I am trying to compile a binary file which requires the HDF5 library. The compiler complains that
/usr/bin/ld: lib/libBVCio.so: undefined reference to `H5::StrType::StrType(H5::PredType const&, unsigned long const&)@HDF5_CPP_1.8.13'
/usr/bin/ld: lib/libBVCio.so: undefined reference to `H5::Attribute::write(H5::DataType const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const@HDF5_CPP_1.8.15.1'
/usr/bin/ld: lib/libBVCio.so: undefined reference to `H5::CommonFG::openDataSet(char const*) const@HDF5_CPP_1.8.9'
/usr/bin/ld: lib/libBVCio.so: undefined reference to `H5::PredType::NATIVE_INT32@HDF5_CPP_1.8.9'
/usr/bin/ld: lib/libBVCio.so: undefined reference to `H5::CompType::~CompType()@HDF5_CPP_1.8.9'
/usr/bin/ld: lib/libBVCio.so: undefined reference to `H5::DSetMemXferPropList::DEFAULT@HDF5_CPP_1.8.9'
...
...
You can see that each error indicates the version tag of the function, such as the 1.8.9 version of H5::CompType::~CompType()@HDF5_CPP_1.8.9. However, I found out the the HDF5 1.8.16 that I manually installed already contains those functions or classes. It is just that somehow the version tag of HDF5 1.8.16 is always Base as shown below.
objdump -T libhdf5_cpp.so.11 | c++filt | grep StrType::StrType
00000000000545ac g DF .text 000000000000003c Base H5::StrType::StrType(H5::StrType const&)
0000000000054460 g DF .text 0000000000000086 Base H5::StrType::StrType(H5::PredType const&, unsigned long const&)
If I check with HDF5 1.10.7, you can see there are the version tag HDF5_CPP_1.8.9. It is just the version tag does not match the one that my source code needs, so I can’t use HDF5 1.10.7.
objdump -T libhdf5_cpp.so.103 | c++filt | grep StrType::StrType
0000000000052310 g DF .text 000000000000001d HDF5_CPP_1.8.9 H5::StrType::StrType(H5::StrType const&)
0000000000052600 g DF .text 0000000000000048 HDF5_CPP_1.10.1 H5::StrType::StrType(H5::H5Location const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
Therefore, I was wondering if I built and installed the HDF5 1.8.16 correctly. I think I installed the HDF5 1.10.7 using sudo apt-get install command, but I need to build and install HDF5 1.8.16 manually from the source files. And my command is very simple. I just followed the instruction in the INSTALL document.
tar -xvf hdf5-1.8.16.tar
cd hdf5-1.8.16
./configure --prefix=/home/ethankao/Software/hdf5-1.8.16/build --enable-fortran --enable-cxx
make
make check
make install prefix=/home/ethankao/Software/hdf5-1.8.16/build
make check-install
Could you please help me with this? Thank you.
Below is the configuration of the my two HDF5 libraries.
1. The manually installed 1.8.16
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.16
Configured on: Mon Mar 18 16:20:25 CET 2024
Configured by: ethankao@Prudens
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux Prudens 6.5.0-25-generic #25~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 20 16:09:15 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries: static, shared
Installation point: /home/ethankao/Software/hdf5-1.8.16/build
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc
CFLAGS:
H5_CFLAGS: -std=c99 -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: /usr/bin/gfortran
Fortran 2003 Compiler:
Fortran Flags:
H5 Fortran Flags:
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: yes
C++ Compiler: /usr/bin/g++
C++ Flags:
H5 C++ Flags:
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: yes
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
Strict File Format Checks: no
Optimization Instrumentation: no
2. Automatically installed 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