Add write_input() before transferring files to remote

pyiron_base/jobs/job/runfunction.py

@@ -72,11 +72,16 @@ def write_input_files_from_input_dict(input_dict: dict, working_directory: str):
         input_dict (dict): hierarchical input dictionary with files_to_create and files_to_copy.
         working_directory (str): path to the working directory
     """
-    for file_name, content in input_dict["files_to_create"].items():
-        with open(os.path.join(working_directory, file_name), "w") as f:
-            f.writelines(content)
-    for file_name, source in input_dict["files_to_copy"].items():
-        shutil.copy(source, os.path.join(working_directory, file_name))
+    if len(os.listdir(working_directory)) == 0:
+        for file_name, content in input_dict["files_to_create"].items():
+            with open(os.path.join(working_directory, file_name), "w") as f:
+                f.writelines(content)
+        for file_name, source in input_dict["files_to_copy"].items():
+            shutil.copy(source, os.path.join(working_directory, file_name))
+    else:
+        state.logger.info(
+            "The working directory is not empty, assuming that input has already been written."
+        )
 
 
 class CalculateFunctionCaller:
@@ -493,6 +498,8 @@ def run_job_with_runmode_queue(job):
             + job.project_hdf5.h5_path
             + " --submit"
         )
+        job.project_hdf5.create_working_directory()
+        job.write_input()
         state.queue_adapter.transfer_file_to_remote(
             file=job.project_hdf5.file_name, transfer_back=False
         )