Bug 830679

Summary:	sci-libs/tensorflow-2.7.0 - undefined reference to 'absl::lts_20211102::Mutex::~Mutex()'
Product:	Gentoo Linux	Reporter:	Hendrik Klug <hendrik.klug>
Component:	Current packages	Assignee:	Jason Zaman <perfinion>
Status:	RESOLVED DUPLICATE
Severity:	normal	CC:	andrewammerlaan, yrusinov
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Attachments:	build log beginning and end of tensorflow build.log Depend on abseil-cpp version 20210324.2

Description Hendrik Klug 2022-01-06 09:49:54 UTC

Build of tensorflow-2.7.0 fails with "undefined reference to 'absl::lts_20211102::Mutex::~Mutex()'"


Output of emerge --info:

Portage 3.0.30 (python 3.9.9-final-0, default/linux/amd64/17.1, gcc-11.2.1, glibc-2.34-r4, 5.10.74-gentoo-x86_64 x86_64)
=================================================================
System uname: Linux-5.10.74-gentoo-x86_64-x86_64-Intel-R-_Core-TM-_i5-7200U_CPU_@_2.50GHz-with-glibc2.34
KiB Mem:    32768976 total,  16106692 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Mon, 03 Jan 2022 07:30:01 +0000
Head commit of repository gentoo: 1587ad86d36059b65545dc4f2dd26430b336fb3f
Timestamp of repository HomeAssistantRepository: Sun, 02 Jan 2022 18:07:16 +0000
Head commit of repository HomeAssistantRepository: 9a2b2086129e8af7c6166ef62f5de1d85bc9f80c

Head commit of repository aclex-pytorch: d195e5446744fa10e40f63e5cc4af74649317fcf

Timestamp of repository brave-overlay: Sun, 02 Jan 2022 11:41:27 +0000
Head commit of repository brave-overlay: 7567bf9c6be52b5a4fdae0ab15163f8e9cf323ef

Timestamp of repository glarbs-overlay: Sun, 02 Jan 2022 11:41:35 +0000
Head commit of repository glarbs-overlay: d82a57d9b09a34b7f2c8a1740c9baee719f93b6a

Timestamp of repository guru: Sun, 02 Jan 2022 19:06:39 +0000
Head commit of repository guru: 804efd24b0665346c811078fb104032e3dc5fda0

Timestamp of repository holgersson-overlay: Sun, 02 Jan 2022 21:36:37 +0000
Head commit of repository holgersson-overlay: 499b15b7af68c18321d8d4a7f79b1689848c7083

Timestamp of repository ppfeufer-gentoo-overlay: Sun, 02 Jan 2022 11:41:32 +0000
Head commit of repository ppfeufer-gentoo-overlay: bc051e394635589ea91db41982d5908ea7343146

Timestamp of repository ricerlay: Sun, 02 Jan 2022 11:41:28 +0000
Head commit of repository ricerlay: cab670b62813e6a68501f5a077fd20f48e4c4cd9

Timestamp of repository science: Sun, 02 Jan 2022 18:07:18 +0000
Head commit of repository science: dae339c5d727a9b4a2495e8a391ce334c587fde6

Timestamp of repository underworld: Sun, 02 Jan 2022 11:41:46 +0000
Head commit of repository underworld: e891a3c72b2668a1f22629831fb94b10436aa003

Head commit of repository chymeric: 9997ccc0d0ac889af9fd78f6b0efa1108f0496b0

sh bash 5.1_p12
ld GNU ld (Gentoo 2.37_p1 p1) 2.37
distcc 3.4 x86_64-pc-linux-gnu [disabled]
app-misc/pax-utils:        1.3.3::gentoo
app-shells/bash:           5.1_p12::gentoo
dev-java/java-config:      2.3.1::gentoo
dev-lang/perl:             5.34.0-r6::gentoo
dev-lang/python:           2.7.18_p13::gentoo, 3.9.9::gentoo, 3.10.1-r1::gentoo
dev-lang/rust:             1.57.0::gentoo
dev-util/cmake:            3.22.1::gentoo
dev-util/meson:            0.60.3::gentoo
sys-apps/baselayout:       2.8::gentoo
sys-apps/openrc:           0.44.10::gentoo
sys-apps/sandbox:          2.29::gentoo
sys-devel/autoconf:        2.13-r1::gentoo, 2.71-r1::gentoo
sys-devel/automake:        1.16.5::gentoo
sys-devel/binutils:        2.37_p1-r1::gentoo
sys-devel/binutils-config: 5.4::gentoo
sys-devel/gcc:             11.2.1_p20211127::gentoo
sys-devel/gcc-config:      2.5-r1::gentoo
sys-devel/libtool:         2.4.6-r6::gentoo
sys-devel/llvm:            13.0.0::gentoo
sys-devel/make:            4.3::gentoo
sys-kernel/linux-headers:  5.15-r3::gentoo (virtual/os-headers)
sys-libs/glibc:            2.34-r4::gentoo
Repositories:

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

HomeAssistantRepository
    location: /var/db/repos/HomeAssistantRepository
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/HomeAssistantRepository.git
    masters: gentoo

aclex-pytorch
    location: /var/db/repos/aclex-pytorch
    sync-type: git
    sync-uri: https://github.com/aclex/pytorch-ebuild
    masters: gentoo

brave-overlay
    location: /var/db/repos/brave-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/brave-overlay.git
    masters: gentoo

glarbs-overlay
    location: /var/db/repos/glarbs-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/glarbs-overlay.git
    masters: gentoo

guru
    location: /var/db/repos/guru
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/guru.git
    masters: gentoo

holgersson-overlay
    location: /var/db/repos/holgersson-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/holgersson-overlay.git
    masters: gentoo

ppfeufer-gentoo-overlay
    location: /var/db/repos/ppfeufer-gentoo-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/ppfeufer-gentoo-overlay.git
    masters: gentoo

ricerlay
    location: /var/db/repos/ricerlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/ricerlay.git
    masters: gentoo

science
    location: /var/db/repos/science
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/science.git
    masters: gentoo

underworld
    location: /var/db/repos/underworld
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/underworld.git
    masters: gentoo

chymeric
    location: /var/db/repos/chymeric
    sync-type: git
    sync-uri: https://github.com/TheChymera/overlay.git
    masters: gentoo
    priority: 8889

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /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 -pipe"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--keep-going"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH 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 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="https://mirror.init7.net/gentoo/"
LANG="en_GB.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j6"
PKGDIR="/var/cache/binpkgs"
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"
SHELL="/bin/fish"
USE="X acl alsa amd64 bluetooth bzip2 cli crypt dbus dri elogind fortran gdbm iconv ipv6 libglvnd libtirpc multilib ncurses nls nptl openmp pam pcre pulseaudio readline savedconfig seccomp split-usr ssl unicode xattr xinerama zlib" ABI_X86="64" ADA_TARGET="gnat_2020" 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="mmx mmxext sse sse2" 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="libinput synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9" RUBY_TARGETS="ruby26 ruby27" USERLAND="GNU" VIDEO_CARDS="intel" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS

Comment 1 Mike Gilbert gentoo-dev

2022-01-06 22:23:29 UTC

Please attach a full build log and change the status back to UNCONFIRMED.

Comment 2 Hendrik Klug 2022-01-07 08:49:06 UTC

Created attachment 761468 [details]
build log

Sorry the build log was too large and was not uploaded.

Comment 3 Larry Sexton 2022-01-14 13:16:34 UTC

Believe I hit the same error when building:

bazel-out/k8-opt/bin/tensorflow/core/profiler/_objs/profiler_analysis_proto_cc_impl/profiler_analysis.grpc.pb.pic.o:profiler_analysis.grpc.pb.cc:function grpc::CompletionQueue::~CompletionQueue(): error: undefined reference to 'absl::lts_20211102::Mutex::~Mutex()'

There were many other errors, I think because it was a large link. As a workaround, I tried setting dev-cpp/abseil-cpp 20210324.2 and net-libs/grpc 1.41.1 and then sci-libs/tensorflow and sci-libs/keras built successfully.

Comment 4 Larry Sexton 2022-01-14 13:19:46 UTC

Created attachment 762158 [details]
beginning and end of tensorflow build.log

partial build.log

Comment 5 Andreas Kölbl 2022-01-16 07:44:17 UTC

Created attachment 762270 [details, diff]
Depend on abseil-cpp version 20210324.2

This workaround does not throw the mentioned Mutex()-Error. Manages to install tensorflow-2.7.0.

Comment 6 Thomas Haschka 2022-01-25 20:25:37 UTC

I can confirm this bug. I just experianced it on my machine!

Comment 7 Benda Xu gentoo-dev

2022-02-08 05:17:59 UTC

Sorry I did not find this bug before reporting bug 832760.

Please give tensorflow-2.8 a try.

*** This bug has been marked as a duplicate of bug 832760 ***