xspew: /var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS//CONFIG/src/SpewMakeInc.c:577: GetArchDef: Assertion `i < l' failed. ERROR 6 IN SYSCMND: './xspew -v 0 -O 1 -A 40 -m 2800 -s 2 -V 1008 -b 64 -f 0 -d s '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS/' -d b '/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared' -D c '-DWALL -DATL_FULL_LAPACK' -D f '-DAdd_ -DF77_INTEGER=int -DStringSunStyle' -C ic '/usr/bin/gcc' -F ic '-O2 -pipe -fPIC -m64' -C sm '/usr/bin/gcc' -F sm '-O2 -pipe -fPIC -m64' -C dm '/usr/bin/gcc' -F dm '-O2 -pipe -fPIC -m64' -C sk '/usr/bin/gcc' -F sk '-O2 -pipe -fPIC -m64' -C dk '/usr/bin/gcc' -F dk '-O2 -pipe -fPIC -m64' -C xc '/usr/bin/gcc' -F xc '-O2 -pipe -fPIC -m64' -C gc '/usr/bin/gcc' -F gc '-O2 -pipe -fPIC -m64' -C if '/usr/bin/x86_64-pc-linux-gnu-gfortran' -F if '-O2 -pipe -fPIC -m64' -Si archdef 1 -Si ieee 1 -Si bozol1 0 -Si latune 1 -Si nof77 0 -Si fko 0 -o Make.inc -t 64 -Ss pmake '$(MAKE) -j66' -Ss f77lib '-L/usr/lib/gcc/x86_64-pc-linux-gnu/4.9.3 -lgfortran ' -Si lapackref 1 -Fa gc '-fPIC'' xconfig exited with 6 Reproducible: Always # emerge --info Portage 2.2.26 (python 3.3.5-final-0, default/linux/amd64/13.0, gcc-4.9.3, glibc-2.21-r1, 4.1.15-gentoo-r1 x86_64) ================================================================= System uname: Linux-4.1.15-gentoo-r1-x86_64-AMD_Opteron-tm-_Processor_6386_SE-with-gentoo-2.2 KiB Mem: 528380724 total, 362108364 free KiB Swap: 272498492 total, 272498492 free Timestamp of repository gentoo: Tue, 26 Jan 2016 10:30:01 +0000 sh bash 4.3_p42-r1 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 app-shells/bash: 4.3_p42-r1::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.10-r1::gentoo, 3.3.5-r2::gentoo, 3.4.3-r1::gentoo dev-util/cmake: 3.3.1-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.19.1::gentoo sys-apps/sandbox: 2.10-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers) sys-libs/glibc: 2.21-r1::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 barzog-overlay location: /var/lib/layman/barzog-overlay masters: gentoo priority: 0 science location: /var/lib/layman/science masters: gentoo priority: 1 sunrise location: /var/lib/layman/sunrise masters: gentoo priority: 2 x-portage location: /usr/local/portage masters: gentoo priority: 3 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /var/bind" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j66" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" USE="X509 aac aacplus aalib accounting acl adns aim aio alpn amd64 ansi apache2 audit automount autotrace bacula-console bash-completion bcmath bidi bind-mysql bittorrent bzip2 calendar caps ccache cdb cgi chipcard chroot command-args corefonts cpudetection cpulimit cracklib cramfs cron crypt cscope css csv ctype curl curlwrappers customlog cvsgraph cxx cyrus dba dbi dbm dbx device-mapper devmap dhcp djvu dlopen dnsdb ecc emf encode enscript exif expat fam fastcgi ffmpeg fftw fits flac flash flatfile fontconfig fpm fpx ftp fuse gd gdal gdbm geoip geos gif gmp graphviz gs gssapi gzip hardened hardenedphp hdf5 hdri hpn http i18n iconv icq icu idea idled idn imagemagick imap imlib imlib2 inifile innodb ipalias iproute2 ipv6 jabber jbig jpeg jpeg2k json kerberos lapack lcms ldap less libwww lm_sensors lmtp logrotate logwatch lzma lzo mbox mcal memlimit mgetty mhash milter mime mimencode ming mmap mmx mp3 mpeg mpm-prefork mppe-mppc multilib mysql mysqli nagios-dns nagios-game nagios-ntp nagios-ping nagios-ssh ncurses netboot netcdf netifrc network nfs nis nls nntp nptl nptlonly oav ocaml ocamlopt odbc ogg oggvorbis openexr openmp openrc openssh openssl pam pam_chroot pam_timestamp pango parse-clocks pcntl pcre pdf pdfkit pdflib perl php pic plotutils png posix postfix postgis postgres postscript procmail proj pwdb python qdbm qemu quotas radius raw readline recode reiserfs rmtp rrdtool rss sample sasl screen sendfile sendmail sensord session sftp sftplogging shaper shared sharedext sieve simplexml slang slp smartcard smime smp sms smtp snmp snortsam soap sockets socks5 spamassassin spell spl sql sqlite sqlite3 sse sse2 sse3 sse4 sse4_1 sse4_2 ssl ssse3 stream subversion svg sysfs syslog sysvipc szip tcpd theora threads tidy tiff tls tokenizer transparent-proxy truetype truetype-fonts type1-fonts udev unicode userlocales utf8 uuid vhosts vim-syntax virtual-users virus-scan vorbis vpx wddx webp withsamplescripts wmf x264 xattr xfs xinetd xls xml xml2 xmlrpc xpm xsl xslt xvid yahoo yaz zlib" ABI_X86="64" APACHE2_MODULES="access http2 auth auth_basic auth_digest authn_default authn_core authn_file authz_core authz_groupfile authz_host authz_user authn_dbm authn_dbd authz_dbd dbd ident imagemap authn_dbd authn_file authn_default authz_groupfile authn_alias authn_anon authz_dbm authz_owner authz_default authz_user auth_digest authz_host alias file_cache echo charset_lite cache disk_cache mem_cache ext_filter case_filter case-filter-in deflate filter mime_magic cern_meta proxy_ajp proxy_balancer expires headers usertrack proxy proxy_connect proxy_ftp proxy_html proxy_http info include cgi cgid dav dav_lock dav_fs vhost_alias speling rewrite log_config logio env setenvif mime status substitute autoindex asis negotiation dir imap actions userdir so unique_id version dumpio log_forensic reqtimeout socache_shmcb unixd proxy_fcgi proxy_wstunnel slotmem_shm ratelimit remoteip lbmethod_bybusyness lbmethod_byrequests lbmethod_bytraffic lbmethod_heartbeat macro" APACHE2_MPMS="event" CURL_SSL="openssl" ELIBC="glibc" FFTOOLS="cws2fws qt-faststart aviocat ismindex" GRUB_PLATFORMS="pc" KERNEL="linux" NGINX_MODULES_HTTP="access auth_basic auth_request autoindex browser charset dav dav_ext fancyindex fastcgi flv geo geoip gunzip gzip gzip_static headers_more image_filter limit_conn limit_req limit_zone memcached metrics mp4 naxsi proxy push push_stream realip referer rewrite secure_link security split_clients spdy sticky stub_status sub upload upload_progress upstream_check upstream_ip_hash userid xslt" NGINX_MODULES_MAIL="smtp imap pop3" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3 python3_4" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" USERLAND="GNU" VIDEO_CARDS="dummy" USE_PYTHON="2.7 3.3 3.4" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 423938 [details] sci-libs/atlas-3.11.38-r1 build.log
Could you explain to me, what this system suppose to be? In *FLAGS you are not using any system specific optimization like "-march", you MAKEOPTS have enormous -j66, the system seems to have 0.5TB RAM...
(In reply to Justin Lecher from comment #2) > Could you explain to me, what this system suppose to be? scientific 4x AMD Opteron(tm) Processor 6386 SE (64 cores) server, it's used by many of my colleagues. > In *FLAGS you are not using any system specific optimization like "-march", > you MAKEOPTS have enormous -j66, the system seems to have 0.5TB RAM... yepp, this is from the last try. In general i go for CFLAGS="-march=bdver2 -fomit-frame-pointer -O2 -pipe", but this fails with the same error. And yes, it haves 512Gb RAM installed.
Have you tried lowering your parallel make, preferably to sequential?
(In reply to Justin Lecher from comment #4) > Have you tried lowering your parallel make, preferably to sequential? same result using: MAKEOPTS="-j" nice -n -19 emerge -1DNu sci-libs/atlas or: MAKEOPTS="-j" nice -n -19 emerge -1DNu sci-libs/atlas
(In reply to Thomas Beutin from comment #5) > (In reply to Justin Lecher from comment #4) > > Have you tried lowering your parallel make, preferably to sequential? > > same result using: > MAKEOPTS="-j" nice -n -19 emerge -1DNu sci-libs/atlas > or: > MAKEOPTS="-j" nice -n -19 emerge -1DNu sci-libs/atlas and even using MAKEOPTS="-j1" does not help ;)
Did you try without "nice"? Atlas is about optimization so you have your system to be as idle as possible and give as much power to the buildsystem as possible.
(In reply to Justin Lecher from comment #7) > Did you try without "nice"? Atlas is about optimization so you have your > system to be as idle as possible and give as much power to the buildsystem > as possible. yepp, i also tried w/o nice - same result. I know the issues about timing problemes during the build (maybe from another package), but the error messages where definitely more specific in such a case (so i excluded this so far). But anyway - this is not the source of the failure.
btw: =sci-libs/atlas-3.10.2::science compiled fine - although it tooks almost 24h... # emerge --info '=sci-libs/atlas-3.10.2::science' Portage 2.2.26 (python 3.3.5-final-0, default/linux/amd64/13.0, gcc-4.9.3, glibc-2.21-r1, 4.1.15-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.1.15-gentoo-r1-x86_64-AMD_Opteron-tm-_Processor_6386_SE-with-gentoo-2.2 KiB Mem: 528380724 total, 573420 free KiB Swap: 272498492 total, 272139308 free Timestamp of repository gentoo: Thu, 04 Feb 2016 09:00:01 +0000 sh bash 4.3_p42-r1 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 app-shells/bash: 4.3_p42-r1::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.10-r1::gentoo, 3.3.5-r2::gentoo, 3.4.3-r1::gentoo dev-util/cmake: 3.3.1-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.19.1::gentoo sys-apps/sandbox: 2.10-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers) sys-libs/glibc: 2.21-r1::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 barzog-overlay location: /var/lib/layman/barzog-overlay masters: gentoo priority: 0 science location: /var/lib/layman/science masters: gentoo priority: 1 sunrise location: /var/lib/layman/sunrise masters: gentoo priority: 2 x-portage location: /usr/local/portage masters: gentoo priority: 3 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=bdver2 -fomit-frame-pointer -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /var/bind" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=bdver2 -fomit-frame-pointer -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j66" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" USE="X509 aac aacplus aalib accounting acl adns aim aio alpn amd64 ansi apache2 audit automount autotrace bacula-console bash-completion bcmath bidi bind-mysql bittorrent bzip2 calendar caps ccache cdb cgi chipcard chroot command-args corefonts cpudetection cpulimit cracklib cramfs cron crypt cscope css csv ctype curl curlwrappers customlog cvsgraph cxx cyrus dba dbi dbm dbx device-mapper devmap dhcp djvu dlopen dnsdb ecc emf encode enscript exif expat fam fastcgi ffmpeg fftw fits flac flash flatfile fontconfig fpm fpx ftp fuse gd gdal gdbm geoip geos gif gmp graphviz gs gssapi gzip hardened hardenedphp hdf5 hdri hpn http i18n iconv icq icu idea idled idn imagemagick imap imlib imlib2 inifile innodb ipalias iproute2 ipv6 jabber jbig jpeg jpeg2k json kerberos lapack lcms ldap less libwww lm_sensors lmtp logrotate logwatch lzma lzo mbox mcal memlimit mgetty mhash milter mime mimencode ming mmap mmx mp3 mpeg mpm-prefork mppe-mppc multilib mysql mysqli nagios-dns nagios-game nagios-ntp nagios-ping nagios-ssh ncurses netboot netcdf netifrc network nfs nis nls nntp nptl nptlonly oav ocaml ocamlopt odbc ogg oggvorbis openexr openmp openrc openssh openssl pam pam_chroot pam_timestamp pango parse-clocks pcntl pcre pdf pdfkit pdflib perl php pic plotutils png posix postfix postgis postgres postscript procmail proj pwdb python qdbm qemu quotas radius raw readline recode reiserfs rmtp rrdtool rss sample sasl screen sendfile sendmail sensord session sftp sftplogging shaper shared sharedext sieve simplexml slang slp smartcard smime smp sms smtp snmp snortsam soap sockets socks5 spamassassin spell spl sql sqlite sqlite3 sse sse2 sse3 sse4 sse4_1 sse4_2 ssl ssse3 stream subversion svg sysfs syslog sysvipc szip tcpd theora threads tidy tiff tls tokenizer transparent-proxy truetype truetype-fonts type1-fonts udev unicode userlocales utf8 uuid vhosts vim-syntax virtual-users virus-scan vorbis vpx wddx webp withsamplescripts wmf x264 xattr xfs xinetd xls xml xml2 xmlrpc xpm xsl xslt xvid yahoo yaz zlib" ABI_X86="64" APACHE2_MODULES="access http2 auth auth_basic auth_digest authn_default authn_core authn_file authz_core authz_groupfile authz_host authz_user authn_dbm authn_dbd authz_dbd dbd ident imagemap authn_dbd authn_file authn_default authz_groupfile authn_alias authn_anon authz_dbm authz_owner authz_default authz_user auth_digest authz_host alias file_cache echo charset_lite cache disk_cache mem_cache ext_filter case_filter case-filter-in deflate filter mime_magic cern_meta proxy_ajp proxy_balancer expires headers usertrack proxy proxy_connect proxy_ftp proxy_html proxy_http info include cgi cgid dav dav_lock dav_fs vhost_alias speling rewrite log_config logio env setenvif mime status substitute autoindex asis negotiation dir imap actions userdir so unique_id version dumpio log_forensic reqtimeout socache_shmcb unixd proxy_fcgi proxy_wstunnel slotmem_shm ratelimit remoteip lbmethod_bybusyness lbmethod_byrequests lbmethod_bytraffic lbmethod_heartbeat macro" APACHE2_MPMS="event" CPU_FLAGS_X86="aes avx fma3 fma4 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3 xop" CURL_SSL="openssl" ELIBC="glibc" FFTOOLS="cws2fws qt-faststart aviocat ismindex" GRUB_PLATFORMS="pc" KERNEL="linux" NGINX_MODULES_HTTP="access auth_basic auth_request autoindex browser charset dav dav_ext fancyindex fastcgi flv geo geoip gunzip gzip gzip_static headers_more image_filter limit_conn limit_req limit_zone memcached metrics mp4 naxsi proxy push push_stream realip referer rewrite secure_link security split_clients spdy sticky stub_status sub upload upload_progress upstream_check upstream_ip_hash userid xslt" NGINX_MODULES_MAIL="smtp imap pop3" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3 python3_4" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" USERLAND="GNU" VIDEO_CARDS="dummy" USE_PYTHON="2.7 3.3 3.4" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= sci-libs/atlas-3.10.2::science was built with the following: USE="fortran lapack threads -doc -generic -static-libs" ABI_X86="64"
(In reply to Thomas Beutin from comment #9) > btw: =sci-libs/atlas-3.10.2::science compiled fine - although it tooks > almost 24h... strange that the older version compiles fine. Could you please report this upstream and add a reference here?
(In reply to Justin Lecher from comment #10) > (In reply to Thomas Beutin from comment #9) > > btw: =sci-libs/atlas-3.10.2::science compiled fine - although it tooks > > almost 24h... > > strange that the older version compiles fine. Could you please report this > upstream and add a reference here? i registered at sf and created a discussion topic (since i'm not allowed to post to their bugs: "Confirmed ATLAS bugs. Users should *NOT* post to this list."). https://sourceforge.net/p/math-atlas/discussion/75123/thread/9d30e1f8/
(In reply to Thomas Beutin from comment #11) > (In reply to Justin Lecher from comment #10) > > (In reply to Thomas Beutin from comment #9) > > > btw: =sci-libs/atlas-3.10.2::science compiled fine - although it tooks > > > almost 24h... > > > > strange that the older version compiles fine. Could you please report this > > upstream and add a reference here? > > i registered at sf and created a discussion topic (since i'm not allowed to > post to their bugs: "Confirmed ATLAS bugs. Users should *NOT* post to this > list."). > > https://sourceforge.net/p/math-atlas/discussion/75123/thread/9d30e1f8/ thanks, let's wait for their response.
Same here, on a more modest new 40-core server (Xeon E5-2630, 64GB Mem). That overflowing counter should be fixable no?
I think upstream has already fixed it on the latest 3.11.41 version
No longer in sci overlay
