Your message dated Fri, 15 Aug 2014 13:22:27 +0000
with message-id <[email protected]>
and subject line Bug#756392: fixed in raxml 8.1.1-1
has caused the Debian Bug report #756392,
regarding enable SIMD and threading support
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.
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--
756392: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=756392
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: raxml
Version: 7.2.8-2
Severity: wishlist
Dear Maintainer,
the current RAxML package contains only the "vanilla" version of RAxML
compiled without support threading or SIMD. Given that typical use cases
of RAxML require days of computation, enabling parallel processing would
improve the utility of the package significantly.
RAxML does not detect the available hardware at runtime. Instead,
separate Makefiles build the various optimized versions. Supported SIMD
variants are: (none), SSE3, AVX and AVX2. Supported threading variants
are: (none), PTHREADS, MPI and HYBRID (both pthreads and MPI).
The makefile names are "Makefile.<SIMD-TYPE><THREAD-TYPE>gcc".
Since most users will have multi-core CPUs and only very few a MPI
environment, focusing on the PTHREAD variants with SIMD extensions
should be a good balance between package complexity and extra value. The
AVX2 extensions apparently do not add much performance. Therefore, I
would suggest building three versions:
- Makefile.PTHREADS.gcc
- Makefile.PTHREADS.SSE3.gcc
- Makefile.PTHREADS.AVX.gcc (depends >= gcc 4.6)
A simple bash wrapper script could then be used to make the appropriate
choice for the user. E.g.:
----
#!/bin/bash
if grep -q avx /proc/cpuinfo; then
exec raxml.PTHREADS.AVX "$@"
elif grep -q sse3 /proc/cpuinfo; then
exec raxml.PTHREADS.SSE3 "$@"
else
exec raxml.PTHREADS.NOSIMD "$@"
fi
----
best regards,
Elmar
--- End Message ---
--- Begin Message ---
Source: raxml
Source-Version: 8.1.1-1
We believe that the bug you reported is fixed in the latest version of
raxml, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated raxml 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 15 Aug 2014 14:40:09 +0200
Source: raxml
Binary: raxml
Architecture: source amd64
Version: 8.1.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
raxml - Randomized Axelerated Maximum Likelihood of phylogenetic trees
Closes: 729537 756392
Changes:
raxml (8.1.1-1) unstable; urgency=medium
.
* New upstream version
* enable SIMD and threading support
Closes: #756392, #729537
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