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lyallp
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Joined: 15 Jul 2004
Posts: 1557
Location: Adelaide/Australia
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 Posted: Mon Dec 11, 2017 7:47 am Post subject: [Solved]emerge core dumps on Verifying ebuild manifests |
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I have a VM of Gentoo in which I have set clang(++) as my primary compiler with only packages that require gcc to successfully compile, such as kernel, glibc, etc, being compiled with gcc.
Unfortunately, and I am unsure as to the root cause, emerge now coredumps during the Verifying ebuild manifest phase.
I don't have gdb installed, I can't re-install portage, in fact, I can't emerge anything.
I tried switching between python 2.7 and 3.4 using eselect, to no avail.
I tried running emerge with --debug but no debug output is generated at the time the core dumps.
I have done an emerge --sync, in case it's a problem in the portage tree
I have built strace manually and tried 'strace emerge strace' and the final output is below.
I manually built gdb and ran emerge using gdb, a stack trace at the crash point is below.
I am unsure as how to proceed, I might try manually building python, but in the meantime, any suggestions?
gdb output. | Code: | Program received signal SIGSEGV, Segmentation fault.
0x00007ffff3e1a58c in blake2b_init_param ()
from /usr/lib64/python3.4/site-packages/pyblake2.cpython-34m.so
(gdb) where
#0 0x00007ffff3e1a58c in blake2b_init_param ()
from /usr/lib64/python3.4/site-packages/pyblake2.cpython-34m.so
#1 0x00007ffff3e19bd5 in ?? ()
from /usr/lib64/python3.4/site-packages/pyblake2.cpython-34m.so
#2 0x000000305491899a in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#3 0x000000305491b70e in ?? () from /usr/lib64/libpython3.4m.so.1.0
#4 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#5 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#6 0x000000305491b786 in ?? () from /usr/lib64/libpython3.4m.so.1.0
#7 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#8 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#9 0x000000305491b786 in ?? () from /usr/lib64/libpython3.4m.so.1.0
#10 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#11 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#12 0x000000305491b786 in ?? () from /usr/lib64/libpython3.4m.so.1.0
#13 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#14 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#15 0x000000305491b786 in ?? () from /usr/lib64/libpython3.4m.so.1.0
#16 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#17 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#18 0x000000305491b786 in ?? () from /usr/lib64/libpython3.4m.so.1.0
#19 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#20 0x000000305491b70e in ?? () from /usr/lib64/libpython3.4m.so.1.0
#21 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#22 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#23 0x000000305491b786 in ?? () from /usr/lib64/libpython3.4m.so.1.0
#24 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#25 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#26 0x000000305491b786 in ?? () from /usr/lib64/libpython3.4m.so.1.0
#27 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#28 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#29 0x000000305491b786 in ?? () from /usr/lib64/libpython3.4m.so.1.0
#30 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#31 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#32 0x000000305491b786 in ?? () from /usr/lib64/libpython3.4m.so.1.0
#33 0x00000030549184cb in PyEval_EvalFrameEx ()
from /usr/lib64/libpython3.4m.so.1.0
#34 0x0000003054912ba7 in PyEval_EvalCodeEx ()
from /usr/lib64/libpython3.4m.so.1.0
#35 0x0000003054911ec5 in PyEval_EvalCode ()
from /usr/lib64/libpython3.4m.so.1.0
#36 0x000000305493e70f in PyRun_FileExFlags ()
from /usr/lib64/libpython3.4m.so.1.0
#37 0x000000305493dc0e in PyRun_SimpleFileExFlags ()
from /usr/lib64/libpython3.4m.so.1.0
#38 0x00000030549556ac in Py_Main () from /usr/lib64/libpython3.4m.so.1.0
#39 0x0000000000400a86 in main ()
(gdb) |
strace output.
| Code: | write(1, ">>> Verifying ebuild manifests\n", 31>>> Verifying ebuild manifests
) = 31
access("/portage/gentoo/dev-util/strace/strace-4.16.ebuild", R_OK) = 0
open("/portage/gentoo/dev-util/strace/Manifest", O_RDONLY|O_CLOEXEC) = 6
fstat(6, {st_mode=S_IFREG|0644, st_size=2425, ...}) = 0
ioctl(6, TCGETS, 0x7ffe45212470) = -1 ENOTTY (Inappropriate ioctl for device)
fstat(6, {st_mode=S_IFREG|0644, st_size=2425, ...}) = 0
lseek(6, 0, SEEK_CUR) = 0
lseek(6, 0, SEEK_CUR) = 0
read(6, "DIST strace-4.16.tar.xz 966668 B"..., 8192) = 2425
read(6, "", 8192) = 0
close(6) = 0
ioctl(1, TCGETS, {B38400 opost isig icanon echo ...}) = 0
stat("/portage/gentoo/dev-util/strace/strace-9999.ebuild", {st_mode=S_IFREG|0644, st_size=1807, ...}) = 0
open("/portage/gentoo/dev-util/strace/strace-9999.ebuild", O_RDONLY|O_CLOEXEC) = 6
fstat(6, {st_mode=S_IFREG|0644, st_size=1807, ...}) = 0
ioctl(6, TCGETS, 0x7ffe45212150) = -1 ENOTTY (Inappropriate ioctl for device)
fstat(6, {st_mode=S_IFREG|0644, st_size=1807, ...}) = 0
lseek(6, 0, SEEK_CUR) = 0
--- SIGSEGV {si_signo=SIGSEGV, si_code=SI_KERNEL, si_addr=NULL} ---
+++ killed by SIGSEGV (core dumped) +++
Segmentation fault
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I see messages in /var/log/message like the following:-
| Code: | Dec 11 17:33:28 gentoo-vm kernel: traps: emerge[4418] general protection ip:7f0fc1c4058c sp:7ffe5714d7f8 error:0 in pyblake2.cpython-34m.so[7f0fc1c3d000+8000]
Dec 11 17:33:57 gentoo-vm kernel: traps: emerge[4430] general protection ip:7fefbbcc058c sp:7ffcdf7c9858 error:0 in pyblake2.cpython-34m.so[7fefbbcbd000+8000]
Dec 11 17:34:24 gentoo-vm kernel: traps: emerge[4442] general protection ip:7f99b989b58c sp:7ffd37d9b118 error:0 in pyblake2.cpython-34m.so[7f99b9898000+8000]
Dec 11 17:35:03 gentoo-vm kernel: traps: emerge[4457] general protection ip:7f0f4142d58c sp:7ffed0a3eb98 error:0 in pyblake2.cpython-34m.so[7f0f4142a000+8000]
Dec 11 17:36:34 gentoo-vm kernel: traps: emerge[4542] general protection ip:7ff2abe7b58c sp:7ffc0791da78 error:0 in pyblake2.cpython-34m.so[7ff2abe78000+8000]
Dec 11 17:36:57 gentoo-vm kernel: traps: emerge[4586] general protection ip:7fa53c7ee52c sp:7fff26354fb8 error:0 in pyblake2.so[7fa53c7eb000+8000]
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emerge --info as follows:-
| Code: | Portage 2.3.13 (python 2.7.14-final-0, default/linux/amd64/13.0/desktop, gcc-7.2.0, glibc-2.25-r9, 4.12.12-gentoo x86_64)
=================================================================
System uname: Linux-4.12.12-gentoo-x86_64-Intel-R-_Core-TM-_i7-7700_CPU_@_3.60GHz-with-gentoo-2.4.1
KiB Mem: 10216148 total, 9557400 free
KiB Swap: 1048572 total, 1048572 free
Timestamp of repository gentoo: Thu, 07 Dec 2017 23:45:02 +0000
Head commit of repository gentoo: 6ef22505bc25ef8a68bef36e38832c7207d7aa68
sh bash 4.3_p48-r1
ld GNU ld (Gentoo 2.29.1 p3) 2.29.1
app-shells/bash: 4.3_p48-r1::gentoo
dev-lang/perl: 5.24.3::gentoo
dev-lang/python: 2.7.14::gentoo, 3.4.5::gentoo
dev-util/cmake: 3.10.0::gentoo
dev-util/pkgconfig: 0.29.2::gentoo
sys-apps/baselayout: 2.4.1-r2::gentoo
sys-apps/openrc: 0.34.9::gentoo
sys-apps/sandbox: 2.10-r4::gentoo
sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo
sys-devel/automake: 1.15.1-r1::gentoo
sys-devel/binutils: 2.29.1-r1::gentoo
sys-devel/gcc: 7.2.0::gentoo
sys-devel/gcc-config: 1.8-r1::gentoo
sys-devel/libtool: 2.4.6-r3::gentoo
sys-devel/make: 4.2.1::gentoo
sys-kernel/linux-headers: 4.4::gentoo (virtual/os-headers)
sys-libs/glibc: 2.25-r9::gentoo
Repositories:
local_repo
location: /portage/local
masters: gentoo
priority: 0
gentoo
location: /portage/gentoo
sync-type: rsync
sync-uri: rsync://mirror.internode.on.net/gentoo-portage
priority: 1
sync-rsync-extra-opts:
ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CC="clang"
CFLAGS="-O2 -mtune=native -march=native -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /lib/udev/rules.d /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/sabnzbd/config"
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"
CXX="clang++"
CXXFLAGS="-O2 -mtune=native -march=native -pipe"
DISTDIR="/portage/gentoo/distfiles"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict 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://mirror.internode.on.net/pub/gentoo ftp://mirror.pacific.net.au/linux/Gentoo http://mymirror.asiaosc.org/gentoo/ http://www.zentek-international.com/mirrors/gentoo/ http://open-systems.ufl.edu/mirrors/gentoo http://www.ibiblio.org/pub/Linux/distributions/gentoo"
LANG="en_AU.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
PKGDIR="/portage/gentoo/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="/tmp"
USE="X a52 aac acl acpi alsa amd64 berkdb bindist bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emacs emboss encode exif fam firefox flac fortran gd gdbm gif glamor gpm iconv ipv6 jpeg lcms ldap libnotify mad mmx mng modules mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds qt3support qt5 readline sdl seccomp session spell sse sse2 sse3 ssl startup-notification svg tcpd tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xattr 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="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache dumpio env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2 sse3 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="efi-64 pc emu" INPUT_DEVICES="evdev" 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" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby22" USERLAND="GNU" VIDEO_CARDS="virtualbox" 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
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...Lyall
Last edited by lyallp on Mon Dec 11, 2017 10:13 am; edited 1 time in total |
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Genone
Retired Dev
Joined: 14 Mar 2003
Posts: 9523
Location: beyond the rim
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| Posted: Mon Dec 11, 2017 9:21 am Post subject: |
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| Well, the issue is clearly with /usr/lib64/python3.4/site-packages/pyblake2.cpython-34m.so which seems to be a new dependency of portage with 2.3.13-r1. Don't know if this is a hard dependency, you could try to rename it temporarily to get portage working again. |
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lyallp
Veteran
Joined: 15 Jul 2004
Posts: 1557
Location: Adelaide/Australia
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| Posted: Mon Dec 11, 2017 9:25 am Post subject: |
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Initially I renamed the pyblake2 shared library and emerge started working.
I subsequently unmerged pyblake2 and emerge still keeps working.
I suspect my next world update pyblake2 will be re-installed and re-break the system.
I will report back on this.
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fedeliallalinea
Administrator
Joined: 08 Mar 2003
Posts: 30894
Location: here
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| Posted: Mon Dec 11, 2017 9:28 am Post subject: |
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Can be related to bug https://bugs.gentoo.org/638428?
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lyallp
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Joined: 15 Jul 2004
Posts: 1557
Location: Adelaide/Australia
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| Posted: Mon Dec 11, 2017 10:10 am Post subject: |
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updating pyblake2 to keyword ~amd64 (1.1.0) fixed the core dump issue for me.
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