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[Bug] Python: OOM-kill when trying to fetch obsm_layers #3064

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ivirshup opened this issue Sep 24, 2024 · 3 comments
Closed

[Bug] Python: OOM-kill when trying to fetch obsm_layers #3064

ivirshup opened this issue Sep 24, 2024 · 3 comments
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@johnkerl @nguyenv

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@ivirshup
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ivirshup commented Sep 24, 2024 •
edited by johnkerl
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Describe the bug

The code in the example below dies with Killed on tiledbsoma 1.14.1, but not on tiledbsoma 1.13

To Reproduce

import tiledbsoma
import cellxgene_census

census = cellxgene_census.open_soma(census_version="2023-12-15")
soma = census["census_data"]["homo_sapiens"]
(
    soma
    .axis_query(
        measurement_name="RNA",
        obs_query=tiledbsoma.AxisQuery(coords=(slice(100),)),
    )
    .to_anndata(
        X_name="raw",
        obsm_layers=["scvi"],
    )
)

You can see more examples on the cellxgene_census CI

Versions (please complete the following information):

  • TileDB-SOMA version: 1.14.1
  • Language and language version (e.g. Python 3.8, R 4.2.2): python 3.11
  • OS (e.g. MacOS, Ubuntu Linux):
  • Note: you can use tiledbsoma.show_package_versions() (Python) or tiledbsoma::show_package_versions() (R)
tiledbsoma.__version__              1.14.1
TileDB core version (libtiledbsoma) 2.26.1
python version                      3.11.9.final.0
OS version                          Linux 6.8.0-1016-aws

Additional context

Upstream of: chanzuckerberg/cellxgene-census#1288
@johnkerl johnkerl self-assigned this Sep 24, 2024
@johnkerl johnkerl changed the title [Bug] python, segfault occurs when trying to fetch obsm_layers [Bug] Python: segfault when trying to fetch obsm_layers Sep 24, 2024
@johnkerl johnkerl changed the title [Bug] Python: segfault when trying to fetch obsm_layers [Bug] Python: apparent OOM-kill when trying to fetch obsm_layers Sep 25, 2024
@johnkerl
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@nguyenv running @ivirshup 's repro with

export SPDLOG_LEVEL=tiledbsoma=trace

I have

...
[2024-09-25 00:44:07.047] [tiledbsoma] [Process: 68934] [Thread: 69912] [debug] [ManagedQuery] submit thread start
[2024-09-25 00:44:09.902] [Process: 68934] [debug] [1727224968354718411-Context: 1] [Query: 10] Done processing tiles
[2024-09-25 00:44:09.903] [Process: 68934] [debug] [1727224968354718411-Context: 1] [Query: 10] Done with iteration, num result tiles 0
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69912] [debug] [ManagedQuery] submit thread done
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ManagedQuery] [scvi] Done waiting for query
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ManagedQuery] [scvi] Buffer soma_dim_0 cells=134217728
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ManagedQuery] [scvi] Buffer soma_dim_1 cells=134217728
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ManagedQuery] [scvi] Buffer soma_data cells=134217728
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] column type l name soma_dim_0 nbuf 2 2 nullable false
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] create array name='soma_dim_0' use_count=4
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ArrowAdapter] release_schema for soma_dim_0
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] release_schema schema->name
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] release_schema schema->format
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] release_schema done
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] column type l name soma_dim_1 nbuf 2 2 nullable false
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] create array name='soma_dim_1' use_count=4
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ArrowAdapter] release_schema for soma_dim_1
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] release_schema schema->name
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] release_schema schema->format
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] release_schema done
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] column type f name soma_data nbuf 2 2 nullable false
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] create array name='soma_data' use_count=4
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ArrowAdapter] release_schema for soma_data
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] release_schema schema->name
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] release_schema schema->format
[2024-09-25 00:44:09.903] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ArrowAdapter] release_schema done
[2024-09-25 00:44:09.904] [tiledbsoma] [Process: 68934] [Thread: 69528] [trace] [ManagedQuery] allocate new buffers
[2024-09-25 00:44:09.904] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ManagedQuery] [scvi] Adding buffer for column 'soma_dim_0'
[2024-09-25 00:44:09.904] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ColumnBuffer] 'soma_dim_0' 1073741824 bytes is_var=false is_nullable=false
[2024-09-25 00:44:09.904] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ManagedQuery] [scvi] Adding buffer for column 'soma_dim_1'
[2024-09-25 00:44:09.904] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ColumnBuffer] 'soma_dim_1' 1073741824 bytes is_var=false is_nullable=false
[2024-09-25 00:44:09.904] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ManagedQuery] [scvi] Adding buffer for column 'soma_data'
[2024-09-25 00:44:09.904] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ColumnBuffer] 'soma_data' 1073741824 bytes is_var=false is_nullable=false
[2024-09-25 00:44:09.904] [tiledbsoma] [Process: 68934] [Thread: 69528] [debug] [ManagedQuery] [scvi] Waiting for query
[2024-09-25 00:44:09.904] [tiledbsoma] [Process: 68934] [Thread: 69913] [debug] [ManagedQuery] submit thread start
Killed

@johnkerl
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@nguyenv this is as far as I got debugging:

  • Repro with Python 3.11
  • MacOS or Linux
  • 16GB RAM; 64GB RAM

I'm guessing either a memory leak or a pagination miswiring ...

@aaronwolen aaronwolen mentioned this issue Sep 25, 2024
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@johnkerl johnkerl mentioned this issue Sep 25, 2024
Merged
@johnkerl johnkerl changed the title [Bug] Python: apparent OOM-kill when trying to fetch obsm_layers [Bug] Python: OOM-kill when trying to fetch obsm_layers Sep 26, 2024
@johnkerl johnkerl mentioned this issue Sep 26, 2024
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@johnkerl
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Fixed in https://github.com/single-cell-data/TileDB-SOMA/releases/tag/1.14.2

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