Downloaded the boot repair disk: 
https://sourceforge.net/projects/boot-repair-cd/
Repaired it. Turns out that a lot of packages were not configured. Also not 
grub.
The package which made the installer to trip over is: libhdf5-openmpi-dev and 
in particular the pre-removal script.
(Reading database ... 1786310 files and directories currently installed.)
Removing libhdf5-openmpi-dev (1.10.7+repack-4ubuntu2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc 
to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
update-alternatives: error: no alternatives for mpi
dpkg: error processing package libhdf5-openmpi-dev (--remove):
 installed libhdf5-openmpi-dev package pre-removal script subprocess returned 
error exit status 2
dpkg: too many errors, stopping
update-alternatives: using /usr/bin/h5pcc.openmpi to provide /usr/bin/h5pcc 
(h5pcc) in auto mode
update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-openmpi.pc 
to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
update-alternatives: error: no alternatives for mpi
dpkg: error while cleaning up:
 installed libhdf5-openmpi-dev package post-installation script subprocess 
returned error exit status 2
Errors were encountered while processing:
 libhdf5-openmpi-dev
Processing was halted because there were too many errors.
E: Sub-process /usr/bin/dpkg returned an error code (1)

So I just deleted these scripts...

root@eeapp:/home/bp1# rm /var/lib/dpkg/info/libhdf5-openmpi-dev.prerm 
root@eeapp:/home/bp1# rm /var/lib/dpkg/info/libhdf5-openmpi-dev.postinst 

... and now the upgrade continues.

Note that this libhdf5-openmpi-dev bug has been around for donkeys. But
I guess for the others it might have been a different script which
bombed during the upgrade.

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https://bugs.launchpad.net/bugs/2065476

Title:
  During boot, after grub selection screen, it appears "error: sparse
  file not allowed - Aborted. Press any key to exit."

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