@@ -20,7 +20,7 @@ import subprocess
 import shutil
 import multiprocessing as mp
 
-GRO_FILE_DIR = "/home/wukevin/software/md_template/mdp/"
+GRO_FILE_DIR = os.path.join(os.path.dirname(__file__), "mdp")
 
 
 def run_gromacs(

scripts/gromacs/gromacs_docker.py

@@ -0,0 +1,50 @@
+"""
+Simple script to wrap the gromacs.py file in an easy to run docker container
+to avoid all the messiness of trying to do mounting and stuff.
+
+Usage: python gromacs_docker.py <input_file> <output_dir>
+"""
+import os
+import shutil
+import tempfile
+import subprocess
+import argparse
+
+
+def build_parser():
+    """Build a basic CLI parser"""
+    parser = argparse.ArgumentParser()
+    parser.add_argument("input_file", help="Input file to run GROMACS on")
+    parser.add_argument("output_dir", help="Output dir to write output files to")
+    return parser
+
+
+def run_gromacs_in_docker(fname: str, out_dir: str):
+    """
+    Run gromacs in docker
+    """
+    assert os.path.isfile(fname), f"Input file {fname} not found"
+    assert shutil.which("nvidia-docker")
+    out_dir = os.path.abspath(out_dir)
+    with tempfile.TemporaryDirectory() as tmpdir:
+        os.chdir(tmpdir)
+        # Copy the file into the directory
+        shutil.copy(fname, tmpdir)
+        # Build and run the command
+        cmd = f"nvidia-docker run -it --rm -v {tmpdir}:/host_pwd --workdir /host_pwd wukevin:gromacs-latest {os.path.basename(fname)}"
+        subprocess.call(cmd, shell=True)
+
+        for fname in os.listdir(tmpdir):
+            shutil.copy(fname, out_dir)
+
+
+def main():
+    """Run script"""
+    args = build_parser().parse_args()
+    if not os.path.isdir(args.output_dir):
+        os.makedirs(args.output_dir)
+    run_gromacs_in_docker(args.input_file, args.output_dir)
+
+
+if __name__ == "__main__":
+    main()