Initial attempt of multi replica

hymd/configure_runtime.py

@@ -115,6 +115,9 @@ def configure_runtime(args_in, comm):
     ap.add_argument(
         "--destdir", default=".", help="Write output to specified directory"
     )
+    ap.add_argument(
+        "--replica-dirs", type=str, nargs="+", default=[], help="Directories to store results for each replica"
+    )
     ap.add_argument(
         "--seed",
         default=None,
@@ -143,12 +146,21 @@ def configure_runtime(args_in, comm):
         type=extant_file,
         help="Gmx-like topology file in toml format"
     )
-    ap.add_argument("config", help="Config .py or .toml input configuration script")
+    ap.add_argument("config", type=extant_file, help="Config .py or .toml input configuration script")
     ap.add_argument("input", help="input.hdf5")
     args = ap.parse_args(args_in)
 
+    # check if we have at least one rank per replica
+    if comm.Get_size() < len(args.replica_dirs):
+        raise ValueError("You should have at least one MPI rank per replica.")
+
+    # block destdir with replicas
+    if (len(args.replica_dirs) > 0) and args.destdir != ".":
+        raise ValueError("You should not specify a destination directory when using replicas.")
+
     if comm.Get_rank() == 0:
         os.makedirs(args.destdir, exist_ok=True)
+
     comm.barrier()
 
     # Safely define seeds
@@ -241,5 +253,5 @@ def extant_file(x):
         # Argparse uses the ArgumentTypeError to give a rejection message like:
         # error: argument input: x does not exist
         raise argparse.ArgumentTypeError("{0} does not exist".format(x))
-    return x
+    return os.path.abspath(x)
 

hymd/file_io.py

@@ -197,20 +197,8 @@ def store_static(
     creator_group = h5md_group.create_group("creator")
     creator_group.attrs["name"] = np.string_("Hylleraas MD")
 
-    # Get HyMD version. Also grab the user email from git config if we
-    # can find it.
+    # Get HyMD version
     creator_group.attrs["version"] = np.string_(get_version())
-    try:
-        import git
-
-        try:
-            reader = repo.config_reader()
-            user_email = reader.get_value("user", "email")
-            author_group.attrs["email"] = np.string_(user_email)
-        except:
-            pass
-    except:
-        pass
 
     h5md.particles_group = h5md.file.create_group("/particles")
     h5md.all_particles = h5md.particles_group.create_group("all")