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cschwan / sage-on-gentoo

(Unofficial) Gentoo Overlay for Sage- and Sage-related ebuilds
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6.10.beta1 fails on Gentoo #376

Closed strogdon closed 9 years ago

strogdon commented 9 years ago

Here I get:

error: [Errno 2] No such file or directory: '/usr/share/sage/ext/notebook-ipython'
 * ERROR: sci-mathematics/sage-9999::sage-on-gentoo failed (install phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line   93:  Called src_install
 *   environment, line 4763:  Called distutils-r1_src_install
 *   environment, line 1327:  Called _distutils-r1_run_foreach_impl 'distutils-r1_python_install'
 *   environment, line  564:  Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_install'
 *   environment, line 4095:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_install'
 *   environment, line 3122:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_install'
 *   environment, line 3120:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_install'
 *   environment, line  894:  Called distutils-r1_run_phase 'distutils-r1_python_install'
 *   environment, line 1296:  Called distutils-r1_python_install
 *   environment, line 1217:  Called esetup.py 'install' '--root=/var/tmp/portage/sci-mathematics/sage-9999/image//_python2.7'
 *   environment, line 1801:  Called die
 * The specific snippet of code:
 *       "${@}" || die
 *

I haven't investigated further.

strogdon commented 9 years ago

I should note that to build sage I did emerge -C sage && emerge -1 sage.

kiwifb commented 9 years ago

I cannot reproduce this. What useflags do you have?

ll /home/extra/portage/sci-mathematics/sage-9999/image/usr/share/sage/ext/notebook-ipython/
total 32K
drwxr-xr-x  2 fbissey fbissey 4.0K Oct 25 21:43 .
drwxr-xr-x 14 fbissey fbissey 4.0K Oct 25 21:43 ..
-rw-r--r--  1 fbissey fbissey 3.4K Oct 25 21:43 logo-64x64.png
-rw-r--r--  1 fbissey fbissey  19K Oct 25 21:43 logo.svg
strogdon commented 9 years ago

Well, Sage is gone, but for a new emerge:

[ebuild  N    #] sci-mathematics/sage-9999  USE="X debug html latex testsuite -arb -bliss -modular_decomposition -pdf" LINGUAS="en -ca -de -fr -hu -it -pt -ru -tr" PYTHON_TARGETS="python2_7"

and

ls -al /var/tmp/portage/sci-mathematics/sage-9999/image/usr/share/
total 12
drwxr-xr-x 3 root root 4096 Oct 24 21:47 .
drwxr-xr-x 3 root root 4096 Oct 24 21:47 ..
drwxr-xr-x 4 root root 4096 Oct 24 21:47 jupyter
kiwifb commented 9 years ago

Yes, I explicitly put code to do that - in conjunction with some code from Jeroen in sage. Troublesome bits, I don't believe there is currently a correct way to do what he wants from a distro perspective from setup.py and I am going to have to accept that.

kiwifb commented 9 years ago

Now I get it, it shouldn't be the only thing, ext should be there amongst others.

kiwifb commented 9 years ago 
ll /home/extra/portage/sci-mathematics/sage-9999/image/usr/share/
total 28K
drwxr-xr-x 7 fbissey fbissey 4.0K Oct 25 21:47 .
drwxr-xr-x 6 fbissey fbissey 4.0K Oct 25 21:43 ..
drwxr-xr-x 2 fbissey fbissey 4.0K Oct 25 21:43 applications
drwxr-xr-x 3 fbissey fbissey 4.0K Oct 25 21:47 doc
drwxr-xr-x 4 fbissey fbissey 4.0K Oct 25 21:43 jupyter
drwxr-xr-x 2 fbissey fbissey 4.0K Oct 25 21:43 pixmaps
drwxr-xr-x 4 fbissey fbissey 4.0K Oct 25 21:43 sage

Do I dare ask if you have a disk space problem? There may be something else in the log that is of interest if you could zip it and send it my way.

strogdon commented 9 years ago

I don't think it's disk related. I get the same in Prefix.

strogdon commented 9 years ago

This is odd. It appears none of the insinto in the ebuild are doing anything? I can't see that anything has changed there since 6.10.beta0. But there must be something.

kiwifb commented 9 years ago

Hum...very strange they should die I believe if they fail. From the failure it is almost like portage thinks it's done it and then cannot find the files. The only thing I can think of, is that on your system portage expect the folder to be created before hand. What version of portage are we talking about?

kiwifb commented 9 years ago

A number of things should have gone under usr/share and usr/share/sage in particular before going to ext. I'll also need emerge --info and version of setuptools and cython I think.

strogdon commented 9 years ago

Gentoo:

[I] dev-python/setuptools
     Available versions:  2.2 7.0 ~8.0.1 ~8.2.1 (~)9.1 12.0.1 ~12.0.3 ~12.0.5 ~15.0 ~15.2 ~16.0 ~17.0 ~17.1.1 ~18.0.1 ~18.1 ~18.2 ~18.2-r2 ~18.2-r3 ~18.3.2 **9999 {test PYTHON_TARGETS="pypy pypy3 python2_7 python3_3 python3_4"}
     Installed versions:  12.0.1(12:10:02 AM 03/08/2015)(-test PYTHON_TARGETS="python2_7 python3_3 -pypy -pypy3 -python3_4")
     Homepage:            https://pypi.python.org/pypi/setuptools
     Description:         a collection of extensions to Distutils

[U] dev-python/cython
     Available versions:  0.22 ~0.22-r5[1] ~0.23.2 (~)0.23.3 (~)0.23.4-r1[1] {doc examples test PYTHON_TARGETS="python2_7 python3_3 python3_4"}
     Installed versions:  0.23.3-r1[1](10:10:46 AM 10/08/2015)(-doc -examples -test PYTHON_TARGETS="python2_7 python3_3 -python3_4")
     Homepage:            http://www.cython.org/ https://pypi.python.org/pypi/Cython
     Description:         A Python to C compiler

[1] "sage-on-gentoo" /var/lib/layman/sage-on-gentoo

[I] sys-apps/portage
     Available versions:  2.2.8-r2 2.2.14 [m]2.2.18 [m]2.2.20 2.2.20.1 ~2.2.22 **9999 {build doc epydoc +ipc pypy2_0 python2 python3 selinux xattr LINGUAS="ru" PYTHON_TARGETS="pypy pypy2_0 python2_6 python2_7 python3_2 python3_3 python3_4"}
     Installed versions:  2.2.20.1(11:19:12 PM 08/18/2015)(ipc -build -doc -epydoc -selinux -xattr LINGUAS="-ru" PYTHON_TARGETS="python2_7 python3_3 -pypy -python3_4")
     Homepage:            https://wiki.gentoo.org/wiki/Project:Portage
     Description:         Portage is the package management and distribution system for Gentoo

Prefix:

[I] dev-python/setuptools
     Available versions:  2.2 7.0 8.0.1 8.2.1 9.1 12.0.1 12.0.3 12.0.5 15.0 15.2 16.0 17.0 17.1.1 18.0.1 18.1 18.2 18.2-r2 18.2-r3 18.3.2 18.4 **9999 {test PYTHON_TARGETS="pypy pypy3 python2_7 python3_3 python3_4 python3_5"}
     Installed versions:  18.4(06:50:33 PM 10/14/2015)(-test PYTHON_TARGETS="python2_7 python3_3 -pypy -pypy3 -python3_4 -python3_5")
     Homepage:            https://pypi.python.org/pypi/setuptools
     Description:         a collection of extensions to Distutils

[U] dev-python/cython
     Available versions:  0.20-r1[2] 0.22 0.22-r5[1] 0.23.2 0.23.3 0.23.4 0.23.4-r1[1] {doc examples test PYTHON_TARGETS="python2_7 python3_3 python3_4 python3_5"}
     Installed versions:  0.23.3-r1[1](05:13:31 PM 10/07/2015)(-doc -examples -test PYTHON_TARGETS="python2_7 python3_3 -python3_4")
     Homepage:            http://www.cython.org/ https://pypi.python.org/pypi/Cython
     Description:         A Python to C compiler

[1] "sage-on-gentoo" /storage/strogdon/gentoo-redlizard/var/lib/layman/sage-on-gentoo
[2] "local-overlay" /storage/strogdon/local-overlay

[I] sys-apps/portage
     Available versions:  2.2.01.21165^t[2] 2.2.01.21313^t[2] [m]2.2.4.22351[3] [m]2.2.6.22374[3] [m]2.2.7[3] [m]2.2.8[1] 2.2.10.1 [m]2.2.10.1[1] 2.2.10.1-r1 [m]2.2.10.1-r1[1] 2.2.14 [m]2.2.14[1] [m]2.2.20 {build doc epydoc (+)ipc prefix-chaining pypy2_0 python2 python3 selinux xattr LINGUAS="pl ru" PYTHON_TARGETS="pypy1_9 pypy2_0 python2_6 python2_7 python3_1 python3_2 python3_3 python3_4"}
     Installed versions:  2.2.14(12:30:52 PM 10/13/2015)(ipc -build -doc -epydoc -prefix-chaining -pypy2_0 -python2 -python3 -selinux -xattr LINGUAS="-ru" PYTHON_TARGETS="python2_7 python3_3 -pypy1_9 -pypy2_0 -python2_6 -python3_1 -python3_2 -python3_4")
     Homepage:            http://www.gentoo.org/proj/en/gentoo-alt/prefix/
     Description:         Prefix branch of the Portage Package Manager, used in Gentoo Prefix

[1] "heroxbd" /storage/strogdon/gentoo-redlizard/var/lib/layman/heroxbd
[2] "prefix-with-glibc" /storage/strogdon/gentoo-prefix-libc/overlay
[3] "rap" /storage/strogdon/prefix-libc

I see cython needs to be updated but it was used with 6.10.beta0. I have =sys-apps/portage-2.2.20 masked in Prefix because I think it does not respect package masks.

strogdon commented 9 years ago

Gentoo: emerge --info

Portage 2.2.20.1 (python 2.7.10-final-0, default/linux/amd64/13.0/desktop, gcc-4.9.3, glibc-2.20-r2, 3.6.11-gentoo x86_64)
=================================================================
System uname: Linux-3.6.11-gentoo-x86_64-Dual-Core_AMD_Opteron-tm-_Processor_2218-with-gentoo-2.2
KiB Mem:     8198876 total,   2077932 free
KiB Swap:    4200984 total,   3744392 free
Timestamp of repository gentoo: Mon, 05 Oct 2015 23:45:01 +0000
sh bash 4.3_p39
ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1
ccache version 3.1.9 [enabled]
app-shells/bash:          4.3_p39::gentoo
dev-java/java-config:     2.2.0::gentoo
dev-lang/perl:            5.20.2::gentoo
dev-lang/python:          2.7.10::gentoo, 3.2.5-r6::gentoo, 3.3.5-r1::gentoo, 3.4.3::gentoo
dev-util/ccache:          3.1.9-r4::gentoo
dev-util/cmake:           3.2.2::gentoo
dev-util/pkgconfig:       0.29::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.17::gentoo
sys-apps/sandbox:         2.6-r1::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69::gentoo
sys-devel/automake:       1.9.6-r3::gentoo, 1.10.3::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:            4.1.2::gentoo, 4.5.4::gentoo, 4.7.3-r1::gentoo, 4.8.5::gentoo, 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: 3.18::gentoo (virtual/os-headers)
sys-libs/glibc:           2.20-r2::gentoo
Repositories:

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

desktop-effects
    location: /var/lib/layman/desktop-effects
    masters: gentoo
    priority: 0

sage-on-gentoo
    location: /var/lib/layman/sage-on-gentoo
    masters: gentoo science
    priority: 1

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

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

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

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

x11
    location: /var/lib/layman/x11
    masters: gentoo
    priority: 6

local-overlay
    location: /usr/local/portage
    masters: gentoo
    priority: 7

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA google-chrome googleearth AdobeFlash-10.3 AdobeFlash-11.x Oracle-BCLA-JavaSE PUEL"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /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-php5.4/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.4/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/splash /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 ccache config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_EXTRA_OPTS="--delete-after --timeout=500"
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="3dnow X Xaw3d a52 aac aalib acl acpi alsa amd64 apache2 audiofile bash-completion berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif glamor gphoto2 gpm gstreamer gtk iconv ieee1394 imlib ipv6 java jpeg lcms ldap lesstif libnotify lm_sensors mad midi mmx mmxext mng modules motif mozilla mp3 mp4 mpeg multilib ncurses nls nptl nsplugin ogg opengl openmp oss pam pango pcre pdf png policykit ppds qt3support qt4 radius readline sdl seccomp session spell sse sse2 ssl startup-notification svg tcl tcpd tiff tk truetype udev udisks unicode upower usb vorbis win32codecs wxwidgets x264 xcb xml xv xvid zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd 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 cgi cgid 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" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext sse sse2 sse3" 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="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-4 php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="nvidia fbdev vesa vga nv" 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"
USE_PYTHON="2.7 3.2 3.3"
Unset:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS
strogdon commented 9 years ago

In the first post there is the error

error: [Errno 2] No such file or directory: '/usr/share/sage/ext/notebook-ipython'

If I create the folder /usr/share/sage/ext/notebook-ipython (on the live system) then the install proceeds properly.

kiwifb commented 9 years ago

That's extremely weird. Checking some stuff.

strogdon commented 9 years ago

Are you able to remove sage (emerge -C sage) and then reinstall it?

kiwifb commented 9 years ago

Yes I reproduce it on gentoo now. I think the trigger is not ext/notebook-ipython but just ext I had a ext/octave folder that I had created manually to deal with a then octave issue some times ago. Still checking prefix, which is weirder because I regularly un-merge sage before merging it again there [the file system performance is quite poor, if I merge on top of an existing install, file collision checking takes about 8 hours, removal just under 10 minutes)

strogdon commented 9 years ago

My prefix has (12 cores) so building is really fast. But the file collision checking is a real pain.

kiwifb commented 9 years ago

Same here on my main gentoo machine (12 cores with hyper threading). And confirmed this time on the prefix, and my alternate patches on the vbraun branch point stuff squarely on the new code installing stuff in /usr/share/jupyter this will need some extra attention.

[426/433] Cythonizing sage/symbolic/expression.pyx
************************************************************************
Traceback (most recent call last):
  File "setup.py", line 627, in <module>
    python_data_files.append(SageKernelSpec.ipython_extra_files()[0])
  File "/home/extra/portage/sci-mathematics/sage-9999/work/sage-9999/src-python2_7/sage/repl/ipython_kernel/install.py", line 237, in ipython_extra_files
    instance._symlink_resources()
  File "/home/extra/portage/sci-mathematics/sage-9999/work/sage-9999/src-python2_7/sage/repl/ipython_kernel/install.py", line 208, in _symlink_resources
    for filename in os.listdir(path):
OSError: [Errno 2] No such file or directory: '/usr/share/sage/ext/notebook-ipython'
************************************************************************
Error building the Sage library
************************************************************************
Finished Cythonizing, time: 98.73 seconds.

My prefix hits the zone where throwing more cores is not useful because of i/o bottleneck:

[frb15@hp1 ~]$ tail -27 /proc/cpuinfo 

processor       : 55
vendor_id       : GenuineIntel
cpu family      : 6
model           : 63
model name      : Intel(R) Xeon(R) CPU E5-4660 v3 @ 2.10GHz
stepping        : 2
microcode       : 0x2e
cpu MHz         : 1200.000
cache size      : 35840 KB
physical id     : 3
siblings        : 14
core id         : 14
cpu cores       : 14
apicid          : 124
initial apicid  : 124
fpu             : yes
fpu_exception   : yes
cpuid level     : 15
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 pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm ida arat epb xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid
bogomips        : 4217.91
clflush size    : 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual
power management:

that's without hyperthreading. When it was first installed it reported 111. 20 threads is probably just maxing out things for sage, and of course there is still the bottleneck of building combinatorial in the the doc.

kiwifb commented 9 years ago

Some of the logic in there will have to be neutered and taken in ebuild, at least for the moment, it is just crappy.

strogdon commented 9 years ago

Not sure if the jupyter notebook ever worked from sage-on-gentoo, but it's a no-go now. Just one more thing.

kiwifb commented 9 years ago

Yes it was, I tested it. Not sure when I will be able to test the new install this morning.

strogdon commented 9 years ago

Oddly, it works in my prefix but not on Gentoo. Perhaps I'm blocking port 8888?

kiwifb commented 9 years ago

Works here for me, and sphere() does also work in a sagemath kernel for me. port blocking is a possibility.

strogdon commented 9 years ago

The jupyter notebook works from vanilla sage on this Gentoo box. I suspect something else is at at fault. From Gentoo a browser window is spawned when the notebook is started (probably indicates the port thing is OK) but when a new sagemath kernel is started I get a dialog box

Connection failed
A connection to the notebook server could not be established. The notebook will continue trying to 
reconnect, but until it does, you will NOT be able to run code. Check your network connection or 
notebook server configuration.

with corresponding segfault

Please wait while the Sage Notebook server starts...
[I 10:07:24.599 NotebookApp] Serving notebooks from local directory: /64bitdev/storage
[I 10:07:24.599 NotebookApp] 0 active kernels
[I 10:07:24.599 NotebookApp] The IPython Notebook is running at: http://localhost:8888/
[I 10:07:24.599 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
START /usr/bin/chromium-browser "http://localhost:8888/tree"
Created new window in existing browser session.
[I 10:07:30.486 NotebookApp] Creating new notebook in
[I 10:07:31.525 NotebookApp] Kernel started: f3a13c3d-3b2d-4b02-aa79-daaae5283d9f
Segmentation fault

Perhaps some component isn't built correctly?

strogdon commented 9 years ago

I believe the dialog box comes from dev-python/notebook.

kiwifb commented 9 years ago

ipykernel versions from gentoo and prefix?

strogdon commented 9 years ago

They are both the same, dev-python/ipykernel-4.0.3. A little debugging when I try to initiate a new sagemath kernel:

sage --notebook=jupyter --debug

[D 15:33:32.254 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 15:33:32.342 NotebookApp] Connecting to: tcp://127.0.0.1:51390
[I 15:33:32.343 NotebookApp] Kernel started: 46b8d2bf-3dc5-4109-b24a-b0ddf21c2aac
[D 15:33:32.343 NotebookApp] Kernel args: {'kernel_name': u'sagemath', 'cwd': u'/64bitdev/storage'}
[D 15:33:32.345 NotebookApp] 201 POST /api/sessions (127.0.0.1) 97.04ms
[D 15:33:32.347 NotebookApp] 200 GET /nbextensions/widgets/notebook/js/widgetarea.js?v=20151028153324 (127.0.0.1) 1.47ms
[D 15:33:32.349 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/init.js?v=20151028153324 (127.0.0.1) 1.10ms
[D 15:33:32.351 NotebookApp] 200 GET /api/contents/Untitled.ipynb/checkpoints?_=1446064411544 (127.0.0.1) 1.35ms
[D 15:33:32.371 NotebookApp] Initializing websocket connection /api/kernels/46b8d2bf-3dc5-4109-b24a-b0ddf21c2aac/channels
[D 15:33:32.373 NotebookApp] Requesting kernel info from 46b8d2bf-3dc5-4109-b24a-b0ddf21c2aac
[D 15:33:32.374 NotebookApp] Connecting to: tcp://127.0.0.1:51658
Segmentation fault

Similar results from 

ipython notebook --debug

or

jupyter-notebook --debug

From vanilla sage

./sage --notebook-jupyter --debug

[D 15:31:31.360 NotebookApp] Native kernel (python2) available from /64bitdev/storage/sage-git_develop/sage/local/lib/python2.7/site-packages/ipykernel/resources
[D 15:31:31.412 NotebookApp] Connecting to: tcp://127.0.0.1:60287
[I 15:31:31.413 NotebookApp] Kernel started: 29fac605-79fa-4ba6-aebb-9f6ade33ea1c
[D 15:31:31.413 NotebookApp] Kernel args: {'kernel_name': u'sagemath', 'cwd': u'/64bitdev/storage/sage-git_develop/sage'}
[D 15:31:31.415 NotebookApp] 201 POST /api/sessions (127.0.0.1) 60.17ms
[D 15:31:31.418 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/init.js (127.0.0.1) 1.34ms
[D 15:31:31.426 NotebookApp] 200 GET /api/contents/Untitled1.ipynb/checkpoints?_=1446064290687 (127.0.0.1) 4.19ms
[D 15:31:31.431 NotebookApp] 304 GET /nbextensions/widgets/notebook/js/widgetarea.js (127.0.0.1) 3.36ms
[D 15:31:31.443 NotebookApp] Initializing websocket connection /api/kernels/29fac605-79fa-4ba6-aebb-9f6ade33ea1c/channels
[D 15:31:31.446 NotebookApp] Requesting kernel info from 29fac605-79fa-4ba6-aebb-9f6ade33ea1c
[D 15:31:31.446 NotebookApp] Connecting to: tcp://127.0.0.1:60708
[D 15:31:31.469 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/manager.js (127.0.0.1) 1.20ms
[D 15:31:31.474 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget.js (127.0.0.1) 1.13ms
[D 15:31:31.478 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_link.js (127.0.0.1) 1.10ms
[D 15:31:31.488 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_bool.js (127.0.0.1) 1.09ms
[D 15:31:31.491 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_button.js (127.0.0.1) 1.06ms
[D 15:31:31.494 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_box.js (127.0.0.1) 1.12ms
[D 15:31:31.508 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_float.js (127.0.0.1) 1.07ms
[D 15:31:31.517 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_image.js (127.0.0.1) 1.07ms
[D 15:31:31.520 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_int.js (127.0.0.1) 1.05ms
[D 15:31:31.533 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_output.js (127.0.0.1) 1.11ms
[D 15:31:31.536 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_selection.js (127.0.0.1) 1.05ms
[D 15:31:31.539 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_selectioncontainer.js (127.0.0.1) 1.11ms
[D 15:31:31.546 NotebookApp] 304 GET /nbextensions/widgets/widgets/js/widget_string.js (127.0.0.1) 1.09ms
[D 15:31:31.556 NotebookApp] 304 GET /static/components/backbone/backbone-min.js (127.0.0.1) 1.07ms
[D 15:31:31.593 NotebookApp] 304 GET /nbextensions/widgets/widgets/css/widgets.min.css (127.0.0.1) 1.11ms
[D 15:31:34.483 NotebookApp] Received kernel info: {u'language_info': {u'mimetype': u'text/x-python', u'nbconvert_exporter': u'python', u'name': u'python', u'pygments_lexer': u'ipython2', u'version': u'2.7.9', u'file_extension': u'.py', u'codemirror_mode': {u'version': 2, u'name': u'ipython'}}, u'implementation': u'sage', u'implementation_version': u'6.10.beta1', u'protocol_version': u'5.0', u'banner': u'\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 SageMath Version 6.10.beta1, Release Date: 2015-10-21              \u2502\n\u2502 Type "notebook()" for the browser-based notebook interface.        \u2502\n\u2502 Type "help()" for help.                                            \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\n\x1b[31m\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2513\n\u2503 Warning: this is a prerelease version, and it may be unstable.     \u2503\n\u2517\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u251b\x1b[0m', u'help_links': [{u'url': u'../kernelspecs/sagemath/doc/index.html', u'text': u'Sage Documentation'}, {u'url': u'../kernelspecs/sagemath/doc/tutorial/index.html', u'text': u'Sage Tutorial'}, {u'url': u'../kernelspecs/sagemath/doc/thematic_tutorials/index.html', u'text': u'Thematic Tutorials'}, {u'url': u'../kernelspecs/sagemath/doc/faq/index.html', u'text': u'FAQs'}, {u'url': u'../kernelspecs/sagemath/doc/prep/index.html', u'text': u'PREP Tutorials'}, {u'url': u'../kernelspecs/sagemath/doc/reference/index.html', u'text': u'Sage Reference'}, {u'url': u'../kernelspecs/sagemath/doc/developer/index.html', u'text': u"Developer's Guide"}, {u'url': u'http://docs.python.org/2.7', u'text': u'Python'}, {u'url': u'http://ipython.org/documentation.html', u'text': u'IPython'}, {u'url': u'http://www.singular.uni-kl.de/Manual/latest/index.htm', u'text': u'Singular'}, {u'url': u'http://gap-system.org/Manuals/doc/ref/chap0.html', u'text': u'GAP'}, {u'url': u'http://docs.scipy.org/doc/numpy/reference/', u'text': u'NumPy'}, {u'url': u'http://docs.scipy.org/doc/scipy/reference/', u'text': u'SciPy'}, {u'url': u'http://docs.sympy.org/latest/index.html', u'text': u'SymPy'}, {u'url': u'http://matplotlib.org/contents.html', u'text': u'Matplotlib'}, {u'url': u'http://help.github.com/articles/github-flavored-markdown', u'text': u'Markdown'}]}
[D 15:31:34.485 NotebookApp] Opening websocket /api/kernels/29fac605-79fa-4ba6-aebb-9f6ade33ea1c/channels
[D 15:31:34.485 NotebookApp] Connecting to: tcp://127.0.0.1:60708
[D 15:31:34.485 NotebookApp] Connecting to: tcp://127.0.0.1:44814
[D 15:31:34.486 NotebookApp] Connecting to: tcp://127.0.0.1:54887

I'm not sure what it's trying to do when it's Requesting kernel info.

kiwifb commented 9 years ago

So to remove cruft and I had a lot:

rm -rf .local/share/jupyter
rm -rf .ipython/kernels/*

I had gobbles of ipython/jupyter kernels in there

So when I start sage --notebook=jupyter --debug and then select the sagemath 9999 kernel I get those:

┌────────────────────────────────────────────────────────────────────┐
│ SageMath Version 6.10.beta1, Release Date: 2015-10-21              │
│ Type "notebook()" for the browser-based notebook interface.        │
│ Type "help()" for help.                                            │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃                                                                         
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛                                                                         
Please wait while the Sage Notebook server starts...
[D 09:57:51.237 NotebookApp] Config changed:
[D 09:57:51.238 NotebookApp] {'NotebookApp': {'log_level': 10}}
[D 09:57:51.238 NotebookApp] Searching [u'/home/fbissey', '/home/fbissey/.jupyter', '/usr/etc/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files
[D 09:57:51.238 NotebookApp] Attempting to load config file jupyter_config.py in path /etc/jupyter
[D 09:57:51.238 NotebookApp] Attempting to load config file jupyter_config.json in path /etc/jupyter
[D 09:57:51.238 NotebookApp] Attempting to load config file jupyter_config.py in path /usr/local/etc/jupyter
[D 09:57:51.239 NotebookApp] Attempting to load config file jupyter_config.json in path /usr/local/etc/jupyter
[D 09:57:51.239 NotebookApp] Attempting to load config file jupyter_config.py in path /usr/etc/jupyter
[D 09:57:51.239 NotebookApp] Attempting to load config file jupyter_config.json in path /usr/etc/jupyter
[D 09:57:51.239 NotebookApp] Attempting to load config file jupyter_config.py in path /home/fbissey/.jupyter
[D 09:57:51.239 NotebookApp] Attempting to load config file jupyter_config.json in path /home/fbissey/.jupyter
[D 09:57:51.239 NotebookApp] Attempting to load config file jupyter_config.py in path /home/fbissey
[D 09:57:51.239 NotebookApp] Attempting to load config file jupyter_config.json in path /home/fbissey
[D 09:57:51.240 NotebookApp] Attempting to load config file jupyter_notebook_config.py in path /etc/jupyter
[D 09:57:51.240 NotebookApp] Attempting to load config file jupyter_notebook_config.json in path /etc/jupyter
[D 09:57:51.240 NotebookApp] Attempting to load config file jupyter_notebook_config.py in path /usr/local/etc/jupyter
[D 09:57:51.240 NotebookApp] Attempting to load config file jupyter_notebook_config.json in path /usr/local/etc/jupyter
[D 09:57:51.240 NotebookApp] Attempting to load config file jupyter_notebook_config.py in path /usr/etc/jupyter
[D 09:57:51.240 NotebookApp] Attempting to load config file jupyter_notebook_config.json in path /usr/etc/jupyter
[D 09:57:51.240 NotebookApp] Attempting to load config file jupyter_notebook_config.py in path /home/fbissey/.jupyter
[D 09:57:51.240 NotebookApp] Attempting to load config file jupyter_notebook_config.json in path /home/fbissey/.jupyter
[D 09:57:51.241 NotebookApp] Attempting to load config file jupyter_notebook_config.py in path /home/fbissey
[D 09:57:51.241 NotebookApp] Attempting to load config file jupyter_notebook_config.json in path /home/fbissey
[I 09:57:51.247 NotebookApp] Writing notebook server cookie secret to /home/fbissey/.local/share/jupyter/runtime/notebook_cookie_secret
[I 09:57:51.278 NotebookApp] Serving notebooks from local directory: /home/fbissey
[I 09:57:51.278 NotebookApp] 0 active kernels 
[I 09:57:51.278 NotebookApp] The IPython Notebook is running at: http://localhost:8888/
[I 09:57:51.278 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[D 09:57:51.499 NotebookApp] Using contents: services/contents
[D 09:57:51.535 NotebookApp] 200 GET /tree (::1) 37.86ms
[D 09:57:51.547 NotebookApp] 304 GET /custom/custom.css (::1) 7.48ms
[D 09:57:51.691 NotebookApp] 200 GET /static/services/contents.js?v=20151029095751 (::1) 0.80ms
[D 09:57:51.697 NotebookApp] 200 GET /custom/custom.js?v=20151029095751 (::1) 0.81ms
[D 09:57:51.714 NotebookApp] 200 GET /api/config/tree?_=1446065871597 (::1) 0.84ms
[D 09:57:51.715 NotebookApp] 200 GET /api/config/common?_=1446065871598 (::1) 0.61ms
[D 09:57:51.721 NotebookApp] 200 GET /api/terminals?_=1446065871599 (::1) 0.51ms
[D 09:57:51.724 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 09:57:51.724 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 09:57:51.724 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 09:57:51.724 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 09:57:51.725 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 09:57:51.725 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 09:57:51.726 NotebookApp] 200 GET /api/kernelspecs (::1) 3.07ms
[D 09:57:51.727 NotebookApp] 200 GET /api/sessions?_=1446065871600 (::1) 0.91ms
[D 09:57:51.728 NotebookApp] 200 GET /api/terminals?_=1446065871601 (::1) 0.50ms
[D 09:57:51.780 NotebookApp] 200 GET /api/contents?type=directory&_=1446065871602 (::1) 30.70ms
[D 09:58:00.136 NotebookApp] 200 GET /api/sessions?_=1446065760013 (::1) 0.67ms
[D 09:58:00.136 NotebookApp] 200 GET /api/terminals?_=1446065760014 (::1) 0.48ms
[D 09:58:00.166 NotebookApp] 200 GET /api/contents?type=directory&_=1446065760015 (::1) 28.80ms
[D 09:58:03.136 NotebookApp] 200 GET /api/sessions?_=1446065702254 (::1) 0.66ms
[D 09:58:03.137 NotebookApp] 200 GET /api/terminals?_=1446065702255 (::1) 0.78ms
[D 09:58:03.167 NotebookApp] 200 GET /api/contents?type=directory&_=1446065702256 (::1) 29.04ms
[D 09:58:06.849 NotebookApp] 200 GET /api/sessions?_=1446065871603 (::1) 0.67ms
[D 09:58:06.850 NotebookApp] 200 GET /api/terminals?_=1446065871604 (::1) 0.48ms
[D 09:58:06.884 NotebookApp] 200 GET /api/contents?type=directory&_=1446065871605 (::1) 29.47ms
[I 09:58:13.021 NotebookApp] Creating new notebook in 
[D 09:58:13.022 NotebookApp] Saving /home/fbissey/Untitled2.ipynb
[I 09:58:13.023 NotebookApp] Writing notebook-signing key to /home/fbissey/.local/share/jupyter/notebook_secret
[D 09:58:13.413 NotebookApp] 201 POST /api/contents (::1) 392.23ms
[D 09:58:13.415 NotebookApp] Using contents: services/contents
[D 09:58:13.447 NotebookApp] 200 GET /notebooks/Untitled2.ipynb?kernel_name=sagemath (::1) 32.51ms
[D 09:58:13.456 NotebookApp] 304 GET /static/components/MathJax/MathJax.js?config=TeX-AMS_HTML-full,Safe&delayStartupUntil=configured (::1) 0.72ms
[D 09:58:13.457 NotebookApp] 304 GET /custom/custom.css (::1) 0.55ms
[D 09:58:13.475 NotebookApp] 304 GET /static/components/MathJax/config/TeX-AMS_HTML-full.js?rev=2.5.3 (::1) 0.66ms
[D 09:58:13.728 NotebookApp] 304 GET /custom/custom.js?v=20151029095751 (::1) 0.71ms
[D 09:58:13.756 NotebookApp] 304 GET /static/components/MathJax/config/Safe.js?rev=2.5.3 (::1) 0.65ms
[D 09:58:13.765 NotebookApp] 200 GET /api/config/notebook?_=1446065893590 (::1) 0.62ms
[D 09:58:13.766 NotebookApp] 200 GET /api/config/common?_=1446065893591 (::1) 0.55ms
[D 09:58:13.834 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 09:58:13.834 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 09:58:13.835 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 09:58:13.835 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 09:58:13.835 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 09:58:13.835 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 09:58:13.836 NotebookApp] 304 GET /api/kernelspecs (::1) 2.37ms
[D 09:58:14.196 NotebookApp] 200 GET /api/contents/Untitled2.ipynb?type=notebook&_=1446065893592 (::1) 341.19ms
[D 09:58:14.197 NotebookApp] 304 GET /static/components/MathJax/extensions/Safe.js?rev=2.5.3 (::1) 0.58ms
[D 09:58:14.198 NotebookApp] 200 GET /nbextensions/widgets/notebook/js/extension.js?v=20151029095751 (::1) 0.63ms
[D 09:58:14.199 NotebookApp] 304 GET /static/components/MathJax/jax/output/HTML-CSS/fonts/STIX-Web/fontdata.js?rev=2.5.3 (::1) 0.51ms
[D 09:58:14.250 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 09:58:14.250 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 09:58:14.259 NotebookApp] Connecting to: tcp://127.0.0.1:33263
[I 09:58:14.259 NotebookApp] Kernel started: 1f9c7c3c-6930-4873-b633-5932f222fd4f
[D 09:58:14.259 NotebookApp] Kernel args: {'kernel_name': u'sagemath', 'cwd': u'/home/fbissey'}
[D 09:58:14.260 NotebookApp] 201 POST /api/sessions (::1) 12.71ms
[D 09:58:14.261 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 09:58:14.262 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 09:58:14.262 NotebookApp] Serving kernel resource from: /usr/share/jupyter/kernels/sagemath
[D 09:58:14.263 NotebookApp] 304 GET /kernelspecs/sagemath/logo-64x64.png (::1) 1.68ms
[D 09:58:14.264 NotebookApp] 200 GET /api/contents/Untitled2.ipynb/checkpoints?_=1446065893593 (::1) 0.81ms
[D 09:58:14.266 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/init.js?v=20151029095751 (::1) 0.73ms
[D 09:58:14.267 NotebookApp] 200 GET /nbextensions/widgets/notebook/js/widgetarea.js?v=20151029095751 (::1) 0.71ms
[D 09:58:14.283 NotebookApp] Initializing websocket connection /api/kernels/1f9c7c3c-6930-4873-b633-5932f222fd4f/channels
[D 09:58:14.284 NotebookApp] Requesting kernel info from 1f9c7c3c-6930-4873-b633-5932f222fd4f
[D 09:58:14.284 NotebookApp] Connecting to: tcp://127.0.0.1:38029
[D 09:58:14.300 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_box.js?v=20151029095751 (::1) 0.83ms
[D 09:58:14.301 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget.js?v=20151029095751 (::1) 0.83ms
[D 09:58:14.302 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_link.js?v=20151029095751 (::1) 0.67ms
[D 09:58:14.304 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_bool.js?v=20151029095751 (::1) 1.24ms
[D 09:58:14.305 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/manager.js?v=20151029095751 (::1) 0.77ms
[D 09:58:14.306 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_button.js?v=20151029095751 (::1) 0.67ms
[D 09:58:14.308 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_float.js?v=20151029095751 (::1) 0.86ms
[D 09:58:14.309 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_image.js?v=20151029095751 (::1) 0.64ms
[D 09:58:14.310 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_int.js?v=20151029095751 (::1) 0.68ms
[D 09:58:14.311 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_output.js?v=20151029095751 (::1) 0.62ms
[D 09:58:14.312 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_selection.js?v=20151029095751 (::1) 0.63ms
[D 09:58:14.313 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_selectioncontainer.js?v=20151029095751 (::1) 0.68ms
[D 09:58:14.314 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_controller.js?v=20151029095751 (::1) 0.61ms
[D 09:58:14.315 NotebookApp] 200 GET /static/components/backbone/backbone-min.js?v=20151029095751 (::1) 0.60ms
[D 09:58:14.317 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/widget_string.js?v=20151029095751 (::1) 0.60ms
[D 09:58:14.338 NotebookApp] 304 GET /nbextensions/widgets/widgets/css/widgets.min.css (::1) 0.67ms
[D 09:58:15.578 NotebookApp] Received kernel info: {'language_info': {'mimetype': 'text/x-python', 'nbconvert_exporter': 'python', 'name': 'python', 'pygments_lexer': 'ipython2', 'version': '2.7.10', 'file_extension': '.py', 'codemirror_mode': {'version': 2, 'name': 'ipython'}}, 'implementation': 'sage', 'implementation_version': '6.10.beta1', 'protocol_version': '5.0', 'banner': u'\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\n\u2502 SageMath Version 6.10.beta1, Release Date: 2015-10-21              \u2502\n\u2502 Type "notebook()" for the browser-based notebook interface.        \u2502\n\u2502 Type "help()" for help.                                            \u2502\n\u2514\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2518\n\x1b[31m\u250f\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2513\n\u2503 Warning: this is a prerelease version, and it may be unstable.     \u2503\n\u2517\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u251b\x1b[0m', 'help_links': [{'url': '../kernelspecs/sagemath/doc/index.html', 'text': 'Sage Documentation'}, {'url': '../kernelspecs/sagemath/doc/tutorial/index.html', 'text': 'Sage Tutorial'}, {'url': '../kernelspecs/sagemath/doc/thematic_tutorials/index.html', 'text': 'Thematic Tutorials'}, {'url': '../kernelspecs/sagemath/doc/faq/index.html', 'text': 'FAQs'}, {'url': '../kernelspecs/sagemath/doc/prep/index.html', 'text': 'PREP Tutorials'}, {'url': '../kernelspecs/sagemath/doc/reference/index.html', 'text': 'Sage Reference'}, {'url': '../kernelspecs/sagemath/doc/developer/index.html', 'text': "Developer's Guide"}, {'url': 'http://docs.python.org/2.7', 'text': 'Python'}, {'url': 'http://ipython.org/documentation.html', 'text': 'IPython'}, {'url': 'http://www.singular.uni-kl.de/Manual/latest/index.htm', 'text': 'Singular'}, {'url': 'http://gap-system.org/Manuals/doc/ref/chap0.html', 'text': 'GAP'}, {'url': 'http://docs.scipy.org/doc/numpy/reference/', 'text': 'NumPy'}, {'url': 'http://docs.scipy.org/doc/scipy/reference/', 'text': 'SciPy'}, {'url': 'http://docs.sympy.org/latest/index.html', 'text': 'SymPy'}, {'url': 'http://matplotlib.org/contents.html', 'text': 'Matplotlib'}, {'url': 'http://help.github.com/articles/github-flavored-markdown', 'text': 'Markdown'}]}
[D 09:58:15.579 NotebookApp] Opening websocket /api/kernels/1f9c7c3c-6930-4873-b633-5932f222fd4f/channels
[D 09:58:15.579 NotebookApp] Connecting to: tcp://127.0.0.1:38029
[D 09:58:15.579 NotebookApp] Connecting to: tcp://127.0.0.1:56561
[D 09:58:15.580 NotebookApp] Connecting to: tcp://127.0.0.1:59687
^C[I 10:00:24.812 NotebookApp] interrupted
Serving notebooks from local directory: /home/fbissey
1 active kernels 
The IPython Notebook is running at: http://localhost:8888/
Shutdown this notebook server (y/[n])? y
[C 10:00:26.436 NotebookApp] Shutdown confirmed
[I 10:00:26.436 NotebookApp] Shutting down kernels
[I 10:00:27.138 NotebookApp] Kernel shutdown: 1f9c7c3c-6930-4873-b633-5932f222fd4f
fb
kiwifb commented 9 years ago

I notice that you don't seem to get messages about finding kernels in /usr/share/jupyter/kernels.

strogdon commented 9 years ago

Yes I had those too. I only showed what appeared after Native kernel (python2) available.

strogdon commented 9 years ago

After removing the cruft I still have the segfault.

kiwifb commented 9 years ago

But you never have a message about finding a sagemath kernel after that message. The corresponding part in my log is:

[D 10:10:33.415 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 10:10:33.425 NotebookApp] Connecting to: tcp://127.0.0.1:60318
[I 10:10:33.426 NotebookApp] Kernel started: 5600ad44-cc2b-4a26-8ed9-564bdfa4d5a3
[D 10:10:33.426 NotebookApp] Kernel args: {'kernel_name': u'sagemath', 'cwd': u'/home/fbissey'}
[D 10:10:33.427 NotebookApp] 201 POST /api/sessions (::1) 13.41ms
[D 10:10:33.428 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/init.js?v=20151029101027 (::1) 0.84ms
[D 10:10:33.429 NotebookApp] 200 GET /nbextensions/widgets/notebook/js/widgetarea.js?v=20151029101027 (::1) 0.63ms
[D 10:10:33.430 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 10:10:33.430 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 10:10:33.430 NotebookApp] Serving kernel resource from: /usr/share/jupyter/kernels/sagemath
[D 10:10:33.431 NotebookApp] 200 GET /kernelspecs/sagemath/logo-64x64.png (::1) 1.60ms
[D 10:10:33.432 NotebookApp] 200 GET /api/contents/Untitled3.ipynb/checkpoints?_=1446066633004 (::1) 0.72ms
[D 10:10:33.452 NotebookApp] Initializing websocket connection /api/kernels/5600ad44-cc2b-4a26-8ed9-564bdfa4d5a3/channels
[D 10:10:33.454 NotebookApp] Requesting kernel info from 5600ad44-cc2b-4a26-8ed9-564bdfa4d5a3
[D 10:10:33.454 NotebookApp] Connecting to: tcp://127.0.0.1:33344
kiwifb commented 9 years ago

Other differences, you have 

[D 15:33:32.345 NotebookApp] 201 POST /api/sessions (127.0.0.1) 97.04ms

vanilla and I have

[D 10:10:33.427 NotebookApp] 201 POST /api/sessions (::1) 13.41ms
strogdon commented 9 years ago

It's there. I didn't post enough.

[I 16:21:49.200 NotebookApp] Creating new notebook in 
[D 16:21:49.203 NotebookApp] Saving /64bitdev/storage/Untitled1.ipynb
[D 16:21:49.287 NotebookApp] 201 POST /api/contents (127.0.0.1) 87.69ms
[D 16:21:49.310 NotebookApp] Using contents: services/contents
[D 16:21:49.360 NotebookApp] 200 GET /notebooks/Untitled1.ipynb?kernel_name=sagemath (127.0.0.1) 51.11ms
[D 16:21:49.384 NotebookApp] 304 GET /static/components/MathJax/MathJax.js?config=TeX-AMS_HTML-full,Safe&delayStartupUntil=configured (127.0.0.1) 1.14ms
[D 16:21:49.396 NotebookApp] 304 GET /custom/custom.css (127.0.0.1) 8.84ms
[D 16:21:49.452 NotebookApp] 304 GET /static/components/MathJax/config/TeX-AMS_HTML-full.js?rev=2.4-beta-2 (127.0.0.1) 1.15ms
[D 16:21:49.820 NotebookApp] 304 GET /custom/custom.js?v=20151028162042 (127.0.0.1) 2.06ms
[D 16:21:49.883 NotebookApp] 304 GET /static/components/MathJax/config/Safe.js?rev=2.4-beta-2 (127.0.0.1) 1.16ms
[D 16:21:49.899 NotebookApp] 200 GET /api/config/notebook?_=1446067309554 (127.0.0.1) 1.58ms
[D 16:21:49.901 NotebookApp] 200 GET /api/config/common?_=1446067309555 (127.0.0.1) 1.06ms
[D 16:21:49.990 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 16:21:49.991 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 16:21:49.992 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 16:21:49.992 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 16:21:49.993 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 16:21:49.994 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 16:21:49.995 NotebookApp] 304 GET /api/kernelspecs (127.0.0.1) 5.85ms
[D 16:21:50.072 NotebookApp] 200 GET /api/contents/Untitled1.ipynb?type=notebook&_=1446067309556 (127.0.0.1) 39.72ms
[D 16:21:50.074 NotebookApp] 200 GET /nbextensions/widgets/notebook/js/extension.js?v=20151028162042 (127.0.0.1) 1.22ms
[D 16:21:50.212 NotebookApp] Found kernel sagemath in /usr/share/jupyter/kernels
[D 16:21:50.212 NotebookApp] Native kernel (python2) available from /usr/lib64/python2.7/site-packages/ipykernel/resources
[D 16:21:50.252 NotebookApp] Connecting to: tcp://127.0.0.1:56429
[I 16:21:50.255 NotebookApp] Kernel started: cc537db3-96fe-42a1-822a-d9ff9a7fd104
[D 16:21:50.255 NotebookApp] Kernel args: {'kernel_name': u'sagemath', 'cwd': u'/64bitdev/storage'}
[D 16:21:50.258 NotebookApp] 201 POST /api/sessions (127.0.0.1) 50.20ms
[D 16:21:50.261 NotebookApp] 200 GET /nbextensions/widgets/widgets/js/init.js?v=20151028162042 (127.0.0.1) 1.78ms
[D 16:21:50.263 NotebookApp] 200 GET /nbextensions/widgets/notebook/js/widgetarea.js?v=20151028162042 (127.0.0.1) 1.61ms
[D 16:21:50.266 NotebookApp] 304 GET /static/components/MathJax/extensions/Safe.js?rev=2.4-beta-2 (127.0.0.1) 1.03ms
[D 16:21:50.269 NotebookApp] 304 GET /static/components/MathJax/jax/output/HTML-CSS/fonts/STIX-Web/fontdata.js?rev=2.4-beta-2 (127.0.0.1) 1.49ms
[D 16:21:50.276 NotebookApp] 200 GET /api/contents/Untitled1.ipynb/checkpoints?_=1446067309557 (127.0.0.1) 6.36ms
[D 16:21:50.280 NotebookApp] Initializing websocket connection /api/kernels/cc537db3-96fe-42a1-822a-d9ff9a7fd104/channels
[D 16:21:50.284 NotebookApp] Requesting kernel info from cc537db3-96fe-42a1-822a-d9ff9a7fd104
[D 16:21:50.284 NotebookApp] Connecting to: tcp://127.0.0.1:34579
Segmentation fault
strogdon commented 9 years ago

Good spot. This also on my prefix

[D 15:56:05.921 NotebookApp] 201 POST /api/sessions (::1) 17.53ms
kiwifb commented 9 years ago

You never get Serving kernel resource from: /usr/share/jupyter/kernels/sagemath could you run it as strace -o nb_trace.txt sage --notebook=jupyter from an empty directory and send me nb_trace.txt (compressed if necessary)?

strogdon commented 9 years ago

Looking a little more closely at my vanilla debug results, (127.0.0.1) appears everywhere and there is no Serving kernel resource from: and yet it works. The problem seems to be in loading the .js files that are provided by dev-python/ipywidgets.

kiwifb commented 9 years ago

Do you have all the links under /usr/share/jupyter/kernels/sagemath/?

strogdon commented 9 years ago

Yes

 ls -l /usr/share/jupyter/kernels/sagemath/
total 4
lrwxrwxrwx 1 root root  27 Oct 27 10:15 doc -> /usr/share/doc/sage/html/en
-rw-r--r-- 1 root root 117 Oct 27 10:00 kernel.json
lrwxrwxrwx 1 root root  51 Oct 27 10:15 logo-64x64.png -> /usr/share/sage/ext/notebook-ipython/logo-64x64.png
lrwxrwxrwx 1 root root  45 Oct 27 10:15 logo.svg -> /usr/share/sage/ext/notebook-ipython/logo.svg
kiwifb commented 9 years ago

I think I have run out of ideas for the day. I don't think it would make a difference but I believe you have ipython installed with USEFLAGS=wxwidgets which was necessary by mistake in the first few iterations of the ipython-4.* ebuild. Can you remove it, along with wxpython, and see how it goes?

strogdon commented 9 years ago

Earlier to day I thought ipython was the problem since I had USE = qt4 wxwidgets. So ipython was rebuilt without them

[I] dev-python/ipython
     Available versions:  2.2.0-r1 ~3.1.0[1] 3.2.1-r1 (~)4.0.0-r2[2] {doc examples matplotlib mongodb nbconvert notebook octave qt4 +smp test wxwidgets PYTHON_TARGETS="python2_7 python3_3 python3_4"}
     Installed versions:  4.0.0-r2[2](10:18:19 AM 10/28/2015)(nbconvert notebook -doc -examples -matplotlib -mongodb -qt4 -smp -test -wxwidgets PYTHON_TARGETS="python2_7 python3_3 -python3_4")
     Homepage:            http://ipython.org/
     Description:         Advanced interactive shell for Python

[1] "sage-on-gentoo" /var/lib/layman/sage-on-gentoo
[2] "science" /var/lib/layman/science

I thought for sure that was the issue, but no. I hadn't thought about removing wxpython which will require rebuilding matplotlib with USE = -wxwidgets. I will report back in the morning (my time) since I don't have enough bandwidth at home to test the notebook.

kiwifb commented 9 years ago

I had noticed calls to what looked like wxpython in your various logs. Influence is far fetched.

strogdon commented 9 years ago

Removing wxpython didn't fix things.

strogdon commented 9 years ago

On a successful connection there is this info that is received:

Received kernel info: {'language_info': {'mimetype': 'text/x-python', ...

which contains a lot of stuff and appears to be a python dict. Do you have any idea where this is generated? I can find bits and pieces of things but not where the entire dictionary is assembled.

kiwifb commented 9 years ago

I don't know either, jupyter_core or jupyter_client are likely suspects.

kiwifb commented 9 years ago

/usr/lib64/python2.7/site-packages/notebook/services/kernels/handlers.py is where it is displayed from. It would ultimately originate from pyzmq.

strogdon commented 9 years ago

In kern.log I have when starting a sagemath kernel:

vanilla sage:

Oct 30 19:08:38 ledaig kernel: netlink: 20 bytes leftover after parsing attributes.
Oct 30 19:08:38 ledaig kernel: netlink: 20 bytes leftover after parsing attributes.
Oct 30 19:08:38 ledaig kernel: netlink: 20 bytes leftover after parsing attributes.

sage-on-gentoo:

Oct 30 19:08:39 ledaig kernel: python2.7[10842]: segfault at 4e7e3bc390 ip 00007f4e8036c46a sp 00007fffaa8675a0 error 6 in socket.so[7f4e8035e000+15000]
Oct 30 19:08:39 ledaig kernel: netlink: 20 bytes leftover after parsing attributes.
Oct 30 19:08:39 ledaig kernel: netlink: 20 bytes leftover after parsing attributes.
Oct 30 19:08:39 ledaig kernel: netlink: 20 bytes leftover after parsing attributes.

So, something is messing with my kernel. This doesn't look good.

kiwifb commented 9 years ago

And that's definitely part of pyzmq, version?

strogdon commented 9 years ago 
[I] dev-python/pyzmq
     Available versions:  14.4.1 ~14.6.0 ~14.7.0 {doc examples green test PYTHON_TARGETS="python2_7 python3_3 python3_4 python3_5"}
     Installed versions:  14.4.1(05:22:18 PM 06/04/2015)(-doc -examples -green -test PYTHON_TARGETS="python2_7 python3_3 -python3_4")
     Homepage:            http://www.zeromq.org/bindings:python https://pypi.python.org/pypi/pyzmq
     Description:         Lightweight and super-fast messaging library built on top of the ZeroMQ library

The same version in Prefix.

kiwifb commented 9 years ago

I have 14.7.0 on both, what about zeromq?