Your message dated Tue, 31 Jan 2017 15:18:28 +0000
with message-id <e1cyacs-000czz...@fasolo.debian.org>
and subject line Bug#853738: fixed in phyml 3:3.2.0+dfsg-6
has caused the Debian Bug report #853738,
regarding phyml: MPI version uses different number of bootstrap steps breaking
applications like seaview
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
853738: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=853738
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: phyml
Source-Version: 3:3.2.0+dfsg-6
We believe that the bug you reported is fixed in the latest version of
phyml, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 853...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated phyml package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 31 Jan 2017 15:16:45 +0100
Source: phyml
Binary: phyml
Architecture: source amd64
Version: 3:3.2.0+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
phyml - Phylogenetic estimation using Maximum Likelihood
Closes: 853737 853738
Changes:
phyml (3:3.2.0+dfsg-6) unstable; urgency=medium
.
* Also provide version without beagle library since it causes trouble
on machines without according graphics hardware
Closes: #853737
* Provide link /usr/bin/phyml-beagle
* Enable to switch of MPI version via environment variable since there
are circumstances when it leads to wrong results
Closes: #853738
* Test single processor and MPI in autopkgtest
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