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@cyrush cyrush commented Dec 8, 2025

Resolves #1472

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cyrush commented Dec 9, 2025

Here are the new sanitizer issues with hdf5 2.0

 =================================================================
==23747==ERROR: LeakSanitizer: detected memory leaks

Direct leak of 96 byte(s) in 4 object(s) allocated from:
    #0 0x55ca5a162b83 in malloc (/home/runner/work/conduit/conduit/build/tests/relay/t_relay_io_hdf5+0xebb83) (BuildId: a10ba7912d38776f3ab781a22b378308bc078595)
    #1 0x7f98b9a60582 in H5FL__malloc /home/runner/work/conduit/conduit/tpls/source/hdf5-2.0.0/src/H5FL.c:211:30
    #2 0x7f98b9a60582 in H5FL_reg_malloc /home/runner/work/conduit/conduit/tpls/source/hdf5-2.0.0/src/H5FL.c:363:34
    #3 0x7f98ba09db44 in H5VL_object_get /home/runner/work/conduit/conduit/tpls/source/hdf5-2.0.0/src/H5VLcallback.c:6082:9

Direct leak of 24 byte(s) in 1 object(s) allocated from:
    #0 0x55ca5a162b83 in malloc (/home/runner/work/conduit/conduit/build/tests/relay/t_relay_io_hdf5+0xebb83) (BuildId: a10ba7912d38776f3ab781a22b378308bc078595)
    #1 0x7f98b9a60582 in H5FL__malloc /home/runner/work/conduit/conduit/tpls/source/hdf5-2.0.0/src/H5FL.c:211:30
    #2 0x7f98b9a60582 in H5FL_reg_malloc /home/runner/work/conduit/conduit/tpls/source/hdf5-2.0.0/src/H5FL.c:363:34
    #3 0x7f98ba0a13a5 in H5VL_introspect_opt_query /home/runner/work/conduit/conduit/tpls/source/hdf5-2.0.0/src/H5VLcallback.c:6655:9

Both of these api calls are part of the H5VL (vol layer) private api

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cyrush commented Dec 9, 2025

This error case:
https://github.com/LLNL/conduit/blob/1254ec2c7b5666247ee09c80f0f778beccd3045a/src/tests/relay/t_relay_io_hdf5.cpp#L551

yields:

HDF5-DIAG: Error detected in HDF5 (2.0.0):
  #000: /home/user/conduit/tpls/source/hdf5-2.0.0/src/H5I.c line 856 in H5Iget_name(): invalid identifier
    major: Object ID
    minor: Inappropriate type
  #001: /home/user/conduit/tpls/source/hdf5-2.0.0/src/H5VLint.c line 1742 in H5VL_vol_object(): can't retrieve object for ID
    major: Virtual Object Layer
    minor: Can't get value
  #002: /home/user/conduit/tpls/source/hdf5-2.0.0/src/H5VLint.c line 1778 in H5VL_vol_object_verify(): not a named datatype
    major: Invalid arguments to routine
    minor: Inappropriate type

_unnamed_0: 
  valid: "true"
  ref_count: 1
  id: 216172782113783930
  type: "datatype"

The error is caught in the next test run.

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cyrush commented Dec 11, 2025

-- Generating done (0.3s)
CMake Warning:
  Manually-specified variables were not used by the project:

    HDF5_ENABLE_Z_LIB_SUPPORT

I found you have to use:

-DHDF5_ENABLE_ZLIB_SUPPORT:BOOL=ON

Setting w/o the type is not sufficient!

-DHDF5_ENABLE_ZLIB_SUPPORT=ON

Wait! It was Z_LIB vs ZLIB

https://github.com/spack/spack-packages/blob/38a07b75e99ab1817fbaa13fd3c4848eabe12e43/repos/spack_repo/builtin/packages/hdf5/package.py#L565

@cyrush cyrush mentioned this pull request Dec 11, 2025
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@JustinPrivitera
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Resolves #1472

@cyrush cyrush merged commit 8ef9e1a into develop Dec 19, 2025
27 of 28 checks passed
@cyrush cyrush deleted the task/2025_12_silo_update branch December 19, 2025 17:16
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Upgrade to Silo 4.12 when it is released

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