g++ compile error: undefined reference to a shared library function which exists

Question

I recently installed the hdf5 library on an ubuntu machine, and am now having trouble linking to the exported functions. I wrote a simple test script readHDF.cpp to explain the issue:

#include <hdf5.h>

int main(int argc, char * argv[])
{
  hid_t     h5_file_id = H5Fopen(argv[1], H5F_ACC_RDWR, H5P_DEFAULT);
  return 0;
}

The compile command is

g++ -Wl,-rpath,$HOME/hdf5/lib -I$HOME/hdf5/include \
    -L$HOME/hdf5/lib -l:$HOME/hdf5/lib/libhdf5.so readHDF.cpp

which returns the following error

/tmp/cc6DXdxV.o: In function `main':  
readHDF.cpp:(.text+0x1f): undefined reference to `H5check_version'  
readHDF.cpp:(.text+0x3c): undefined reference to `H5Fopen'  
collect2: ld returned 1 exit status

I am confused because the nm command seems to say that the function has been exported:

nm -C $HOME/hdf5/lib/libhdf5.so | grep H5check_version

which returns

0000000000034349 T H5check_version

and a similar result for H5Fopen. Any thoughts on what might be going wrong? Not sure if it helps, but if I comment out the H5Fopen portion of the script, then it compiles fine:

#include <hdf5.h>

int main(int argc, char * argv[])
{
hid_t     h5_file_id;// = H5Fopen(argv[1], H5F_ACC_RDWR, H5P_DEFAULT);
return 0;
}

Also there are multiple versions of hdf5 installed on the server which are used by various python modules such as h5py and tables, but I couldn't get any of them to work, so I installed this version in my local directory and changed the rpath options for g++ linker.

Devotee

Answer 1

Ok, solved. The issue was in the placement of the -lhdf5 in the compile command. Apparently -lhdf5 should be placed after readHDF.cpp. For instance g++ -Wl,-rpath=$HOME/hdf5/lib -L$HOME/hdf5/lib -I$HOME/hdf5/include readHDF.cpp -lhdf5 will compile with no problems, but g++ -Wl,-rpath=$HOME/hdf5/lib -L$HOME/hdf5/lib -I$HOME/hdf5/include -lhdf5 readHDF.cpp will fail with the undefined reference errors. Interestingly, this was only a problem for Ubuntu 12.04, as both compile commands worked for Ubuntu 10.04.

Found the answer with explanation at this post:

undefined reference to symbol even when nm indicates that this symbol is present

I guess placing -lXXX after the script is safer practice.

Devotee

Strange. Putting -lhdf5 before the script, and everything works fine. When I put it after the script, it gives libraries errors. – Neritic

+500 if i could – Zworykin

Can confirm that this also fixed the same problem on Windows with Cygwin – Hurwit

Answer 2

This is not a bug. See C++ shared library undefined reference to `FooClass::SayHello()'

"Recent versions of GCC reuqire that you put the object files and libraries in the order that they depend on each other ..."

Raynell

Answer 3

You forgot to put -lhdf5 in the compile command. Also, there's no need for -l:$HOME/hdf5/lib/libhdf5.so

This should work: $ g++ -Wl,-rpath,$HOME/hdf5/lib -I$HOME/hdf5/include -L$HOME/hdf5/lib -lhdf5 readHDF5.cpp

Machiavelli

I tried that originally and it gave the same error. There are multiple versions of libhdf5.so* in $HOME/hdf5/lib for instance libhdf5.so.6 and libhdf5.so.6.0.3 etc so I though that being more specific would help, but it didn't. – Devotee

And what about the -lhdf5? I can reproduce the exact linker error you have in your question on my machine, and adding -lhdf5 solves the problem. – Machiavelli

Yeah, adding the -lhdf5 didn't help. It is a very strange bug. I installed in exactly the same way on an Ubuntu 10 machine and it worked ok. – Devotee