HDF5 library version mismatched error

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最新推荐文章于 2025-07-14 17:41:07 发布

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本文链接：https://blog.youkuaiyun.com/qq_23944915/article/details/95937725

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博客指出运行时出现HDF5库版本不匹配错误，编译应用的HDF5头文件版本与链接的库版本不一致，可能导致数据损坏或段错误。给出了重新编译应用、检查共享库设置等解决建议，还提及可通过设置环境变量禁用警告。

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[ RUN ] RMSPropSolverTest/1.TestLeastSquaresUpdateWithEverythingAccum
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.17, library is 1.10.4
SUMMARY OF THE HDF5 CONFIGURATION
=================================

General Information:
-------------------
HDF5 Version: 1.10.4
Configured on: Wed Dec 19 18:26:52 UTC 2018
Configured by: root@3dad7c19-81ba-4672-4f33-547177f88490
Host system: x86_64-conda_cos6-linux-gnu
Uname information: Linux 3dad7c19-81ba-4672-4f33-547177f88490 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /home/lsz/anaconda2

Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high

Linking Options:
----------------
Libraries: static, shared
Statically Linked Executables:
LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/home/lsz/anaconda2/lib -L/home/lsz/anaconda2/lib
H5_LDFLAGS:
AM_LDFLAGS: -L/home/lsz/anaconda2/lib
Extra libraries: -lrt -lpthread -lz -ldl -lm
Archiver: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar
AR_FLAGS: cr
Ranlib: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib

Languages:
----------
C: yes
C Compiler: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/home/lsz/anaconda2/include
C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/home/lsz/anaconda2/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
H5 C Flags: -std=c99 -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -finline-functions -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -O
AM C Flags:
Shared C Library: yes
Static C Library: yes

Fortran: yes
Fortran Compiler: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran
Fortran Flags:
H5 Fortran Flags: -pedantic -Wall -Wextra -Wunderflow -Wimplicit-interface -Wsurprising -Wno-c-binding-type -s -O2
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes

C++: yes
C++ Compiler: /tmp/build/80754af9/hdf5_1545243905949/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++
C++ Flags: -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/home/lsz/anaconda2/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
H5 C++ Flags: -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -finline-functions -s -O
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: yes

Java: no

Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Threadsafety: yes
Default API mapping: v110
With deprecated public symbols: yes
I/O filters (external): deflate(zlib)
MPE: no
Direct VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: yes
Memory allocation sanity checks: no
Metadata trace file: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
Bye...
*** Aborted at 1563133170 (unix time) try "date -d @1563133170" if you are using GNU date ***
PC: @ 0x7f48f3f59428 gsignal
*** SIGABRT (@0x7562) received by PID 30050 (TID 0x7f48cc8f5240) from PID 30050; stack trace: ***
@ 0x7f48f9db9390 (unknown)
@ 0x7f48f3f59428 gsignal
@ 0x7f48f3f5b02a abort
@ 0x7f48f9827f4c (unknown)
@ 0x7f48fa82bd63 caffe::HDF5DataLayer<>::LoadHDF5FileData()
@ 0x7f48fa826166 caffe::HDF5DataLayer<>::LayerSetUp()
@ 0x7f48fa7556ff caffe::Net<>::Init()
@ 0x7f48fa756cbe caffe::Net<>::Net()
@ 0x7f48fa7b674a caffe::Solver<>::InitTrainNet()
@ 0x7f48fa7b7d15 caffe::Solver<>::Init()
@ 0x7f48fa7b802f caffe::Solver<>::Solver()
@ 0xa6dcfe caffe::SGDSolver<>::SGDSolver()
@ 0xa6ee1c caffe::RMSPropSolverTest<>::InitSolver()
@ 0xa6ecf0 caffe::GradientBasedSolverTest<>::InitSolverFromProtoString()
@ 0xa2e1a0 caffe::GradientBasedSolverTest<>::RunLeastSquaresSolver()
@ 0xa5915f caffe::GradientBasedSolverTest<>::CheckAccumulation()
@ 0xe66513 testing::internal::HandleExceptionsInMethodIfSupported<>()
@ 0xe5f44a testing::Test::Run()
@ 0xe5f598 testing::TestInfo::Run()
@ 0xe5f6a5 testing::TestCase::Run()
@ 0xe6123f testing::internal::UnitTestImpl::RunAllTests()
@ 0xe61563 testing::UnitTest::Run()
@ 0x8cdd4d main
@ 0x7f48f3f44830 __libc_start_main
@ 0x8d5289 _start
@ 0x0 (unknown)
Aborted (core dumped)
src/caffe/test/CMakeFiles/runtest.dir/build.make:57: recipe for target 'src/caffe/test/CMakeFiles/runtest' failed
make[3]: *** [src/caffe/test/CMakeFiles/runtest] Error 134
CMakeFiles/Makefile2:360: recipe for target 'src/caffe/test/CMakeFiles/runtest.dir/all' failed
make[2]: *** [src/caffe/test/CMakeFiles/runtest.dir/all] Error 2
CMakeFiles/Makefile2:367: recipe for target 'src/caffe/test/CMakeFiles/runtest.dir/rule' failed
make[1]: *** [src/caffe/test/CMakeFiles/runtest.dir/rule] Error 2
Makefile:253: recipe for target 'runtest' failed
make: *** [runtest] Error 2
(base) lsz@RQ-Lab-DL-pc:~/Downloads/caffe-master-ori/build$ conda install -c anaconda hdf5=1.88.17
WARNING: The conda.compat module is deprecated and will be removed in a future release.
Collecting package metadata: / failed