Add option to write flux log files#519

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Merged
jan-janssen merged 22 commits into from
Dec 20, 2024
Merged

Add option to write flux log files #519

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48a8e68
Add option to write flux log files
jan-janssen Dec 13, 2024
d14ebbd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 13, 2024
114ff49
Add tests and docstrings
jan-janssen Dec 13, 2024
e7371b7
Merge remote-tracking branch 'origin/flux_log_files' into flux_log_files
jan-janssen Dec 13, 2024
03659b6
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
9d66651
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
f02ce72
Add test
jan-janssen Dec 17, 2024
5234add
fix tests
jan-janssen Dec 17, 2024
14405a2
extensions
jan-janssen Dec 17, 2024
38125a5
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
9ef5180
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
c94f0ad
remove pmi
jan-janssen Dec 20, 2024
e930b79
disable new tests
jan-janssen Dec 20, 2024
aaf3b1e
test cwd
jan-janssen Dec 20, 2024
eb1e6f8
abspath
jan-janssen Dec 20, 2024
a2a076e
create new directory
jan-janssen Dec 20, 2024
655bb07
do not remove
jan-janssen Dec 20, 2024
7704d57
cwd
jan-janssen Dec 20, 2024
e0ed2b7
fix working directory
jan-janssen Dec 20, 2024
1e22aa8
fix makedir
jan-janssen Dec 20, 2024
482cb8f
try higher level
jan-janssen Dec 20, 2024
5d0046d
Merge branch 'main' into flux_log_files
jan-janssen Dec 20, 2024
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -45,6 +45,7 @@ class Executor:
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -95,6 +96,7 @@ def __init__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -117,6 +119,7 @@ def __new__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand DownExpand Up@@ -153,6 +156,7 @@ def __new__(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -198,6 +202,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
pysqa_config_directory=pysqa_config_directory,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
Expand All@@ -215,6 +220,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand All@@ -235,6 +241,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand Down
3 changes: 3 additions & 0 deletions executorlib/cache/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,7 @@
from executorlib.standalone.inputcheck import (
check_executor,
check_flux_executor_pmi_mode,
check_flux_log_files,
check_hostname_localhost,
check_max_workers_and_cores,
check_nested_flux_executor,
Expand DownExpand Up@@ -88,6 +89,7 @@ def create_file_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -109,6 +111,7 @@ def create_file_executor(
check_hostname_localhost(hostname_localhost=hostname_localhost)
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
return FileExecutor(
cache_directory=cache_directory,
resource_dict=resource_dict,
Expand Down
6 changes: 6 additions & 0 deletions executorlib/interactive/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -11,6 +11,7 @@
from executorlib.standalone.inputcheck import (
check_command_line_argument_lst,
check_executor,
check_flux_log_files,
check_gpus_per_worker,
check_init_function,
check_nested_flux_executor,
Expand DownExpand Up@@ -163,6 +164,7 @@ def create_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
init_function: Optional[callable] = None,
Expand DownExpand Up@@ -193,6 +195,7 @@ def create_executor(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an Executor
running on a different compute node within the same allocation. And in principle
Expand DownExpand Up@@ -222,6 +225,7 @@ def create_executor(
resource_dict["flux_executor"] = flux_executor
resource_dict["flux_executor_pmi_mode"] = flux_executor_pmi_mode
resource_dict["flux_executor_nesting"] = flux_executor_nesting
resource_dict["flux_log_files"] = flux_log_files
if block_allocation:
resource_dict["init_function"] = init_function
max_workers = validate_number_of_cores(
Expand DownExpand Up@@ -250,6 +254,7 @@ def create_executor(
elif backend == "slurm_allocation":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
if block_allocation:
resource_dict["init_function"] = init_function
return InteractiveExecutor(
Expand All@@ -272,6 +277,7 @@ def create_executor(
elif backend == "local":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
check_gpus_per_worker(gpus_per_worker=resource_dict["gpus_per_core"])
check_command_line_argument_lst(
command_line_argument_lst=resource_dict["slurm_cmd_args"]
Expand Down
9 changes: 9 additions & 0 deletions executorlib/interactive/flux.py
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -33,6 +33,7 @@ class FluxPythonSpawner(BaseSpawner):
flux_executor (flux.job.FluxExecutor, optional): The FluxExecutor instance. Defaults to None.
flux_executor_pmi_mode (str, optional): The PMI option. Defaults to None.
flux_executor_nesting (bool, optional): Whether to use nested FluxExecutor. Defaults to False.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
"""

def __init__(
Expand All@@ -45,6 +46,7 @@ def __init__(
flux_executor: Optional[flux.job.FluxExecutor] = None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
):
super().__init__(
cwd=cwd,
Expand All@@ -56,6 +58,7 @@ def __init__(
self._flux_executor = flux_executor
self._flux_executor_pmi_mode = flux_executor_pmi_mode
self._flux_executor_nesting = flux_executor_nesting
self._flux_log_files = flux_log_files
self._future = None

def bootup(
Expand DownExpand Up@@ -99,6 +102,12 @@ def bootup(
jobspec.setattr_shell_option("pmi", self._flux_executor_pmi_mode)
if self._cwd is not None:
jobspec.cwd = self._cwd
if self._flux_log_files and self._cwd is not None:
jobspec.stderr = os.path.join(self._cwd, "flux.err")
jobspec.stdout = os.path.join(self._cwd, "flux.out")
elif self._flux_log_files:
jobspec.stderr = os.path.abspath("flux.err")
jobspec.stdout = os.path.abspath("flux.out")
self._future = self._flux_executor.submit(jobspec)

def shutdown(self, wait: bool = True):
Expand Down
10 changes: 10 additions & 0 deletions executorlib/standalone/inputcheck.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -147,6 +147,16 @@ def check_flux_executor_pmi_mode(flux_executor_pmi_mode: Optional[str]) -> None:
)


def check_flux_log_files(flux_log_files: Optional[bool]) -> None:
"""
Check if flux_log_files is True and raise a ValueError if it is.
"""
if flux_log_files:
raise ValueError(
"The flux_log_files parameter is only supported for the flux framework backend."
)


def check_pysqa_config_directory(pysqa_config_directory: Optional[str]) -> None:
"""
Check if pysqa_config_directory is None and raise a ValueError if it is not.
Expand Down
44 changes: 44 additions & 0 deletions tests/test_executor_backend_flux.py
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Original file line numberDiff line numberDiff line change
Expand Up@@ -100,6 +100,50 @@ def test_single_task(self):
[[(1, 2, 0), (1, 2, 1)], [(2, 2, 0), (2, 2, 1)], [(3, 2, 0), (3, 2, 1)]],
)

def test_output_files_cwd(self):
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
os.makedirs(dirname, exist_ok=True)
file_stdout = os.path.join(dirname, "flux.out")
file_stderr = os.path.join(dirname, "flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1, "cwd": dirname},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_output_files_abs(self):
file_stdout = os.path.abspath("flux.out")
file_stderr = os.path.abspath("flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_internal_memory(self):
with Executor(
max_cores=1,
Expand Down
5 changes: 5 additions & 0 deletions tests/test_shared_input_check.py
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -7,6 +7,7 @@
check_executor,
check_init_function,
check_nested_flux_executor,
check_flux_log_files,
check_pmi,
check_plot_dependency_graph,
check_refresh_rate,
Expand DownExpand Up@@ -67,6 +68,10 @@ def test_check_nested_flux_executor(self):
with self.assertRaises(ValueError):
check_nested_flux_executor(nested_flux_executor=True)

def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
Comment on lines +71 to +73

@coderabbitaicoderabbitaiBotDec 13, 2024

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🛠️ Refactor suggestion

Enhance test coverage with additional test cases.

The current test only verifies that flux_log_files=True raises a ValueError. Consider adding test cases for:

  • flux_log_files=False (valid case)
  • Non-boolean values (invalid case)
 def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
+ # Valid case should not raise+ check_flux_log_files(flux_log_files=False)+ # Non-boolean values should raise+ with self.assertRaises(TypeError):+ check_flux_log_files(flux_log_files="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
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
# Valid case should not raise
check_flux_log_files(flux_log_files=False)
# Non-boolean values should raise
withself.assertRaises(TypeError):
check_flux_log_files(flux_log_files="True")


def test_check_plot_dependency_graph(self):
with self.assertRaises(ValueError):
check_plot_dependency_graph(plot_dependency_graph=True)
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" + '
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Add option to write flux log files#519

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Merged
jan-janssen merged 22 commits into from
Dec 20, 2024
Merged

Add option to write flux log files #519

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48a8e68
Add option to write flux log files
jan-janssen Dec 13, 2024
d14ebbd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 13, 2024
114ff49
Add tests and docstrings
jan-janssen Dec 13, 2024
e7371b7
Merge remote-tracking branch 'origin/flux_log_files' into flux_log_files
jan-janssen Dec 13, 2024
03659b6
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
9d66651
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
f02ce72
Add test
jan-janssen Dec 17, 2024
5234add
fix tests
jan-janssen Dec 17, 2024
14405a2
extensions
jan-janssen Dec 17, 2024
38125a5
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
9ef5180
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
c94f0ad
remove pmi
jan-janssen Dec 20, 2024
e930b79
disable new tests
jan-janssen Dec 20, 2024
aaf3b1e
test cwd
jan-janssen Dec 20, 2024
eb1e6f8
abspath
jan-janssen Dec 20, 2024
a2a076e
create new directory
jan-janssen Dec 20, 2024
655bb07
do not remove
jan-janssen Dec 20, 2024
7704d57
cwd
jan-janssen Dec 20, 2024
e0ed2b7
fix working directory
jan-janssen Dec 20, 2024
1e22aa8
fix makedir
jan-janssen Dec 20, 2024
482cb8f
try higher level
jan-janssen Dec 20, 2024
5d0046d
Merge branch 'main' into flux_log_files
jan-janssen Dec 20, 2024
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -45,6 +45,7 @@ class Executor:
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -95,6 +96,7 @@ def __init__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -117,6 +119,7 @@ def __new__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand DownExpand Up@@ -153,6 +156,7 @@ def __new__(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -198,6 +202,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
pysqa_config_directory=pysqa_config_directory,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
Expand All@@ -215,6 +220,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand All@@ -235,6 +241,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand Down
3 changes: 3 additions & 0 deletions executorlib/cache/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,7 @@
from executorlib.standalone.inputcheck import (
check_executor,
check_flux_executor_pmi_mode,
check_flux_log_files,
check_hostname_localhost,
check_max_workers_and_cores,
check_nested_flux_executor,
Expand DownExpand Up@@ -88,6 +89,7 @@ def create_file_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -109,6 +111,7 @@ def create_file_executor(
check_hostname_localhost(hostname_localhost=hostname_localhost)
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
return FileExecutor(
cache_directory=cache_directory,
resource_dict=resource_dict,
Expand Down
6 changes: 6 additions & 0 deletions executorlib/interactive/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -11,6 +11,7 @@
from executorlib.standalone.inputcheck import (
check_command_line_argument_lst,
check_executor,
check_flux_log_files,
check_gpus_per_worker,
check_init_function,
check_nested_flux_executor,
Expand DownExpand Up@@ -163,6 +164,7 @@ def create_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
init_function: Optional[callable] = None,
Expand DownExpand Up@@ -193,6 +195,7 @@ def create_executor(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an Executor
running on a different compute node within the same allocation. And in principle
Expand DownExpand Up@@ -222,6 +225,7 @@ def create_executor(
resource_dict["flux_executor"] = flux_executor
resource_dict["flux_executor_pmi_mode"] = flux_executor_pmi_mode
resource_dict["flux_executor_nesting"] = flux_executor_nesting
resource_dict["flux_log_files"] = flux_log_files
if block_allocation:
resource_dict["init_function"] = init_function
max_workers = validate_number_of_cores(
Expand DownExpand Up@@ -250,6 +254,7 @@ def create_executor(
elif backend == "slurm_allocation":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
if block_allocation:
resource_dict["init_function"] = init_function
return InteractiveExecutor(
Expand All@@ -272,6 +277,7 @@ def create_executor(
elif backend == "local":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
check_gpus_per_worker(gpus_per_worker=resource_dict["gpus_per_core"])
check_command_line_argument_lst(
command_line_argument_lst=resource_dict["slurm_cmd_args"]
Expand Down
9 changes: 9 additions & 0 deletions executorlib/interactive/flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,6 +33,7 @@ class FluxPythonSpawner(BaseSpawner):
flux_executor (flux.job.FluxExecutor, optional): The FluxExecutor instance. Defaults to None.
flux_executor_pmi_mode (str, optional): The PMI option. Defaults to None.
flux_executor_nesting (bool, optional): Whether to use nested FluxExecutor. Defaults to False.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
"""

def __init__(
Expand All@@ -45,6 +46,7 @@ def __init__(
flux_executor: Optional[flux.job.FluxExecutor] = None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
):
super().__init__(
cwd=cwd,
Expand All@@ -56,6 +58,7 @@ def __init__(
self._flux_executor = flux_executor
self._flux_executor_pmi_mode = flux_executor_pmi_mode
self._flux_executor_nesting = flux_executor_nesting
self._flux_log_files = flux_log_files
self._future = None

def bootup(
Expand DownExpand Up@@ -99,6 +102,12 @@ def bootup(
jobspec.setattr_shell_option("pmi", self._flux_executor_pmi_mode)
if self._cwd is not None:
jobspec.cwd = self._cwd
if self._flux_log_files and self._cwd is not None:
jobspec.stderr = os.path.join(self._cwd, "flux.err")
jobspec.stdout = os.path.join(self._cwd, "flux.out")
elif self._flux_log_files:
jobspec.stderr = os.path.abspath("flux.err")
jobspec.stdout = os.path.abspath("flux.out")
self._future = self._flux_executor.submit(jobspec)

def shutdown(self, wait: bool = True):
Expand Down
10 changes: 10 additions & 0 deletions executorlib/standalone/inputcheck.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -147,6 +147,16 @@ def check_flux_executor_pmi_mode(flux_executor_pmi_mode: Optional[str]) -> None:
)


def check_flux_log_files(flux_log_files: Optional[bool]) -> None:
"""
Check if flux_log_files is True and raise a ValueError if it is.
"""
if flux_log_files:
raise ValueError(
"The flux_log_files parameter is only supported for the flux framework backend."
)


def check_pysqa_config_directory(pysqa_config_directory: Optional[str]) -> None:
"""
Check if pysqa_config_directory is None and raise a ValueError if it is not.
Expand Down
44 changes: 44 additions & 0 deletions tests/test_executor_backend_flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -100,6 +100,50 @@ def test_single_task(self):
[[(1, 2, 0), (1, 2, 1)], [(2, 2, 0), (2, 2, 1)], [(3, 2, 0), (3, 2, 1)]],
)

def test_output_files_cwd(self):
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
os.makedirs(dirname, exist_ok=True)
file_stdout = os.path.join(dirname, "flux.out")
file_stderr = os.path.join(dirname, "flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1, "cwd": dirname},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_output_files_abs(self):
file_stdout = os.path.abspath("flux.out")
file_stderr = os.path.abspath("flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_internal_memory(self):
with Executor(
max_cores=1,
Expand Down
5 changes: 5 additions & 0 deletions tests/test_shared_input_check.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,6 +7,7 @@
check_executor,
check_init_function,
check_nested_flux_executor,
check_flux_log_files,
check_pmi,
check_plot_dependency_graph,
check_refresh_rate,
Expand DownExpand Up@@ -67,6 +68,10 @@ def test_check_nested_flux_executor(self):
with self.assertRaises(ValueError):
check_nested_flux_executor(nested_flux_executor=True)

def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
Comment on lines +71 to +73

@coderabbitaicoderabbitaiBotDec 13, 2024

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🛠️ Refactor suggestion

Enhance test coverage with additional test cases.

The current test only verifies that flux_log_files=True raises a ValueError. Consider adding test cases for:

  • flux_log_files=False (valid case)
  • Non-boolean values (invalid case)
 def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
+ # Valid case should not raise+ check_flux_log_files(flux_log_files=False)+ # Non-boolean values should raise+ with self.assertRaises(TypeError):+ check_flux_log_files(flux_log_files="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
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
# Valid case should not raise
check_flux_log_files(flux_log_files=False)
# Non-boolean values should raise
withself.assertRaises(TypeError):
check_flux_log_files(flux_log_files="True")


def test_check_plot_dependency_graph(self):
with self.assertRaises(ValueError):
check_plot_dependency_graph(plot_dependency_graph=True)
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('^' + ".*" + '
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Add option to write flux log files#519

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Merged
jan-janssen merged 22 commits into from
Dec 20, 2024
Merged

Add option to write flux log files #519

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48a8e68
Add option to write flux log files
jan-janssen Dec 13, 2024
d14ebbd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 13, 2024
114ff49
Add tests and docstrings
jan-janssen Dec 13, 2024
e7371b7
Merge remote-tracking branch 'origin/flux_log_files' into flux_log_files
jan-janssen Dec 13, 2024
03659b6
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
9d66651
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
f02ce72
Add test
jan-janssen Dec 17, 2024
5234add
fix tests
jan-janssen Dec 17, 2024
14405a2
extensions
jan-janssen Dec 17, 2024
38125a5
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
9ef5180
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
c94f0ad
remove pmi
jan-janssen Dec 20, 2024
e930b79
disable new tests
jan-janssen Dec 20, 2024
aaf3b1e
test cwd
jan-janssen Dec 20, 2024
eb1e6f8
abspath
jan-janssen Dec 20, 2024
a2a076e
create new directory
jan-janssen Dec 20, 2024
655bb07
do not remove
jan-janssen Dec 20, 2024
7704d57
cwd
jan-janssen Dec 20, 2024
e0ed2b7
fix working directory
jan-janssen Dec 20, 2024
1e22aa8
fix makedir
jan-janssen Dec 20, 2024
482cb8f
try higher level
jan-janssen Dec 20, 2024
5d0046d
Merge branch 'main' into flux_log_files
jan-janssen Dec 20, 2024
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -45,6 +45,7 @@ class Executor:
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -95,6 +96,7 @@ def __init__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -117,6 +119,7 @@ def __new__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand DownExpand Up@@ -153,6 +156,7 @@ def __new__(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -198,6 +202,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
pysqa_config_directory=pysqa_config_directory,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
Expand All@@ -215,6 +220,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand All@@ -235,6 +241,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand Down
3 changes: 3 additions & 0 deletions executorlib/cache/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,7 @@
from executorlib.standalone.inputcheck import (
check_executor,
check_flux_executor_pmi_mode,
check_flux_log_files,
check_hostname_localhost,
check_max_workers_and_cores,
check_nested_flux_executor,
Expand DownExpand Up@@ -88,6 +89,7 @@ def create_file_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -109,6 +111,7 @@ def create_file_executor(
check_hostname_localhost(hostname_localhost=hostname_localhost)
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
return FileExecutor(
cache_directory=cache_directory,
resource_dict=resource_dict,
Expand Down
6 changes: 6 additions & 0 deletions executorlib/interactive/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -11,6 +11,7 @@
from executorlib.standalone.inputcheck import (
check_command_line_argument_lst,
check_executor,
check_flux_log_files,
check_gpus_per_worker,
check_init_function,
check_nested_flux_executor,
Expand DownExpand Up@@ -163,6 +164,7 @@ def create_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
init_function: Optional[callable] = None,
Expand DownExpand Up@@ -193,6 +195,7 @@ def create_executor(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an Executor
running on a different compute node within the same allocation. And in principle
Expand DownExpand Up@@ -222,6 +225,7 @@ def create_executor(
resource_dict["flux_executor"] = flux_executor
resource_dict["flux_executor_pmi_mode"] = flux_executor_pmi_mode
resource_dict["flux_executor_nesting"] = flux_executor_nesting
resource_dict["flux_log_files"] = flux_log_files
if block_allocation:
resource_dict["init_function"] = init_function
max_workers = validate_number_of_cores(
Expand DownExpand Up@@ -250,6 +254,7 @@ def create_executor(
elif backend == "slurm_allocation":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
if block_allocation:
resource_dict["init_function"] = init_function
return InteractiveExecutor(
Expand All@@ -272,6 +277,7 @@ def create_executor(
elif backend == "local":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
check_gpus_per_worker(gpus_per_worker=resource_dict["gpus_per_core"])
check_command_line_argument_lst(
command_line_argument_lst=resource_dict["slurm_cmd_args"]
Expand Down
9 changes: 9 additions & 0 deletions executorlib/interactive/flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,6 +33,7 @@ class FluxPythonSpawner(BaseSpawner):
flux_executor (flux.job.FluxExecutor, optional): The FluxExecutor instance. Defaults to None.
flux_executor_pmi_mode (str, optional): The PMI option. Defaults to None.
flux_executor_nesting (bool, optional): Whether to use nested FluxExecutor. Defaults to False.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
"""

def __init__(
Expand All@@ -45,6 +46,7 @@ def __init__(
flux_executor: Optional[flux.job.FluxExecutor] = None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
):
super().__init__(
cwd=cwd,
Expand All@@ -56,6 +58,7 @@ def __init__(
self._flux_executor = flux_executor
self._flux_executor_pmi_mode = flux_executor_pmi_mode
self._flux_executor_nesting = flux_executor_nesting
self._flux_log_files = flux_log_files
self._future = None

def bootup(
Expand DownExpand Up@@ -99,6 +102,12 @@ def bootup(
jobspec.setattr_shell_option("pmi", self._flux_executor_pmi_mode)
if self._cwd is not None:
jobspec.cwd = self._cwd
if self._flux_log_files and self._cwd is not None:
jobspec.stderr = os.path.join(self._cwd, "flux.err")
jobspec.stdout = os.path.join(self._cwd, "flux.out")
elif self._flux_log_files:
jobspec.stderr = os.path.abspath("flux.err")
jobspec.stdout = os.path.abspath("flux.out")
self._future = self._flux_executor.submit(jobspec)

def shutdown(self, wait: bool = True):
Expand Down
10 changes: 10 additions & 0 deletions executorlib/standalone/inputcheck.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -147,6 +147,16 @@ def check_flux_executor_pmi_mode(flux_executor_pmi_mode: Optional[str]) -> None:
)


def check_flux_log_files(flux_log_files: Optional[bool]) -> None:
"""
Check if flux_log_files is True and raise a ValueError if it is.
"""
if flux_log_files:
raise ValueError(
"The flux_log_files parameter is only supported for the flux framework backend."
)


def check_pysqa_config_directory(pysqa_config_directory: Optional[str]) -> None:
"""
Check if pysqa_config_directory is None and raise a ValueError if it is not.
Expand Down
44 changes: 44 additions & 0 deletions tests/test_executor_backend_flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -100,6 +100,50 @@ def test_single_task(self):
[[(1, 2, 0), (1, 2, 1)], [(2, 2, 0), (2, 2, 1)], [(3, 2, 0), (3, 2, 1)]],
)

def test_output_files_cwd(self):
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
os.makedirs(dirname, exist_ok=True)
file_stdout = os.path.join(dirname, "flux.out")
file_stderr = os.path.join(dirname, "flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1, "cwd": dirname},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_output_files_abs(self):
file_stdout = os.path.abspath("flux.out")
file_stderr = os.path.abspath("flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_internal_memory(self):
with Executor(
max_cores=1,
Expand Down
5 changes: 5 additions & 0 deletions tests/test_shared_input_check.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,6 +7,7 @@
check_executor,
check_init_function,
check_nested_flux_executor,
check_flux_log_files,
check_pmi,
check_plot_dependency_graph,
check_refresh_rate,
Expand DownExpand Up@@ -67,6 +68,10 @@ def test_check_nested_flux_executor(self):
with self.assertRaises(ValueError):
check_nested_flux_executor(nested_flux_executor=True)

def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
Comment on lines +71 to +73

@coderabbitaicoderabbitaiBotDec 13, 2024

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🛠️ Refactor suggestion

Enhance test coverage with additional test cases.

The current test only verifies that flux_log_files=True raises a ValueError. Consider adding test cases for:

  • flux_log_files=False (valid case)
  • Non-boolean values (invalid case)
 def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
+ # Valid case should not raise+ check_flux_log_files(flux_log_files=False)+ # Non-boolean values should raise+ with self.assertRaises(TypeError):+ check_flux_log_files(flux_log_files="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
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
# Valid case should not raise
check_flux_log_files(flux_log_files=False)
# Non-boolean values should raise
withself.assertRaises(TypeError):
check_flux_log_files(flux_log_files="True")


def test_check_plot_dependency_graph(self):
with self.assertRaises(ValueError):
check_plot_dependency_graph(plot_dependency_graph=True)
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('^' + ".*" + '
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Add option to write flux log files#519

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Merged
jan-janssen merged 22 commits into from
Dec 20, 2024
Merged

Add option to write flux log files #519

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48a8e68
Add option to write flux log files
jan-janssen Dec 13, 2024
d14ebbd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 13, 2024
114ff49
Add tests and docstrings
jan-janssen Dec 13, 2024
e7371b7
Merge remote-tracking branch 'origin/flux_log_files' into flux_log_files
jan-janssen Dec 13, 2024
03659b6
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
9d66651
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
f02ce72
Add test
jan-janssen Dec 17, 2024
5234add
fix tests
jan-janssen Dec 17, 2024
14405a2
extensions
jan-janssen Dec 17, 2024
38125a5
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
9ef5180
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
c94f0ad
remove pmi
jan-janssen Dec 20, 2024
e930b79
disable new tests
jan-janssen Dec 20, 2024
aaf3b1e
test cwd
jan-janssen Dec 20, 2024
eb1e6f8
abspath
jan-janssen Dec 20, 2024
a2a076e
create new directory
jan-janssen Dec 20, 2024
655bb07
do not remove
jan-janssen Dec 20, 2024
7704d57
cwd
jan-janssen Dec 20, 2024
e0ed2b7
fix working directory
jan-janssen Dec 20, 2024
1e22aa8
fix makedir
jan-janssen Dec 20, 2024
482cb8f
try higher level
jan-janssen Dec 20, 2024
5d0046d
Merge branch 'main' into flux_log_files
jan-janssen Dec 20, 2024
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -45,6 +45,7 @@ class Executor:
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -95,6 +96,7 @@ def __init__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -117,6 +119,7 @@ def __new__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand DownExpand Up@@ -153,6 +156,7 @@ def __new__(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -198,6 +202,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
pysqa_config_directory=pysqa_config_directory,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
Expand All@@ -215,6 +220,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand All@@ -235,6 +241,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand Down
3 changes: 3 additions & 0 deletions executorlib/cache/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,7 @@
from executorlib.standalone.inputcheck import (
check_executor,
check_flux_executor_pmi_mode,
check_flux_log_files,
check_hostname_localhost,
check_max_workers_and_cores,
check_nested_flux_executor,
Expand DownExpand Up@@ -88,6 +89,7 @@ def create_file_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -109,6 +111,7 @@ def create_file_executor(
check_hostname_localhost(hostname_localhost=hostname_localhost)
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
return FileExecutor(
cache_directory=cache_directory,
resource_dict=resource_dict,
Expand Down
6 changes: 6 additions & 0 deletions executorlib/interactive/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -11,6 +11,7 @@
from executorlib.standalone.inputcheck import (
check_command_line_argument_lst,
check_executor,
check_flux_log_files,
check_gpus_per_worker,
check_init_function,
check_nested_flux_executor,
Expand DownExpand Up@@ -163,6 +164,7 @@ def create_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
init_function: Optional[callable] = None,
Expand DownExpand Up@@ -193,6 +195,7 @@ def create_executor(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an Executor
running on a different compute node within the same allocation. And in principle
Expand DownExpand Up@@ -222,6 +225,7 @@ def create_executor(
resource_dict["flux_executor"] = flux_executor
resource_dict["flux_executor_pmi_mode"] = flux_executor_pmi_mode
resource_dict["flux_executor_nesting"] = flux_executor_nesting
resource_dict["flux_log_files"] = flux_log_files
if block_allocation:
resource_dict["init_function"] = init_function
max_workers = validate_number_of_cores(
Expand DownExpand Up@@ -250,6 +254,7 @@ def create_executor(
elif backend == "slurm_allocation":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
if block_allocation:
resource_dict["init_function"] = init_function
return InteractiveExecutor(
Expand All@@ -272,6 +277,7 @@ def create_executor(
elif backend == "local":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
check_gpus_per_worker(gpus_per_worker=resource_dict["gpus_per_core"])
check_command_line_argument_lst(
command_line_argument_lst=resource_dict["slurm_cmd_args"]
Expand Down
9 changes: 9 additions & 0 deletions executorlib/interactive/flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,6 +33,7 @@ class FluxPythonSpawner(BaseSpawner):
flux_executor (flux.job.FluxExecutor, optional): The FluxExecutor instance. Defaults to None.
flux_executor_pmi_mode (str, optional): The PMI option. Defaults to None.
flux_executor_nesting (bool, optional): Whether to use nested FluxExecutor. Defaults to False.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
"""

def __init__(
Expand All@@ -45,6 +46,7 @@ def __init__(
flux_executor: Optional[flux.job.FluxExecutor] = None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
):
super().__init__(
cwd=cwd,
Expand All@@ -56,6 +58,7 @@ def __init__(
self._flux_executor = flux_executor
self._flux_executor_pmi_mode = flux_executor_pmi_mode
self._flux_executor_nesting = flux_executor_nesting
self._flux_log_files = flux_log_files
self._future = None

def bootup(
Expand DownExpand Up@@ -99,6 +102,12 @@ def bootup(
jobspec.setattr_shell_option("pmi", self._flux_executor_pmi_mode)
if self._cwd is not None:
jobspec.cwd = self._cwd
if self._flux_log_files and self._cwd is not None:
jobspec.stderr = os.path.join(self._cwd, "flux.err")
jobspec.stdout = os.path.join(self._cwd, "flux.out")
elif self._flux_log_files:
jobspec.stderr = os.path.abspath("flux.err")
jobspec.stdout = os.path.abspath("flux.out")
self._future = self._flux_executor.submit(jobspec)

def shutdown(self, wait: bool = True):
Expand Down
10 changes: 10 additions & 0 deletions executorlib/standalone/inputcheck.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -147,6 +147,16 @@ def check_flux_executor_pmi_mode(flux_executor_pmi_mode: Optional[str]) -> None:
)


def check_flux_log_files(flux_log_files: Optional[bool]) -> None:
"""
Check if flux_log_files is True and raise a ValueError if it is.
"""
if flux_log_files:
raise ValueError(
"The flux_log_files parameter is only supported for the flux framework backend."
)


def check_pysqa_config_directory(pysqa_config_directory: Optional[str]) -> None:
"""
Check if pysqa_config_directory is None and raise a ValueError if it is not.
Expand Down
44 changes: 44 additions & 0 deletions tests/test_executor_backend_flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -100,6 +100,50 @@ def test_single_task(self):
[[(1, 2, 0), (1, 2, 1)], [(2, 2, 0), (2, 2, 1)], [(3, 2, 0), (3, 2, 1)]],
)

def test_output_files_cwd(self):
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
os.makedirs(dirname, exist_ok=True)
file_stdout = os.path.join(dirname, "flux.out")
file_stderr = os.path.join(dirname, "flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1, "cwd": dirname},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_output_files_abs(self):
file_stdout = os.path.abspath("flux.out")
file_stderr = os.path.abspath("flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_internal_memory(self):
with Executor(
max_cores=1,
Expand Down
5 changes: 5 additions & 0 deletions tests/test_shared_input_check.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,6 +7,7 @@
check_executor,
check_init_function,
check_nested_flux_executor,
check_flux_log_files,
check_pmi,
check_plot_dependency_graph,
check_refresh_rate,
Expand DownExpand Up@@ -67,6 +68,10 @@ def test_check_nested_flux_executor(self):
with self.assertRaises(ValueError):
check_nested_flux_executor(nested_flux_executor=True)

def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
Comment on lines +71 to +73

@coderabbitaicoderabbitaiBotDec 13, 2024

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🛠️ Refactor suggestion

Enhance test coverage with additional test cases.

The current test only verifies that flux_log_files=True raises a ValueError. Consider adding test cases for:

  • flux_log_files=False (valid case)
  • Non-boolean values (invalid case)
 def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
+ # Valid case should not raise+ check_flux_log_files(flux_log_files=False)+ # Non-boolean values should raise+ with self.assertRaises(TypeError):+ check_flux_log_files(flux_log_files="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
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
# Valid case should not raise
check_flux_log_files(flux_log_files=False)
# Non-boolean values should raise
withself.assertRaises(TypeError):
check_flux_log_files(flux_log_files="True")


def test_check_plot_dependency_graph(self):
with self.assertRaises(ValueError):
check_plot_dependency_graph(plot_dependency_graph=True)
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

Add option to write flux log files#519

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Merged
jan-janssen merged 22 commits into from
Dec 20, 2024
Merged

Add option to write flux log files #519

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22 commits
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48a8e68
Add option to write flux log files
jan-janssen Dec 13, 2024
d14ebbd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 13, 2024
114ff49
Add tests and docstrings
jan-janssen Dec 13, 2024
e7371b7
Merge remote-tracking branch 'origin/flux_log_files' into flux_log_files
jan-janssen Dec 13, 2024
03659b6
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
9d66651
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
f02ce72
Add test
jan-janssen Dec 17, 2024
5234add
fix tests
jan-janssen Dec 17, 2024
14405a2
extensions
jan-janssen Dec 17, 2024
38125a5
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
9ef5180
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
c94f0ad
remove pmi
jan-janssen Dec 20, 2024
e930b79
disable new tests
jan-janssen Dec 20, 2024
aaf3b1e
test cwd
jan-janssen Dec 20, 2024
eb1e6f8
abspath
jan-janssen Dec 20, 2024
a2a076e
create new directory
jan-janssen Dec 20, 2024
655bb07
do not remove
jan-janssen Dec 20, 2024
7704d57
cwd
jan-janssen Dec 20, 2024
e0ed2b7
fix working directory
jan-janssen Dec 20, 2024
1e22aa8
fix makedir
jan-janssen Dec 20, 2024
482cb8f
try higher level
jan-janssen Dec 20, 2024
5d0046d
Merge branch 'main' into flux_log_files
jan-janssen Dec 20, 2024
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -45,6 +45,7 @@ class Executor:
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -95,6 +96,7 @@ def __init__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -117,6 +119,7 @@ def __new__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand DownExpand Up@@ -153,6 +156,7 @@ def __new__(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -198,6 +202,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
pysqa_config_directory=pysqa_config_directory,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
Expand All@@ -215,6 +220,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand All@@ -235,6 +241,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand Down
3 changes: 3 additions & 0 deletions executorlib/cache/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,7 @@
from executorlib.standalone.inputcheck import (
check_executor,
check_flux_executor_pmi_mode,
check_flux_log_files,
check_hostname_localhost,
check_max_workers_and_cores,
check_nested_flux_executor,
Expand DownExpand Up@@ -88,6 +89,7 @@ def create_file_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -109,6 +111,7 @@ def create_file_executor(
check_hostname_localhost(hostname_localhost=hostname_localhost)
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
return FileExecutor(
cache_directory=cache_directory,
resource_dict=resource_dict,
Expand Down
6 changes: 6 additions & 0 deletions executorlib/interactive/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -11,6 +11,7 @@
from executorlib.standalone.inputcheck import (
check_command_line_argument_lst,
check_executor,
check_flux_log_files,
check_gpus_per_worker,
check_init_function,
check_nested_flux_executor,
Expand DownExpand Up@@ -163,6 +164,7 @@ def create_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
init_function: Optional[callable] = None,
Expand DownExpand Up@@ -193,6 +195,7 @@ def create_executor(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an Executor
running on a different compute node within the same allocation. And in principle
Expand DownExpand Up@@ -222,6 +225,7 @@ def create_executor(
resource_dict["flux_executor"] = flux_executor
resource_dict["flux_executor_pmi_mode"] = flux_executor_pmi_mode
resource_dict["flux_executor_nesting"] = flux_executor_nesting
resource_dict["flux_log_files"] = flux_log_files
if block_allocation:
resource_dict["init_function"] = init_function
max_workers = validate_number_of_cores(
Expand DownExpand Up@@ -250,6 +254,7 @@ def create_executor(
elif backend == "slurm_allocation":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
if block_allocation:
resource_dict["init_function"] = init_function
return InteractiveExecutor(
Expand All@@ -272,6 +277,7 @@ def create_executor(
elif backend == "local":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
check_gpus_per_worker(gpus_per_worker=resource_dict["gpus_per_core"])
check_command_line_argument_lst(
command_line_argument_lst=resource_dict["slurm_cmd_args"]
Expand Down
9 changes: 9 additions & 0 deletions executorlib/interactive/flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,6 +33,7 @@ class FluxPythonSpawner(BaseSpawner):
flux_executor (flux.job.FluxExecutor, optional): The FluxExecutor instance. Defaults to None.
flux_executor_pmi_mode (str, optional): The PMI option. Defaults to None.
flux_executor_nesting (bool, optional): Whether to use nested FluxExecutor. Defaults to False.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
"""

def __init__(
Expand All@@ -45,6 +46,7 @@ def __init__(
flux_executor: Optional[flux.job.FluxExecutor] = None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
):
super().__init__(
cwd=cwd,
Expand All@@ -56,6 +58,7 @@ def __init__(
self._flux_executor = flux_executor
self._flux_executor_pmi_mode = flux_executor_pmi_mode
self._flux_executor_nesting = flux_executor_nesting
self._flux_log_files = flux_log_files
self._future = None

def bootup(
Expand DownExpand Up@@ -99,6 +102,12 @@ def bootup(
jobspec.setattr_shell_option("pmi", self._flux_executor_pmi_mode)
if self._cwd is not None:
jobspec.cwd = self._cwd
if self._flux_log_files and self._cwd is not None:
jobspec.stderr = os.path.join(self._cwd, "flux.err")
jobspec.stdout = os.path.join(self._cwd, "flux.out")
elif self._flux_log_files:
jobspec.stderr = os.path.abspath("flux.err")
jobspec.stdout = os.path.abspath("flux.out")
self._future = self._flux_executor.submit(jobspec)

def shutdown(self, wait: bool = True):
Expand Down
10 changes: 10 additions & 0 deletions executorlib/standalone/inputcheck.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -147,6 +147,16 @@ def check_flux_executor_pmi_mode(flux_executor_pmi_mode: Optional[str]) -> None:
)


def check_flux_log_files(flux_log_files: Optional[bool]) -> None:
"""
Check if flux_log_files is True and raise a ValueError if it is.
"""
if flux_log_files:
raise ValueError(
"The flux_log_files parameter is only supported for the flux framework backend."
)


def check_pysqa_config_directory(pysqa_config_directory: Optional[str]) -> None:
"""
Check if pysqa_config_directory is None and raise a ValueError if it is not.
Expand Down
44 changes: 44 additions & 0 deletions tests/test_executor_backend_flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -100,6 +100,50 @@ def test_single_task(self):
[[(1, 2, 0), (1, 2, 1)], [(2, 2, 0), (2, 2, 1)], [(3, 2, 0), (3, 2, 1)]],
)

def test_output_files_cwd(self):
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
os.makedirs(dirname, exist_ok=True)
file_stdout = os.path.join(dirname, "flux.out")
file_stderr = os.path.join(dirname, "flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1, "cwd": dirname},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_output_files_abs(self):
file_stdout = os.path.abspath("flux.out")
file_stderr = os.path.abspath("flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_internal_memory(self):
with Executor(
max_cores=1,
Expand Down
5 changes: 5 additions & 0 deletions tests/test_shared_input_check.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,6 +7,7 @@
check_executor,
check_init_function,
check_nested_flux_executor,
check_flux_log_files,
check_pmi,
check_plot_dependency_graph,
check_refresh_rate,
Expand DownExpand Up@@ -67,6 +68,10 @@ def test_check_nested_flux_executor(self):
with self.assertRaises(ValueError):
check_nested_flux_executor(nested_flux_executor=True)

def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
Comment on lines +71 to +73

@coderabbitaicoderabbitaiBotDec 13, 2024

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🛠️ Refactor suggestion

Enhance test coverage with additional test cases.

The current test only verifies that flux_log_files=True raises a ValueError. Consider adding test cases for:

  • flux_log_files=False (valid case)
  • Non-boolean values (invalid case)
 def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
+ # Valid case should not raise+ check_flux_log_files(flux_log_files=False)+ # Non-boolean values should raise+ with self.assertRaises(TypeError):+ check_flux_log_files(flux_log_files="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
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
# Valid case should not raise
check_flux_log_files(flux_log_files=False)
# Non-boolean values should raise
withself.assertRaises(TypeError):
check_flux_log_files(flux_log_files="True")


def test_check_plot_dependency_graph(self):
with self.assertRaises(ValueError):
check_plot_dependency_graph(plot_dependency_graph=True)
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('^' + ".*" + '
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Add option to write flux log files#519

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Merged
jan-janssen merged 22 commits into from
Dec 20, 2024
Merged

Add option to write flux log files #519

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48a8e68
Add option to write flux log files
jan-janssen Dec 13, 2024
d14ebbd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 13, 2024
114ff49
Add tests and docstrings
jan-janssen Dec 13, 2024
e7371b7
Merge remote-tracking branch 'origin/flux_log_files' into flux_log_files
jan-janssen Dec 13, 2024
03659b6
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
9d66651
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
f02ce72
Add test
jan-janssen Dec 17, 2024
5234add
fix tests
jan-janssen Dec 17, 2024
14405a2
extensions
jan-janssen Dec 17, 2024
38125a5
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
9ef5180
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
c94f0ad
remove pmi
jan-janssen Dec 20, 2024
e930b79
disable new tests
jan-janssen Dec 20, 2024
aaf3b1e
test cwd
jan-janssen Dec 20, 2024
eb1e6f8
abspath
jan-janssen Dec 20, 2024
a2a076e
create new directory
jan-janssen Dec 20, 2024
655bb07
do not remove
jan-janssen Dec 20, 2024
7704d57
cwd
jan-janssen Dec 20, 2024
e0ed2b7
fix working directory
jan-janssen Dec 20, 2024
1e22aa8
fix makedir
jan-janssen Dec 20, 2024
482cb8f
try higher level
jan-janssen Dec 20, 2024
5d0046d
Merge branch 'main' into flux_log_files
jan-janssen Dec 20, 2024
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -45,6 +45,7 @@ class Executor:
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -95,6 +96,7 @@ def __init__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -117,6 +119,7 @@ def __new__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand DownExpand Up@@ -153,6 +156,7 @@ def __new__(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -198,6 +202,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
pysqa_config_directory=pysqa_config_directory,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
Expand All@@ -215,6 +220,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand All@@ -235,6 +241,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand Down
3 changes: 3 additions & 0 deletions executorlib/cache/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,7 @@
from executorlib.standalone.inputcheck import (
check_executor,
check_flux_executor_pmi_mode,
check_flux_log_files,
check_hostname_localhost,
check_max_workers_and_cores,
check_nested_flux_executor,
Expand DownExpand Up@@ -88,6 +89,7 @@ def create_file_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -109,6 +111,7 @@ def create_file_executor(
check_hostname_localhost(hostname_localhost=hostname_localhost)
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
return FileExecutor(
cache_directory=cache_directory,
resource_dict=resource_dict,
Expand Down
6 changes: 6 additions & 0 deletions executorlib/interactive/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -11,6 +11,7 @@
from executorlib.standalone.inputcheck import (
check_command_line_argument_lst,
check_executor,
check_flux_log_files,
check_gpus_per_worker,
check_init_function,
check_nested_flux_executor,
Expand DownExpand Up@@ -163,6 +164,7 @@ def create_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
init_function: Optional[callable] = None,
Expand DownExpand Up@@ -193,6 +195,7 @@ def create_executor(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an Executor
running on a different compute node within the same allocation. And in principle
Expand DownExpand Up@@ -222,6 +225,7 @@ def create_executor(
resource_dict["flux_executor"] = flux_executor
resource_dict["flux_executor_pmi_mode"] = flux_executor_pmi_mode
resource_dict["flux_executor_nesting"] = flux_executor_nesting
resource_dict["flux_log_files"] = flux_log_files
if block_allocation:
resource_dict["init_function"] = init_function
max_workers = validate_number_of_cores(
Expand DownExpand Up@@ -250,6 +254,7 @@ def create_executor(
elif backend == "slurm_allocation":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
if block_allocation:
resource_dict["init_function"] = init_function
return InteractiveExecutor(
Expand All@@ -272,6 +277,7 @@ def create_executor(
elif backend == "local":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
check_gpus_per_worker(gpus_per_worker=resource_dict["gpus_per_core"])
check_command_line_argument_lst(
command_line_argument_lst=resource_dict["slurm_cmd_args"]
Expand Down
9 changes: 9 additions & 0 deletions executorlib/interactive/flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,6 +33,7 @@ class FluxPythonSpawner(BaseSpawner):
flux_executor (flux.job.FluxExecutor, optional): The FluxExecutor instance. Defaults to None.
flux_executor_pmi_mode (str, optional): The PMI option. Defaults to None.
flux_executor_nesting (bool, optional): Whether to use nested FluxExecutor. Defaults to False.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
"""

def __init__(
Expand All@@ -45,6 +46,7 @@ def __init__(
flux_executor: Optional[flux.job.FluxExecutor] = None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
):
super().__init__(
cwd=cwd,
Expand All@@ -56,6 +58,7 @@ def __init__(
self._flux_executor = flux_executor
self._flux_executor_pmi_mode = flux_executor_pmi_mode
self._flux_executor_nesting = flux_executor_nesting
self._flux_log_files = flux_log_files
self._future = None

def bootup(
Expand DownExpand Up@@ -99,6 +102,12 @@ def bootup(
jobspec.setattr_shell_option("pmi", self._flux_executor_pmi_mode)
if self._cwd is not None:
jobspec.cwd = self._cwd
if self._flux_log_files and self._cwd is not None:
jobspec.stderr = os.path.join(self._cwd, "flux.err")
jobspec.stdout = os.path.join(self._cwd, "flux.out")
elif self._flux_log_files:
jobspec.stderr = os.path.abspath("flux.err")
jobspec.stdout = os.path.abspath("flux.out")
self._future = self._flux_executor.submit(jobspec)

def shutdown(self, wait: bool = True):
Expand Down
10 changes: 10 additions & 0 deletions executorlib/standalone/inputcheck.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -147,6 +147,16 @@ def check_flux_executor_pmi_mode(flux_executor_pmi_mode: Optional[str]) -> None:
)


def check_flux_log_files(flux_log_files: Optional[bool]) -> None:
"""
Check if flux_log_files is True and raise a ValueError if it is.
"""
if flux_log_files:
raise ValueError(
"The flux_log_files parameter is only supported for the flux framework backend."
)


def check_pysqa_config_directory(pysqa_config_directory: Optional[str]) -> None:
"""
Check if pysqa_config_directory is None and raise a ValueError if it is not.
Expand Down
44 changes: 44 additions & 0 deletions tests/test_executor_backend_flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -100,6 +100,50 @@ def test_single_task(self):
[[(1, 2, 0), (1, 2, 1)], [(2, 2, 0), (2, 2, 1)], [(3, 2, 0), (3, 2, 1)]],
)

def test_output_files_cwd(self):
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
os.makedirs(dirname, exist_ok=True)
file_stdout = os.path.join(dirname, "flux.out")
file_stderr = os.path.join(dirname, "flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1, "cwd": dirname},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_output_files_abs(self):
file_stdout = os.path.abspath("flux.out")
file_stderr = os.path.abspath("flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_internal_memory(self):
with Executor(
max_cores=1,
Expand Down
5 changes: 5 additions & 0 deletions tests/test_shared_input_check.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,6 +7,7 @@
check_executor,
check_init_function,
check_nested_flux_executor,
check_flux_log_files,
check_pmi,
check_plot_dependency_graph,
check_refresh_rate,
Expand DownExpand Up@@ -67,6 +68,10 @@ def test_check_nested_flux_executor(self):
with self.assertRaises(ValueError):
check_nested_flux_executor(nested_flux_executor=True)

def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
Comment on lines +71 to +73

@coderabbitaicoderabbitaiBotDec 13, 2024

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🛠️ Refactor suggestion

Enhance test coverage with additional test cases.

The current test only verifies that flux_log_files=True raises a ValueError. Consider adding test cases for:

  • flux_log_files=False (valid case)
  • Non-boolean values (invalid case)
 def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
+ # Valid case should not raise+ check_flux_log_files(flux_log_files=False)+ # Non-boolean values should raise+ with self.assertRaises(TypeError):+ check_flux_log_files(flux_log_files="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
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
# Valid case should not raise
check_flux_log_files(flux_log_files=False)
# Non-boolean values should raise
withself.assertRaises(TypeError):
check_flux_log_files(flux_log_files="True")


def test_check_plot_dependency_graph(self):
with self.assertRaises(ValueError):
check_plot_dependency_graph(plot_dependency_graph=True)
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('^' + ".*" + '
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Add option to write flux log files#519

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Merged
jan-janssen merged 22 commits into from
Dec 20, 2024
Merged

Add option to write flux log files #519

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48a8e68
Add option to write flux log files
jan-janssen Dec 13, 2024
d14ebbd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 13, 2024
114ff49
Add tests and docstrings
jan-janssen Dec 13, 2024
e7371b7
Merge remote-tracking branch 'origin/flux_log_files' into flux_log_files
jan-janssen Dec 13, 2024
03659b6
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
9d66651
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
f02ce72
Add test
jan-janssen Dec 17, 2024
5234add
fix tests
jan-janssen Dec 17, 2024
14405a2
extensions
jan-janssen Dec 17, 2024
38125a5
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
9ef5180
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
c94f0ad
remove pmi
jan-janssen Dec 20, 2024
e930b79
disable new tests
jan-janssen Dec 20, 2024
aaf3b1e
test cwd
jan-janssen Dec 20, 2024
eb1e6f8
abspath
jan-janssen Dec 20, 2024
a2a076e
create new directory
jan-janssen Dec 20, 2024
655bb07
do not remove
jan-janssen Dec 20, 2024
7704d57
cwd
jan-janssen Dec 20, 2024
e0ed2b7
fix working directory
jan-janssen Dec 20, 2024
1e22aa8
fix makedir
jan-janssen Dec 20, 2024
482cb8f
try higher level
jan-janssen Dec 20, 2024
5d0046d
Merge branch 'main' into flux_log_files
jan-janssen Dec 20, 2024
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -45,6 +45,7 @@ class Executor:
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -95,6 +96,7 @@ def __init__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -117,6 +119,7 @@ def __new__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand DownExpand Up@@ -153,6 +156,7 @@ def __new__(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -198,6 +202,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
pysqa_config_directory=pysqa_config_directory,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
Expand All@@ -215,6 +220,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand All@@ -235,6 +241,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand Down
3 changes: 3 additions & 0 deletions executorlib/cache/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,7 @@
from executorlib.standalone.inputcheck import (
check_executor,
check_flux_executor_pmi_mode,
check_flux_log_files,
check_hostname_localhost,
check_max_workers_and_cores,
check_nested_flux_executor,
Expand DownExpand Up@@ -88,6 +89,7 @@ def create_file_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -109,6 +111,7 @@ def create_file_executor(
check_hostname_localhost(hostname_localhost=hostname_localhost)
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
return FileExecutor(
cache_directory=cache_directory,
resource_dict=resource_dict,
Expand Down
6 changes: 6 additions & 0 deletions executorlib/interactive/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -11,6 +11,7 @@
from executorlib.standalone.inputcheck import (
check_command_line_argument_lst,
check_executor,
check_flux_log_files,
check_gpus_per_worker,
check_init_function,
check_nested_flux_executor,
Expand DownExpand Up@@ -163,6 +164,7 @@ def create_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
init_function: Optional[callable] = None,
Expand DownExpand Up@@ -193,6 +195,7 @@ def create_executor(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an Executor
running on a different compute node within the same allocation. And in principle
Expand DownExpand Up@@ -222,6 +225,7 @@ def create_executor(
resource_dict["flux_executor"] = flux_executor
resource_dict["flux_executor_pmi_mode"] = flux_executor_pmi_mode
resource_dict["flux_executor_nesting"] = flux_executor_nesting
resource_dict["flux_log_files"] = flux_log_files
if block_allocation:
resource_dict["init_function"] = init_function
max_workers = validate_number_of_cores(
Expand DownExpand Up@@ -250,6 +254,7 @@ def create_executor(
elif backend == "slurm_allocation":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
if block_allocation:
resource_dict["init_function"] = init_function
return InteractiveExecutor(
Expand All@@ -272,6 +277,7 @@ def create_executor(
elif backend == "local":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
check_gpus_per_worker(gpus_per_worker=resource_dict["gpus_per_core"])
check_command_line_argument_lst(
command_line_argument_lst=resource_dict["slurm_cmd_args"]
Expand Down
9 changes: 9 additions & 0 deletions executorlib/interactive/flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,6 +33,7 @@ class FluxPythonSpawner(BaseSpawner):
flux_executor (flux.job.FluxExecutor, optional): The FluxExecutor instance. Defaults to None.
flux_executor_pmi_mode (str, optional): The PMI option. Defaults to None.
flux_executor_nesting (bool, optional): Whether to use nested FluxExecutor. Defaults to False.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
"""

def __init__(
Expand All@@ -45,6 +46,7 @@ def __init__(
flux_executor: Optional[flux.job.FluxExecutor] = None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
):
super().__init__(
cwd=cwd,
Expand All@@ -56,6 +58,7 @@ def __init__(
self._flux_executor = flux_executor
self._flux_executor_pmi_mode = flux_executor_pmi_mode
self._flux_executor_nesting = flux_executor_nesting
self._flux_log_files = flux_log_files
self._future = None

def bootup(
Expand DownExpand Up@@ -99,6 +102,12 @@ def bootup(
jobspec.setattr_shell_option("pmi", self._flux_executor_pmi_mode)
if self._cwd is not None:
jobspec.cwd = self._cwd
if self._flux_log_files and self._cwd is not None:
jobspec.stderr = os.path.join(self._cwd, "flux.err")
jobspec.stdout = os.path.join(self._cwd, "flux.out")
elif self._flux_log_files:
jobspec.stderr = os.path.abspath("flux.err")
jobspec.stdout = os.path.abspath("flux.out")
self._future = self._flux_executor.submit(jobspec)

def shutdown(self, wait: bool = True):
Expand Down
10 changes: 10 additions & 0 deletions executorlib/standalone/inputcheck.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -147,6 +147,16 @@ def check_flux_executor_pmi_mode(flux_executor_pmi_mode: Optional[str]) -> None:
)


def check_flux_log_files(flux_log_files: Optional[bool]) -> None:
"""
Check if flux_log_files is True and raise a ValueError if it is.
"""
if flux_log_files:
raise ValueError(
"The flux_log_files parameter is only supported for the flux framework backend."
)


def check_pysqa_config_directory(pysqa_config_directory: Optional[str]) -> None:
"""
Check if pysqa_config_directory is None and raise a ValueError if it is not.
Expand Down
44 changes: 44 additions & 0 deletions tests/test_executor_backend_flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -100,6 +100,50 @@ def test_single_task(self):
[[(1, 2, 0), (1, 2, 1)], [(2, 2, 0), (2, 2, 1)], [(3, 2, 0), (3, 2, 1)]],
)

def test_output_files_cwd(self):
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
os.makedirs(dirname, exist_ok=True)
file_stdout = os.path.join(dirname, "flux.out")
file_stderr = os.path.join(dirname, "flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1, "cwd": dirname},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_output_files_abs(self):
file_stdout = os.path.abspath("flux.out")
file_stderr = os.path.abspath("flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_internal_memory(self):
with Executor(
max_cores=1,
Expand Down
5 changes: 5 additions & 0 deletions tests/test_shared_input_check.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,6 +7,7 @@
check_executor,
check_init_function,
check_nested_flux_executor,
check_flux_log_files,
check_pmi,
check_plot_dependency_graph,
check_refresh_rate,
Expand DownExpand Up@@ -67,6 +68,10 @@ def test_check_nested_flux_executor(self):
with self.assertRaises(ValueError):
check_nested_flux_executor(nested_flux_executor=True)

def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
Comment on lines +71 to +73

@coderabbitaicoderabbitaiBotDec 13, 2024

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🛠️ Refactor suggestion

Enhance test coverage with additional test cases.

The current test only verifies that flux_log_files=True raises a ValueError. Consider adding test cases for:

  • flux_log_files=False (valid case)
  • Non-boolean values (invalid case)
 def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
+ # Valid case should not raise+ check_flux_log_files(flux_log_files=False)+ # Non-boolean values should raise+ with self.assertRaises(TypeError):+ check_flux_log_files(flux_log_files="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
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
# Valid case should not raise
check_flux_log_files(flux_log_files=False)
# Non-boolean values should raise
withself.assertRaises(TypeError):
check_flux_log_files(flux_log_files="True")


def test_check_plot_dependency_graph(self):
with self.assertRaises(ValueError):
check_plot_dependency_graph(plot_dependency_graph=True)
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); } })(); })();
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Add option to write flux log files#519

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Merged
jan-janssen merged 22 commits into from
Dec 20, 2024
Merged

Add option to write flux log files #519

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48a8e68
Add option to write flux log files
jan-janssen Dec 13, 2024
d14ebbd
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 13, 2024
114ff49
Add tests and docstrings
jan-janssen Dec 13, 2024
e7371b7
Merge remote-tracking branch 'origin/flux_log_files' into flux_log_files
jan-janssen Dec 13, 2024
03659b6
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
9d66651
Merge remote-tracking branch 'origin/main' into flux_log_files
jan-janssen Dec 17, 2024
f02ce72
Add test
jan-janssen Dec 17, 2024
5234add
fix tests
jan-janssen Dec 17, 2024
14405a2
extensions
jan-janssen Dec 17, 2024
38125a5
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
9ef5180
Update test_executor_backend_flux.py
jan-janssen Dec 19, 2024
c94f0ad
remove pmi
jan-janssen Dec 20, 2024
e930b79
disable new tests
jan-janssen Dec 20, 2024
aaf3b1e
test cwd
jan-janssen Dec 20, 2024
eb1e6f8
abspath
jan-janssen Dec 20, 2024
a2a076e
create new directory
jan-janssen Dec 20, 2024
655bb07
do not remove
jan-janssen Dec 20, 2024
7704d57
cwd
jan-janssen Dec 20, 2024
e0ed2b7
fix working directory
jan-janssen Dec 20, 2024
1e22aa8
fix makedir
jan-janssen Dec 20, 2024
482cb8f
try higher level
jan-janssen Dec 20, 2024
5d0046d
Merge branch 'main' into flux_log_files
jan-janssen Dec 20, 2024
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7 changes: 7 additions & 0 deletions executorlib/__init__.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -45,6 +45,7 @@ class Executor:
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -95,6 +96,7 @@ def __init__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -117,6 +119,7 @@ def __new__(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand DownExpand Up@@ -153,6 +156,7 @@ def __new__(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
pysqa_config_directory (str, optional): path to the pysqa config directory (only for pysqa based backend).
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an
Expand DownExpand Up@@ -198,6 +202,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
pysqa_config_directory=pysqa_config_directory,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
Expand All@@ -215,6 +220,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand All@@ -235,6 +241,7 @@ def __new__(
flux_executor=flux_executor,
flux_executor_pmi_mode=flux_executor_pmi_mode,
flux_executor_nesting=flux_executor_nesting,
flux_log_files=flux_log_files,
hostname_localhost=hostname_localhost,
block_allocation=block_allocation,
init_function=init_function,
Expand Down
3 changes: 3 additions & 0 deletions executorlib/cache/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -10,6 +10,7 @@
from executorlib.standalone.inputcheck import (
check_executor,
check_flux_executor_pmi_mode,
check_flux_log_files,
check_hostname_localhost,
check_max_workers_and_cores,
check_nested_flux_executor,
Expand DownExpand Up@@ -88,6 +89,7 @@ def create_file_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
pysqa_config_directory: Optional[str] = None,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
Expand All@@ -109,6 +111,7 @@ def create_file_executor(
check_hostname_localhost(hostname_localhost=hostname_localhost)
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
return FileExecutor(
cache_directory=cache_directory,
resource_dict=resource_dict,
Expand Down
6 changes: 6 additions & 0 deletions executorlib/interactive/executor.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -11,6 +11,7 @@
from executorlib.standalone.inputcheck import (
check_command_line_argument_lst,
check_executor,
check_flux_log_files,
check_gpus_per_worker,
check_init_function,
check_nested_flux_executor,
Expand DownExpand Up@@ -163,6 +164,7 @@ def create_executor(
flux_executor=None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
hostname_localhost: Optional[bool] = None,
block_allocation: bool = False,
init_function: Optional[callable] = None,
Expand DownExpand Up@@ -193,6 +195,7 @@ def create_executor(
flux_executor (flux.job.FluxExecutor): Flux Python interface to submit the workers to flux
flux_executor_pmi_mode (str): PMI interface to use (OpenMPI v5 requires pmix) default is None (Flux only)
flux_executor_nesting (bool): Provide hierarchically nested Flux job scheduler inside the submitted function.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
hostname_localhost (boolean): use localhost instead of the hostname to establish the zmq connection. In the
context of an HPC cluster this essential to be able to communicate to an Executor
running on a different compute node within the same allocation. And in principle
Expand DownExpand Up@@ -222,6 +225,7 @@ def create_executor(
resource_dict["flux_executor"] = flux_executor
resource_dict["flux_executor_pmi_mode"] = flux_executor_pmi_mode
resource_dict["flux_executor_nesting"] = flux_executor_nesting
resource_dict["flux_log_files"] = flux_log_files
if block_allocation:
resource_dict["init_function"] = init_function
max_workers = validate_number_of_cores(
Expand DownExpand Up@@ -250,6 +254,7 @@ def create_executor(
elif backend == "slurm_allocation":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
if block_allocation:
resource_dict["init_function"] = init_function
return InteractiveExecutor(
Expand All@@ -272,6 +277,7 @@ def create_executor(
elif backend == "local":
check_executor(executor=flux_executor)
check_nested_flux_executor(nested_flux_executor=flux_executor_nesting)
check_flux_log_files(flux_log_files=flux_log_files)
check_gpus_per_worker(gpus_per_worker=resource_dict["gpus_per_core"])
check_command_line_argument_lst(
command_line_argument_lst=resource_dict["slurm_cmd_args"]
Expand Down
9 changes: 9 additions & 0 deletions executorlib/interactive/flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -33,6 +33,7 @@ class FluxPythonSpawner(BaseSpawner):
flux_executor (flux.job.FluxExecutor, optional): The FluxExecutor instance. Defaults to None.
flux_executor_pmi_mode (str, optional): The PMI option. Defaults to None.
flux_executor_nesting (bool, optional): Whether to use nested FluxExecutor. Defaults to False.
flux_log_files (bool, optional): Write flux stdout and stderr files. Defaults to False.
"""

def __init__(
Expand All@@ -45,6 +46,7 @@ def __init__(
flux_executor: Optional[flux.job.FluxExecutor] = None,
flux_executor_pmi_mode: Optional[str] = None,
flux_executor_nesting: bool = False,
flux_log_files: bool = False,
):
super().__init__(
cwd=cwd,
Expand All@@ -56,6 +58,7 @@ def __init__(
self._flux_executor = flux_executor
self._flux_executor_pmi_mode = flux_executor_pmi_mode
self._flux_executor_nesting = flux_executor_nesting
self._flux_log_files = flux_log_files
self._future = None

def bootup(
Expand DownExpand Up@@ -99,6 +102,12 @@ def bootup(
jobspec.setattr_shell_option("pmi", self._flux_executor_pmi_mode)
if self._cwd is not None:
jobspec.cwd = self._cwd
if self._flux_log_files and self._cwd is not None:
jobspec.stderr = os.path.join(self._cwd, "flux.err")
jobspec.stdout = os.path.join(self._cwd, "flux.out")
elif self._flux_log_files:
jobspec.stderr = os.path.abspath("flux.err")
jobspec.stdout = os.path.abspath("flux.out")
self._future = self._flux_executor.submit(jobspec)

def shutdown(self, wait: bool = True):
Expand Down
10 changes: 10 additions & 0 deletions executorlib/standalone/inputcheck.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -147,6 +147,16 @@ def check_flux_executor_pmi_mode(flux_executor_pmi_mode: Optional[str]) -> None:
)


def check_flux_log_files(flux_log_files: Optional[bool]) -> None:
"""
Check if flux_log_files is True and raise a ValueError if it is.
"""
if flux_log_files:
raise ValueError(
"The flux_log_files parameter is only supported for the flux framework backend."
)


def check_pysqa_config_directory(pysqa_config_directory: Optional[str]) -> None:
"""
Check if pysqa_config_directory is None and raise a ValueError if it is not.
Expand Down
44 changes: 44 additions & 0 deletions tests/test_executor_backend_flux.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -100,6 +100,50 @@ def test_single_task(self):
[[(1, 2, 0), (1, 2, 1)], [(2, 2, 0), (2, 2, 1)], [(3, 2, 0), (3, 2, 1)]],
)

def test_output_files_cwd(self):
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
os.makedirs(dirname, exist_ok=True)
file_stdout = os.path.join(dirname, "flux.out")
file_stderr = os.path.join(dirname, "flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1, "cwd": dirname},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_output_files_abs(self):
file_stdout = os.path.abspath("flux.out")
file_stderr = os.path.abspath("flux.err")
with Executor(
max_cores=1,
resource_dict={"cores": 1},
flux_executor=self.executor,
backend="flux_allocation",
block_allocation=True,
flux_log_files=True,
) as p:
output = p.map(calc, [1, 2, 3])
self.assertEqual(
list(output),
[1, 2, 3],
)
self.assertTrue(os.path.exists(file_stdout))
self.assertTrue(os.path.exists(file_stderr))
os.remove(file_stdout)
os.remove(file_stderr)

def test_internal_memory(self):
with Executor(
max_cores=1,
Expand Down
5 changes: 5 additions & 0 deletions tests/test_shared_input_check.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -7,6 +7,7 @@
check_executor,
check_init_function,
check_nested_flux_executor,
check_flux_log_files,
check_pmi,
check_plot_dependency_graph,
check_refresh_rate,
Expand DownExpand Up@@ -67,6 +68,10 @@ def test_check_nested_flux_executor(self):
with self.assertRaises(ValueError):
check_nested_flux_executor(nested_flux_executor=True)

def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
Comment on lines +71 to +73

@coderabbitaicoderabbitaiBotDec 13, 2024

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🛠️ Refactor suggestion

Enhance test coverage with additional test cases.

The current test only verifies that flux_log_files=True raises a ValueError. Consider adding test cases for:

  • flux_log_files=False (valid case)
  • Non-boolean values (invalid case)
 def test_check_flux_log_files(self):
with self.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
+ # Valid case should not raise+ check_flux_log_files(flux_log_files=False)+ # Non-boolean values should raise+ with self.assertRaises(TypeError):+ check_flux_log_files(flux_log_files="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
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
deftest_check_flux_log_files(self):
withself.assertRaises(ValueError):
check_flux_log_files(flux_log_files=True)
# Valid case should not raise
check_flux_log_files(flux_log_files=False)
# Non-boolean values should raise
withself.assertRaises(TypeError):
check_flux_log_files(flux_log_files="True")


def test_check_plot_dependency_graph(self):
with self.assertRaises(ValueError):
check_plot_dependency_graph(plot_dependency_graph=True)
Expand Down