update to use abs run_dir paths by default (#820)

src/fairchem/core/common/flags.py

@@ -8,6 +8,7 @@
 from __future__ import annotations
 
 import argparse
+import os
 from pathlib import Path
 
 
@@ -48,7 +49,7 @@ def add_core_args(self) -> None:
         )
         self.parser.add_argument(
             "--run-dir",
-            default="./",
+            default=os.path.abspath("./"),
             type=str,
             help="Directory to store checkpoint/log/result directory",
         )