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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jan-janssen merged 5 commits into from
Jul 3, 2025
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 5 additions & 3 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff 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

@coderabbitaicoderabbitaiBotJul 2, 2025

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ 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)
ifnotcommand:
raiseValueError("Command list cannot be empty")
# Extract folder name safely
last_arg=command[-1]
if"_i.h5"inlast_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
ifnotfolderorfolderin (".", ".."):
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
View file
Open in desktop
Original file line numberDiff line numberDiff 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
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all \u003cpre\u003e\u003ccode\u003e blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks"); } } catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); } })(); (function(){ try { var __m = "github.com"; var __re = new RegExp('^' + "github\\.com" + '
Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jan-janssen merged 5 commits into from
Jul 3, 2025
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 5 additions & 3 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff 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

@coderabbitaicoderabbitaiBotJul 2, 2025

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ 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)
ifnotcommand:
raiseValueError("Command list cannot be empty")
# Extract folder name safely
last_arg=command[-1]
if"_i.h5"inlast_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
ifnotfolderorfolderin (".", ".."):
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
View file
Open in desktop
Original file line numberDiff line numberDiff 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
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix"); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jan-janssen merged 5 commits into from
Jul 3, 2025
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 5 additions & 3 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff 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

@coderabbitaicoderabbitaiBotJul 2, 2025

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ 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)
ifnotcommand:
raiseValueError("Command list cannot be empty")
# Extract folder name safely
last_arg=command[-1]
if"_i.h5"inlast_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
ifnotfolderorfolderin (".", ".."):
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
View file
Open in desktop
Original file line numberDiff line numberDiff 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
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length \u003e 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms"); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jan-janssen merged 5 commits into from
Jul 3, 2025
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 5 additions & 3 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff 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

@coderabbitaicoderabbitaiBotJul 2, 2025

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ 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)
ifnotcommand:
raiseValueError("Command list cannot be empty")
# Extract folder name safely
last_arg=command[-1]
if"_i.h5"inlast_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
ifnotfolderorfolderin (".", ".."):
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
View file
Open in desktop
Original file line numberDiff line numberDiff 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
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + '
Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jan-janssen merged 5 commits into from
Jul 3, 2025
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 5 additions & 3 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff 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

@coderabbitaicoderabbitaiBotJul 2, 2025

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ 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)
ifnotcommand:
raiseValueError("Command list cannot be empty")
# Extract folder name safely
last_arg=command[-1]
if"_i.h5"inlast_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
ifnotfolderorfolderin (".", ".."):
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
View file
Open in desktop
Original file line numberDiff line numberDiff 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
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jan-janssen merged 5 commits into from
Jul 3, 2025
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 5 additions & 3 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff 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

@coderabbitaicoderabbitaiBotJul 2, 2025

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ 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)
ifnotcommand:
raiseValueError("Command list cannot be empty")
# Extract folder name safely
last_arg=command[-1]
if"_i.h5"inlast_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
ifnotfolderorfolderin (".", ".."):
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
View file
Open in desktop
Original file line numberDiff line numberDiff 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
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers"); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jan-janssen merged 5 commits into from
Jul 3, 2025
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 5 additions & 3 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff 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

@coderabbitaicoderabbitaiBotJul 2, 2025

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ 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)
ifnotcommand:
raiseValueError("Command list cannot be empty")
# Extract folder name safely
last_arg=command[-1]
if"_i.h5"inlast_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
ifnotfolderorfolderin (".", ".."):
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
View file
Open in desktop
Original file line numberDiff line numberDiff 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
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })();
Skip to content

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

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
jan-janssen merged 5 commits into from
Jul 3, 2025
Merged

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

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 5 additions & 3 deletions executorlib/task_scheduler/file/queue_spawner.py
View file
Open in desktop
Original file line numberDiff line numberDiff 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

@coderabbitaicoderabbitaiBotJul 2, 2025

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

⚠️ 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)
ifnotcommand:
raiseValueError("Command list cannot be empty")
# Extract folder name safely
last_arg=command[-1]
if"_i.h5"inlast_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
ifnotfolderorfolderin (".", ".."):
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
View file
Open in desktop
Original file line numberDiff line numberDiff 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