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Add patch to fix arm segfault in nmslib during ingestion #1541

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merged 1 commit into from
Mar 14, 2024
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Add patch to fix arm segfault in nmslib during ingestion #1541

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3 changes: 3 additions & 0 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,9 @@ jobs:
rm ../../patches/faiss/0001-Custom-patch-to-support-multi-vector.patch
git apply --ignore-space-change --ignore-whitespace --3way ../../patches/faiss/0002-Custom-patch-to-support-AVX2-Linux-CI.patch
rm ../../patches/faiss/0002-Custom-patch-to-support-AVX2-Linux-CI.patch
cd ../nmslib
git apply --ignore-space-change --ignore-whitespace --3way ../../patches/nmslib/0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch
rm ../../patches/nmslib/0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch
working-directory: ${{ github.workspace }}

- name: Setup Java ${{ matrix.java }}
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3 changes: 3 additions & 0 deletions .github/workflows/test_security.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,9 @@ jobs:
rm ../../patches/faiss/0001-Custom-patch-to-support-multi-vector.patch
git apply --ignore-space-change --ignore-whitespace --3way ../../patches/faiss/0002-Custom-patch-to-support-AVX2-Linux-CI.patch
rm ../../patches/faiss/0002-Custom-patch-to-support-AVX2-Linux-CI.patch
cd ../nmslib
git apply --ignore-space-change --ignore-whitespace --3way ../../patches/nmslib/0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch
rm ../../patches/nmslib/0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch
working-directory: ${{ github.workspace }}

- name: Setup Java ${{ matrix.java }}
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -21,6 +21,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
### Bug Fixes
* Disable sdc table for HNSWPQ read-only indices [#1518](https://github.com/opensearch-project/k-NN/pull/1518)
* Switch SpaceType.INNERPRODUCT's vector similarity function to MAXIMUM_INNER_PRODUCT [#1532](https://github.com/opensearch-project/k-NN/pull/1532)
* Add patch to fix arm segfault in nmslib during ingestion [#1541](https://github.com/opensearch-project/k-NN/pull/1541)
### Infrastructure
* Manually install zlib for win CI [#1513](https://github.com/opensearch-project/k-NN/pull/1513)
### Documentation
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13 changes: 13 additions & 0 deletions jni/CMakeLists.txt
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Expand Up @@ -87,6 +87,19 @@ if (${CONFIG_NMSLIB} STREQUAL ON OR ${CONFIG_ALL} STREQUAL ON OR ${CONFIG_TEST}
execute_process(COMMAND git submodule update --init -- external/nmslib WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
endif ()

# Check if patch exist, this is to skip git apply during CI build. See CI.yml with ubuntu.
find_path(PATCH_FILE NAMES 0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch PATHS ${CMAKE_CURRENT_SOURCE_DIR}/patches/nmslib NO_DEFAULT_PATH)

# If it exists, apply patches
if (EXISTS ${PATCH_FILE})
message(STATUS "Applying custom patches.")
execute_process(COMMAND git apply --ignore-space-change --ignore-whitespace --3way ${CMAKE_CURRENT_SOURCE_DIR}/patches/nmslib/0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/nmslib ERROR_VARIABLE ERROR_MSG RESULT_VARIABLE RESULT_CODE)

if(RESULT_CODE)
message(FATAL_ERROR "Failed to apply patch:\n${ERROR_MSG}")
endif()
endif()

add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/nmslib/similarity_search)

add_library(${TARGET_LIB_NMSLIB} SHARED ${CMAKE_CURRENT_SOURCE_DIR}/src/org_opensearch_knn_jni_NmslibService.cpp ${CMAKE_CURRENT_SOURCE_DIR}/src/nmslib_wrapper.cpp)
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31 changes: 31 additions & 0 deletions jni/patches/nmslib/0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch
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@@ -0,0 +1,31 @@
From aa1ca485c0ab8b79dae1fb5c1567149c5f61b533 Mon Sep 17 00:00:00 2001
From: John Mazanec <[email protected]>
Date: Thu, 14 Mar 2024 12:22:06 -0700
Subject: [PATCH] Initialize maxlevel during add from enterpoint->level

Signed-off-by: John Mazanec <[email protected]>
---
similarity_search/src/method/hnsw.cc | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/similarity_search/src/method/hnsw.cc b/similarity_search/src/method/hnsw.cc
index 35b372c..e9a725e 100644
--- a/similarity_search/src/method/hnsw.cc
+++ b/similarity_search/src/method/hnsw.cc
@@ -542,8 +542,12 @@ namespace similarity {

NewElement->init(curlevel, maxM_, maxM0_);

- int maxlevelcopy = maxlevel_;
+ // Get the enterpoint at this moment and then use it to set the
+ // max level that is used. Copying maxlevel from this->maxlevel_
+ // can lead to race conditions during concurrent insertion. See:
+ // https://github.com/nmslib/nmslib/issues/544
HnswNode *ep = enterpoint_;
+ int maxlevelcopy = ep->level;
if (curlevel < maxlevelcopy) {
const Object *currObj = ep->getData();

--
2.39.3 (Apple Git-146)

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