Error in configuring HDF5 on Ubuntu 18.04 with Intel Compilers


I’m trying to install the HDF5 compression libraries with the Intel Compilers suite (Intel Parallel Studio XE 2018.2.046). With the same suite I’ve compiled both szip and zlib and I’m proceeding to configure HDF, but the configuration stops with the error:

checking size of size_t… configure: error: in `/home/modelstation/Downloads/hdf5-1.10.2’: configure: error: cannot compute sizeof (size_t)

On HDF FAQ I’ve seen that it could’ve been a problem with SZIP/ZLIB to LD_LIBRARY_PATH but this doesn’t seem to be the case. In fact, on the Intel Developer Forum, someone highlighted an incompatibility with the newest version of Ubuntu (see here).

Since I cannot follow the workaround suggested in that page, I was wondering if anyone found a solution or is there a patch for this bug.

Thank you!

P.S.: I would attach the log file, but I cannot since I am a new user


Does the version of zlib matter, and might you try the cmake hdf5 build (using the supplied zlib/szip tgz files). The supplied zlib tgz file is based on v1.2.8.



Hi Federico,
Can you send your config.log file to the helpdesk?: