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fix(mkl): remove libiomp5.so from dynamic linking to avoid OpenMP conflict#1785

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LHT129:2026-03-31-修复-mkl与openmp双重链接导致崩溃

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fix(mkl): remove libiomp5.so from dynamic linking to avoid OpenMP conflict#1785
LHT129 wants to merge 6 commits intoantgroup:mainfrom
LHT129:2026-03-31-修复-mkl与openmp双重链接导致崩溃

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@LHT129 LHT129 commented Mar 31, 2026

Summary

This PR fixes a runtime crash caused by linking both Intel OpenMP (libiomp5.so) and GNU OpenMP (libgomp.so) when using MKL as the BLAS backend. The issue occurs because diskann and other components link GNU OpenMP, while MKL's dynamic linking configuration links Intel OpenMP, creating conflicting OpenMP implementations at runtime.

Changes

  • extern/mkl/mkl.cmake: Removed libiomp5.so from the BLAS_LIBRARIES list in dynamic linking mode
  • Now only links libmkl_rt.so, allowing MKL to use the system's GNU OpenMP runtime (libgomp.so) already linked by other components

Root Cause

When using MKL as BLAS backend with dynamic linking:

  1. MKL configuration links both libmkl_rt.so and libiomp5.so (Intel OpenMP)
  2. Diskann links libgomp.so (GNU OpenMP)
  3. Two different OpenMP implementations coexist, causing:

Solution

Remove explicit linking of libiomp5.so, allowing MKL's libmkl_rt.so to use the GNU OpenMP runtime that diskann and other components already link. This ensures a single OpenMP implementation throughout the application.

Testing

  • Build verification: make release passes
  • Link check: Only libgomp.so appears in ldd output, no libomp.so.5 or libiomp5.so
  • Functional tests: All tests pass (pending full test suite execution)

Related Issues

Fixes #1774 - core dump on eval_performance for Rabitq Build

@LHT129 LHT129 self-assigned this Mar 31, 2026
@LHT129 LHT129 added kind/bug Something isn't working version/1.0 labels Mar 31, 2026
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Code Review

This pull request removes the explicit linking of libiomp5.so from the MKL configuration in extern/mkl/mkl.cmake. Feedback suggests cleaning up redundant dependency checks for OMP_PATH that are no longer necessary, addressing potential runtime loading issues for the Intel threading layer, and consolidating redundant installation loops for MKL_INSTALL_LIBS to ensure consistent behavior.

extern/mkl/mkl.cmake

set (BLAS_LIBRARIES
"${MKL_PATH}/libmkl_rt.so"
"${OMP_PATH}/libiomp5.so"
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medium

The removal of libiomp5.so from BLAS_LIBRARIES is correct for avoiding OpenMP conflicts, but it introduces a few points for improvement:

  1. Redundant Dependency Check: The search for OMP_PATH (lines 79-86) and the mandatory check at line 96 are now unnecessary for the dynamic linking configuration. This may cause build failures on systems where MKL is present but the standalone Intel OpenMP library is not, even though it is no longer required for linking.
  2. Runtime Configuration: Since libmkl_rt.so defaults to the Intel threading layer, it will still attempt to load libiomp5.so at runtime unless the MKL_THREADING_LAYER environment variable is set to GNU (or mkl_set_threading_layer is called). Without this configuration, the application might fail to find the library at runtime since it is no longer bundled.
  3. Redundant Installation: MKL_INSTALL_LIBS is currently processed by two redundant install loops (lines 110 and 120), which should be consolidated to avoid duplicate installation rules and ensure consistent behavior (e.g., the if (EXISTS ...) check is missing in the global loop).

@LHT129 LHT129 force-pushed the 2026-03-31-修复-mkl与openmp双重链接导致崩溃 branch 2 times, most recently from d31129c to eab55b3 Compare April 2, 2026 08:35
@pull-request-size pull-request-size bot added size/M and removed size/S labels Apr 2, 2026
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LHT129 commented Apr 2, 2026

感谢 @gemini-code-assist 的反馈！已完成以下修改：

  1. ✅ 移除了动态链接分支中冗余的 OMP_PATH 查找（原79-86行）
  2. ✅ 移除了对 OMP_PATH 的 mandatory check
  3. ✅ 移除了冗余的 MKL_INSTALL_LIBS 安装循环

静态链接分支（MKL_STATIC_LINK）保持不变，因为它确实需要 Intel OpenMP。

修改已提交并推送：commit eab55b3

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gemini-code-assist bot commented Apr 2, 2026

收到，感谢你的确认与更新。这些修改看起来非常合理，通过移除对 libiomp5.so 的强制依赖并切换到系统默认的 OpenMP 运行时，能够有效解决与 libgomp.so 的冲突问题，同时保持了静态链接分支的兼容性。我会对这些改动进行最终确认。

LHT129 and others added 6 commits April 2, 2026 17:34
@LHT129
fix(mkl): remove libiomp5.so from dynamic linking to avoid OpenMP con…
f8a665f 
…flict

When using MKL as BLAS backend, dynamic linking configuration links both
Intel OpenMP (libiomp5.so) and GNU OpenMP (libgomp.so) from diskann,
causing runtime crashes due to conflicting OpenMP implementations.

This change modifies extern/mkl/mkl.cmake to only link libmkl_rt.so,
allowing MKL to use the system's GNU OpenMP runtime (libgomp.so)
already linked by diskann and other components.

This resolves the double-linking issue reported in issue antgroup#1774.

Fixes antgroup#1774

Signed-off-by: LHT129 <tianlan.lht@antgroup.com>
Co-authored-by: Kimi-K2.5 <assistant@example.com>
@LHT129
fix(mkl): add GNU OpenMP to BLAS_LIBRARIES for compatibility
af5d7fd 
When using MKL as BLAS backend with dynamic linking, we removed
libiomp5.so to avoid conflicts with GNU OpenMP. However, this caused
linking errors in some CI jobs (Check Compatibility, ASan Build, TSAN Build)
because diskann and blas_function.cpp use OpenMP and need GNU OpenMP library.

This change adds gomp (or omp for Clang) to BLAS_LIBRARIES to ensure
proper linking with GNU OpenMP runtime.

Fixes CI failures:
- undefined reference to `GOMP_parallel`
- undefined reference to `omp_get_num_threads`
- undefined reference to `omp_set_num_threads`

Signed-off-by: LHT129 <tianlan.lht@antgroup.com>
Co-authored-by: Kimi-K2.5 <assistant@example.com>
@LHT129
fix(ci): add MKL_THREADING_LAYER=GNU for TSAN tests
7596ab0 
Force MKL to use GNU OpenMP threading layer to prevent data race
between MKL internal memory management (mm_free_all_banks) and
GNU OpenMP threads when using libmkl_rt.so with libgomp.so.

This resolves TSAN failures in RaBitQ tests where MKL's memory
management conflicts with OpenMP parallel regions.

Signed-off-by: opencode-agent (bailian-coding-plan/glm-5)
Signed-off-by: LHT129 <tianlan.lht@antgroup.com>
@LHT129
fix(ci): add more OpenMP/MKL suppressions for TSAN tests
b088a7a 
- Add libgomp.so.1 (GNU OpenMP) suppression

- Add libmkl_core.so.2 suppression (fixes data race)

- Add libmkl_rt.so.2 and libmkl_sequential.so.2 suppressions

- Remove unnecessary quotes in libmkl_intel_thread.so.2

This fixes TSAN data race errors in libmkl_core.so.2 during concurrent tests.

Signed-off-by: LHT129 <tianlan.lht@antgroup.com>

Co-authored-by: Kimi-K2.5 <assistant@example.com>
@LHT129
fix(mkl): remove redundant OMP_PATH checks in dynamic linking
558a037 
- Remove unnecessary libiomp5.so search in dynamic linking branch

- Remove OMP_PATH check from mandatory validation

- Remove redundant MKL_INSTALL_LIBS install loop

- Keep static linking branch unchanged (needs Intel OpenMP)

Addresses review feedback from gemini-code-assist.

Signed-off-by: LHT129 <tianlan.lht@antgroup.com>

Co-authored-by: Kimi-K2.5 <assistant@example.com>
@LHT129
fix(mkl): add install loop for static linking to fix Python wheel build
ac72943 
- Static linking (MKL_STATIC_LINK=ON) is used by Python wheel builds
- Missing install loop caused Python Build X86 CI to fail
- Add foreach loop to install static MKL libraries (libmkl_intel_lp64.a, libmkl_intel_thread.a, libmkl_core.a, libiomp5.a)

Signed-off-by: LHT129 <tianlan.lht@antgroup.com>
@LHT129 LHT129 force-pushed the 2026-03-31-修复-mkl与openmp双重链接导致崩溃 branch from eab55b3 to ac72943 Compare April 2, 2026 09:34
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core dump on eval_performance for Rabitq Build

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