Summary: | sci-libs/tensorflow-1.14 with dev-libs/jsoncpp-1.9 - In file included from tensorflow/core/platform/cloud/gcs_file_system.cc:29: bazel-out/host/genfiles/external/jsoncpp_git/include/json/config.h:127:10: fatal error: allocator.h: No such file or directory | ||
---|---|---|---|
Product: | Gentoo Linux | Reporter: | Harris Landgarten <harrisl> |
Component: | Current packages | Assignee: | Jason Zaman <perfinion> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | jarausch, jouni.kosonen, me, tb |
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: |
build log
tensorflow-jsoncpp-1.9.patch |
Description
Harris Landgarten
2019-07-04 16:47:31 UTC
1) Please attach the entire build log to this bug report. 2) Please post your `emerge --info` output in a comment. *** Bug 689238 has been marked as a duplicate of this bug. *** Created attachment 582122 [details] build log Same issue here. Attached build.log emerge --info (note, lto is disabled for tensorflow using custom package.env): Portage 2.3.68 (python 3.6.8-final-0, default/linux/amd64/17.1/desktop/plasma/systemd, gcc-9.1.0, glibc-2.29-r2, 5.1.12-gentoo x86_64) ================================================================= System uname: Linux-5.1.12-gentoo-x86_64-Intel-R-_Core-TM-_i7-6700K_CPU_@_4.00GHz-with-gentoo-2.6 KiB Mem: 32905500 total, 25202120 free KiB Swap: 18874364 total, 18874364 free Timestamp of repository gentoo: Fri, 05 Jul 2019 17:00:01 +0000 Head commit of repository gentoo: d61d24f4818eef45f8e7ba2e4a7c508ad5bdfb43 sh bash 5.0_p7 ld GNU gold (Gentoo 2.32 p2 2.32.0) 1.16 app-shells/bash: 5.0_p7::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.30.0::gentoo dev-lang/python: 2.7.16-r100::sage-on-gentoo, 3.6.8::Local, 3.7.3::Local dev-util/cmake: 3.14.5::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.6-r1::gentoo sys-apps/sandbox: 2.17::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, 9.1.0-r1::gentoo sys-devel/gcc-config: 2.0::gentoo sys-devel/libtool: 2.4.6-r5::gentoo sys-devel/make: 4.2.1-r4::gentoo sys-kernel/linux-headers: 5.1::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-extra-opts: sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 Local location: /usr/local/portage masters: gentoo priority: 0 archenroot location: /var/lib/layman/archenroot masters: gentoo priority: 50 atom location: /var/lib/layman/atom masters: gentoo priority: 50 gamerlay location: /var/lib/layman/gamerlay masters: gentoo priority: 50 games-overlay location: /var/lib/layman/games-overlay masters: gentoo priority: 50 interactive-fiction location: /var/lib/layman/interactive-fiction masters: gentoo priority: 50 java location: /var/lib/layman/java masters: gentoo priority: 50 sage-on-gentoo location: /var/lib/layman/sage-on-gentoo masters: gentoo science priority: 50 sakaki-tools location: /var/lib/layman/sakaki-tools masters: gentoo priority: 50 science location: /var/lib/layman/science masters: gentoo priority: 50 steam-overlay location: /var/lib/layman/steam-overlay masters: gentoo priority: 50 Installed sets: @toolchain ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="@FREE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=native -flto=8 -fuse-linker-plugin -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /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 -march=native -flto=8 -fuse-linker-plugin -pipe -fvisibility-inlines-hidden" 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" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs 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 splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://de-mirror.org/gentoo/ http://mirror.netcologne.de/gentoo/ http://ftp.halifax.rwth-aachen.de/gentoo/ http://ftp.spline.inf.fu-berlin.de/mirrors/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/" LANG="en_US.utf-8" LC_ALL="en_US.utf-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -O2 -march=native -Wl,--as-needed -Wl,-O1 -Wl,--hash-style=gnu -flto=8 -fuse-linker-plugin" LINGUAS="en en-US nl" MAKEOPTS="-j8" 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 a52 aac acl acpi activities alsa amd64 avx avx2 berkdb bluetooth boost branding btrfs bzip2 c++0x cairo caps cdda cdr clang cli crypt cryptsetup cuda cups cxx dbus declarative dhclient dri dts dvd dvdr emboss encode exif extraengine fam fat ffmpeg flac flash fontconfig gdbm gif git glamor gmp gpg gpm graphics graphite gtk iconv icu inotify ipv6 jpeg jpeg2k kdbus kde kipi kwallet latex lcms ldap libnotify libtirpc linguas_en linguas_nl lto luatex lzma lzo mad mathml mmx mng mono mp3 mp4 mpeg mpx multilib ncurses nls nptl ntfs ogg openal opencv opengl openmp pam pango pcre pdf phonon plasma plymouth png policykit ppds pulseaudio python qml qt5 r600-llvm-compiler readline s3tc science sdl seccomp semantic-desktop spell sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 startup-notification steamfonts streaming subversion svg systemd tcpd theora threads tiff trayicon truetype udev udisks unicode upower usb vaapi vdpau vlc vorbis vpx widevine widgets wxwidgets x264 x265 xa xattr xcb xcomposite xetex 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="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx sse sse2 ssse3 sse3 sse4_1 sse4_2 mmxext avx avx2 aes fma3 mpx" 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="pc efi-64" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" L10N="en en_US nl" 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 pypy python3_7" RUBY_TARGETS="ruby25" USERLAND="GNU" VIDEO_CARDS="nvidia" 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, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS I was hit by this as well. Confirming that jsoncpp-1.9.0 breaks things. Either masking this version of jsoncpp or setting the dependency in the tensorflow ebuild to ~jsoncpp-1.8.4 resolved this error. (In reply to Martin H from comment #4) > I was hit by this as well. Confirming that jsoncpp-1.9.0 breaks things. > Either masking this version of jsoncpp or setting the dependency in the > tensorflow ebuild to ~jsoncpp-1.8.4 resolved this error. Hi, I have the same error. Unfortunately masking jsoncpp, forcing a downgrade to jsoncpp-1.8.4 does not resolve things for me but the same error remains. (In reply to Fredrik Fyring from comment #5) > (In reply to Martin H from comment #4) > > I was hit by this as well. Confirming that jsoncpp-1.9.0 breaks things. > > Either masking this version of jsoncpp or setting the dependency in the > > tensorflow ebuild to ~jsoncpp-1.8.4 resolved this error. > > Hi, > > I have the same error. Unfortunately masking jsoncpp, forcing a downgrade to > jsoncpp-1.8.4 does not resolve things for me but the same error remains. Sorry, was a bit quick. I now have another error, but still related to allocator in jsoncpp: ERROR: /var/tmp/portage/sci-libs/tensorflow-1.14.0/work/tensorflow-1.14.0-python3_7/tensorflow/cc/BUILD:492:1: Linking of rule '//tensorflow/cc:ops/string_ops_gen_cc' failed (Exit 1): crosstool_wrapper_driver_is_not_gcc failed: error executing command (cd /var/tmp/portage/sci-libs/tensorflow-1.14.0/work/tensorflow-1.14.0-python3_7-bazel-base/execroot/org_tensorflow && \ exec env - \ PATH=/var/tmp/portage/sci-libs/tensorflow-1.14.0/temp/python3.7/bin:/usr/lib/portage/python3.7/ebuild-helpers/xattr:/usr/lib/portage/python3.7/ebuild-helpers:/usr/lib/llvm/8/bin:/usr/lib/llvm/7/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/lib64/subversion/bin:/opt/cuda/bin \ PWD=/proc/self/cwd \ external/local_config_cuda/crosstool/clang/bin/crosstool_wrapper_driver_is_not_gcc @bazel-out/host/bin/tensorflow/cc/ops/string_ops_gen_cc-2.params) Execution platform: @bazel_tools//platforms:host_platform /usr/bin/ld: /usr/lib64/libjsoncpp.so.19: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream()@GLIBCXX_3.4.26' (In reply to Fredrik Fyring from comment #5) > (In reply to Martin H from comment #4) > > I was hit by this as well. Confirming that jsoncpp-1.9.0 breaks things. > > Either masking this version of jsoncpp or setting the dependency in the > > tensorflow ebuild to ~jsoncpp-1.8.4 resolved this error. > > Hi, > > I have the same error. Unfortunately masking jsoncpp, forcing a downgrade to > jsoncpp-1.8.4 does not resolve things for me but the same error remains. This is still happening with dev-libs/jsoncpp-1.9.1, currently going stable in bug 690878 : Execution platform: @bazel_tools//platforms:host_platform In file included from tensorflow/contrib/cloud/kernels/gcs_config_ops.cc:18: In file included from bazel-out/k8-opt/bin/external/jsoncpp_git/include/json/json.h:9: In file included from bazel-out/k8-opt/bin/external/jsoncpp_git/include/json/autolink.h:9: bazel-out/k8-opt/bin/external/jsoncpp_git/include/json/config.h:132:10: fatal error: 'allocator.h' file not found #include "allocator.h" ^~~~~~~~~~~~~ 1 error generated. Created attachment 585226 [details, diff]
tensorflow-jsoncpp-1.9.patch
jsoncpp-1.9* unconditionally #includes "allocator.h" in the unamalgamated config, jsoncpp-1.8.4 didn't.
Tensorflow doesn't point the compilation machinery to the existing headers, it softlinks the list of required headers to its own source tree and "allocator.h" is not on the list.
I think the attached patch to tensorflow should be enough to fix the situation, but it'll take quite a few hours to verify on my machine. The file existed already with jsoncpp-1.8.4, it just didn't get used, so this shouldn't break anything.
Confirming that the patch in comment 8 above did allow tensorflow-1.14 to build here against jsoncpp-1.9.1. Protip: if you have net-libs/google-cloud-cpp installed and then bump up net-libs/grpc to a new minor version, rebuild net-libs/google-cloud-cpp afterwards unless you enjoy wasting a few hours on tensorflow rebuild that then fails because the classes and typedefs of those two conflict. With an API that volatile net-libs/google-cloud-cpp really needs a subslot dependency on net-libs/grpc. > Sorry, was a bit quick. I now have another error, but still related to
> allocator in jsoncpp:
>
> ERROR:
> /var/tmp/portage/sci-libs/tensorflow-1.14.0/work/tensorflow-1.14.0-python3_7/
> tensorflow/cc/BUILD:492:1: Linking of rule
> '//tensorflow/cc:ops/string_ops_gen_cc' failed (Exit 1):
> crosstool_wrapper_driver_is_not_gcc failed: error executing command
> (cd
> /var/tmp/portage/sci-libs/tensorflow-1.14.0/work/tensorflow-1.14.0-python3_7-
> bazel-base/execroot/org_tensorflow && \
> exec env - \
>
> PATH=/var/tmp/portage/sci-libs/tensorflow-1.14.0/temp/python3.7/bin:/usr/lib/
> portage/python3.7/ebuild-helpers/xattr:/usr/lib/portage/python3.7/ebuild-
> helpers:/usr/lib/llvm/8/bin:/usr/lib/llvm/7/bin:/usr/local/sbin:/usr/local/
> bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/lib64/subversion/bin:/opt/
> cuda/bin \
> PWD=/proc/self/cwd \
>
> external/local_config_cuda/crosstool/clang/bin/
> crosstool_wrapper_driver_is_not_gcc
> @bazel-out/host/bin/tensorflow/cc/ops/string_ops_gen_cc-2.params)
> Execution platform: @bazel_tools//platforms:host_platform
> /usr/bin/ld: /usr/lib64/libjsoncpp.so.19: undefined reference to
> `std::__cxx11::basic_ostringstream<char, std::char_traits<char>,
> std::allocator<char> >::basic_ostringstream()@GLIBCXX_3.4.26'
>
I have same problem with jsoncpp-1.9.1 and tensorflow-jsoncpp-1.9.patch:
ERROR: /var/tmp/portage/sci-libs/tensorflow-1.14.0/work/tensorflow-1.14.0-python3_7/tensorflow/cc/BUILD:492:1: Linking of rule '//tensorflow/cc:ops/random_ops_gen_cc' failed (Exit 1): crosstool_wrapper_driver_is_not_gcc failed: error executing command
(cd /var/tmp/portage/sci-libs/tensorflow-1.14.0/work/tensorflow-1.14.0-python3_7-bazel-base/execroot/org_tensorflow && \
exec env - \
PATH=/var/tmp/portage/sci-libs/tensorflow-1.14.0/temp/python3.7/bin:/usr/lib/portage/python3.7/ebuild-helpers/xattr:/usr/lib/portage/python3.7/ebuild-helpers:/usr/lib/llvm/8/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/opt/cuda/bin \
PWD=/proc/self/cwd \
external/local_config_cuda/crosstool/clang/bin/crosstool_wrapper_driver_is_not_gcc @bazel-out/host/bin/tensorflow/cc/ops/random_ops_gen_cc-2.params)
Execution platform: @bazel_tools//platforms:host_platform
/usr/bin/ld: /usr/lib64/libjsoncpp.so.21: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream()@GLIBCXX_3.4.26'
collect2: error: ld returned 1 exit status
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b684f751b6ad2029191c65b50ce0eacc4de001a3 commit b684f751b6ad2029191c65b50ce0eacc4de001a3 Author: Jason Zaman <perfinion@gentoo.org> AuthorDate: 2019-08-02 14:21:01 +0000 Commit: Jason Zaman <perfinion@gentoo.org> CommitDate: 2019-08-03 11:55:38 +0000 sci-libs/tensorflow-1.14.0-r1: Fix build issues - Header paths were mangled - Jsoncpp-1.9 build error - Newer GRPC needed a bumped google-cloud-cpp dep - Build failed with python2 if future was not installed - Add tensorflow_cc pkgconfig file Closes: https://bugs.gentoo.org/688594 Closes: https://bugs.gentoo.org/689282 Closes: https://bugs.gentoo.org/690212 Package-Manager: Portage-2.3.69, Repoman-2.3.16 Signed-off-by: Jason Zaman <perfinion@gentoo.org> ...ll_headers-fix-paths-of-generated-headers.patch | 38 ++++++++++++++++++ ...jsoncpp-update-header-symlinks-for-jsoncp.patch | 27 +++++++++++++ ...g-generate-tensorflow_cc-pkg-config-entry.patch | 46 ++++++++++++++++++++++ ...source-builtins-does-not-exist-in-python2.patch | 25 ++++++++++++ ...w-1.14.0.ebuild => tensorflow-1.14.0-r1.ebuild} | 16 +++++--- 5 files changed, 146 insertions(+), 6 deletions(-) |