WRF compile problem libhdf5_fortran.so: undefined reference to `H5Oget_info'

[Zhanghc]

Dear all,

I am doing WRF compiling.
I typed the following in the command line: ./configure, and I choose 16 (dm+sm) INTEL (ifort/icc), it succeeded.
When I typed the following in the command line: ./compile em_real >&log.compile ,
I got the following error,which I couldn’t understand.


/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libhdf5_fortran.so: undefined reference to `H5Oget_info'
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libhdf5_fortran.so: undefined reference to `H5Sencode'
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libhdf5_fortran.so: undefined reference to `H5Oget_info_by_idx'
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libhdf5_fortran.so: undefined reference to `H5Rdereference'
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libhdf5_fortran.so: undefined reference to `H5Lget_info_by_idx'
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/libhdf5_fortran.so: undefined reference to `H5Lget_info'
0.58user 3.98system 0:04.83elapsed 94%CPU (0avgtext+0avgdata 470592maxresident)k
0inputs+94920outputs (0major+80717minor)pagefaults 0swaps
make[1]: [em_real] Error 1 (ignored)


I would appreciate it if you would take the time out of your busy schedule to check out my posts and give suggestions.
Best regards,
Hongchi

 

[kwerner]

Hongchi,
It looks like you're trying to compile WRF with NetCDF4 options (e.g., compression), which requires the HDF5 libraries. If you don't care about compression, you can ask it to compile without that option by setting the environment variable

export NETCDF_classic=1

Afterward, you'll need to clean the code and reconfigure before recompiling again

./clean -a
./configure

If you do intent to use compression, you'll need to make sure you have HDF5 installed and that you point to it in your path. You may need to ask a systems administrator at your institution to help you with this if you're unsure.

Also, if you're not familiar with using dm+sm, you should probably just stick with the dmpar option, as we've seen better results with this option.