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Bug 704274 - dev-python/jupyter_core-4.4.0 with dev-python/ipykernel-4.6.1-r2 - RuntimeError: This event loop is already running
Summary: dev-python/jupyter_core-4.4.0 with dev-python/ipykernel-4.6.1-r2 - RuntimeErr...
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2019-12-30 14:03 UTC by Thomas Haschka
Modified: 2020-03-27 20:24 UTC (History)
0 users

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


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Description Thomas Haschka 2019-12-30 14:03:16 UTC
running:
ipython notebook

does not work on a current stable ( non keyworded ) installation.
This seems to be due to version incompatibilities of ipykernel, tornado and or 
other packages. 

Unmasking the following set leaded to an installation that works:
dev-python/jupyter_console ~amd64
dev-python/jupyter_core ~amd64
dev-python/jupyter_client ~amd64
dev-python/backcall ~amd64
dev-python/prompt_toolkit ~amd64
dev-python/ipyparallel ~amd64
dev-python/ipython ~amd64
dev-python/ipykernel ~amd64

I hence recommand either to stabelize or keyword packages in a way so that the different versions work together. 

Running an ipython notebook seems to work at first glance but one cannot connect to the kernel ( i.e. it fails running whatever python code in the notebook ) with the following error which seems to be tornado related:

[I 14:39:06.006 NotebookApp] KernelRestarter: restarting kernel (4/5), new random ports
Traceback (most recent call last):
  File "/usr/lib64/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/usr/lib64/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/usr/lib64/python3.6/site-packages/ipykernel_launcher.py", line 16, in <module>
    app.launch_new_instance()
  File "/usr/lib64/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/usr/lib64/python3.6/site-packages/ipykernel/kernelapp.py", line 477, in start
    ioloop.IOLoop.instance().start()
  File "/usr/lib64/python3.6/site-packages/tornado/platform/asyncio.py", line 132, in start
    self.asyncio_loop.run_forever()
  File "/usr/lib64/python3.6/asyncio/base_events.py", line 425, in run_forever
    raise RuntimeError('This event loop is already running')
RuntimeError: This event loop is already running
[W 14:39:09.017 NotebookApp] KernelRestarter: restart failed

however trying different (i.e. downgrading tornado to tornado 4 did not resolve the problem ) the problem was only resolved by unmasking the packages above. 

Reproducible: Always

Steps to Reproduce:
1. install a current gentoo stable system. emerge dev-python/notebook 
2. open a browser or an other ipython notebook client
3. try to run code in the client, which will utterly fail
Actual Results:  
the ipython kernel can not be started from the jupyter client: 
[I 14:39:06.006 NotebookApp] KernelRestarter: restarting kernel (4/5), new random ports
Traceback (most recent call last):
  File "/usr/lib64/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/usr/lib64/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/usr/lib64/python3.6/site-packages/ipykernel_launcher.py", line 16, in <module>
    app.launch_new_instance()
  File "/usr/lib64/python3.6/site-packages/traitlets/config/application.py", line 658, in launch_instance
    app.start()
  File "/usr/lib64/python3.6/site-packages/ipykernel/kernelapp.py", line 477, in start
    ioloop.IOLoop.instance().start()
  File "/usr/lib64/python3.6/site-packages/tornado/platform/asyncio.py", line 132, in start
    self.asyncio_loop.run_forever()
  File "/usr/lib64/python3.6/asyncio/base_events.py", line 425, in run_forever
    raise RuntimeError('This event loop is already running')
RuntimeError: This event loop is already running
[W 14:39:09.017 NotebookApp] KernelRestarter: restart failed

Expected Results:  
kernel starts and connects to the notebook

Portage 2.3.79 (python 3.6.9-final-0, default/linux/amd64/17.0/no-multilib, gcc-9.2.0, glibc-2.29-r7, 4.19.82-gentoo x86_64)
=================================================================
System uname: Linux-4.19.82-gentoo-x86_64-Intel-R-_Core-TM-_i7-8700_CPU_@_3.20GHz-with-gentoo-2.6
KiB Mem:     7940132 total,   5447844 free
KiB Swap:    5092300 total,   5092300 free
Timestamp of repository gentoo: Mon, 30 Dec 2019 10:00:01 +0000
Head commit of repository gentoo: 5de3a9337121c670602ba5c5e1e5c5aa37909e88
sh bash 4.4_p23-r1
ld GNU ld (Gentoo 2.32 p2) 2.32.0
app-shells/bash:          4.4_p23-r1::gentoo
dev-lang/perl:            5.30.1::gentoo
dev-lang/python:          2.7.17::gentoo, 3.6.9::gentoo
dev-util/cmake:           3.14.6::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/openrc:          0.41.2::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.16.1-r1::gentoo
sys-devel/binutils:       2.32-r1::gentoo
sys-devel/gcc:            9.2.0-r2::gentoo
sys-devel/gcc-config:     2.1::gentoo
sys-devel/libtool:        2.4.6-r3::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 4.19::gentoo (virtual/os-headers)
sys-libs/glibc:           2.29-r7::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-max-age: 24
    sync-rsync-extra-opts: 
    sync-rsync-verify-jobs: 1

localebuilds
    location: /localebuilds
    masters: gentoo

gnu-elpa
    location: /var/lib/layman/gnu-elpa
    masters: gentoo
    priority: 50

melpa
    location: /var/lib/layman/melpa
    masters: gnu-elpa gentoo
    priority: 50

melpa-stable
    location: /var/lib/layman/melpa-stable
    masters: gnu-elpa gentoo
    priority: 50

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE swiss-prot freedist linux-firmware linux-fw-redistributable no-source-code STRIDE SURF vmd free-noncomm Intel-SDP"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -march=native -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -march=native -pipe"
DISTDIR="/usr/portage/distfiles"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR"
FCFLAGS="-O2 -march=native -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict news parallel-fetch pid-sandbox preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -march=native -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="en de fr"
MAKEOPTS="-j6"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
USE="X acl alsa amd64 berkdb bluetooth bzip2 cli crypt cxx dbus dri fontconfig fortran freetype gdbm gif iconv ipv6 jpeg lcms libtirpc mp3 ncurses nls nptl opengl openmp pam pcre pdf png readline seccomp split-usr ssl svg tcpd threads tiff truetype unicode vaapi vorbis vpx webp x264 x265 xattr xft zlib" ABI_X86="64" ADA_TARGET="gnat_2018" 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="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="en de fr" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" NETBEANS_MODULES="apisupport cnd groovy gsf harness ide identity j2ee java mobility nb php profiler soa visualweb webcommon websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="intel i965" 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_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Kobboi 2020-03-01 15:53:19 UTC
I am getting a similar error running portage 2.3.90:



christophe@tanagra ~ $ sudo emerge -1Gav gnome-boxes --quiet

 * IMPORTANT: 1 news items need reading for repository 'gentoo'.
 * Use eselect news read to view new items.

[binary  N    ] app-misc/scrub-2.6.1 
[binary  N    ] sys-apps/dmidecode-3.2  USE="(-selinux)" 
[binary  N    ] dev-libs/yajl-2.1.0-r2  USE="-static-libs" ABI_X86="(64) -32 (-x32)" 
[binary  N    ] acct-group/qemu-0 
[binary  N    ] acct-user/qemu-0 
[binary  N    ] net-analyzer/openbsd-netcat-1.190 
[binary  N    ] app-emulation/libvirt-6.0.0-r1  USE="caps dbus libvirtd macvtap nls policykit qemu udev vepa -apparmor -audit -dtrace -firewalld -fuse -glusterfs -iscsi -iscsi-direct -libssh -lvm -lxc -nfs -numa (-openvz) -parted -pcap -phyp -rbd -sasl (-selinux) -virt-network -virtualbox -wireshark-plugins -xen -zfs" 
[binary  N    ] net-misc/spice-gtk-0.37-r2  USE="gtk3 introspection policykit pulseaudio smartcard usbredir vala -libressl -lz4 -mjpeg -sasl -static-libs -webdav" 
[binary  N    ] app-cdr/cdrtools-3.02_alpha09-r2  USE="acl nls unicode -caps -filecaps (-selinux)" 
[binary  N    ] app-emulation/libvirt-glib-3.0.0  USE="introspection nls vala" 
[binary  N    ] virtual/cdrtools-0 
[binary  N    ] gnome-extra/gnome-boxes-3.32.2  USE="-rdp" 

Would you like to merge these packages? [Yes/No] y
>>> Running pre-merge checks for acct-group/qemu-0
>>> Running pre-merge checks for acct-user/qemu-0
>>> Running pre-merge checks for gnome-extra/gnome-boxes-3.32.2
 * You need KVM support in your kernel to use GNOME Boxes local VM support!
>>> Emerging binary (1 of 12) app-misc/scrub-2.6.1::gentoo
>>> Jobs: 0 of 12 complete, 1 running               Load avg: 1.28, 1.32, 1.35Exception in callback SequentialTaskQueue._task_exit(<_emerge.Binp...x7fe7038103a8>)(<Future finis...dy running',)>)
handle: <Handle SequentialTaskQueue._task_exit(<_emerge.Binp...x7fe7038103a8>)(<Future finis...dy running',)>)>
Traceback (most recent call last):
  File "/usr/lib64/python3.6/asyncio/events.py", line 145, in _run
    self._callback(*self._args)
  File "/usr/lib64/python3.6/site-packages/_emerge/SequentialTaskQueue.py", line 65, in _task_exit
    future.result()
  File "/usr/lib64/python3.6/site-packages/portage/util/futures/compat_coroutine.py", line 113, in _next
    future = self._generator.throw(previous.exception())
  File "/usr/lib64/python3.6/site-packages/_emerge/SequentialTaskQueue.py", line 54, in _task_coroutine
    yield task.async_start()
  File "/usr/lib64/python3.6/site-packages/portage/util/futures/compat_coroutine.py", line 113, in _next
    future = self._generator.throw(previous.exception())
  File "/usr/lib64/python3.6/site-packages/_emerge/AsynchronousTask.py", line 31, in async_start
    yield self._async_start()
  File "/usr/lib64/python3.6/site-packages/portage/util/futures/compat_coroutine.py", line 107, in _next
    future = next(self._generator)
  File "/usr/lib64/python3.6/site-packages/_emerge/AsynchronousTask.py", line 44, in _async_start
    self._start()
  File "/usr/lib64/python3.6/site-packages/_emerge/BinpkgFetcher.py", line 44, in _start
    AsyncTaskFuture(future=fetcher.async_lock()),
  File "/usr/lib64/python3.6/site-packages/_emerge/BinpkgFetcher.py", line 232, in async_lock
    self._lock_obj.start()
  File "/usr/lib64/python3.6/site-packages/_emerge/AsynchronousTask.py", line 52, in start
    self._start()
  File "/usr/lib64/python3.6/site-packages/_emerge/AsynchronousLock.py", line 47, in _start
    self.scheduler.run_until_complete(self._async_start())
  File "/usr/lib64/python3.6/site-packages/portage/util/_eventloop/asyncio_event_loop.py", line 140, in _run_until_complete
    return self._loop.run_until_complete(future)
  File "/usr/lib64/python3.6/asyncio/base_events.py", line 475, in run_until_complete
    self.run_forever()
  File "/usr/lib64/python3.6/asyncio/base_events.py", line 429, in run_forever
    raise RuntimeError('This event loop is already running')
RuntimeError: This event loop is already running
--Return--
> /usr/lib64/python3.6/site-packages/portage/util/_eventloop/asyncio_event_loop.py(81)_internal_caller_exception_handler()->None
-> pdb.set_trace()
(Pdb)
Comment 2 Kobboi 2020-03-01 17:07:04 UTC
I logged https://bugs.gentoo.org/711178 as an issue specifically with portage version 2.3.90 (not with 2.3.89)
Comment 3 Zac Medico gentoo-dev 2020-03-01 18:53:00 UTC

*** This bug has been marked as a duplicate of bug 711178 ***
Comment 4 Zac Medico gentoo-dev 2020-03-01 18:55:25 UTC
(In reply to Kobboi from comment #1)
>     AsyncTaskFuture(future=fetcher.async_lock()),
>   File "/usr/lib64/python3.6/site-packages/_emerge/BinpkgFetcher.py", line
> 232, in async_lock
>     self._lock_obj.start()
>   File "/usr/lib64/python3.6/site-packages/_emerge/AsynchronousTask.py",
> line 52, in start
>     self._start()
>   File "/usr/lib64/python3.6/site-packages/_emerge/AsynchronousLock.py",
> line 47, in _start
>     self.scheduler.run_until_complete(self._async_start())
>   File
> "/usr/lib64/python3.6/site-packages/portage/util/_eventloop/
> asyncio_event_loop.py", line 140, in _run_until_complete
>     return self._loop.run_until_complete(future)
>   File "/usr/lib64/python3.6/asyncio/base_events.py", line 475, in
> run_until_complete
>     self.run_forever()
>   File "/usr/lib64/python3.6/asyncio/base_events.py", line 429, in
> run_forever
>     raise RuntimeError('This event loop is already running')
> RuntimeError: This event loop is already running
> --Return--
> > /usr/lib64/python3.6/site-packages/portage/util/_eventloop/asyncio_event_loop.py(81)_internal_caller_exception_handler()->None
> -> pdb.set_trace()
> (Pdb)

That's bug 711178.
Comment 5 Benda Xu gentoo-dev 2020-03-02 04:03:56 UTC
Hi I have no clue of what's going on here. Kobboi's comment seems to have no relation with Thomas Haschka's.
Comment 6 Benda Xu gentoo-dev 2020-03-02 04:06:21 UTC
(In reply to Thomas Haschka from comment #0)
> running:
> ipython notebook
> 
> does not work on a current stable ( non keyworded ) installation.
> This seems to be due to version incompatibilities of ipykernel, tornado and
> or 
> other packages. 
> 
> Unmasking the following set leaded to an installation that works:
> dev-python/jupyter_console ~amd64
> dev-python/jupyter_core ~amd64
> dev-python/jupyter_client ~amd64
> dev-python/backcall ~amd64
> dev-python/prompt_toolkit ~amd64
> dev-python/ipyparallel ~amd64
> dev-python/ipython ~amd64
> dev-python/ipykernel ~amd64
> 
> I hence recommand either to stabelize or keyword packages in a way so that
> the different versions work together. 

Please go ahead to file a stabilization request.
Comment 7 Michał Górny archtester Gentoo Infrastructure gentoo-dev Security 2020-03-27 20:24:19 UTC
Old version removed.  Please reopen if you can reproduce with current.