我正在尝试编译需要 HDF5 的 C++ 代码。我还使用 conda 环境来管理 Python 中后处理所需的包，以及启动调用基于 C++ 的可执行文件的参数组合运行。除了系统上安装的发行版之外，此 conda env 还包含 h5py 和其他 HDF5 发行版。
CMake 能够正确配置，并且可以在基础环境中构建。但是，当在激活 h5py 的 conda 环境中构建（这是调用参数组合运行的可执行文件所必需的）时，我最终出现以下错误：
[100%] Linking CXX executable simulation
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_global_init@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_perform@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_slist_free_all@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_setopt@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_init@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_slist_append@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_cleanup@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_global_cleanup@CURL_OPENSSL_4'
collect2: error: ld returned 1 exit status
gmake[3]: *** [src/CMakeFiles/simulation.dir/build.make:597: src/simulation] Error 1
gmake[2]: *** [CMakeFiles/Makefile2:2032: src/CMakeFiles/simulation.dir/all] Error 2
gmake[1]: *** [CMakeFiles/Makefile2:2039: src/CMakeFiles/simulation.dir/rule] Error 2
gmake: *** [Makefile:963: simulation] Error 2
在激活的conda env中使用cmake -B./build/
进行配置可以工作，但发现错误的HDF5版本（系统版本，而不是h5py版本）：
CMAKE_SOURCE_DIR: /home/path/to/my/env
-- HDF5 CXX compiler wrapper is unable to compile a minimal HDF5 program.
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so (found version "1.10.7") found components: CXX
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0")
-- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so (found version "1.10.7")
-- Found Boost: /usr/include (found version "1.74.0") found components: system serialization
CMake Warning at build/_deps/highfive-src/CMakeLists.txt:117 (message):
Unit tests have been DISABLED.
-- Detected CPPZMQ Version - 4.10.0
-- cppzmq v4.10.0
-- Using the multi-header code from /home/path/to/my/env/build/_deps/json-src/include/
-- Configuring done
-- Generating done
-- Build files have been written to: /home/path/to/my/env/build
激活 conda env 时运行 h5cc -showconfig
显示 h5py 附带的 HDF5 版本 1.14.2 正在使用中：
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/my/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/my/envlib -Wl,-rpath-link,/home/path/to/my/envlib -L/home/path/to/my/envlib
H5_LDFLAGS:
AM_LDFLAGS: -L/home/path/to/my/envlib -L/home/path/to/my/envlib
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/my/envinclude
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/my/envinclude -I/home/path/to/my/envinclude
C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/path/to/my/envinclude -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/my/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/my/envinclude -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/my/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 conda env 停用并且仅激活 base env 时，版本为 1.10.7:
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
在我的 CMakeLists.txt 中，我使用以下相关行：
find_package(HDF5 REQUIRED COMPONENTS CXX)
link_directories(${HDF5_LIBRARY_DIRS})
include_directories(${HDF5_INCLUDE_DIRS})
...
#### COMPILER FLAGS ###
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++2a")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -larmadillo -lhdf5") # required for mlpack
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ljson") # required for SwarmRL integration
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS} -O3 -march=native") # optimized
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS} -g -Wall -Wextra -Wpedantic -Wdouble-promotion -Wformat=2 -Wformat-truncation -Wundef -fno-common -Wconversion -Wmisleading-indentation") # debugging
# other flags: -Wshadow
添加 -lcurl
标志没有帮助。我的相关 CMakeCache.txt 部分如下所示，表明设置了版本 1.10 路径（而不是 1.14 路径！）：
//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
//Path to a library.
HDF5_CXX_LIBRARY_crypto:FILEPATH=/usr/lib/x86_64-linux-gnu/libcrypto.so
//Path to a library.
HDF5_CXX_LIBRARY_curl:FILEPATH=/usr/lib/x86_64-linux-gnu/libcurl.so
//Path to a library.
HDF5_CXX_LIBRARY_dl:FILEPATH=/usr/lib/x86_64-linux-gnu/libdl.a
//Path to a library.
HDF5_CXX_LIBRARY_hdf5:FILEPATH=/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
//Path to a library.
HDF5_CXX_LIBRARY_hdf5_cpp:FILEPATH=/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so
//Path to a library.
HDF5_CXX_LIBRARY_m:FILEPATH=/usr/lib/x86_64-linux-gnu/libm.so
//Path to a library.
HDF5_CXX_LIBRARY_pthread:FILEPATH=/usr/lib/x86_64-linux-gnu/libpthread.a
//Path to a library.
HDF5_CXX_LIBRARY_sz:FILEPATH=/usr/lib/x86_64-linux-gnu/libsz.so
//Path to a library.
HDF5_CXX_LIBRARY_z:FILEPATH=/usr/lib/x86_64-linux-gnu/libz.so
康达环境：
name: myenv
channels: # strict channel priority enforced! order matters
- conda-forge
- bioconda
- defaults
dependencies:
- python=3.10
- snakemake=7.32
- matplotlib
- pandas
- seaborn
- scipy
- yaml
- pyyaml
- graphviz
- ffmpeg
- numba
- h5py
- pytables
- jupyter
我怀疑 cmake 配置 HDF5 版本 (1.10.7) 与由于 conda env (1.14.2) 而处于活动状态的版本不匹配。我想我需要在 CMake 中指定要使用哪些 HDF5 库。
理想情况下，我可以使用 h5py 附带的版本，以实现更好的依赖管理。
我怎样才能解决这个问题（以最优雅的方式）？谢谢您的帮助！
具体操作方法如下：
1.设置 HDF5_ROOT CMake 变量以指向 conda 环境中的 HDF5 安装。您可以在运行 CMake 之前设置此变量。 重击
cmake -B./build/ -DHDF5_ROOT=/path/to/your/conda/env
Activate your conda environment*
conda activate myenv
*Run CMake with the HDF5_ROOT variable set*
cmake -B./build/ -DHDF5_ROOT=/path/to/your/conda/env
* Build your project*
cmake --build ./build/
如果遇到任何其他问题，您可能需要调整其他 CMake 变量，例如 HDF5_CXX_INCLUDE_DIR 和 HDF5_CXX_LIBRARY，以指向 conda 环境中的正确位置。
通过适当设置这些变量，您可以确保 CMake 使用 conda 环境提供的 HDF5 版本，从而使您能够更有效地管理依赖关系。