A configure option is available to disable file locking:

-disable-libtool-lock 

You can also set the HDF5_USE_FILE_LOCKING environment variable to FALSE to disable file locking. This was added to HDF5-1.10.6, and is described in the release notes:

fcntl(2)-based file locking incorrectly passed the lock argument struct
instead of a pointer to the struct, causing errors on systems where
flock(2) is not available.

File locking is used when files are opened to enforce SWMR semantics. A
lock operation takes place on all file opens unless the
HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE".
flock(2) is preferentially used, with fcntl(2) locks as a backup if
flock(2) is unavailable on a system (if neither is available, the lock
operation fails). On these systems, the file lock will often fail, which
causes HDF5 to not open the file and report an error.

This bug only affects POSIX systems. Win32 builds on Windows use a no-op
locking call which always succeeds. Systems which exhibit this bug will
have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output.

This bug affects HDF5 1.10.0 through 1.10.5.