I get several errors while updating blas-atlas from 3.7.11-r1 to 3.8.0 Reproducible: Always Steps to Reproduce: 1. just emerge blas-atlas :-) Actual Results: emerge failed Expected Results: emerge succeded Result of 'emerge --info': Portage 2.1.3.19 (default-linux/x86/2007.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.22-gentoo-r8 i686) ================================================================= System uname: 2.6.22-gentoo-r8 i686 AMD Sempron(tm) 2800+ Timestamp of tree: Wed, 19 Dec 2007 07:16:01 +0000 app-shells/bash: 3.2_p17 dev-java/java-config: 1.3.7, 2.0.33-r1 dev-lang/python: 2.4.4-r6 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.9-r2 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.3.16 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.22-r2 ACCEPT_KEYWORDS="x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=i686 -O2 -pipe -mmmx -msse -m3dnow" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=i686 -O2 -pipe -mmmx -msse -m3dnow" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://mirror.exp.dc.uba.ar/gentoo/ http://gentoo.cites.uiuc.edu/pub/gentoo/" LC_ALL="en_US.utf8" LINGUAS="en es es_AR" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_EXTRA_OPTS="--timeout=600" 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 --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/portage/local/layman/enlightenment /usr/portage/local/layman/science /usr/local/portage" SYNC="rsync://mirror.exp.dc.uba.ar/gentoo-portage" USE="3dnow 3dnowext X aac acl acpi alsa apache2 apm arts asf audiofile avi bash-completion berkdb bitmap-fonts bzip2 bzlib cairo cdb cdparanoia cdr cli cracklib crypt cscope cups curl dbus doc dri dvd dvdread emboss encode exif f77 fam ffmpeg firefox flac foomaticdb fortran gcj gd gdbm gif glut gmp gnome gpm graphviz gstreamer gtk gtk2 gtkhtml iconv idn imagemagick imlib ipv6 isdnlog java jpeg kde lapack lcms ldap libg++ libwww lua mad mbox midi mikmod mmx mmxext mng motif mozilla mp3 mpeg mpi mudflap mysql ncurses nls nptl nptlonly nsplugin ntpl nvidia ogg oggvorbis opengl openmp oss pam pcre pdflib perl php png pppd python qt quicktime readline recode reflection samba sdl session slang spell spl sqlite ssl svga szip tcltk tcpd tetex threads tiff tk truetype truetype-fonts type1-fonts udev unicode usb vim-with-x vorbis win32codecs x86 xml xorg xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en es es_AR" USERLAND="GNU" VIDEO_CARDS="nv fbdev" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS
Created attachment 138892 [details] part of the log file from emerge (total log is over 5000 Kb)
Please attach the whole log (bzipped).
Created attachment 138913 [details] whole log file, bzipped
Hi Matías, Thanks much for your report and, unfortunately, you're suffering from a problem that pops up on K7 CPUs that we've yet to diagnose. In any case, could you please post the content of /var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/include/dXover.h Is there any chance I could get temporary access to your box for some testing? Otherwise I will have to go upstream with this issue. Thanks, Markus
I had this problem too, but syncing (and updating several packages, see below) and re-trying made it go away. I had a brief look at the faulty dXover.h file. If contained beginning include-guards and then three DEFINEs, but no ending include-guard -- hence the missing-#endif error message. After syncing, the dXover.h header file was much longer, and the include-guard was correctly terminated. The faulty header file looked like this #ifndef _FOOBAR #define _FOOBAR #define foo bar #define foo bar #define foo bar (the defines were not identical) Between trying, I updated the following packages: mldonkey dejavu xkeyboard-config libX11 libSM gdb libexif cups libXpm libXi libXxf86dga libXcursor libXtst imlib libXaw linux-headers gnuconfig gmp gettext inputproto libICE xf86dgaproto gpm libXfont glproto xorg-server gnupg Soory for flooding. I realize most of these package updates are probably irrelevant, but I thought I'd give you all the info.
Thanks for you note, I appreciate it! Was this on a K7 as well or a different type of chip; also what version of gcc do you have? In Matías case, atlas' crossover point detection routine fails to converge resulting in the half baked include file. Unfortunately I am not quite sure why this happens and I have asked him to file a bug upstream about this. In don't think that the problem is related to any of the packages you upgraded, but I could imagine that the routine fails if there is too much background noise, i.e., other processes running on the machine, during compilation. It could also be an issue with gcc-4.1 but I don't have any evidence for this either. Best, Markus
My Athlon-XP 3000 system has locked up twice trying to compile this package... I left it running so I didn't witness the lockup, but the system was totally unresponsive when I came back (X was not running and the console would not even give login:, network access was also down). In the hopes that this information is of any use, here is what I found in my logs: current:Dec 25 20:34:47 [kernel] [23762.277861] xsfc[14095]: segfault at 4067b140 eip 08048de2 esp bfb50700 error 4 current:Dec 25 20:37:18 [kernel] [23913.207681] xsfc[15034]: segfault at 40681120 eip 08048de2 esp bfd208d0 error 4 current:Dec 25 20:40:41 [kernel] [24115.614388] xsfc[16177]: segfault at 40685140 eip 08048e4f esp bffa8af8 error 4 log-2007-12-26-00:12:58:Dec 25 11:48:57 [kernel] [ 7395.216157] xsfc[14060]: segfault at 4067b140 eip 08048de2 esp bffbe040 error 4 log-2007-12-26-00:12:58:Dec 25 11:51:36 [kernel] [ 7553.142381] xsfc[15001]: segfault at 40681120 eip 08048de2 esp bf8d0950 error 4 log-2007-12-26-00:12:58:Dec 25 11:55:11 [kernel] [ 7767.805308] xsfc[16146]: segfault at 40685140 eip 08048e4f esp bfcbbcc8 error 4
Hi Charles, Please make sure that this is not related to any hardware issues such as bad memory. Compilation of blas or any other package for that matter should never lock up your box like that. Also, could you please provide us with your emerge --info? Thanks, Markus
I've tried on two different (but similar Athlon XP systems; the second will not build but did not lock up). A third, a hardened gentoo system, does build this package.
Hi Charles, Could you please post your emerge --info. I suspect that this is something that upstream needs to look at. Would you mind filing a bug with them? Thanks, Markus
On my computer the package doesn't build too. Here some information: ********************* make[5]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/tune/blas/ger' i686-pc-linux-gnu-gcc -c -DL2SIZE=4194304 -I/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/include -I/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/..//include -I/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_K7 -DATL_CPUMHZ=2205 -DATL_SSE1 -DATL_3DNow -DATL_GAS_x8632 -march=athlon-xp -O3 -m32 -o ATL_dger.o -DDREAL -I/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/tune/blas/ger ATL_ger.c In Datei, eingefügt von /var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/..//include/atlas_lvl3.h:42, von ATL_ger.c:33: /var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/include/dXover.h:1:1: Fehler: unbeendetes #ifndef make[5]: *** [ATL_dger.o] Fehler 1 make[5]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/tune/blas/ger' make[4]: *** [dr1case] Fehler 2 make[4]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/tune/blas/ger' xr1search: /var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/..//tune/blas/ger/r1search.c:472: RunCases: Assertion `imax' failed. ATL_ger1_axpy.c : 0.00 ATL_ger1_4x4_1.c : 0.00 ATL_ger1_1x4_0.c : 0.00 ATL_ger1_8x4_0.c : 0.00 ATL_ger1_SSE.c : 0.00 make[3]: *** [res/dR1RES] Abgebrochen make[3]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/tune/blas/ger' make[2]: *** [/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/tune/blas/ger/res/dR1RES] Fehler 2 make[2]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/bin' ERROR 776 DURING R1TUNE!!. CHECK INSTALL_LOG/dR1TUNE.LOG FOR DETAILS. make[2]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/bin' cd /var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build ; make error_report make[3]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build' make -f Make.top error_report make[4]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build' uname -a 2>&1 >> bin/INSTALL_LOG/ERROR.LOG i686-pc-linux-gnu-gcc -v 2>&1 >> bin/INSTALL_LOG/ERROR.LOG Es werden eingebaute Spezifikationen verwendet. Ziel: i686-pc-linux-gnu Konfiguriert mit: /var/tmp/portage/sys-devel/gcc-4.1.2/work/gcc-4.1.2/configure --prefix=/usr --bindir=/usr/i686-pc-linux-gnu/gcc-bin/4.1.2 --includedir=/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/include --datadir=/usr/share/gcc-data/i686-pc-linux-gnu/4.1.2 --mandir=/usr/share/gcc-data/i686-pc-linux-gnu/4.1.2/man --infodir=/usr/share/gcc-data/i686-pc-linux-gnu/4.1.2/info --with-gxx-include-dir=/usr/lib/gcc/i686-pc-linux-gnu/4.1.2/include/g++-v4 --host=i686-pc-linux-gnu --build=i686-pc-linux-gnu --disable-altivec --enable-nls --without-included-gettext --with-system-zlib --disable-checking --disable-werror --enable-secureplt --disable-libunwind-exceptions --disable-multilib --enable-libmudflap --disable-libssp --disable-libgcj --with-arch=i686 --enable-languages=c,c++,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit --enable-clocale=gnu Thread-Modell: posix gcc-Version 4.1.2 (Gentoo 4.1.2 p1.0.1) i686-pc-linux-gnu-gcc -V 2>&1 >> bin/INSTALL_LOG/ERROR.LOG i686-pc-linux-gnu-gcc: Die Option »-V« muss ein Argument haben make[4]: [error_report] Fehler 1 (ignoriert) i686-pc-linux-gnu-gcc --version 2>&1 >> bin/INSTALL_LOG/ERROR.LOG tar cf error_K732SSE1.tar Make.inc bin/INSTALL_LOG/* gzip --best error_K732SSE1.tar mv error_K732SSE1.tar.gz error_K732SSE1.tgz make[4]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build' make[3]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build' make[2]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build/bin' Error report error_<ARCH>.tgz has been created in your top-level ATLAS directory. Be sure to include this file in any help request. cat: ../../CONFIG/error.txt: Datei oder Verzeichnis nicht gefunden cat: ../../CONFIG/error.txt: Datei oder Verzeichnis nicht gefunden make[1]: *** [build] Fehler 255 make[1]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.8.0/work/ATLAS/gentoo-build' make: *** [build] Fehler 2 * * ERROR: sci-libs/blas-atlas-3.8.0 failed. * Call stack: * ebuild.sh, line 1701: Called dyn_compile * ebuild.sh, line 1039: Called qa_call 'src_compile' * ebuild.sh, line 44: Called src_compile * blas-atlas-3.8.0.ebuild, line 102: Called die * The specific snippet of code: * emake -j1 || die "emake failed" * The die message: * emake failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-libs/blas-atlas-3.8.0/temp/build.log'. * ************************ Portage 2.1.3.19 (default-linux/x86/2007.0/desktop, gcc-4.1.2, glibc-2.6.1-r0, 2.6.23.1 i686) ================================================================= System uname: 2.6.23.1 i686 AMD Athlon(tm) XP 3200+ Timestamp of tree: Tue, 05 Feb 2008 11:00:01 +0000 distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] app-shells/bash: 3.2_p17-r1 dev-java/java-config: 1.3.7, 2.1.4 dev-lang/python: 2.3.5-r3, 2.4.4-r6 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.10-r5 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="x86" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=athlon-xp -O3" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/splash /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=athlon-xp -O3" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo/ http://gentoo.oregonstate.edu/ http://www.ibiblio.org/pub/Linux/distributions/gentoo" LANG="de_DE@euro" LC_ALL="de_DE@euro" LINGUAS="de" 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 --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext X a52 aac acl acpi aim alsa arts asf bash-completion berkdb bitmap-fonts bzip2 cairo cdr cli cracklib crypt cups dbus dga dmx dri dvd dvdr dvdread emboss encode esd evo fam firefox flac fluidsynth fortran gdbm gif gimp gnome gpm gstreamer gtk hal hbci iconv icq imap ipv6 isdnlog jack jpeg kde kerberos ladcca ldap libpng mad maps midi mikmod mmx mmxext mp3 mpeg mudflap ncurses network nls nntp nptl nptlonly nsplugin ofx ogg openal opengl openmp oss pam pcre pdf perl png ppds pppd python qt3 qt3support qt4 quicktime readline real reflection sdl sensord session spell spl sqlite sse ssl stencil-buffer svg tcltk tcpd tetex tiff truetype truetype-fonts type1-fonts unicode usb vorbis win32codecs wxwindows x86 xml xorg xv xvid zlib" ALSA_CARDS="emu10k1" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse aiptek" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de" LIRC_DEVICES="serial" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, MAKEOPTS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 142720 [details] error log
This looks like the same K7 error that the others have been reporting. PLEASE file a bug with upstream about this since I don't have the proper hardware to do anything about it and please keep us informed about any progress. Thanks in advance! Markus
Who or what is upstream?
Hi Wilfried, My apologies for not being clear enough on this. Upstream refers to the original developer(s) of the atlas package. You can file a bug at their bugtracker https://sourceforge.net/tracker/?atid=379483&group_id=23725&func=browse Before you do so please read through http://math-atlas.sourceforge.net/faq.html#help for instructions on what to post. Thanks, Markus
Does the new blas-atlas-3.8.1 solve this issue or does it persist? Thanks, Markus
blas-atlas-3.8.1 does solve the issue for me. I changed resolution to FIXED (I guess this is what I have to do; please reopen it otherwise).
Hi Matías, Thanks for your response and I am glad to hear that these K7 issues seem to be fixed now (closing as FIXED was absolutely correct BTW). cheers, Markus
