[Debian-med-packaging] Bug#853738: phyml: MPI version uses different number of bootstrap steps breaking applications like seaview

[Andreas Tille]

Package: phyml
Severity: grave
Justification: renders package unusable

Hi,

for optimisation reasons the bootstrap parameter (-b) is not matched
exactly in phyml but rather adjusted to an optimized usage of processors
by the following algorithm:

    (nBootstrap / nProzessors + 1) * nProzessors

(see src/mpi_boot.c line 26 and 27).  While this is OK for manual
inspection of the results it breaks applications like seaview which
is using the number of given bootstrap processes as 100% for a
quality measure.  If this number increases unexpectedly the measure
will become above 100% which is no sensible result.

As a workaround it would be needed to either determine the number
of processors to fullfill the relation

    nBootstrap % nProzessors = 0

which results in unchanged number of bootstrap steps or simply
set nProcessors=1 (disable multiprocessing at all).

Kind regards

       Andreas.

-- System Information:
Debian Release: 8.7
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages phyml depends on:
ii  libc6  2.19-18+deb8u7

phyml recommends no packages.

phyml suggests no packages.