Skip to content

preload PyPI nvidia-*-cu12 libs so _core.so resolves cuBLAS symbols#267

Merged
jameslehoux merged 1 commit intomasterfrom
claude/upbeat-mccarthy-f1mNN
Apr 30, 2026
Merged

preload PyPI nvidia-*-cu12 libs so _core.so resolves cuBLAS symbols#267
jameslehoux merged 1 commit intomasterfrom
claude/upbeat-mccarthy-f1mNN

Conversation

@jameslehoux
Copy link
Copy Markdown

Reported on Colab from a fresh pip install openimpala-cuda:

ImportError: .../openimpala/_core.cpython-312-...so:
  undefined symbol: cublasSetStream_v2

The openimpala-cuda wheel auditwheel-excludes libcublas.so.12 (and libcudart, libcusparse, libcurand, libnvJitLink) to fit under PyPI's 320 MiB cap, then declares the matching nvidia-*-cu12 packages as runtime deps. Those PyPI wheels install their .so's under site-packages/nvidia/<component>/lib/, which the dynamic linker does NOT search by default — so when Python tries to load _core.so, ld.so can't find libcublas.so.12 and the cuBLAS symbols stay unresolved.

Fix mirrors what PyTorch, CuPy, and JAX all do: at the top of openimpala/init.py, ctypes.CDLL each lib with RTLD_GLOBAL so its symbols join the global namespace before any compiled extension import. Try the bare soname first (so HPC nodes with system CUDA on LD_LIBRARY_PATH win) and fall back to the PyPI bundled path if not found.

Load order matters:

  • libcudart.so.12 first (most CUDA libs depend on it)
  • libnvJitLink.so.12
  • libcublasLt.so.12 BEFORE libcublas.so.12 (cublas links against cublasLt at the symbol level)
  • libcusparse.so.12, libcurand.so.10

No-op on the pure-Python wheel (the nvidia/ site-packages dir doesn't exist) and on non-Linux platforms (sys.platform check).

Reported on Colab from a fresh `pip install openimpala-cuda`:

    ImportError: .../openimpala/_core.cpython-312-...so:
      undefined symbol: cublasSetStream_v2

The openimpala-cuda wheel auditwheel-excludes libcublas.so.12 (and
libcudart, libcusparse, libcurand, libnvJitLink) to fit under PyPI's
320 MiB cap, then declares the matching nvidia-*-cu12 packages as
runtime deps. Those PyPI wheels install their .so's under
``site-packages/nvidia/<component>/lib/``, which the dynamic linker
does NOT search by default — so when Python tries to load _core.so,
ld.so can't find libcublas.so.12 and the cuBLAS symbols stay
unresolved.

Fix mirrors what PyTorch, CuPy, and JAX all do: at the top of
openimpala/__init__.py, ctypes.CDLL each lib with RTLD_GLOBAL so its
symbols join the global namespace before any compiled extension
import. Try the bare soname first (so HPC nodes with system CUDA on
LD_LIBRARY_PATH win) and fall back to the PyPI bundled path if not
found.

Load order matters:
- libcudart.so.12 first (most CUDA libs depend on it)
- libnvJitLink.so.12
- libcublasLt.so.12 BEFORE libcublas.so.12 (cublas links against
  cublasLt at the symbol level)
- libcusparse.so.12, libcurand.so.10

No-op on the pure-Python wheel (the nvidia/ site-packages dir doesn't
exist) and on non-Linux platforms (sys.platform check).

https://claude.ai/code/session_011dJ5Bwq4Tnr8wxH597XJFf
@jameslehoux jameslehoux merged commit bcf82b2 into master Apr 30, 2026
6 checks passed
@github-actions
Copy link
Copy Markdown

Performance Benchmark Results

Size Solver Wall Time (s) Tortuosity Expected Rel. Error Iters Status
64³ pcg 0.6116 0.984375 0.984375 0.00e+00 1 PASS
64³ flexgmres 0.3812 0.984375 0.984375 0.00e+00 N/A PASS
64³ bicgstab 0.3723 0.984375 0.984375 0.00e+00 N/A PASS
64³ gmres 0.3737 0.984375 0.984375 0.00e+00 N/A PASS
128³ pcg 7.2852 0.992188 0.992188 0.00e+00 1 PASS
128³ flexgmres 5.1587 0.992188 0.992188 0.00e+00 N/A PASS
128³ bicgstab 5.0971 0.992188 0.992188 0.00e+00 N/A PASS
128³ gmres 5.1276 0.992188 0.992188 0.00e+00 N/A PASS

Fastest solver: bicgstab at 64³ (0.3723s)

Benchmark: uniform block (analytical τ = (N-1)/N)

@github-actions
Copy link
Copy Markdown

Code Coverage Report

------------------------------------------------------------------------------
                           GCC Code Coverage Report
Directory: .
------------------------------------------------------------------------------
File                                       Lines     Exec  Cover   Missing
------------------------------------------------------------------------------
src/io/CathodeWrite.cpp                       95       83    87%   40-41,97-100,115-116,182-185
src/io/CathodeWrite.H                          1        1   100%
src/io/DatReader.cpp                         135      105    77%   26-27,30,35,92-93,99-100,107-109,135-137,141,144-148,152-155,162,164,208-209,242,245
src/io/DatReader.H                             1        1   100%
src/io/HDF5Reader.cpp                        344       84    24%   40-41,43-44,46-49,52,54-56,58-59,62,64-66,68-74,92-93,126-128,144-145,154-157,174-180,182-187,204,213-215,217,219-228,230-233,236-238,240-251,253-258,266,266,266,266,266,266,266,270,270,270,270,270,270,270,274,276,278,280,282,288,290,297,297,297,297,297,297,297,301,301,301,301,301,301,301,305,305,305,305,305,305,305-306,306,306,306,306,306,306,309,309,309,309,309,309,309-310,310,310,310,310,310,310-311,311,311,311,311,311,311,313,313,313,313,313,313,313-314,314,314,314,314,314,314-315,315,315,315,315,315,315,319,319,319,319,319,319,319,324,324,324,324,324,324,324-325,325,325,325,325,325,325-326,326,326,326,326,326,326-327,327,327,327,327,327,327,332,332,332,332,332,332,332,337,337,337,337,337,337,337-338,338,338,338,338,338,338,343,343,343,343,343,343,343,350,350,350,350,350,350,350,357-358,432-435,437-440
src/io/HDF5Reader.H                            3        3   100%
src/io/ImageLoader.cpp                        61       42    68%   25,38,48,60-62,64-70,72,77,89-90,92,94
src/io/RawReader.cpp                         266      135    50%   49-50,89-90,111-112,115-117,120-121,140-142,155-157,166-168,174-177,185-186,192-196,200-204,209-212,219-224,231-237,271,273-274,276,283-284,301,312,314,318,325,327,331-334,338,346-347,353-355,361-363,365-366,369,372,374,377-380,382-384,386,388-389,391,393-394,396,398-399,401,403-404,406,410-411,413,417-418,420,425,465,471-472,521-524,538,540-542,544,546-548,558,562-564,566,588
src/io/RawReader.H                             1        1   100%
src/io/TiffReader.cpp                        384      130    33%   59-65,67-69,71-73,75-77,79-80,82-84,86-88,90-92,94-96,98-99,101-103,106-108,111-112,114-117,119,122,124-127,143-144,148-150,152-158,160,186,210,217,226,228-231,240,242-245,248,255,288-293,306,309-317,319-320,323-327,331-335,338-342,344-348,351-357,359-363,367,369,375-377,379-393,396,398-402,404-409,413-418,420-425,428-429,432-434,555-575,577-578,581-588,590,593-609,612-614,670,673-674,677-683,685,689-700,702-703
src/io/TiffReader.H                            5        5   100%
src/props/BoundaryCondition.H                131       74    56%   63,68,70,216,224-229,233-236,238-244,247-249,252-253,255,258-261,264-265,271-272,274-279,285-287,290-296,299,303,365-366,371,373
src/props/ConnectedComponents.cpp             69       67    97%   94-95
src/props/ConnectedComponents.H                4        4   100%
src/props/DeffTensor.cpp                      62       59    95%   122,128-129
src/props/Diffusion.cpp                      510      378    74%   93-94,97-98,103-104,106-116,118,123-132,134-141,144-150,153-157,159-163,165,168-173,175-177,179,182-184,186-187,190-191,193,195-198,200,202-203,288-289,297-298,300,349,359-360,368-371,373-375,404-413,415,453,461,465-467,526-527,533,535,539,547,581,610,638,646,735-736,739-740,757-760,771-772,774,824
src/props/EffDiffFillMtx.H                   120      106    88%   58,216-217,221-225,229,231-235
src/props/EffectiveDiffusivityHypre.cpp      389      347    89%   189-191,193-197,305,367-370,479,612-615,617-619,621-624,633-636,643,672,684-687,689-691,693,705,716,718
src/props/EffectiveDiffusivityHypre.H          7        7   100%
src/props/FloodFill.cpp                       84       81    96%   94-95,203
src/props/HypreStructSolver.cpp              343      210    61%   87-88,121,133-134,145,299,309,311,314,346,356,358,361,367-370,372-376,378-379,381-385,388-389,391-392,394,397-398,401-402,404-407,409-413,415-416,418-422,425-426,428-429,431,434-435,438-439,441-443,445-451,453-457,460-461,463-464,466,469-470,473,475-477,479-485,487-491,494-495,497-498,500,503-504,507,509-511,513-516,518-522,525-526,528-529,531,534-535,538,541-542,555
src/props/HypreStructSolver.H                  6        6   100%
src/props/MacroGeometry.H                     17       17   100%
src/props/ParticleSizeDistribution.cpp        11       11   100%
src/props/ParticleSizeDistribution.H           6        6   100%
src/props/PercolationCheck.cpp                53       46    86%   32-33,49-51,68,73
src/props/PercolationCheck.H                   4        4   100%
src/props/PhysicsConfig.H                     90       89    98%   150
src/props/ResultsJSON.H                      225      222    98%   242,395,416
src/props/REVStudy.cpp                       151      128    84%   72,83-91,159,170-173,175,183-186,188-190
src/props/SolverConfig.H                      32       20    62%   30,32,37-44,75-76
src/props/SpecificSurfaceArea.cpp             56       55    98%   59
src/props/SpecificSurfaceArea.H                6        6   100%
src/props/ThroughThicknessProfile.cpp         38       38   100%
src/props/ThroughThicknessProfile.H            5        5   100%
src/props/Tortuosity.H                         2        2   100%
src/props/TortuosityDirect.cpp               219      191    87%   81-83,86,100-106,113-114,125,134,140,202-209,226,394,424,433
src/props/TortuosityDirect.H                   5        5   100%
src/props/TortuosityHypre.cpp                784      563    71%   149-150,155-156,240-243,246-248,311,335-337,340-341,343,353-355,358-360,390-393,573,597,601,622,639-640,642-644,646-655,657,660-664,668-670,673-680,682-686,690-692,694-696,698-707,709-713,715-726,728-731,733,743,749-752,754-756,765-768,770-772,788,791-792,815-820,831-834,836,873,878-881,884-886,890-893,895,897-900,902,907-909,911,960,969,974,977-982,998-1001,1015-1019,1024-1029,1039-1043,1048-1053,1058-1062,1065-1068,1075-1078,1089,1098,1100,1104,1106,1128,1159-1160,1246-1248,1374-1377
src/props/TortuosityHypre.H                   15       15   100%
src/props/TortuosityHypreFill.H              127       98    77%   85,203,205-212,237-239,241-245,247-248,250,252,255-256,258-262
src/props/TortuosityKernels.H                 97       53    54%   52,56-60,62-65,69-74,76-80,84-85,90,129,143,157,243,245-248,250-253,257-260,262-265
src/props/TortuosityMLMG.cpp                  99       91    91%   160,181-183,185-186,193,206
src/props/TortuosityMLMG.H                     1        1   100%
src/props/TortuositySolverBase.cpp           301      237    78%   70-72,74-75,94-101,104,106,142-145,200,203,205,255,280,298,327,391,394-396,398,406-409,411-417,422,427-429,435-436,438-440,454,460,464-465,467,478,492,496-498,500,502,506
src/props/TortuositySolverBase.H              13       13   100%
src/props/VolumeFraction.cpp                  25       25   100%
src/props/VolumeFraction.H                     4        4   100%
------------------------------------------------------------------------------
TOTAL                                       5407     3874    71%
------------------------------------------------------------------------------


Generated by CI — coverage data from gcovr

@codecov
Copy link
Copy Markdown

codecov Bot commented Apr 30, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.

📢 Thoughts on this report? Let us know!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant