Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 567682 - [science overlay] sci-libs/atlas-3.11.38-r1 - all cpus are set to performance but emerge fails due to cpu throttling
Summary: [science overlay] sci-libs/atlas-3.11.38-r1 - all cpus are set to performance...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Library (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2015-12-06 22:00 UTC by Juergen Rose
Modified: 2015-12-14 11:40 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments

Note You need to log in before you can comment on or make changes to this bug.
Description Juergen Rose 2015-12-06 22:00:56 UTC
'emerge -v1 atlas' fails with:
...
Architecture configured as  Corei2 (28)
/var/tmp/portage/sci-libs/atlas-3.11.38-r1/temp/ccsEmMaq.o: In function `ATL_tmpnam':
/var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp'

Clock rate configured as 1200Mhz

Maximum number of threads configured as  8
CPU Throttling apparently enabled!
It appears you have cpu throttling enabled, which makes timings
unreliable and an ATLAS install nonsensical.  Aborting.
See ATLAS/INSTALL.txt for further information
xconfig exited with 1
 * ERROR: sci-libs/atlas-3.11.38-r1::science failed (configure phase):
 *   configure in /var/tmp/portage/sci-libs/atlas-3.11.38-r1/work/ATLAS_shared failed
...
root@lynx:/root(21)# cat  /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor
performance
performance
performance
performance
performance
performance
performance
performance




root@lynx:/root(22)# emerge --info '=sci-libs/atlas-3.11.38-r1::science'
Portage 2.2.26 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop, gcc-4.9.3, glibc-2.22-r1, 4.3.0-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.3.0-gentoo-x86_64-Intel-R-_Core-TM-_i7-3630QM_CPU_@_2.40GHz-with-gentoo-2.2
KiB Mem:    15207056 total,   1048288 free
KiB Swap:   50331644 total,  49898264 free
Timestamp of repository gentoo: Sun, 29 Nov 2015 11:00:01 +0000
sh bash 4.3_p42
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
distcc[20812] (dcc_trace_version) distcc 3.2rc1 x86_64-pc-linux-gnu; built Nov 12 2015 10:53:53 [disabled]
app-shells/bash:          4.3_p42::gentoo
dev-java/java-config:     2.2.0::gentoo
dev-lang/perl:            5.22.0::gentoo
dev-lang/python:          2.7.10-r10::sage-on-gentoo, 3.4.3-r2::gentoo, 3.5.0-r1::gentoo
dev-util/cmake:           3.4.0-r1::gentoo
dev-util/pkgconfig:       0.29::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.18.3::gentoo
sys-apps/sandbox:         2.9::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r1::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.11.6-r1::gentoo, 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:     1.8::gentoo
sys-devel/libtool:        2.4.6-r1::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers)
sys-libs/glibc:           2.22-r1::gentoo
Repositories:

gentoo
    location: /usr/portage_lynx
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

sage-on-gentoo
    location: /var/lib/layman/sage-on-gentoo
    masters: gentoo science
    priority: 0

science
    location: /var/lib/layman/science
    masters: gentoo
    priority: 1

sunrise
    location: /var/lib/layman/sunrise
    masters: gentoo
    priority: 2

x11
    location: /var/lib/layman/x11
    masters: gentoo
    priority: 3

ago
    location: /var/lib/layman/ago
    masters: gentoo
    priority: 4

tlp
    location: /var/lib/layman/tlp
    masters: gentoo
    priority: 5

local
    location: /usr/local/portage
    masters: gentoo
    priority: 6

g-cpan
    location: /var/lib/cpan
    masters: gentoo
    priority: 7

g-octave
    location: /var/lib/g-octave
    masters: gentoo
    priority: 8

Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/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="-march=native -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="-march=native -O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j9"
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="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 amr ao apache2 apng applet archive armadillo arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cilk cli cmake collada consolekit cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples excel exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx ftp fuse gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hdaps hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jadetex java jbig jit john jpeg jpeg2k kate kde kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libgda libkms libnotify libsamplerate lirc live lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mpi-threads mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg opencl opencv openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm pstricks pulseaudio python q16 q32 qemu qhull qt3support qt4 qt5 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool rtlsdr sage samba sasl schroedinger science sdk sdl seccomp secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap sockets sound soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tbb tcl tcpd tex tex4ht texmacs theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l v4l2 vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx vtk wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" APACHE2_MPMS="worker" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog sensors thermal" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" CURL_SSL="nss" DVB_CARDS="usb-wt220u dvb_usb_rtl28xxu" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev synaptics void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd SureElec" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en fr ru" LIRC_DEVICES="devinput" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON





root@lynx:/root(23)# emerge -pqv '=sci-libs/atlas-3.11.38-r1::science'
[ebuild     U ] sci-libs/atlas-3.11.38-r1 [3.11.38] USE="doc fortran lapack threads -generic -ifko -static-libs"
Comment 1 Justin Lecher (RETIRED) gentoo-dev 2015-12-07 13:45:16 UTC
What does

zgrep PSTATE /proc/config.gz

give?

Do you have any other scaling technology enabled?
Comment 2 Juergen Rose 2015-12-07 14:27:33 UTC
(In reply to Justin Lecher from comment #1)
> What does
> 
> zgrep PSTATE /proc/config.gz
> 
> give?
> 
> Do you have any other scaling technology enabled?

PSTATE is not set. I have still set CONFIG_X86_P4_CLOCKMOD=m:

root@lynx:/usr/src/linux(12)# gzip  -dc /proc/config.gz | grep -U30 PSTATE
CONFIG_ACPI_APEI=y
CONFIG_ACPI_APEI_GHES=y
# CONFIG_ACPI_APEI_PCIEAER is not set
CONFIG_ACPI_APEI_EINJ=m
# CONFIG_ACPI_APEI_ERST_DEBUG is not set
# CONFIG_ACPI_EXTLOG is not set
# CONFIG_PMIC_OPREGION is not set
# CONFIG_SFI is not set

#
# CPU Frequency scaling
#
CONFIG_CPU_FREQ=y
CONFIG_CPU_FREQ_GOV_COMMON=y
CONFIG_CPU_FREQ_STAT=y
CONFIG_CPU_FREQ_STAT_DETAILS=y
# CONFIG_CPU_FREQ_DEFAULT_GOV_PERFORMANCE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_POWERSAVE is not set
# CONFIG_CPU_FREQ_DEFAULT_GOV_USERSPACE is not set
CONFIG_CPU_FREQ_DEFAULT_GOV_ONDEMAND=y
# CONFIG_CPU_FREQ_DEFAULT_GOV_CONSERVATIVE is not set
CONFIG_CPU_FREQ_GOV_PERFORMANCE=y
CONFIG_CPU_FREQ_GOV_POWERSAVE=m
CONFIG_CPU_FREQ_GOV_USERSPACE=m
CONFIG_CPU_FREQ_GOV_ONDEMAND=y
CONFIG_CPU_FREQ_GOV_CONSERVATIVE=m

#
# CPU frequency scaling drivers
#
# CONFIG_X86_INTEL_PSTATE is not set
# CONFIG_X86_PCC_CPUFREQ is not set
CONFIG_X86_ACPI_CPUFREQ=m
# CONFIG_X86_POWERNOW_K8 is not set
# CONFIG_X86_SPEEDSTEP_CENTRINO is not set
CONFIG_X86_P4_CLOCKMOD=m

#
# shared options
#
CONFIG_X86_SPEEDSTEP_LIB=m

#
# CPU Idle
#
CONFIG_CPU_IDLE=y
CONFIG_CPU_IDLE_GOV_LADDER=y
CONFIG_CPU_IDLE_GOV_MENU=y
# CONFIG_ARCH_NEEDS_CPU_IDLE_COUPLED is not set
CONFIG_INTEL_IDLE=y

#
# Memory power savings
#
# CONFIG_I7300_IDLE is not set

#
# Bus options (PCI etc.)
#
CONFIG_PCI=y
CONFIG_PCI_DIRECT=y
Comment 3 Justin Lecher (RETIRED) gentoo-dev 2015-12-07 14:57:49 UTC
(In reply to Juergen Rose from comment #2)
> (In reply to Justin Lecher from comment #1)
> > What does
> > 
> > zgrep PSTATE /proc/config.gz
> > 
> > give?
> > 
> > Do you have any other scaling technology enabled?
> 
> PSTATE is not set. I have still set CONFIG_X86_P4_CLOCKMOD=m:
>

Any idea how to detect if clockmod is active?
Comment 4 Juergen Rose 2015-12-08 23:54:55 UTC
(In reply to Justin Lecher from comment #3)
> (In reply to Juergen Rose from comment #2)
> > (In reply to Justin Lecher from comment #1)
> > > What does
> > > 
> > > zgrep PSTATE /proc/config.gz
> > > 
> > > give?
> > > 
> > > Do you have any other scaling technology enabled?
> > 
> > PSTATE is not set. I have still set CONFIG_X86_P4_CLOCKMOD=m:
> >
> 
> Any idea how to detect if clockmod is active?

'cpupower -c 0,1,2,3,4,5,6,7 frequency-info' does not show anything about 1200Mhz. 'lsmod | grep clock' does not show anything about Clock:

root@lynx:/root(10)# cpupower -c 0,1,2,3,4,5,6,7 frequency-info | grep 120
root@lynx:/root(11)#  lsmod | grep -i clock
root@lynx:/root(12)#
Comment 5 Justin Lecher (RETIRED) gentoo-dev 2015-12-09 09:08:43 UTC
(In reply to Juergen Rose from comment #4)
> (In reply to Justin Lecher from comment #3)
> > (In reply to Juergen Rose from comment #2)
> > > (In reply to Justin Lecher from comment #1)
> > > > What does
> > > > 
> > > > zgrep PSTATE /proc/config.gz
> > > > 
> > > > give?
> > > > 
> > > > Do you have any other scaling technology enabled?
> > > 
> > > PSTATE is not set. I have still set CONFIG_X86_P4_CLOCKMOD=m:
> > >
> > 
> > Any idea how to detect if clockmod is active?
> 
> 'cpupower -c 0,1,2,3,4,5,6,7 frequency-info' does not show anything about
> 1200Mhz. 'lsmod | grep clock' does not show anything about Clock:
> 
> root@lynx:/root(10)# cpupower -c 0,1,2,3,4,5,6,7 frequency-info | grep 120
> root@lynx:/root(11)#  lsmod | grep -i clock
> root@lynx:/root(12)#

We need some hint here from you. I cannot test this.
Comment 6 Juergen Rose 2015-12-10 08:39:41 UTC
After removing the CONFIG_X86_P4_CLOCKMOD kernel flag and booting with the resulting new kernel I could compile atlas-3.11.38-r1 without difficulties:

root@lynx:/root(2)# gzip  -dc /proc/config.gz | grep -U5 PSTATE
CONFIG_CPU_FREQ_GOV_CONSERVATIVE=m

#
# CPU frequency scaling drivers
#
# CONFIG_X86_INTEL_PSTATE is not set
# CONFIG_X86_PCC_CPUFREQ is not set
CONFIG_X86_ACPI_CPUFREQ=m
# CONFIG_X86_POWERNOW_K8 is not set
# CONFIG_X86_SPEEDSTEP_CENTRINO is not set
# CONFIG_X86_P4_CLOCKMOD is not set

root@lynx:/root(3)# genlop -t atlas | tail

     Thu Nov 12 01:56:09 2015 >>> sci-libs/atlas-3.10.1-r2
       merge time: 9 minutes and 18 seconds.

     Fri Dec  4 10:31:04 2015 >>> sci-libs/atlas-3.11.38
       merge time: 1 hour, 37 minutes and 21 seconds.

     Wed Dec  9 15:24:28 2015 >>> sci-libs/atlas-3.11.38-r1
       merge time: 1 hour, 36 minutes and 40 seconds.
Comment 7 Justin Lecher (RETIRED) gentoo-dev 2015-12-11 08:50:58 UTC
(In reply to Juergen Rose from comment #6)
> After removing the CONFIG_X86_P4_CLOCKMOD kernel flag and booting with the
> resulting new kernel I could compile atlas-3.11.38-r1 without difficulties:
> 

So we need to have at least a way to detect if not disable these throttlings.
Comment 8 Guilherme Amadio gentoo-dev 2015-12-11 09:42:28 UTC
(In reply to Justin Lecher from comment #7)
> (In reply to Juergen Rose from comment #6)
> > After removing the CONFIG_X86_P4_CLOCKMOD kernel flag and booting with the
> > resulting new kernel I could compile atlas-3.11.38-r1 without difficulties:
> > 
> 
> So we need to have at least a way to detect if not disable these throttlings.

If it's a kernel config, then it may not be possible to disable, but it might make sense to add warnings about the kernel config in the ebuild by using the linux-info eclass. Have a look at sys-power/powertop for an example.
Comment 9 Justin Lecher (RETIRED) gentoo-dev 2015-12-14 11:40:06 UTC
commit 6ff188a81f27d09a7a6eb304d91afc3a5caea7d4
Author: Justin Lecher <jlec@gentoo.org>
Date:   Mon Dec 14 12:39:34 2015 +0100
    
    sci-libs/atlas: Warn if incompatible kernel config is set
    
    Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=567682
    
    Package-Manager: portage-2.2.26
    Signed-off-by: Justin Lecher <jlec@gentoo.org>