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

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.

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.

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 ..."

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