我在基于 C++ 的软件中使用 HDF5，该软件是使用 CMake 构建的。
我曾经有两个 HDF5 版本，一个来自 Anaconda 附带的 h5py (1.14.x)，另一个是使用 apt (1.10.x) 安装时附带的。
这种不匹配导致了错误
libhdf5 undefined reference to curl_global_init@CURL_OPENSSL_4现在我重新安装了所有东西，但我什至无法达到以前的状态。
尝试构建时，我收到以下错误：
cmake -B./build/
-- The CXX compiler identification is GNU 11.4.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMAKE_SOURCE_DIR: /home/ac141173/repos/ResoBee
-- HDF5 CXX compiler wrapper is unable to compile a minimal HDF5 program.
CMake Error at /usr/local/share/cmake-3.24/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find HDF5 (missing: HDF5_LIBRARIES CXX) (found version "1.10.7")
Call Stack (most recent call first):
/usr/local/share/cmake-3.24/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
/usr/local/share/cmake-3.24/Modules/FindHDF5.cmake:1007 (find_package_handle_standard_args)
CMakeLists.txt:59 (find_package)
-- Configuring incomplete, errors occurred!
由于某种原因，CMake 无法再找到任何 HDF5 库。
当激活带有 h5py 的 conda 环境时，
h5cc -showconfig SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.14.2
Configured on: Sun Aug 20 20:09:14 UTC 2023
Configured by: conda@8701a29b7fa1
Host system: x86_64-conda-linux-gnu
Uname information: Linux 8701a29b7fa1 5.15.0-1041-azure #48-Ubuntu SMP Tue Jun 20 20:34:08 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /home/path/to/conda/env
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: shared
Statically Linked Executables:
LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/path/to/conda/env/lib -Wl,-rpath-link,/home/path/to/conda/env/lib -L/home/path/to/conda/env/lib
H5_LDFLAGS:
AM_LDFLAGS: -L/home/path/to/conda/env/lib -L/home/path/to/conda/env/lib
Extra libraries: -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm
Archiver: /home/conda/feedstock_root/build_artifacts/hdf5_1692561980689/_build_env/bin/x86_64-conda-linux-gnu-ar
AR_FLAGS: cr
Ranlib: /home/conda/feedstock_root/build_artifacts/hdf5_1692561980689/_build_env/bin/x86_64-conda-linux-gnu-ranlib
Languages:
----------
C: yes
C Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1692561980689/_build_env/bin/x86_64-conda-linux-gnu-cc
CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/path/to/conda/env/include
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API -I/home/conda/feedstock_root/build_artifacts/hdf5_1692561980689/work/src/H5FDsubfiling
AM_CPPFLAGS: -I/home/path/to/conda/env/include -I/home/path/to/conda/env/include
C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/path/to/conda/env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_1692561980689/work=/usr/local/src/conda/hdf5-1.14.2 -fdebug-prefix-map=/home/path/to/conda/env=/usr/local/src/conda-prefix
H5 C Flags: -std=c99 -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wshadow -Wundef -Wwrite-strings -pedantic -Wno-c++-compat -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wc11-c2x-compat -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -s -Wbad-function-cast -Wcast-align -Wformat -Wimplicit-function-declaration -Wint-to-pointer-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign -Wpointer-to-int-cast -Wredundant-decls -Wstrict-prototypes -Wswitch -Wunused-but-set-variable -Wunused-variable -Wunused-function -Wunused-parameter -Wincompatible-pointer-types -Wint-conversion -Wshadow -Wrestrict -Wcast-function-type -Wmaybe-uninitialized -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wstrict-overflow=2 -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3
AM C Flags:
Shared C Library: yes
Static C Library: no
Fortran: yes
Fortran Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1692561980689/_build_env/bin/x86_64-conda-linux-gnu-gfortran
Fortran Flags:
H5 Fortran Flags: -std=f2008 -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Winteger-division -Wfrontend-loop-interchange -fdiagnostics-urls=never -fno-diagnostics-color -s -Wno-unused-dummy-argument -Wno-array-temporaries -O3
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: no
Module Directory: ${includedir}
C++: yes
C++ Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1692561980689/_build_env/bin/x86_64-conda-linux-gnu-c++
C++ Flags: -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/path/to/conda/env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_1692561980689/work=/usr/local/src/conda/hdf5-1.14.2 -fdebug-prefix-map=/home/path/to/conda/env=/usr/local/src/conda-prefix
H5 C++ Flags: -std=c++11 -Wall -Wcast-qual -Wconversion -Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wnon-virtual-dtor -Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wno-deprecated-copy -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -s -Wcast-align -Wmissing-declarations -Wpacked -Wredundant-decls -Wswitch -Wunused-but-set-variable -Wunused-function -Wunused-variable -Wunused-parameter -Wshadow -O3
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: no
Java: no
Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Dimension scales w/ new references: no
Build HDF5 Tests: yes
Build HDF5 Tools: yes
Build GIF Tools: yes
Threadsafety: yes
Default API mapping: v114
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
Map (H5M) API: no
Direct VFD: yes
Mirror VFD: no
Subfiling VFD: no
(Read-Only) S3 VFD: yes
(Read-Only) HDFS VFD: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: yes
Function stack tracing: no
Use file locking: best-effort
Strict file format checks: no
Optimization instrumentation: no
当基础环境被激活时，就会产生
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.10.7
Configured on: Wed, 08 Dec 2021 23:33:27 +0000
Configured by: Debian
Host system: x86_64-pc-linux-gnu
Uname information: Debian
Byte sex: little-endian
Installation point: /usr
Flavor name: serial
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,-Bsymbolic-functions -flto=auto -Wl,-z,relro
H5_LDFLAGS: -Wl,--version-script,$(top_srcdir)/debian/map_serial.ver
AM_LDFLAGS:
Extra libraries: -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: x86_64-linux-gnu-ranlib
Languages:
----------
C: yes
C Compiler: /usr/bin/gcc
CPPFLAGS: -Wdate-time -D_FORTIFY_SOURCE=2
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
C Flags: -g -O2 -ffile-prefix-map=$(top_srcdir)=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
H5 C Flags: -std=c99 -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3 -Werror=bad-function-cast -Werror=declaration-after-statement -Werror=implicit-function-declaration -Werror=missing-declarations -Werror=missing-prototypes -Werror=nested-externs -Werror=old-style-definition -Werror=packed -Werror=pointer-sign -Werror=pointer-to-int-cast -Werror=redundant-decls -Werror=strict-prototypes -Werror=switch -Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align -Wunused-but-set-variable -Wformat -Werror=incompatible-pointer-types -Werror=shadow -Wcast-function-type -Wmaybe-uninitialized
AM C Flags:
Shared C Library: yes
Static C Library: yes
Fortran: yes
Fortran Compiler: /usr/bin/gfortran
Fortran Flags: -g -O2 -ffile-prefix-map=$(top_srcdir)=. -flto=auto -ffat-lto-objects -fstack-protector-strong
H5 Fortran Flags: -std=f2008 -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Wuse-without-only -Winteger-division -Wfrontend-loop-interchange -s -O3
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: yes
C++ Compiler: /usr/bin/g++
C++ Flags: -g -O2 -ffile-prefix-map=$(top_srcdir)=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security
H5 C++ Flags: -Wall -Wcast-qual -Wconversion -Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor -Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -fstdarg-opt -s -O3 -Wcast-align -Wmissing-declarations -Werror=packed -Werror=redundant-decls -Werror=switch -Wunused-but-set-variable -Werror=unused-function -Werror=unused-variable -Wunused-parameter -Werror=shadow
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: yes
Java: yes
Java Compiler: /usr/bin/java (openjdk 11.0.13 2021-10-19)
Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Build HDF5 Tests: yes
Build HDF5 Tools: yes
Threadsafety: yes
Default API mapping: v18
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
MPE: no
Direct VFD: no
Mirror VFD: no
(Read-Only) S3 VFD: yes
(Read-Only) HDFS VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Function stack tracing: no
Use file locking: best-effort
Strict file format checks: no
Optimization instrumentation: no
我尝试卸载所有库（例如 Boost 和 OpenMP）。重新安装后，Boost和OpenMP又找到了，没有任何问题，但是HDF5就找不到了。
我尝试使用
set(LD_LIBRARY_PATH)include(FetchContent)
find_package(HDF5 REQUIRED COMPONENTS CXX)
link_directories(${HDF5_LIBRARY_DIRS})
include_directories(${HDF5_INCLUDE_DIRS})
在我的
CMakeCache.txt
//HDF5 CXX Wrapper compiler. Used only to detect HDF5 compile
// flags.
HDF5_CXX_COMPILER_EXECUTABLE:FILEPATH=/usr/bin/h5c++
//Path to a file.
HDF5_CXX_INCLUDE_DIR:PATH=/usr/include/hdf5/serial
//HDF5 file differencing tool.
HDF5_DIFF_EXECUTABLE:FILEPATH=/usr/bin/h5diff
//The directory containing a CMake configuration file for HDF5.
HDF5_DIR:PATH=HDF5_DIR-NOTFOUND
//HDF5 library compiled with parallel IO support
HDF5_IS_PARALLEL:BOOL=FALSE
//Path to a library.
HDF5_hdf5_LIBRARY_DEBUG:FILEPATH=HDF5_hdf5_LIBRARY_DEBUG-NOTFOUND
//Path to a library.
HDF5_hdf5_LIBRARY_RELEASE:FILEPATH=HDF5_hdf5_LIBRARY_RELEASE-NOTFOUND
//Path to a library.
HDF5_hdf5_cpp_LIBRARY_DEBUG:FILEPATH=HDF5_hdf5_cpp_LIBRARY_DEBUG-NOTFOUND
//Path to a library.
HDF5_hdf5_cpp_LIBRARY_RELEASE:FILEPATH=HDF5_hdf5_cpp_LIBRARY_RELEASE-NOTFOUND
//ADVANCED property for variable: HDF5_CXX_COMPILER_EXECUTABLE
HDF5_CXX_COMPILER_EXECUTABLE-ADVANCED:INTERNAL=1
//Result of TRY_COMPILE
HDF5_CXX_COMPILER_NO_INTERROGATE:INTERNAL=FALSE
//ADVANCED property for variable: HDF5_CXX_INCLUDE_DIR
HDF5_CXX_INCLUDE_DIR-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_DIFF_EXECUTABLE
HDF5_DIFF_EXECUTABLE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_IS_PARALLEL
HDF5_IS_PARALLEL-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_hdf5_LIBRARY_DEBUG
HDF5_hdf5_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_hdf5_LIBRARY_RELEASE
HDF5_hdf5_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_hdf5_cpp_LIBRARY_DEBUG
HDF5_hdf5_cpp_LIBRARY_DEBUG-ADVANCED:INTERNAL=1
//ADVANCED property for variable: HDF5_hdf5_cpp_LIBRARY_RELEASE
HDF5_hdf5_cpp_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
这表明没有找到正确的路径。
理想情况下，我可以只使用 h5py 附带的一个 HDF5 版本，以实现可重复性。 我怎样才能实现这个目标？我想我需要告诉 CMake 在哪里寻找库，但我不知道如何。但为什么以前不告诉这些信息就可以无缝运行，而现在却不能了？
谢谢您的帮助！
更新：我根据 CMakeCache.txt 路径进行了一些挖掘，发现变量 libdir 中存储的路径指向我手动删除的路径，
"${prefix}/lib/x86_64-linux-gnu"cat /usr/bin/h5c++
#! /bin/sh
#
# Copyright by The HDF Group.
# Copyright by the Board of Trustees of the University of Illinois.
# All rights reserved.
#
# This file is part of HDF5. The full HDF5 copyright notice, including
# terms governing use, modification, and redistribution, is contained in
# the COPYING file, which can be found at the root of the source code
# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.
# If you do not have access to either file, you may request a copy from
# [email protected].
#
############################################################################
## ##
## Things You May Have to Modify: ##
## ##
## If the following paths don't point to the place were HDF5 is installed ##
## on your system (i.e., you received a binary distribution or moved the ##
## files from the originally installed directory to another directory) ##
## then modify them accordingly to represent the new paths. ##
## ##
############################################################################
prefix="/usr"
exec_prefix="${prefix}"
libdir="${prefix}/lib/x86_64-linux-gnu"
libdevdir="${prefix}/lib/x86_64-linux-gnu/hdf5/serial"
includedir="${prefix}/include/hdf5/serial"
HL="hl"
我解决了！ （不是原来的问题，而是这个问题）
解决方案是清除所有 HDF5 软件包并重新安装它们，使用
sudo apt-get remove --purge $(dpkg -l | grep 'hdf5' | awk '{print $2}')仅使用remove不会产生一组新的配置文件，所以似乎需要purge。然后当然删除构建目录并再次构建，然后它应该可以工作。