Valgrind: Syscall param write(buf) points to uninitialised byte(s)

[garrison]

When run under valgrind, the MatrixRoundTrip.LongDouble test emits a warning:

==3258== Syscall param write(buf) points to uninitialised byte(s)
==3258==    at 0x4F621E7: write (write.c:26)
==3258==    by 0x4960BAB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x495A427: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x493985A: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x4A3C30A: H5PB_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x49441AC: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x4905602: H5D__flush_sieve_buf (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x48F7F15: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x4905706: H5D__flush_real (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x4905804: H5D_close (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x49061E5: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x49B4E1F: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==  Address 0x55ece92 is 18 bytes inside a block of size 200 alloc'd
==3258==    at 0x483B7F3: malloc (in /usr/lib/x86_64-linux-gnu/valgrind/vgpreload_memcheck-amd64-linux.so)
==3258==    by 0x4964641: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x4964E58: H5FL_blk_malloc (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x4965059: H5FL_blk_calloc (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x48F739D: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x4AF5910: H5VM_opvv (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x48F6F67: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x4911FE8: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x4912849: H5D__select_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x48F8036: H5D__contig_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x490BEB0: H5D__write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258==    by 0x490C69C: H5Dwrite (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.103.0.0)
==3258== 

I am not sure if this is a problem with eigen3-hdf5 or is entirely an issue with the underlying library. It might even be benign, in which case we should add a suppression. Once this is resolved, we should run valgrind with --error-exitcode=1 so CI fails if any new error is introduced.

[garrison]

I just reproduced this in a Ubuntu 16.04 (xenial) Docker container, both on the latest commit (f161974) and in the commit this test was introduced (9804313). Here's the output:

==4176== Syscall param write(buf) points to uninitialised byte(s)
==4176==    at 0x5BCA3C0: __write_nocancel (syscall-template.S:84)
==4176==    by 0x4EE4893: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EDEEEC: H5FD_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4ECF976: H5F__accum_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4ED21D3: H5F_block_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EB1500: H5D__flush_sieve_buf (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EAA298: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EB1644: H5D__flush_real (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EB1810: H5D_close (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4F2DCA5: H5I_dec_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4F2DD5D: H5I_dec_app_ref (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4F2DF7D: H5I_dec_app_ref_always_close (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==  Address 0x7374d32 is 18 bytes inside a block of size 200 alloc'd
==4176==    at 0x4C2DB8F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==4176==    by 0x4EE77AD: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EE7E38: H5FL_blk_malloc (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EE7F44: H5FL_blk_calloc (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EA9874: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x5031919: H5VM_opvv (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EA929C: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EBA4AB: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EBAD1C: H5D__select_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EAA359: H5D__contig_write (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EB4C54: ??? (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176==    by 0x4EB5129: H5Dwrite (in /usr/lib/x86_64-linux-gnu/libhdf5_serial.so.10.1.0)
==4176== 

so I think this may indeed be from the underlying library, especially because it only appears in the tests for long double.