emerge --update to blas-atlas-3.9.21 fails: BEST CASE 60 percent of L1, MFLOP=377.93 BEGIN L2-BLOCKED TUNING 1:ATL_gerk_axpy.c gets 377.91 MFLOPS 2:ATL_gerk_4x4_1.c gets 377.93 MFLOPS 3:ATL_gerk_1x4_0.c gets 377.91 MFLOPS 4:ATL_gerk_8x4_0.c gets 377.91 MFLOPS DONE L2-BLOCKED TUNING, CHOSE 'ATL_gerk_4x4_1.c' (377.93) M N lda percL1 mflop ====== ====== ====== ====== ========== 2300 2300 2300 150 377.91 2300 2300 2300 800 377.91 2300 2300 2300 450 377.93 2300 2300 2300 300 377.91 2300 2300 2300 200 377.91 2300 2300 2300 250 377.91 2300 2300 2300 350 377.93 2300 2300 2300 400 377.93 2300 2300 2300 600 377.91 2300 2300 2300 500 377.91 2300 make[3]: *** [res/dR1SUMM] Segmentation fault make[3]: Leaving directory `/scratch/tmp/portage/sci-libs/blas-atlas-3.9.21/work/ATLAS/gentoo-build/tune/blas/ger' make[2]: *** [/scratch/tmp/portage/sci-libs/blas-atlas-3.9.21/work/ATLAS/gentoo-build/tune/blas/ger/res/dR1SUMM] Error 2 make[2]: Leaving directory `/scratch/tmp/portage/sci-libs/blas-atlas-3.9.21/work/ATLAS/gentoo-build/bin' ERROR 955 DURING R1TUNE!!. CHECK INSTALL_LOG/dR1TUNE.LOG FOR DETAILS. make[2]: Entering directory `/scratch/tmp/portage/sci-libs/blas-atlas-3.9.21/work/ATLAS/gentoo-build/bin' I could not locate any core file in the build directories. Reproducible: Always Steps to Reproduce: 1.emerge --update blas-atlas 2. 3. Actual Results: segfault in atlas tuning Expected Results: installed atlas-blas library dev-java/java-config: 1.3.7-r1, 2.1.10 dev-lang/python: 2.4.6, 2.5.4-r4, 2.6.4, 3.1.1-r1 dev-python/pycrypto: 2.1.0_beta1 dev-util/cmake: 2.8.0-r2 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.2 sys-devel/binutils: 2.16.1-r3, 2.17-r1, 2.18-r3 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="*" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium4m -msse2 -pipe -fno-omit-frame-pointer" 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 /var/bind /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-O2 -march=pentium4m -msse2 -pipe -fno-omit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" GENTOO_MIRRORS="ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://ftp.sh.cvut.cz/MIRRORS/gentoo ftp://mirror.switch.ch/mirror/gentoo/ http://gentoo.supp.name/ " LANG="C" LDFLAGS="-Wl,-O1" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/scratch/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="X Xaw3d a52 aac aalib ac3 acl acpi alsa amr berkdb blas bluetooth bonobo branding bzip2 cairo cddb cdparanoia cdr cli consolekit cracklib crypt cxx dbus dri dts dv dvb dvd dvdnav dvdr dvdread eds emboss encode evo exif extra fam ffmpeg firefox flac fortran ftp gcj gd gdbm gif gnome gphoto2 gpm gps graphics gsm gstreamer gtk hal http hwac3 icc iconv ieee1394 imagemagick imap ipv6 jabber java javascript jpeg jpeg2k kde kpathsea lapack ldap lesstif libnotify libwww lirc lm_sensors lprng mad mbox mikmod mime mmap mmx mng modules mozilla mp3 mp4 mpeg mpi mudflap music mysql nas ncurses nls nptl nptlonly nsplugin obex ogg opengl openmp paste64 pcmcia pcre pdf perl plotutils png posix ppds pppd pstricks publishers python qt3support qt4 quicktime readline reflection samba scanner science sdl session sharedmem smartcard sndfile sockets socks5 sox spell spl sse sse2 ssl startup-notification svg svga sysfs tcl tcltk tcpd tetex threads thunar tiff tk truetype unicode usb usrp v4l v4l2 vcd vorbis wifi win32codecs wxwindows x264 x86 xine xml xmms xorg xpm xv xvid zlib zrtp" 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 mmap_emul 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 evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="radeon radeon-hd vesa sc fbdev v4l vga" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Please, attach full build.log.
I have the same error.
root@thinkpad:/home/rose(60)# emerge --info =sci-libs/blas-atlas-3.9.21 Portage 2.1.7.17 (default/linux/x86/10.0/desktop, gcc-4.4.2, glibc-2.11-r1, 2.6.32-gentoo-r3 i686) ================================================================= System Settings ================================================================= System uname: Linux-2.6.32-gentoo-r3-i686-Intel-R-_Pentium-R-_M_processor_2.00GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 04 Feb 2010 00:00:01 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] ccache version 2.4 [disabled] app-shells/bash: 4.0_p37 dev-java/java-config: 2.1.10 dev-lang/python: 2.6.4-r1, 3.1.1-r1 dev-python/pycrypto: 2.1.0 dev-util/ccache: 2.4-r8 dev-util/cmake: 2.8.0-r2 sys-apps/baselayout: 2.0.1 sys-apps/openrc: 0.6.0-r1 sys-apps/sandbox: 2.2 sys-devel/autoconf: 2.13, 2.65 sys-devel/automake: 1.4_p6, 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20 sys-devel/gcc: 3.4.6-r2, 4.4.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="x86 ~x86" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=pentium-m -fomit-frame-pointer" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=pentium-m -fomit-frame-pointer" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -march=pentium-m -fomit-frame-pointer" GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ rsync://ftp.fi.muni.cz/pub/linux/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://vlaai.snt.ipv6.utwente.nl/pub/os/linux/gentoo/" LDFLAGS="-Wl,-O1" LINGUAS="de fr" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages/" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/dotnet /var/lib/layman/java-overlay /var/lib/layman/lordvan /var/lib/layman/science /var/lib/layman/x11 /var/lib/layman/zugaina /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X Xaw3d a52 aac acl acpi administrator afs alsa amrr ao aotuv apache2 asf aspell atlas audacious audiofile automount bash-completion beagle berkdb blas bluetooth boo boost branding bzip2 c++ cairo cardbus cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib crypt cups curl cxx daap dbus device-mapper dga dia djvu doc dri ds2490 dts dv dvb dvd dvdr dvi dxr3 eds elf emacs emboss encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk foomaticdb fortran fpx fts3 fuse galago garmin gd gdal gdbm geolocation geos gif gimp ginac git glade glib glitz gml gmp gnokii gnome gnome-keyring gnuplot gnutls gphoto2 gpm graphics graphtft graphviz gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hlapi http httpd iconv icq icu id3 ide imagemagick imap innodb ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kde kdrive kerberos kexi kpathsea ladspa lame lapack laptop latex lcms ldap libffi libgda libnotify libsamplerate lirc lua lzo mad madwifi mail maildir mailwrapper math matroska mikmod mmx mmxext mng modules mono motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pam pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python qemu qhull qt3support qt4 quicktime readline reflection reiserfs rle romio rpc rrdcgi rrdtool samba sasl science sdl semantic-desktop server session slang slp smbclient sndfile snmp soup sox speex spell spl sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora thinkpad threads thunar thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wifi win32codecs wmf wxwidgets x264 x86 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0 ac97_codec emu10k1 emu10k1x" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul 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" DVB_CARDS="usb-wt220u" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev synaptics " KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="radeon vesa displaylink" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= sci-libs/blas-atlas-3.9.21 was built with the following: USE="doc -debug"
Created attachment 218469 [details] bzip2ed /var/tmp/portage/sci-libs/blas-atlas-3.9.21/temp/build.log
Almost the same error happens with blas-atlas-3.9.21-r1, now with gcc-4.4.3 at an other i686 computer: emerge -uvND blas-atlas: ... DONE STAGE 2-3-5 at 19:44 BEGIN STAGE 2-3-6: GER TUNE at 19:44 make -f Makefile INSTALL_LOG/zR1SUMM pre=z 2>&1 | ./xatlas_tee INSTALL_LOG/zR1TUNE.LOG make[2]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/bin' cd /var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger ; make res/zR1SUMM pre=z make[3]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger' ./xr1ksearch -p z Read in L1 Cache size as = 128KB. make[3]: *** [res/zR1SUMM] Segmentation fault make[3]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger' make[2]: *** [/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger/res/zR1SUMM] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/bin'
In /var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/bin/INSTALL_LOG/zR1TUNE.LOG I find: ... * BEGAN ATLAS3.9.21 INSTALL OF SECTION 2-3-7 ON 02/09/2010 AT 19:44 * ... make[2]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/bin' cd /var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger ; make res/zR1SUMM pre=z make[3]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger' ./xr1ksearch -p z Read in L1 Cache size as = 128KB. make[3]: *** [res/zR1SUMM] Segmentation fault make[3]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger' make[2]: *** [/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger/res/zR1SUMM] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/bin'
(In reply to comment #6) > make[2]: Leaving directory > `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/bin' > From your logs I can't unfortunately tell what the problem is. atlas recognizes your CPU as a P-M for which is doesn't have any arch defaults and hence does a full blown bootstrap which eventually causes the segfault. In addition, your CPU seems to have CPU throttling enabled (at least atlas thinks so). Before we go any further can you please make sure to turn throttling off completely and then try again. If that still fails, could you dial your CFLAGS back to -O2 and see how far that gets you. @Jiri: Could you please post your logs as well!
Hi Markus, what is the best way to turn off cpu throttling, change the BIOS settings, pass ACPI=off at boot command line or just stop cpufreqd? Regards
Markus, what do mean exactly by "dial your CFLAGS back to -O2"? My CFLAGS are set to '-O2 -march=pentium-m -fomit-frame-pointer'. Should I remove 'march=pentium-m -fomit-frame-pointer' from CFLAGS?
I have here an old P4 system without HT. root@tiger:/root(31)# cat /proc/cpuinfo processor : 0 vendor_id : GenuineIntel cpu family : 15 model : 2 model name : Intel(R) Pentium(R) 4 CPU 1.60GHz stepping : 4 cpu MHz : 1600.000 cache size : 512 KB fdiv_bug : no hlt_bug : no f00f_bug : no coma_bug : no fpu : yes fpu_exception : yes cpuid level : 2 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm up pebs bts bogomips : 3200.06 clflush size : 64 cache_alignment : 128 address sizes : 36 bits physical, 32 bits virtual power management: Cpufread is stopped, scaling governor is performance, cur_freq's are equal to max_freq and there is on one cpu in /sys/devices/system/cpu: root@tiger:/root(32)# /etc/init.d/cpufreqd status * status: stopped root@tiger:/root(33)# cat /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor performance root@tiger:/root(34)# cat /sys/devices/system/cpu/cpu0/cpufreq/scaling_driver p4-clockmod root@tiger:/root(35)# cat /sys/devices/system/cpu/cpu0/cpufreq/scaling_cur_freq 1600000 root@tiger:/root(36)# cat /sys/devices/system/cpu/cpu0/cpufreq/cpuinfo_cur_freq 1600000 root@tiger:/root(37)# cat /sys/devices/system/cpu/cpu0/cpufreq/cpuinfo_max_freq 1600000 root@tiger:/root(38)# ll -d /sys/devices/system/cpu/cpu[0-9] drwxr-xr-x 5 root root 0 Feb 16 12:51 /sys/devices/system/cpu/cpu0/ 'emerge blas-atlas' fails with: root@tiger:/root(39)# emerge -vuND blas-atlas ... BEST CASE 300 percent of L1, MFLOP=176.36 BEST Lmake[3]: *** [res/dR1SUMM] Segmentation fault make[3]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger' make[2]: *** [/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/tune/blas/ger/res/dR1SUMM] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.21-r1/work/ATLAS/gentoo-build/bin' Have I really to disable throttling in the BIOS?
I've just added blas/lapack-atlas-3.9.23 to portage. Please see if that fixes your problems. > > Have I really to disable throttling in the BIOS? > First off, I don't really think the problems are related to throttling issues but it is worth a try. Second, and more importantly, please don't treat blas-atlas as a regular package compilation since it is not. In order to obtain the best possible performance on your particular machine atlas goes through a large number of tests and benchmarks to find the optimal set of parameters. This will only work if the CPU delivers consistent performance during the whole procedure. Any additional system load will interfere and certainly any type of throttling. If you have a lot of interference your atlas install will be suboptimal and potentially even worse than if you would have just emerge the blas/lapack reference ebuilds. Hard to say, really. Best, Markus
I of course understand that there is performance measurement involved in the atlas installation - it's already in its acronym. I thought that echo performance > /sys/devices/system/cpu/cpu0,1/cpufreq/scaling_governor before the emerge is sufficient. However, I think in no case should the tuning test programs crash by a coredump, right? The problem is that find . -name '*core*' in the install workdir did not reveal any core file, so we do not know exactly what crashed. I thought the sandbox process involved in emerge allows coredumps to be created, or should I perhaps try (in tcsh) 'unlimit coredumpsize; emerge ...'?
> any core file, so we do not know exactly what crashed. Maybe first try fist if the new blas-atlas-3.9.23 works for you. I agree that it is very unlikely that the crash is due to CPU throttling - then again, weird things happen ;) The best would be to compile blas-atlas with debugging symbols and after a crash cd into /var/tmp and run the segfaulting command within gdb to get a backtrace or at least trigger a core dump (you might have to adjust ulimit -c). In any case, does atlas recognize your CPU as PM as in Juergen's case? I've tried compiling atlas on my old P4m an all is well. Thanks, Markus
Created attachment 220391 [details] core file with debug symbols crash generated using blas 3.9.23 and gcc 4.4.3 p1.0
The bug persists in version 3.9.23 compiled with gcc (Gentoo 4.4.3 p1.0) 4.4.3. It crashes in directory /scratch/tmp/portage/sci-libs/blas-atlas-3.9.23/work/ATLAS/gentoo-build/tune/blas/ger crashed executable ./xr1ksearch -p d Read in L1 Cache size as = 32KB. Cases read in: ID=1 ROUT='ATL_gerk_axpy.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=1 XU=16 \ LDAMUL=0 FYU=0 X87=0 ID=2 ROUT='ATL_gerk_4x4_1.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=4 \ LDAMUL=0 FYU=0 X87=0 ID=3 ROUT='ATL_gerk_1x4_0.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=1 \ LDAMUL=0 FYU=0 X87=0 ID=4 ROUT='ATL_gerk_8x4_0.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=8 \ LDAMUL=0 FYU=0 X87=0 ID=6 ROUT='ATL_dgerk_4x8_sse.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=3 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=8 \ LDAMUL=16 FYU=0 X87=0 BEGIN BASIC KERNEL TESTS: Kernel ATL_gerk_axpy.c(1) passes basic test Kernel ATL_gerk_4x4_1.c(2) passes basic test Kernel ATL_gerk_1x4_0.c(3) passes basic test Kernel ATL_gerk_8x4_0.c(4) passes basic test Kernel ATL_dgerk_4x8_sse.c(6) passes basic test DONE BASIC KERNEL TESTS: Surviving cases: ID=1 ROUT='ATL_gerk_axpy.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=1 XU=16 \ LDAMUL=0 FYU=0 X87=0 ID=2 ROUT='ATL_gerk_4x4_1.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=4 \ LDAMUL=0 FYU=0 X87=0 ID=3 ROUT='ATL_gerk_1x4_0.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=1 \ LDAMUL=0 FYU=0 X87=0 ID=4 ROUT='ATL_gerk_8x4_0.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=8 \ LDAMUL=0 FYU=0 X87=0 ID=6 ROUT='ATL_dgerk_4x8_sse.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=3 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=8 \ LDAMUL=16 FYU=0 X87=0 BEGIN L1-BLOCKED TUNING 1:ATL_gerk_axpy.c gets 377.91 MFLOPS 2:ATL_gerk_4x4_1.c gets 377.91 MFLOPS 3:ATL_gerk_1x4_0.c gets 377.93 MFLOPS 4:ATL_gerk_8x4_0.c gets 377.91 MFLOPS DONE L1-BLOCKED TUNING, CHOSE 'ATL_gerk_1x4_0.c' (377.93) M N lda percL1 mflop ====== ====== ====== ====== ========== 2300 2300 2300 50 377.91 2300 2300 2300 100 377.91 2300 2300 2300 74 377.91 2300 2300 2300 62 330.68 2300 2300 2300 56 377.91 2300 2300 2300 52 377.91 2300 2300 2300 54 377.91 2300 2300 2300 58 377.91 2300 2300 2300 60 377.93 2300 2300 2300 68 377.91 2300 2300 2300 64 377.91 2300 2300 2300 66 377.91 2300 2300 2300 70 377.91 2300 2300 2300 72 377.91 2300 2300 2300 86 377.93 2300 2300 2300 80 330.68 2300 2300 2300 76 377.91 2300 2300 2300 78 377.91 2300 2300 2300 82 377.91 2300 2300 2300 84 377.93 2300 2300 2300 92 377.91 2300 2300 2300 88 377.91 2300 2300 2300 90 377.91 2300 2300 2300 96 377.91 2300 2300 2300 94 377.91 2300 2300 2300 98 377.91 BEST CASE 60 percent of L1, MFLOP=377.93 BEGIN L2-BLOCKED TUNING 1:ATL_gerk_axpy.c gets 377.91 MFLOPS 2:ATL_gerk_4x4_1.c gets 377.91 MFLOPS 3:ATL_gerk_1x4_0.c gets 377.91 MFLOPS 4:ATL_gerk_8x4_0.c gets 377.91 MFLOPS DONE L2-BLOCKED TUNING, CHOSE 'ATL_gerk_axpy.c' (377.91) M N lda percL1 mflop ====== ====== ====== ====== ========== 2300 2300 2300 150 377.93 2300 2300 2300 800 377.91 2300 2300 2300 450 377.93 2300 2300 2300 300 377.93 2300 2300 2300 200 377.91 2300 2300 2300 250 377.91 2300 2300 2300 350 377.91 2300 2300 2300 400 377.91 2300 2300 2300 600 377.93 2300 2300 2300 500 377.91 2300 2300 2300 550 377.91 2300 2300 2300 700 377.91 2300 2300 2300 650 377.91 2300 2300 2300 750 377.93 BEST CASE 150 percent of L1, MFLOP=377.93 BEST L1-blocked kernel: ID=3 ROUT='ATL_gerk_1x4_0.c' AUTH='R. Clint Whaley' \ CacheElts=2457 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=1 \ LDAMUL=0 FYU=0 X87=0 \ MFLOP=3.779258e+02 BEST L2-blocked kernel: ID=1 ROUT='ATL_gerk_axpy.c' AUTH='R. Clint Whaley' \ CacheElts=6144 SSE=0 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=1 XU=16 \ LDAMUL=0 FYU=0 X87=0 \ MFLOP=3.779258e+02,3.779123e+02 BEGIN RESTRICTED OUT-OF-CACHE TUNING 6:ATL_dgerk_4x8_sse.c gets 377.91 MFLOPS ID=6 ROUT='ATL_dgerk_4x8_sse.c' AUTH='R. Clint Whaley' \ CacheElts=0 SSE=3 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=8 \ LDAMUL=16 FYU=0 X87=0 \ MFLOP=0.000000e+00,0.000000e+00,3.779123e+02 BEGIN RESTRICTED L1-BLOCKED TUNING TUNING 6:ATL_dgerk_4x8_sse.c gets 377.91 MFLOPS ID=6 ROUT='ATL_dgerk_4x8_sse.c' AUTH='R. Clint Whaley' \ CacheElts=2457 SSE=3 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=8 \ LDAMUL=16 FYU=0 X87=0 \ MFLOP=3.779123e+02,0.000000e+00,3.779123e+02 BEGIN RESTRICTED in-L1 TUNING TUNING ID=6 ROUT='ATL_dgerk_4x8_sse.c' AUTH='R. Clint Whaley' \ CacheElts=2457 SSE=3 alignA=0 alignY=0 alignX=0 minX=0 minY=0 YU=4 XU=8 \ LDAMUL=16 FYU=0 X87=0 \ MFLOP=3.779123e+02,0.000000e+00,3.779123e+02,0.000000e+00,inf BEGIN RESTRICTED in-L2 TUNING TUNING Segmentation fault (core dumped) Core was generated by `./xr1ksearch -p d'. Program terminated with signal 11, Segmentation fault. #0 0x080490eb in CloneR1Node (dup=0x0) at /usr/include/bits/string3.h:52 52 return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); (gdb) bt #0 0x080490eb in CloneR1Node (dup=0x0) at /usr/include/bits/string3.h:52 #1 0x0804c7a9 in main (nargs=3, args=0xbf9b8d04) at /scratch/tmp/portage/sci-libs/blas-atlas-3.9.23/work/ATLAS/gentoo-build/..//tune/blas/ger/r1ksearch.c:629 (gdb) From the header: __extern_always_inline void * __NTH (memcpy (void *__restrict __dest, __const void *__restrict __src, size_t __len)) { return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest));// LINE 52 }
The third run of TimeAllKernelsForContext (with imf = 4) returns NULL. This is because TimeR1Kernel returns -1.2352e+19 (for my system, Intel Core 2 Quad Q2800 @2.33GHz). Contents of res/dr16_435x8_444_0_a0x0x0 3 0 -1.235200e+19 -1.235200e+19 inf
Have to rm res/dr1* before running ./xr1ksearch -p d Problem appears to be that ./xdr1ktime -m 435 -n 8 -l 444 -C 4192 -Fx 16 -Fy 16 -Fa 16 occasionally returns a negative number e.g. -1.2352e+19 as its median. e.g.: # ./xdr1ktime -m 435 -n 8 -l 444 -C 4192 -Fx 16 -Fy 16 -Fa 16 GER1: M=435, N=8, lda=444, AF=[16,16,16], AM=[0,0,0], alpha=1.000000e+00: M=435, N=8, lda=444, nreps=186, time=5.370968e-06, mflop=1297.35 M=435, N=8, lda=444, nreps=186, time=-5.641194e-22, mflop=-12351995227830953984.00 M=435, N=8, lda=444, nreps=186, time=-5.641194e-22, mflop=-12351995227830953984.00 NSAMPLES=3, MAX=-12351995227830953984.00, MIN=1297.35, AVG=-8234663485220635648.00, MED=-12351995227830953984.00 Something a little wrong, it would seem.
Ah, it's the time that's the issue: capella ger # ./xdr1ktime -m 435 -n 8 -l 444 -C 4192 -Fx 16 -Fy 16 -Fa 16 GER1: M=435, N=8, lda=444, AF=[16,16,16], AM=[0,0,0], alpha=1.000000e+00: M=435, N=8, lda=444, nreps=186, time=0.000000e+00, mflop=inf M=435, N=8, lda=444, nreps=186, time=5.370968e-06, mflop=1297.35 M=435, N=8, lda=444, nreps=186, time=-5.641194e-22, mflop=-12351995227830953984.00 NSAMPLES=3, MAX=-12351995227830953984.00, MIN=1297.35, AVG=inf, MED=inf First pass: time=0 (??); second pass: time reasonable (and mflops makes sense); third pass: done in negative time! (half a negative zeptosecond; impressive, given that according to [1] (via [2]) 100 attoseconds is the shortest measured period of time). 1. http://news.bbc.co.uk/2/hi/science/nature/3486160.stm 2. http://en.wikipedia.org/wiki/Zeptosecond
Problem seems to be that time00 is returning almost-but-not-quite identical doubles before and after the test loop, if it was over quicker than the resolution of time00. It looks like it's supposed to have a resolution of 2e-4 seconds (kernel tick?). OK, in this case time00 is ATL_cputime. We're using the default implementation, which calls getrusage: #include <stdlib.h> #include <sys/time.h> #include <sys/resource.h> double ATL_cputime(void) { struct rusage ruse; getrusage(RUSAGE_SELF, &ruse); return( (double)(ruse.ru_utime.tv_sec+ruse.ru_utime.tv_usec/1000000.0) ); } So... decimal rounding fail, I guess. Easiest fix would probably be to make r1time coerce time delta to nonnegative.
Created attachment 220561 [details, diff] zerotime.patch Suggested patch.
(In reply to comment #20) > Created an attachment (id=220561) [details] > zerotime.patch > > Suggested patch. > Hi Ed, Great work, thanks a lot. Would you mind sending this upstream. I'd like them to have a look to make sure there isn't anything more fundamental broken in this case. Thanks, Markus
Filed request upstream: https://sourceforge.net/tracker/?func=detail&aid=2959857&group_id=23725&atid=379483
While I could emerge blas-atlas in the last two weeks: root@thinkpad:/root(38)# genlop -t blas-atlas | tail Sun Jan 24 04:20:37 2010 >>> sci-libs/blas-atlas-3.9.21 merge time: 3 hours, 31 minutes and 6 seconds. Sat Feb 13 16:13:07 2010 >>> sci-libs/blas-atlas-3.9.21-r1 merge time: 3 hours, 43 minutes and 45 seconds. Fri Feb 19 15:38:15 2010 >>> sci-libs/blas-atlas-3.9.23 merge time: 4 hours, 24 minutes and 57 seconds. Now 'emerge blas-atlas-3.9.23-r1' fails again with the old error: BEGIN STAGE 2-3-6: GER TUNE at 22:06 make -f Makefile INSTALL_LOG/zR1SUMM pre=z 2>&1 | ./xatlas_tee INSTALL_LOG/zR1TUNE.LOG make[2]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/bin' cd /var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/tune/blas/ger ; make res/zR1SUMM pre=z make[3]: Entering directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/tune/blas/ger' ./xr1ksearch -p z Read in L1 Cache size as = 32KB. make[3]: *** [res/zR1SUMM] Segmentation fault make[3]: Leaving directory `/var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/tune/blas/ger' make[2]: *** [/var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/tune/blas/ger/res/zR1SUMM] Error 2
(In reply to comment #23) > While I could emerge blas-atlas in the last two weeks: > > root@thinkpad:/root(38)# genlop -t blas-atlas | tail > > Sun Jan 24 04:20:37 2010 >>> sci-libs/blas-atlas-3.9.21 > merge time: 3 hours, 31 minutes and 6 seconds. > > Sat Feb 13 16:13:07 2010 >>> sci-libs/blas-atlas-3.9.21-r1 > merge time: 3 hours, 43 minutes and 45 seconds. > > Fri Feb 19 15:38:15 2010 >>> sci-libs/blas-atlas-3.9.23 > merge time: 4 hours, 24 minutes and 57 seconds. > > Now 'emerge blas-atlas-3.9.23-r1' fails again with the old error: > BEGIN STAGE 2-3-6: GER TUNE at 22:06 > make -f Makefile INSTALL_LOG/zR1SUMM pre=z 2>&1 | ./xatlas_tee > INSTALL_LOG/zR1TUNE.LOG > make[2]: Entering directory > `/var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/bin' > cd > /var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/tune/blas/ger > ; make res/zR1SUMM pre=z > make[3]: Entering directory > `/var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/tune/blas/ger' > ./xr1ksearch -p z > > Read in L1 Cache size as = 32KB. > make[3]: *** [res/zR1SUMM] Segmentation fault > make[3]: Leaving directory > `/var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/tune/blas/ger' > make[2]: *** > [/var/tmp/portage/sci-libs/blas-atlas-3.9.23-r1/work/ATLAS/gentoo-build/tune/blas/ger/res/zR1SUMM] > Error 2 > Yeah something is totaly screwed up with that version.
Hopefully it is fixed now.
I installed now 3.9.23-r1 succesfully. Jiri
Could we leave this open until we are really sure it works fine? -r1 has some big changes which aren't as flawless as I would like.
As I am trying to fix the two -r1 ebuild for *-atlas I reemerged the package multiple times. What I observed was, that this segf is randomly in time. So from ten emerges of the same ebuild w/o modifications 3-5 segf. But only on x86 for me.
*** Bug 315769 has been marked as a duplicate of this bug. ***
I can confirm this "random" behaviour (with sci-libs/blas-atlas-3.9.23-r2). After multiple failed attempts, it just managed to build without the segfault. The only thing I changed was to try to reduce CPU load by shutting down background processes, but I doubt that this is related to the problem.
Emerge of 3.9.23-r4 worked in my case on the first attempt, using gcc 4.4.3.
Dropped all atlas packages from tree. Please use sci-libs/atlas from sci overlay. If problem still exist with that package, please reopen the bug or file a new one.
