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SlurmClusterExecutor - create a separate working directory for each job #698

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Merged
merged 5 commits into from
Jul 3, 2025
Merged

SlurmClusterExecutor - create a separate working directory for each job #698

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981b77e
SlurmClusterExecutor - create a separate working directory for each job
jan-janssen Jul 2, 2025
cab77e3
The cache directory is a mandatory input
jan-janssen Jul 2, 2025
9535958
extend tests
jan-janssen Jul 2, 2025
da6f689
test length after successful execution
jan-janssen Jul 2, 2025
0d9ce2b
fix
jan-janssen Jul 2, 2025
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8 changes: 5 additions & 3 deletions executorlib/task_scheduler/file/queue_spawner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,18 +10,19 @@

def execute_with_pysqa(
command: list,
cache_directory: str,
task_dependent_lst: Optional[list[int]] = None,
file_name: Optional[str] = None,
resource_dict: Optional[dict] = None,
config_directory: Optional[str] = None,
backend: Optional[str] = None,
cache_directory: Optional[str] = None,
) -> Optional[int]:
"""
Execute a command by submitting it to the queuing system

Args:
command (list): The command to be executed.
cache_directory (str): The directory to store the HDF5 files.
task_dependent_lst (list): A list of subprocesses that the current subprocess depends on. Defaults to [].
file_name (str): Name of the HDF5 file which contains the Python function
resource_dict (dict): resource dictionary, which defines the resources used for the execution of the function.
Expand All @@ -30,7 +31,6 @@ def execute_with_pysqa(
}
config_directory (str, optional): path to the config directory.
backend (str, optional): name of the backend used to spawn tasks.
cache_directory (str): The directory to store the HDF5 files.

Returns:
int: queuing system ID
Expand All @@ -50,7 +50,9 @@ def execute_with_pysqa(
if "cwd" in resource_dict and resource_dict["cwd"] is not None:
cwd = resource_dict["cwd"]
else:
cwd = cache_directory
folder = command[-1].split("_i.h5")[0]
cwd = os.path.join(cache_directory, folder)
os.makedirs(cwd, exist_ok=True)
Comment on lines +53 to +55
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@coderabbitai coderabbitai bot Jul 2, 2025

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⚠️ Potential issue

Add input validation and improve robustness of folder name extraction.

The current implementation has several potential issues:

  1. Missing input validation: No check if command is empty, which would cause IndexError on command[-1]
  2. Brittle string parsing: The code assumes command[-1] contains "_i.h5", but if it doesn't, the entire string becomes the folder name
  3. Path security: The folder name comes from user input and could contain path traversal characters like "../"

Consider this more robust implementation:

-            folder = command[-1].split("_i.h5")[0]
-            cwd = os.path.join(cache_directory, folder)
-            os.makedirs(cwd, exist_ok=True)
+            if not command:
+                raise ValueError("Command list cannot be empty")
+            
+            # Extract folder name safely
+            last_arg = command[-1]
+            if "_i.h5" in last_arg:
+                folder = last_arg.split("_i.h5")[0]
+            else:
+                # Fallback: use basename without extension
+                folder = os.path.splitext(os.path.basename(last_arg))[0]
+            
+            # Sanitize folder name to prevent path traversal
+            folder = os.path.basename(folder)  # Remove any path components
+            if not folder or folder in (".", ".."):
+                folder = "default_job"
+            
+            cwd = os.path.join(cache_directory, folder)
+            os.makedirs(cwd, exist_ok=True)
📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change
folder = command[-1].split("_i.h5")[0]
cwd = os.path.join(cache_directory, folder)
os.makedirs(cwd, exist_ok=True)
if not command:
raise ValueError("Command list cannot be empty")
# Extract folder name safely
last_arg = command[-1]
if "_i.h5" in last_arg:
folder = last_arg.split("_i.h5")[0]
else:
# Fallback: use basename without extension
folder = os.path.splitext(os.path.basename(last_arg))[0]
# Sanitize folder name to prevent path traversal
folder = os.path.basename(folder) # Remove any path components
if not folder or folder in (".", ".."):
folder = "default_job"
cwd = os.path.join(cache_directory, folder)
os.makedirs(cwd, exist_ok=True)
🤖 Prompt for AI Agents 
In executorlib/task_scheduler/file/queue_spawner.py around lines 53 to 55, add
validation to ensure the command list is not empty before accessing command[-1]
to prevent IndexError. Check if the last element contains the expected "_i.h5"
substring before splitting; if not, handle it gracefully or raise an error.
Sanitize the extracted folder name to remove or neutralize any path traversal
characters like "../" to avoid security risks. Use a safe method to construct
the folder path and then create the directory with os.makedirs as before.

submit_kwargs = {
"command": " ".join(command),
"dependency_list": [str(qid) for qid in task_dependent_lst],
Expand Down
14 changes: 14 additions & 0 deletions tests/test_fluxclusterexecutor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,20 @@ def test_executor(self):
fs1 = exe.submit(mpi_funct, 1)
self.assertFalse(fs1.done())
self.assertEqual(fs1.result(), [(1, 2, 0), (1, 2, 1)])
self.assertEqual(len(os.listdir("executorlib_cache")), 4)
self.assertTrue(fs1.done())

def test_executor_no_cwd(self):
with FluxClusterExecutor(
resource_dict={"cores": 2},
block_allocation=False,
cache_directory="executorlib_cache",
) as exe:
cloudpickle_register(ind=1)
fs1 = exe.submit(mpi_funct, 1)
self.assertFalse(fs1.done())
self.assertEqual(fs1.result(), [(1, 2, 0), (1, 2, 1)])
self.assertEqual(len(os.listdir("executorlib_cache")), 2)
self.assertTrue(fs1.done())

def tearDown(self):
Expand Down
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