cc -O3 -march=pentium4 -mmmx -msse -msse2 -msse3 -pipe -c -o util_dp_sim.o util_dp_sim.c util_dp_sim.c: In function `sim_pair_wise_lalign': util_dp_sim.c:1016: internal compiler error: in simplify_gen_subreg, at simplify-rtx.c:3558 Please submit a full bug report, with preprocessed source if appropriate. See <URL:http://bugs.gentoo.org/> for instructions. Preprocessed source stored into /var/tmp/portage/t-coffee-3.18/temp/ccFN9EEB.out file, please attach this to your bugreport. make: *** [util_dp_sim.o] Error 1 !!! ERROR: sci-biology/t-coffee-3.18 failed. !!! Function src_compile, Line 31, Exitcode 2 !!! ERROR: sci-biology/t-coffee-3.18 failed. # emerge info Portage 2.0.53 (default-linux/x86/2005.1, gcc-3.4.4, glibc-2.3.5-r3, 2.6.13.2 i686) ================================================================= System uname: 2.6.13.2 i686 Intel(R) Pentium(R) 4 CPU 3.00GHz Gentoo Base System version 1.12.0_pre11 dev-lang/python: 2.3.5, 2.4.2 sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r1 sys-devel/binutils: 2.16.1-r1 sys-devel/libtool: 1.5.20-r1 virtual/os-headers: 2.6.11-r3 ACCEPT_KEYWORDS="x86 ~x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O3 -march=pentium4 -mmmx -msse -msse2 -msse3 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/2/share/config /usr/kde/3/share/config /usr/lib/X11/xkb /usr/lib/mozilla/defaults/pref /usr/share/config /usr/spool/PBS /var/qmail/control" CONFIG_PROTECT_MASK="/etc/gconf /etc/terminfo /etc/texmf/web2c /etc/env.d" CXXFLAGS="-O2 -mcpu=i686 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks sandbox sfperms strict" GENTOO_MIRRORS="ftp://ftp.muni.cz/pub/linux/gentoo" PKGDIR="/usr/portage/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="x86 FFmpeg X Xaw3d aalib acpi alsa apache2 apm avi berkdb bidi bitmap-fonts bzip2 caca cdr crypt cscope curl dba divx divx4 divx4linux divx5 divx5linux dvd dvdr dvdread eds emacs emacs-w3 emboss encode exif expat f77 faad faad2 fam fame ffmpeg flash foomaticdb fortran fvwm fvwm2 gb gd gdbm ggi gif glut gpm gstreamer gtk gtk2 gtkhtml i8x0 icc imagemagick imlib imlib2 innodb ipv6 ithreads java javascript jpeg lcms leim libg++ libwww live lzo mad mcal mesa mikmod mmx mmx2 mng motif mozilla mp3 mpeg mule mysql ncurses network nls nptl ogg opengl oss pam pda pdflib perl plotutils png ppds pthread pthreads python qt qtx quicktime readline rtc samba sdl slang slp spell sse sse2 sse3 ssl tcltk tcpd tetex theora thread threads tiff truetype truetype-fonts type1-fonts udev unicode usb v4l v4l2 vorbis win32 winvidix wmf xml xml2 xmms xosd xv xvid xvmc zeo zlib video_cards_radeon userland_GNU kernel_linux elibc_glibc" Unset: ASFLAGS, CTARGET, LANG, LC_ALL, LDFLAGS, LINGUAS, MAKEOPTS, PORTDIR_OVERLAY # Using -O2 does not help.
Created attachment 74230 [details] ccFN9EEB.out
Thanks for reporting. Using -O2 will not solve the problem, but -O0 actually will. (I have not benchmarked how slow t-coffee actually is when not optimised at all, but it might be a problem when extracting the aligned sequences and iterating the alignment multiple times.) Since this is a reproducable GCC 3.4 specific compiler error, I am CCing the toolchain team. It is not specific to version 3.18. (The latest version, 3.27, is also affected.)
I have added a warning message to the ebuild for version 3.27. I checked different CFLAGS combinations, and it seems users of the stable version (2.66) are not affected at all. Unfortunately, this version is now masked since the archive may no longer be downloaded. Curse restricting downloading for grant purposes. :\
Yeah, I had to use CFLAGS="" emerge -u t-coffee :( This bug should be really filed to gcc guys. The preprocessed file should make them able to fix it in a moment.
(In reply to comment #2) > Thanks for reporting. Using -O2 will not solve the problem, but -O0 actually > will. Please note that "-O1" also works fine. "-O1 -funit-at-a-time" fails however.
This is a problem in gcc-3.4 all the way up to mainline. Putting to reso->upstream until we get a patch.
ribosome, can you make it strip all -O[123] flags in the meanwhile? It's a bit annoying to just have the compile be broken.
Anything new on this? I am still getting this problem with gcc-3.4.5 but not with gcc-3.3.6. Maybe running temporarily gcc-config(1) would be a better temporary fix for this.
ribosome - I suggest adding -fno-unit-at-a-time with gcc-3.4.x; e.g. adding: [[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time in src_compile() prior to the make. This gets it to compile at -O2 for me; you may also want to try -O3 and -Os as they're popular. Since I'm not a biologist I have no idea what the application does so can't check that it actually works 8-)
(In reply to comment #9) > ribosome - I suggest adding -fno-unit-at-a-time with gcc-3.4.x; e.g. adding: > > [[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time > > in src_compile() prior to the make. This gets it to compile at -O2 for me; you > may also want to try -O3 and -Os as they're popular. Since I'm not a biologist > I have no idea what the application does so can't check that it actually works > 8-) > Added to the ebuild. Thanks for the suggestion.
