Public bug reported:
I installed the PHYLIP software and ran a set of data with the fitch
tool. It took 17:39 minutes which seemed very long. I then downloaded
the source code with the 'apt-get source phylip' command and checked the
make file. It reads:
...
CFLAGS = -g
#
# An optimized one for gcc
#CFLAGS = -O3 -DUNX -fomit-frame-pointer
...
So it compiles with the debug flag and no optimization. I then
uncommented the line with the optimization flags, compiled and ran the
same set of data with the same settings as before. This time it took
8:49 minutes or about twice as fast.
ProblemType: Bug
DistroRelease: Ubuntu 14.04
Package: phylip 1:3.695-1
ProcVersionSignature: Ubuntu 3.13.0-48.80-generic 3.13.11-ckt16
Uname: Linux 3.13.0-48-generic x86_64
NonfreeKernelModules: vtsspp sep3_15 pax nvidia
ApportVersion: 2.14.1-0ubuntu3.8
Architecture: amd64
CurrentDesktop: Unity
Date: Sat Apr 4 00:28:38 2015
Dependencies:
gcc-4.9-base 4.9.1-0ubuntu1
libc6 2.19-0ubuntu6.6
libgcc1 1:4.9.1-0ubuntu1
multiarch-support 2.19-0ubuntu6.6
InstallationDate: Installed on 2014-12-31 (93 days ago)
InstallationMedia: Ubuntu 14.04.1 LTS "Trusty Tahr" - Release amd64 (20140722.2)
SourcePackage: phylip
UpgradeStatus: No upgrade log present (probably fresh install)
** Affects: phylip (Ubuntu)
Importance: Undecided
Status: New
** Tags: amd64 apport-bug trusty
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https://bugs.launchpad.net/bugs/1440240
Title:
PHYLIP seems to be debug compiled with no optimization
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