Comment (by Roland Haas):

Ok, that explains it then. I have adapted your fix and pushed it as git hash 7090973 "HDF5: make h5check compile even if _GNU_SOURCE is defined" of ExternalLibraries-HDF5

I cannot find where _GNU_SOURCE shows up in the docs or tutorials either, but it is used in a couple of simfactory option lists (which all use a system compiled HDF5 library) so having the fix is a good idea anyway just in case we ever need to build our own HDF5 library on those machines.

You already seem to have a workaround, alternatively I would have suggested compiling without -D_GNU_SOURCE which ought not be required, in particular if you already use -std=gnuc11 and -std=gnu++11 anyway.

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Ticket URL: https://bitbucket.org/einsteintoolkit/tickets/issues/2492/h5check-fails-to-build