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Path fixes

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This commit is contained in:
Kevin Wu
2023-03-09 23:35:17 -08:00
parent 403e747368
commit 372ec85564
1 changed files with 3 additions and 1 deletions
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4
scripts/gromacs/gromacs_docker.py
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@@ -31,6 +31,7 @@ def run_gromacs_in_docker(fname: str, out_dir: str, gpu: int = 0):
fname = os.path.abspath(fname)
bname = os.path.splitext(os.path.basename(fname))[0]
orig_dir = os.getcwd()
with tempfile.TemporaryDirectory() as tmpdir:
logging.info(f"Running {fname} via docker in temporary directory {tmpdir}")
assert not os.listdir(tmpdir)
@@ -53,6 +54,7 @@ def run_gromacs_in_docker(fname: str, out_dir: str, gpu: int = 0):
)
logging.info(f"Copying {src_fname} to {dest_fname} in {out_dir}")
shutil.copy(os.path.join(tmpdir, fname), os.path.join(out_dir, dest_fname))
os.chdir(orig_dir) # Restore directory
def main():
@@ -60,7 +62,7 @@ def main():
args = build_parser().parse_args()
if not os.path.isdir(args.output_dir):
os.makedirs(args.output_dir)
for fname in args.input_file:
for fname in [os.path.abspath(f) for f in args.input_file]:
run_gromacs_in_docker(fname, args.output_dir, gpu=args.gpu)