[Debian-med-packaging] Please verify whether pyhml has done the expected number of bootstraps which is not guaranteed when using MPI

[Andreas Tille]

Hi Manolo,

as you know from my last mail I created a wrapper inside the Debian
package of phyml which uses MPI if available.  This resulted in quite
some gain of speed.  However, we realised that it also might cause a
problem since phyml "decides" itself how many bootstrap steps it takes
depending from the amount of processors can be used.  I have described
the issue in Debian bug #853738[1] and fixed the bug in a way which
allows the user to call seaview like:

   PHYMLCPUS=8 seaview *.fna

when intending to do for instance 1000 bootstrap steps.  This works
since 1000%8=0.  However, for other numbers of CPUs for instance when
calling

   PHYMLCPUS=16 seaview *.fna

phyml would do

   (1000 / 16 + 1) * 16 = 1008

bootstrap processes.  From phyml perspective this does not matter but
the effect in seaview is that if 1000 bootstraps are considered 100%
some values might end up beeing 101% which is nonsense.

So I wonder whether you could please consider parsing the phyml output
for changed numbers of bootstraps to adjust the base of the calculations
that are based on the effective number of bootstraps.

Kind regards

      Andreas.

[1] https://bugs.debian.org/853738

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