I'm trying to link hdf5 to c++ code (Mac) - c++

I have the files:
main.cpp, tools.cpp, tools.h, integrator.cpp, and integrator.h.
I have tried to link HDF5 to this code (it compiles/links just fine without hdf5 stuff).
Here's what I am using to compile:
g++ -Wall -Werror -pedantic -std=c++1y -I /usr/local/include -L/usr/local/lib -lhdf5 -lhdf5_hl -lhdf5_cpp main.cpp tools.cpp integrator.cpp
The error I get is complete nonsense to me:
"__ZN2H56H5FileC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjRKNS_17FileCreatPropListERKNS_15FileAccPropListE", referenced from:
_main in cc76aLiD.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
However, sure enough, if I take out all the HDF5 commands in my code but keep the #include "H5Cpp.h" at the top of main.cpp it works. This seems odd to me because I would assume it would fail here too?
Anyone have any suggestions to try?
I'm using a Mac if that is relevant. Thanks!

Maybe you want also link with -lhdf5_hl_cpp. If you had used cmake, as I suggested today, you would not have such issues.

Related

vscode g++ Link failure : Undefined symbols for architecture x86_64

Basic Info:
system: macOS High Sierra(10.13.6)
editor : vs code(latest version)
Compiler: g++ (Xcode)
Target:deploy GLFW + GLAD
Question Description:
Recently, I'm learning to do some Computer Graphics related work. Everything is going smooth. However, when i create a window to test the env.Link error happened:
Undefined symbols for architecture x86_64:
"_gladLoadGLLoader", referenced from:
_main in main-5c211c.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
The terminal process terminated with exit code: 1
It seems I have not link some third party file. I
have fixed exactly the same problem by add "-lglfw" args to g++ when using functions in glfw3.h.
But when meeting glad related function : gladLoadGLLoader, I don't know how to do.
Something I have done:
Can find the head file.
#include glad/glad.h
#include GLFW/glfw3.h
Have put the file "glad.c" in workspace.
Try to Add "g++ -framework XXXXX" , But doesn't work.
Try to Add "g++ -lglfw3", But doesn't work.
Add "g++ -L or I /usr/lib or /usr/local/lib or /usr/local/include", But doesn't work.
Just tell the g++ to compile glad.c by adding "glad.c" to args. I thought glad.c will be compiled by default. Although I am not clear what happened, the problem is resolved anyway.
Add glad.c into Build Phases->Compile Sources

libgtest.so error adding symbols: DSO missing from command line

I have been using gtests for unit testing a personal project. Last week I upgraded to the LTS version of Linux Mint. Unfortunately, after that event, I haven't been able to compile my project due to gtests linking problems.
The following error is being issued:
/usr/bin/x86_64-linux-gnu-ld: build/tests/policies/roundrobin_tests.o: undefined reference to symbol '_ZN7testing4TestC2Ev'
/home/myuser/Documents/googletest-release-1.8.0/googletest/libgtest.so: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
I have generated both libgtest.so and libgtest_main.so through CMake 3.10.2. The gtest version is the release-1.8.0, the same I used to have before.
Those libraries are located in /usr/lib and the corresponding include folder has also been copied to /usr/include. I made sure that this location is in my ld path and that is not the problem.
My compiler is g++ v7.3.0 and the command Im using to compile the testes is:
g++ -std=c++14 -Wall -O3 -Iinclude build/tests/policies/roundrobin_tests.o -lgtest_main -pthread -o bin/policies/roundrobin_tests
I have tried altering the order of the elements in the command, explicitly adding -L/usr/lib and -I/usr/include without luck. A funny fact is that if I take off the -pthread flag, the error is still the same.
The same command was used before and the only difference is the compiler version I am using now as I used g++ 5.4.0 before. Any insights on how to solve this?
edit: Just tested the same process with g++ 5.4.0 and CMake 3.5 and the same problems ocurred.

ld: symbol(s) not found for architecture

First of all I want to say I realise this has been asked a dozen times, and I've read countless solutions without any luck so therefore I'm asking again.
I'm using OS X Mavericks 10.9.5, writing in Sublime 3 and compiling using terminal with g++
I'm trying to compile this simple file (test.cpp)
#include <iostream>
#include <SDL2/SDL.h>
int main () {
if(SDL_Init(SDL_INIT_VIDEO)) {
std::cout << "I made it this far" << std::endl;
}
return 0;
}
Compiler line :
g++ test.cpp
This returns the error :
Undefined symbols for architecture x86_64:
"_SDL_Init", referenced from:
_main in test-ebbae4.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
So, I've tried adding a lot of different flags, -m32 only changes the result to throw Undefined symbols for architecture i386: and ld: symbol(s) not found for architecture i386
I've tried different -arch variations, but I can't seem to get it to work. also played around with -l -I flags but I'm not sure I know what they do/how they could help..
Does anyone have a clue what to do next?
EDIT : Some additional information. I've tried using the .framework for SDL2, that didn't change anything, currently I'm using SDL2 installed through compilation of the source. Headers located in usr/local/SDL2
g++ test.cpp
You should specify the SDL library, too:
g++ test.cpp -lsdl2
You might need to include a path if its not well known to the compiler driver:
g++ test.cpp -L/path/to/the/library -lsdl2

Boost Thread Destructor Undefined Symbol

I'm using OSX Mountain Lion. I just downloaded, unpacked, and built boost 1.52.0 using the instructions supplied from the boost website: http://www.boost.org/doc/libs/1_52_0/more/getting_started/unix-variants.html. I left the default installation prefix at /usr/local, meaning that the libraries are installed in /usr/local/lib and the header files are in /usr/local/include. I have verified that the libraries and headers are present there and recently modified.
I'm attempting to compile the boost asynchronous I/O example found here: http://www.boost.org/doc/libs/1_52_0/doc/html/boost_asio/tutorial/tuttimer5/src.html (source).
Here is my compilation command:
g++ -Wall -c -g -I/usr/local/include src/test1.cpp -o src/test1.o
where src/test1.cpp is the example source file. Here is my linking command (and error):
g++ -Wall -L/usr/local/lib -lboost_thread -lboost_system src/test1.o -o bin/test1
Undefined symbols for architecture x86_64:
"boost::thread::~thread()", referenced from:
_main in test1.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
I have tried using both Apple's clang++ 4.0 and g++ 4.6.0. I get the same undefined symbol error from both programs.
Other people seem to have had trouble compiling this code sample as well. I am aware of this question: C++ / Boost: Undefined Symbols in example? and this one: Linker error when compiling boost.asio example. However, each of these problems seems to have been fixed by adding the appropriate switches (-lboost_thread and -lboost_system) to the command line. I already have those. I have also tried adding -lpthread without luck.
Thank you for taking time to look at my question! Any help is appreciated. :)
Just ran into this same problem, and I found that reverting to Boost 1.49 fixes the problem. Download links for Boost 1.49 are here:
http://www.boost.org/users/history/version_1_49_0.html
Before installing 1.49, I removed 1.52 by deleting /usr/local/include/boost and /usr/local/lib/*boost*. Not sure what changed between 1.49 and 1.52 to cause this problem, or whether Boost 1.50 or 1.51 will work.
Put the libraries you link with last on the command line.
The GNU linker uses kind of reverse lookup of dependencies, so if file A depends on library B, B should come after A on the command line.

Trouble using SFML with GCC and OS X

I've been trying to get SFML working for a while now and I've been trying to get it working using GCC. I'm on OS X by the way. I followed the standard Linux instructions and using the Linux 64-bit download however when it comes to compiling...
g++ -o testing main.cpp -lsfml-system
This happens:
main.cpp: In function ‘int main()’:
main.cpp:7: error: ‘class sf::Clock’ has no member named ‘GetElapsedTime’
main.cpp:9: error: ‘class sf::Clock’ has no member named ‘GetElapsedTime’
main.cpp:10: error: ‘Sleep’ is not a member of ‘sf’
So I thought it could be due to not using includes, so I changed my gcc compile command to:
g++ -o testing main.cpp -I ~/SFML-1.6/include/ -lsfml-system
and now I'm getting this error:
ld: warning: ignoring file /usr/local/lib/libsfml-system.so, file was built for unsupported file format which is not the architecture being linked (x86_64)
Undefined symbols for architecture x86_64:
"sf::Clock::Clock()", referenced from:
_main in ccZEiB7b.o
"sf::Clock::GetElapsedTime() const", referenced from:
_main in ccZEiB7b.o
"sf::Sleep(float)", referenced from:
_main in ccZEiB7b.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status**
And I have no idea what to do to fix it.
Short answer
Add the -arch i386 (on mac) or -m32 (on linux) flag
Long answer
Your sfml-system library was built in 32 bits whereas you are trying to compile your program in 64 bits. So your program cannot link to the library.
Recompile SFML in 64 bits if possible and you should be able to compile your program in 64 bits.
SFML expects you to use frameworks on OS X. Open the SFML folder and copy all the folders under lib64 to /Library/Frameworks (that is, copy SFML.framework, sfml-system.framework, etc. to /Library/Frameworks).
Once you've installed the frameworks, you can use them by passing the -framework command to g++ like so:
g++ -o testing main.cpp -framework SFML -framework sfml-system