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Fix leiden hanging when insufficient shared memory is available. #989

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Merged
merged 2 commits into from
Mar 28, 2025
Merged

Fix leiden hanging when insufficient shared memory is available. #989

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df54636
Fix leiden hanging when insufficient shared memory
DriesSchaumont Mar 25, 2025
66a9d3b
Undo container image change
DriesSchaumont Mar 25, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,8 @@

# BUG FIXES

* `cluster/leiden`: Fix an issue where insufficient shared memory (size of `/dev/shm`) causes the processing to hang.

* `utils/subset_vars`: Convert .var column used for subsetting of dtype "boolean" to dtype "bool" when it doesn't contain NaN values (PR #959).

* `resources_test_scripts/annotation_test_data.sh`: Add a layer to the annotation reference dataset with log normalized counts (PR #960).
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16 changes: 15 additions & 1 deletion src/cluster/leiden/script.py
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Expand Up @@ -45,7 +45,7 @@
"uns_name": "leiden",
"output_compression": "gzip",
}
meta = {"cpus": 8, "resources_dir": "."}
meta = {"cpus": 8, "resources_dir": "src/utils"}
## VIASH END

sys.path.append(meta["resources_dir"])
Expand All @@ -55,6 +55,13 @@
_shared_logger_name = "leiden"


# Function to check available space in /dev/shm
def get_available_shared_memory():
shm_path = "/dev/shm"
shm_stats = os.statvfs(shm_path)
return shm_stats.f_bsize * shm_stats.f_bavail


class SharedNumpyMatrix:
def __init__(
self,
Expand All @@ -70,6 +77,13 @@ def __init__(
def from_numpy(
cls, memory_manager: managers.SharedMemoryManager, array: npt.ArrayLike
):
available_shared_memory = get_available_shared_memory()
n_bytes_required = array.nbytes
if available_shared_memory < n_bytes_required:
raise ValueError(
"Not enough shared memory (/dev/shm) is available to load the data. "
f"Required amount: {n_bytes_required}, available: {available_shared_memory}."
)
shm = memory_manager.SharedMemory(size=array.nbytes)
array_in_shared_memory = np.ndarray(
array.shape, dtype=array.dtype, buffer=shm.buf
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