g++ compile error: undefined reference to a shared library function which exists
g++, hdf5, ld, shared-libraries, undefined-reference
Solution
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.
Problem
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.