Bug 143094

Summary:	sci-biology/mrbayes crashes on 64-bit architectures
Product:	Gentoo Linux	Reporter:	dawe <daweonline>
Component:	Current packages	Assignee:	Olivier Fisette (RETIRED) <ribosome>
Status:	RESOLVED UPSTREAM
Severity:	normal	CC:	amd64, daweonline, toffolidan
Priority:	High
Version:	unspecified
Hardware:	All
OS:	Other
URL:	http://mrbayes.csit.fsu.edu/
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	full backtrace for SIGSEGV backtrace in utf-8

Description dawe 2006-08-07 08:13:49 UTC

Hi there, I've found that mrbayes crashes as you try the sumt function on a 64-bit platform. I've tried this on amd64, on alpha and on ia64. 
I've seen that there are several reports on this behavior on
http://sourceforge.net/tracker/index.php
It seems that the bug has not been yet solved.

d

Comment 1 Jakub Moc (RETIRED) gentoo-dev

2006-08-07 08:18:16 UTC

- the link doesn't work.
- emerge --info missing
- we need a backtrace

http://www.gentoo.org/proj/en/qa/backtraces.xml

Comment 2 dawe 2006-08-08 08:38:06 UTC

Hi there. I've missed a lot of stuff in previous bug report, sorry.
If you still need I'll give emerge --info at the end of this. BTW, the problem is related to sizeof(long) that is 8 bytes on 64-bit platforms and 4 bytes on 32 bit ones. I've successfully modified the source to handle this and I'm now producing a patchset to submit. I have some problems in writing a portage-compatible patch :-(
I'm also going to produce a valuable backtrace, in the meanwhile just be informed of this workaround

cheers

d

emerge --info for amd64:

Portage 2.1.1_pre3-r3 (default-linux/amd64/2005.1, gcc-3.4.6, glibc-2.3.5-r0, 2.6.15-gentoo-r7-smp x86_64)
=================================================================
System uname: 2.6.15-gentoo-r7-smp x86_64 AMD Opteron(tm) Processor 252
Gentoo Base System version 1.6.12
app-admin/eselect-compiler: [Not Present]
dev-lang/python:     2.3.5, 2.4.3-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     [Not Present]
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.18.1
sys-devel/autoconf:  2.13, 2.59-r6
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.5
sys-devel/binutils:  2.17
sys-devel/gcc-config: 1.3.13-r2
sys-devel/libtool:   1.5.18-r1
virtual/os-headers:  2.6.11-r2
ACCEPT_KEYWORDS="amd64 ~amd64"
AUTOCLEAN="yes"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-mtune=k8 -O3 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib/X11/xkb"
CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/terminfo /etc/texmf/web2c"
CXXFLAGS="-mtune=k8 -O3 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoaddcvs autoconfig ccache distcc distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j3"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="amd64 avi berkdb bitmap-fonts cli crypt cups dlloader dri eds emboss encode foomaticdb fortran gif gnome gpm gstreamer gtk gtk2 imlib ipv6 isdnlog jpeg kde lzw lzw-tiff mp3 mpeg ncurses nls opengl pam pcre pdflib perl png pppd python qt qt3 qt4 quicktime readline reflection sdl session spell spl ssl tcpd threads tiff truetype-fonts type1-fonts usb xorg xpm xv zlib elibc_glibc input_devices_keyboard input_devices_mouse input_devices_evdev kernel_linux userland_GNU"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS


emerge --info for ia64:

Portage 2.1.1_pre3-r3 (default-linux/ia64/2005.0, gcc-4.0.3/vanilla, glibc-2.4-r3, 2.6.12-gentoo-r9IA64 ia64)
=================================================================
System uname: 2.6.12-gentoo-r9IA64 ia64 Itanium 2
Gentoo Base System version 1.12.1
app-admin/eselect-compiler: 2.0.0_rc2-r1
dev-lang/python:     2.3.5, 2.4.3-r1
dev-python/pycrypto: 2.0.1-r5
dev-util/ccache:     [Not Present]
dev-util/confcache:  [Not Present]
sys-apps/sandbox:    1.2.18.1
sys-devel/autoconf:  2.13, 2.60
sys-devel/automake:  1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2
sys-devel/binutils:  2.16.1-r3
sys-devel/gcc-config: 1.3.13-r3
sys-devel/libtool:   1.5.22
virtual/os-headers:  2.6.11-r6
ACCEPT_KEYWORDS="ia64 ~ia64"
AUTOCLEAN="yes"
CBUILD="ia64-unknown-linux-gnu"
CFLAGS="-O3 -pipe"
CHOST="ia64-unknown-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib/X11/xkb /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/"
CONFIG_PROTECT_MASK="/etc/env.d /etc/eselect/compiler /etc/gconf /etc/terminfo"
CXXFLAGS="-O3 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict"
GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo http://distfiles.gentoo.org http://www.ibiblio.org/pub/Linux/distributions/gentoo"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/usr/local/portage"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="ia64 X berkdb bitmap-fonts cli crypt cups dlloader dri eds encode foomaticdb fortran gdbm gif gnome gpm gstreamer gtk gtk2 imlib ipv6 isdnlog jpeg kde libg++ libwww mikmod motif mysql ncurses nls nptl nptlonly ogg oggvorbis opengl oss pam pcre pdflib perl png pppd python qt quicktime readline reflection sdl session spell spl ssl tcpd threads truetype truetype-fonts type1-fonts vorbis xml2 xmms xorg xv zlib elibc_glibc input_devices_keyboard input_devices_mouse input_devices_evdev kernel_linux userland_GNU"
Unset:  CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_RSYNC_EXTRA_OPTS

Comment 3 dawe 2006-08-09 02:09:11 UTC

Created attachment 93833 [details]
full backtrace for SIGSEGV

Comment 4 dawe 2006-08-09 02:13:11 UTC

Here there's the link to bug report page on sourceforge...
http://sourceforge.net/tracker/?group_id=129302&atid=714418

Comment 5 Jakub Moc (RETIRED) gentoo-dev

2006-08-09 02:15:08 UTC

(In reply to comment #3)
> Created an attachment (id=93833) [edit]
> full backtrace for SIGSEGV

Eh, can you attach something readable please?

Comment 6 Jan Kundrát (RETIRED) gentoo-dev

2006-08-09 02:40:03 UTC

Created attachment 93835 [details]
backtrace in utf-8

`iconv -f utf-16 -t utf-8 old-attachment > new-attachment`

Comment 7 Jan Kundrát (RETIRED) gentoo-dev

2006-08-09 02:40:55 UTC

Readable backtrace attached :)

Comment 8 Jakub Moc (RETIRED) gentoo-dev

2006-08-09 02:46:47 UTC

Thanks jkt.

Comment 9 dawe 2006-08-09 03:00:42 UTC

(In reply to comment #8)

whooops! Sorry.

Comment 10 Olivier Fisette (RETIRED) gentoo-dev

2006-09-12 13:49:31 UTC

Thanks for the report. I removed AMD64 support from the ebuilds pending upstream fixing the issue.

Comment 11 daniel 2009-03-18 15:13:14 UTC

(In reply to comment #10)
> Thanks for the report. I removed AMD64 support from the ebuilds pending
> upstream fixing the issue.
> 
Hi people,

Mrbayes compiled under 32 or 64 bit runs fine on my linux mint 64 bit but except when I try to sum trees (sumt command) returning a segmentation fault. In the same system I can sum trees in the virtualbox WinXP. I tried to understand what is written in this thread but I am a beginner. Please if somebody could tell me a step by step how to fix this I will greatly apprciate.

thanks

dani