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Bug 815244 - sci-libs/tensorflow-2.5.0-r1 build fails with dev-libs/cudnn-8.2.4.15
Summary: sci-libs/tensorflow-2.5.0-r1 build fails with dev-libs/cudnn-8.2.4.15
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Jason Zaman
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2021-09-28 16:23 UTC by Oscar
Modified: 2021-10-25 01:11 UTC (History)
4 users (show)

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


Attachments
build.log (build.log.bz2,6.86 KB, application/x-bzip)
2021-09-28 17:49 UTC, Oscar
Details

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Description Oscar 2021-09-28 16:23:06 UTC
Hi, 
after updating to dev-libs/cudnn-8.2.4.15, tensorflow compilation crashes.

Reproducible: Always




Portage 3.0.20 (python 3.9.6-final-0, default/linux/amd64/17.1, gcc-10.3.0, glibc-2.33-r1, 5.10.61-gentoo-x86_64 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.10.61-gentoo-x86_64-x86_64-Intel-R-_Core-TM-_i7-3770K_CPU_@_3.50GHz-with-glibc2.33
KiB Mem:    16330596 total,   2869380 free
KiB Swap:   31280120 total,  31075576 free
Timestamp of repository gentoo: Mon, 27 Sep 2021 13:30:01 +0000
Head commit of repository gentoo: 9d10222f9cc77e635102de328685af93d95466d4
sh bash 5.1_p8
ld GNU ld (Gentoo 2.36.1 p5) 2.36.1
app-shells/bash:          5.1_p8::gentoo
dev-java/java-config:     2.3.1::gentoo
dev-lang/perl:            5.34.0-r2::gentoo
dev-lang/python:          3.9.6_p2::gentoo
dev-lang/rust:            1.53.0::gentoo
dev-util/cmake:           3.20.5::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/openrc:          0.43.5::gentoo
sys-apps/sandbox:         2.24::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.16.4::gentoo
sys-devel/binutils:       2.36.1-r2::gentoo, 2.37_p1::gentoo
sys-devel/gcc:            10.3.0-r2::gentoo
sys-devel/gcc-config:     2.4::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.10::gentoo (virtual/os-headers)
sys-libs/glibc:           2.33-r1::gentoo
Repositories:

gentoo
    location: /var/db/repos/gentoo
    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: 

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

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=ivybridge -O3 -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="-march=ivybridge -O3 -pipe"
DISTDIR="/var/cache/distfiles"
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="-march=native -O3 -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 qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=native -O3 -pipe"
GENTOO_MIRRORS="https://ftp.halifax.rwth-aachen.de/gentoo/"
LANG="de_DE.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j9"
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"
USE="X acl amd64 bluetooth bzip2 cli crypt dbus dri elogind fortran gdbm iconv ipv6 libglvnd libtirpc multilib ncurses nls nptl nvidia openmp pam pcre pulseaudio readline seccomp split-usr ssl tcpd unicode xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2019" 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 mmxext sse sse2 aes avx f16c pclmul popcnt 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="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="NVPTX X86" 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" USERLAND="GNU" VIDEO_CARDS="nvidia" 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:  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, RUSTFLAGS

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

sci-libs/tensorflow-2.5.0-r1::gentoo was built with the following:
USE="cuda python xla -mpi" ABI_X86="(64)" CPU_FLAGS_X86="avx sse sse2 sse3 sse4_1 sse4_2 -avx2 -fma3 -fma4" PYTHON_TARGETS="python3_9 -python3_8"
CFLAGS="-march=ivybridge -O3 -pipe -msse -msse2 -msse3 -msse4.1 -msse4.2 -mavx"
CXXFLAGS="-march=ivybridge -O3 -pipe -msse -msse2 -msse3 -msse4.1 -msse4.2 -mavx"
Comment 1 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2021-09-28 17:38:20 UTC
Please share the build.log in full (compressed if necessary).
Comment 2 Oscar 2021-09-28 17:49:07 UTC
Created attachment 741798 [details]
build.log
Comment 3 Petru 2021-09-29 02:05:35 UTC
I've encountered the same build error, which seems to be fixed upstream starting with version 2.6.0, 2.5.1 is still broken (still has the buggy code). I found the explanation here https://www.gitmemory.com/issue/tensorflow/tensorflow/48652/823594730 (sory this doesn't seem to be the original post)
Comment 4 Oscar 2021-09-29 12:57:18 UTC
(In reply to scantlight from comment #3)
> I've encountered the same build error, which seems to be fixed upstream
> starting with version 2.6.0, 2.5.1 is still broken (still has the buggy
> code). I found the explanation here
> https://www.gitmemory.com/issue/tensorflow/tensorflow/48652/823594730 (sory
> this doesn't seem to be the original post)

Hi,
thanks for the tip. I followed the suggested instructions and swapped from 
output.append(outputs)
to
outputs.append(output), 
which seems to make more sense concerning the function's return value. 
It compiles!, well, it started compiling...
Comment 5 foufou33 2021-09-30 06:51:10 UTC
(In reply to Oscar from comment #4)
> (In reply to scantlight from comment #3)
> > I've encountered the same build error, which seems to be fixed upstream
> > starting with version 2.6.0, 2.5.1 is still broken (still has the buggy
> > code). I found the explanation here
> > https://www.gitmemory.com/issue/tensorflow/tensorflow/48652/823594730 (sory
> > this doesn't seem to be the original post)
> 
> Hi,
> thanks for the tip. I followed the suggested instructions and swapped from 
> output.append(outputs)
> to
> outputs.append(output), 
> which seems to make more sense concerning the function's return value. 
> It compiles!, well, it started compiling...
this seems to be the fix 
https://github.com/tensorflow/tensorflow/commit/c8e4f2aa633c4f9b803fdeb5d8463f002387a2bf.patch
or at least as you said compilation starts (and still going on)
Comment 6 Oscar 2021-09-30 11:33:20 UTC
(In reply to foufou33 from comment #5)
> this seems to be the fix 
> https://github.com/tensorflow/tensorflow/commit/
> c8e4f2aa633c4f9b803fdeb5d8463f002387a2bf.patch
> or at least as you said compilation starts (and still going on)

yes, that's the one. The build finished
Comment 7 Larry the Git Cow gentoo-dev 2021-10-25 01:11:25 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3ee1f4fa9a7bae90ab9452aa9570775cc7c15f00

commit 3ee1f4fa9a7bae90ab9452aa9570775cc7c15f00
Author:     Jason Zaman <perfinion@gentoo.org>
AuthorDate: 2021-10-24 21:34:06 +0000
Commit:     Jason Zaman <perfinion@gentoo.org>
CommitDate: 2021-10-25 01:08:44 +0000

    sci-libs/tensorflow: Fix build with >=CUDA-11.3
    
    Closes: https://bugs.gentoo.org/815244
    Package-Manager: Portage-3.0.20, Repoman-3.0.3
    Signed-off-by: Jason Zaman <perfinion@gentoo.org>

 sci-libs/tensorflow/Manifest                       |   3 +-
 .../files/0008-patch-ruy-for-gcc-11.patch          |  37 --
 sci-libs/tensorflow/tensorflow-2.5.0-r1.ebuild     | 413 ---------------------
 ...-2.5.0-r2.ebuild => tensorflow-2.5.0-r3.ebuild} |   8 +-
 4 files changed, 5 insertions(+), 456 deletions(-)