Undefined symbol ompi_mpi_info_null for HDF5 - Ubuntu 16.04

Question

I was trying to compile a package in Ubuntu 16.04 that requires HDF5. When compiling HDF5 I encounter this problem:

ImportError: /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.10: undefined symbol: ompi_mpi_info_null

Is this indicating that I don't have openMPI? Pretty sure I have that as well checked from synaptic... I have libopenmpi-dev and libopenmpi1.10 already installed...

Answer 1

ImportError looks like a Python error. What is the software stack that you are using?

Is your application code parallel? I suggest to make sure that both OpenMPI and HDF5 are up-to-date, use the serial version of HDF5 if parallel is not needed, install h5py (if that is what you are using).