Bug 691492 – sci-libs/tensorflow-1.13.1 - In file included from tensorflow/core/platform/cloud/gcs_file_system.cc:29: bazel-out/k8-opt/genfiles/external/jsoncpp_git/include/json/config.h:132:10: fatal error: allocator.h: No such file or directory

• Status: RESOLVED OBSOLETE
• Product: Gentoo Linux

[Description Matthias Coppens 2019-08-05 13:12:02 UTC]

Created attachment 585764 [details]
build.log

Because of some library update, tensorflow needed to get updated.  When running emerge @preserved-rebuild, tensorflow failed to build.

I've already tried rebuilding tensorflow with bazel-0.20.0 (instead of bazel-0.22.0), but that resulted in the same build error.


$ emerge --info '=sci-libs/tensorflow-1.13.1::gentoo'

Portage 2.3.69 (python 3.6.5-final-0, default/linux/amd64/17.1/systemd, gcc-8.3.0, glibc-2.29-r2, 4.19.57-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-4.19.57-gentoo-x86_64-Intel-R-_Core-TM-_i7-5500U_CPU_@_2.40GHz-with-gentoo-2.6
KiB Mem:     8061240 total,   3028580 free
KiB Swap:   31249996 total,  30986000 free
Timestamp of repository gentoo: Sun, 04 Aug 2019 19:00:01 +0000
Head commit of repository gentoo: 1d2c71e6c79621707379b4d6e9109f1c2c3502e6
sh dash 0.5.9.1-r3
ld GNU ld (Gentoo 2.32 p2) 2.32.0
ccache version 3.7.1 [enabled]
app-shells/bash:          4.4_p23-r1::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.28.2-r1::gentoo
dev-lang/python:          2.7.15::gentoo, 3.6.5::gentoo
dev-util/ccache:          3.7.1::gentoo
dev-util/cmake:           3.14.6::gentoo
sys-apps/baselayout:      2.6-r1::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:            8.3.0-r1::gentoo
sys-devel/gcc-config:     2.0::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-r2::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-jobs: 1
    sync-rsync-verify-max-age: 24
    sync-rsync-extra-opts: 

localrepo
    location: /usr/local/portage
    masters: gentoo

haskell
    location: /var/lib/layman/haskell
    masters: gentoo
    priority: 50

pentoo
    location: /var/lib/layman/pentoo
    masters: gentoo
    priority: 50

sorrow
    location: /var/lib/layman/sorrow
    masters: gentoo
    priority: 50

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=native"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /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 -march=native"
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 -pipe -march=native"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs ccache 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 sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=native"
GENTOO_MIRRORS="http://mirrors.soeasyto.com/distfiles.gentoo.org/ http://mirrors.evowise.com/gentoo/ http://mirror.leaseweb.com/gentoo/ http://gentoo.mirrors.ovh.net/gentoo-distfiles/ https://mirrors.evowise.com/gentoo/ https://mirrors.soeasyto.com/distfiles.gentoo.org/ http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/ http://mirror.netcologne.de/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo http://www.mirrorservice.org/sites/distfiles.gentoo.org/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j5"
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 aac acl alsa amd64 berkdb branding bzip2 cli crypt cups cxx dri exif fish-completion fortran gdbm gtk iconv icu ipv6 jpeg libtirpc mp3 mp4 mpeg multilib ncurses networkmanager nls nptl openmp pam pcre png pulseaudio qt5 readline seccomp split-usr ssl systemd tcpd udev unicode wayland x264 xattr xinerama 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="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 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" 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" USERLAND="GNU" VIDEO_CARDS="fbdev intel nouveau dummy v4l" 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, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

=================================================================
                        Package Settings
=================================================================

sci-libs/tensorflow-1.13.1::gentoo was built with the following:
USE="python -cuda -mpi" ABI_X86="(64)" CPU_FLAGS_X86="avx avx2 fma3 sse sse2 sse3 sse4_1 sse4_2 -fma4" PYTHON_TARGETS="python2_7 python3_6 -python3_5 -python3_7"
CFLAGS="-O2 -pipe -march=native -msse -msse2 -msse3 -msse4.1 -msse4.2 -mavx -mavx2 -mfma"
CXXFLAGS="-O2 -pipe -march=native -msse -msse2 -msse3 -msse4.1 -msse4.2 -mavx -mavx2 -mfma"

[Comment 1 Thomas Beutin 2019-08-05 14:17:52 UTC]

In file included from bazel-out/k8-opt/genfiles/external/jsoncpp_git/include/json/autolink.h:9,
                 from bazel-out/k8-opt/genfiles/external/jsoncpp_git/include/json/json.h:9,
                 from tensorflow/core/platform/cloud/gcs_file_system.cc:29:
bazel-out/k8-opt/genfiles/external/jsoncpp_git/include/json/config.h:132:10: fatal error: allocator.h: No such file or directory
 #include "allocator.h"
          ^~~~~~~~~~~~~
compilation terminated.

[Comment 2 Thomas Beutin 2019-08-05 14:18:58 UTC]

Seems to be a dupe of bug 689282

[Comment 3 Matthias Coppens 2019-08-05 15:32:52 UTC]

(In reply to Thomas Beutin from comment #2)
> Seems to be a dupe of bug 689282

I am currently compiling in my localrepo, where I've cp'ed all files/tensorflow-1.14.0* to files/tensorflow-1.13.0*, and I've had no errors so far.  This indeed seems to be the solution.

[Comment 4 Matthias Coppens 2019-08-05 16:13:19 UTC]

(In reply to coppens.matthias.abc from comment #3)
> (In reply to Thomas Beutin from comment #2)
> > Seems to be a dupe of bug 689282
> 
> I am currently compiling in my localrepo, where I've cp'ed all
> files/tensorflow-1.14.0* to files/tensorflow-1.13.0*, and I've had no errors
> so far.  This indeed seems to be the solution.

Nevermind, didn't work.

[Comment 5 Matthias Coppens 2019-08-05 22:17:58 UTC]

Created attachment 585840 [details, diff]
This patch for the ebuild fixed it for me

This fixed it for me by using 4 of the patches from bug 689282.  I'm not sure if all patches are necessary, but it now builds without problems.

[Comment 6 Thomas Beutin 2019-08-06 15:08:42 UTC]

(In reply to coppens.matthias.abc from comment #5)
> Created attachment 585840 [details, diff] [details, diff]
> This patch for the ebuild fixed it for me
> 
> This fixed it for me by using 4 of the patches from bug 689282.  I'm not
> sure if all patches are necessary, but it now builds without problems.

I can confirm the successful compilation of sci-libs/tensorflow-1.13.1 on my system.

I suggest to change the bug summary to something more descriptive (see bug 689282) and than close it.

[Comment 7 Jason Zaman 2019-12-08 10:38:09 UTC]

I removed tf-1.13 already, thanks tho.