Removal of netcdf and hdf5 system-level library installations

June 14, 2017
Conte, Halstead, Radon, Rice, Snyder

Research Computing has begun removing several libraries installed at the system-level that should be provided by the module command. These libraries include netcdf, hdf5, and several related packages. This change should have limited impact as module installations of these packages are not changing and most people should be using the module versions.

These packages are being removed at the system-level because these types of libraries should be managed at the "module" level. These packages were inadvertently installed but have not been tuned and optimized for use on the clusters. Some software compilations may have accidentally picked up these packages, rather than the "module" package, or may have picked up some combination of system-level packages and module packages. Anyone with software linked against these libraries may have had issues with the software mixing versions.

Many scientific applications are very sensitive to the compilers used to build software and its libraries, so by removing these packages at the system-level, and by the "module" command's enforcement of only loading one of a package at the time, you can be sure your code is being compiled with exactly the same version of the library and not scrambled with other versions that were not asked for.

There were a couple of our own module installations that fell victim to this scrambling of libraries which we have fixed. If your software does not use netcdf or hdf5, or your software does and you are loading a netcdf or hdf5 module, you will not be impacted. If you see an error such as:

error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory

You will need to ensure you are loading a netcdf or hdf5 module and you may need to recompile your code to ensure you are picking up the library version from the module.

Please let us know at rcac-help@purdue.edu if you have any questions.

Originally posted: June 14, 2017  2:59pm

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