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Bug 869629 - =media-gfx/openvdb-9.0.0-r4[cuda] - sandbox violation during src_configure
Summary: =media-gfx/openvdb-9.0.0-r4[cuda] - sandbox violation during src_configure
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Adrian
URL:
Whiteboard:
Keywords: PullRequest
: 870580 (view as bug list)
Depends on:
Blocks:
 
Reported: 2022-09-10 23:49 UTC by Bernd
Modified: 2022-09-25 01:27 UTC (History)
3 users (show)

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


Attachments
openvdb-9.0.0-r4:20220910-164913.log (openvdb-9.0.0-r4:20220910-164913.log,8.80 KB, text/plain)
2022-09-10 23:50 UTC, Bernd
Details

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Description Bernd 2022-09-10 23:49:00 UTC
After a boost triggered rebuild, the package no longer build with the cuda USE flag:

-- Check for working CUDA compiler: /opt/cuda/bin/nvcc - skipped
 * ACCESS DENIED:  open_wr:       /dev/nvidiactl
 * ACCESS DENIED:  open_wr:       /dev/nvidiactl
 * ACCESS DENIED:  open_wr:       /dev/nvidiactl
 * ACCESS DENIED:  open_wr:       /dev/nvidiactl
 * ACCESS DENIED:  open_wr:       /dev/nvidiactl
 * ACCESS DENIED:  open_wr:       /dev/nvidiactl
 * ACCESS DENIED:  open_wr:       /dev/nvidiactl
 * ACCESS DENIED:  open_wr:       /dev/nvidiactl
-- Detecting CUDA compile features
-- Detecting CUDA compile features - done

My last rebuild was early July, so the reason could be related to other package updates.

Reproducible: Always

Steps to Reproduce:
1. emerge >=boost-1.80.0 (not sure if necessary, the upgrade triggered the rebuild)
2. USE=cuda emerge openvdb
3.



Portage 3.0.36 (python 3.10.7-final-0, default/linux/amd64/17.1/systemd, gcc-11.3.1, glibc-2.35-r8, 5.19.8-gentoo-0 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.19.8-gentoo-0-x86_64-AMD_Ryzen_7_3800X_8-Core_Processor-with-glibc2.35
KiB Mem:    32822700 total,   6390452 free
KiB Swap:   33554428 total,  33239400 free
Head commit of repository guru: e9b5432c4460478e3fda14907a252325e6264d3c

Timestamp of repository steam-overlay: Wed, 07 Sep 2022 08:26:00 +0000
Head commit of repository steam-overlay: 78208ca83614c4cc031ca8f8ec9b023a5c9c3b1e

Head commit of repository qt: 943f1f45e69cee8a1c159244f91d822042f35b2d

Head commit of repository science: 070f86d184cddd2d2fb02fe2f8930a29dba4ee7d

Head commit of repository gentoo-git: 29a1061bbfbc3be4209fadaa2eef96ddb9542780

Head commit of repository waebbl: 7886a666096237e29d5df7a2eab1fd91b9130c24

Timestamp of repository gentoo: Sat, 10 Sep 2022 08:42:38 +0000
Head commit of repository gentoo: b42138f5c986665c237813b8f07eed2ee05b829f

sh bash 5.1_p16-r2
ld GNU ld (Gentoo 2.39 p4) 2.39.0
app-misc/pax-utils:        1.3.5::gentoo
app-shells/bash:           5.1_p16-r2::gentoo
dev-java/java-config:      2.3.1::gentoo
dev-lang/perl:             5.36.0::gentoo
dev-lang/python:           3.10.7::gentoo, 3.11.0_rc1_p2::gentoo
dev-lang/rust:             1.62.1::gentoo
dev-util/cmake:            3.24.1::gentoo
dev-util/meson:            0.63.2::gentoo
sys-apps/baselayout:       2.8-r2::gentoo
sys-apps/sandbox:          2.29::gentoo
sys-apps/systemd:          251.4::gentoo
sys-devel/autoconf:        2.13-r2::gentoo, 2.71-r2::gentoo
sys-devel/automake:        1.16.5::gentoo
sys-devel/binutils:        2.39-r2::gentoo
sys-devel/binutils-config: 5.4.1::gentoo
sys-devel/clang:           13.0.1::gentoo, 14.0.6-r1::gentoo, 15.0.0::gentoo
sys-devel/gcc:             11.3.1_p20220909::gentoo, 12.2.0::gentoo
sys-devel/gcc-config:      2.5-r1::gentoo
sys-devel/libtool:         2.4.7::gentoo
sys-devel/lld:             15.0.0::gentoo
sys-devel/llvm:            13.0.1::gentoo, 14.0.6-r2::gentoo, 15.0.0::gentoo
sys-devel/make:            4.3::gentoo
sys-kernel/linux-headers:  5.19::gentoo (virtual/os-headers)
sys-libs/glibc:            2.35-r8::gentoo
sys-libs/libselinux:       3.4::gentoo
Repositories:

guru
    location: /mnt/data/code/github/portage-overlays/guru
    sync-type: git
    sync-uri: git@git.gentoo.org:repo/proj/guru.git
    masters: gentoo
    priority: -1000

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

qt
    location: /mnt/data/code/github/portage-overlays/qt
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/qt.git
    masters: gentoo
    priority: 60

science
    location: /mnt/data/code/github/portage-overlays/sci
    sync-type: git
    sync-uri: git://github.com/waebbl/sci.git
    masters: gentoo
    priority: 60

gentoo-git
    location: /mnt/data/code/github/portage-overlays/gentoo-git
    sync-type: git
    sync-uri: https://github.com/waebbl/gentoo.git
    masters: gentoo
    priority: 99

waebbl
    location: /mnt/data/code/github/portage-overlays/waebbl
    sync-type: git
    sync-uri: https://github.com/waebbl/waebbl-gentoo.git
    masters: gentoo
    priority: 99

gentoo
    location: /var/db/repos/gentoo
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/gentoo.git
    priority: 100

Installed sets: @3D, @Qt6, @admin-tools, @desktop, @dev-tools, @docs, @esteam, @fonts, @games, @net-tools, @science
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check"
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 -pipe -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--complete-graph --keep-going --fail-clean --usepkg --buildpkg --buildpkg-exclude='x11-drivers/nvidia-drivers virtual/* acct-user/* acct-group/* app-eselect/* dev-util/nvidia-cuda-toolkit' --autounmask=n --binpkg-respect-use=y --binpkg-changed-deps=y"
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 -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg buildpkg-live buildsyspkg cgroup clean-logs config-protect-if-modified distlocks downgrade-backup ebuild-locks fail-clean fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-elog split-log strict strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe -march=znver2 -frecord-gcc-switches -fstack-protector-strong -fstack-check"
GENTOO_MIRRORS="https://ftp.fau.de/gentoo/ https://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/         https://ftp.halifax.rwth-aachen.de/gentoo/"
INSTALL_MASK="/usr/share/locale -/usr/share/locale/de* -/usr/share/locale/en*"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0"
MAKEOPTS="-j8"
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/bash"
USE="X acl alsa amd64 branding bzip2 cli crypt dbus dri egl emacs fortran gdbm gif gnome gtk-doc iconv ipv6 jpeg jpeg2k kde lcms libglvnd libinput libtirpc man multilib ncurses networkmanager nls nptl offensive ogg opengl openmp pam pcre pic png policykit pulseaudio python qml qt5 readline seccomp sound split-usr ssl svg systemd tga theora threads tiff udev unicode vorbis webp wifi x264 x265 xattr xpm zlib zstd" 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="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sha sse sse2 sse3 sse4_1 sse4_2 sse4a 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" GRUB_PLATFORMS="pc multiboot qemu" INPUT_DEVICES="libinput wacom" KERNEL="linux" L10N="de de-DE en en-GB en-US" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver" LLVM_TARGETS="NVPTX WebAssembly" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_10" PYTHON_TARGETS="python3_10" RUBY_TARGETS="ruby31" STEAMGAMES="witcher2" USERLAND="GNU" VIDEO_CARDS="dummy fbdev nvidia vesa" 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, 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

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

media-gfx/openvdb-9.0.0-r4::gentoo was built with the following:
USE="abi9-compat blosc cuda nanovdb numpy python utils zlib -abi6-compat -abi7-compat -abi8-compat -doc -static-libs -test" ABI_X86="(64)" CPU_FLAGS_X86="avx sse4_2" PYTHON_SINGLE_TARGET="python3_10 -python3_8 -python3_9"
FEATURES="fail-clean protect-owned sign unmerge-logs usersandbox xattr buildsyspkg sfperms split-elog news strict ebuild-locks unmerge-orphans merge-sync binpkg-dostrip preserve-libs config-protect-if-modified distlocks userpriv downgrade-backup split-log qa-unresolved-soname-deps userfetch fixlafiles unknown-features-warn strict-keepdir network-sandbox clean-logs binpkg-docompress assume-digests buildpkg-live cgroup parallel-fetch usersync binpkg-logs ipc-sandbox pid-sandbox sandbox buildpkg multilib-strict"
Comment 1 Bernd 2022-09-10 23:50:31 UTC
Created attachment 804541 [details]
openvdb-9.0.0-r4:20220910-164913.log

build log
Comment 2 Stephan Hartmann (RETIRED) gentoo-dev 2022-09-18 08:05:31 UTC
*** Bug 870580 has been marked as a duplicate of this bug. ***
Comment 3 Larry the Git Cow gentoo-dev 2022-09-25 01:27:45 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c098bb4532b66d37ee7bd1e1878d332711d008ad

commit c098bb4532b66d37ee7bd1e1878d332711d008ad
Author:     Bernd Waibel <waebbl-gentoo@posteo.net>
AuthorDate: 2022-09-11 08:05:05 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2022-09-25 01:27:16 +0000

    media-gfx/openvdb: fix build with cuda
    
    Allow write to /dev/nvidiactl for cmake configuration to work properly
    Remove abi6-compat USE flag. V6 ABI compatibility is not available in v9.
    
    Closes: https://bugs.gentoo.org/869629
    Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
    Closes: https://github.com/gentoo/gentoo/pull/27204
    Signed-off-by: Sam James <sam@gentoo.org>

 media-gfx/openvdb/openvdb-9.0.0-r4.ebuild | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

Additionally, it has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d089d928deeb9d0ff8226f23ca9168058fecf337

commit d089d928deeb9d0ff8226f23ca9168058fecf337
Author:     Bernd Waibel <waebbl-gentoo@posteo.net>
AuthorDate: 2022-09-14 06:56:47 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2022-09-25 01:27:15 +0000

    media-gfx/openvdb: add 9.1.0
    
    - Bump to EAPI 8, add support for Python 3.11
    - Add support for OpenVDB AX
    - Drop obsolete ABI 6 compatibility, add cmake options if deprecated ABIs are
            requested
    - Drop zlib USE flag, we depend on sys-libs/zlib anyway
    - Improve dependecies: some deps are only needed for the vdb_render binary,
            toggled by the utils USE flag
    - Include changes from PR #27204
    
    Additional notes:
    - OpenVDB AX can be used for custom manipulation of VDB data via an expression language. It needs <llvm-14 and will fail to configure or build with llvm-14 and above.
    - Lowest compatible ABI is 7, so I removed abi6-compat USE flag. Additionally the package needs an extra cmake option to actually build the deprecated ABIs
    - Zlib is required by enabling blosc or building OpenVDB AX.
      If it's found by NanoVDB or if blosc is enabled in addition to nanovdb (the ebuild default), nanovdb builds in support for zlib.
      Other configurations don't look for zlib, although it's enabled by the default cmake configuration.
      As we uncodtionally depend on it anyway, I think the USE flag has no real use.
    - Dependency on OpenGL, glew, OpenEXR or libpng is only needed by the vdb_render binary, which is enabled through the utils USE flag.
      So I moved the dependencies for this packages. I had no issues with this changed dependency settings.
    
    Bug: https://bugs.gentoo.org/869629
    Closes: https://bugs.gentoo.org/851855
    Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
    Closes: https://github.com/gentoo/gentoo/pull/27251
    Signed-off-by: Sam James <sam@gentoo.org>

 media-gfx/openvdb/Manifest                         |   1 +
 .../openvdb-9.1.0-disable-failing-tests.patch      | 111 +++++++++++++
 media-gfx/openvdb/metadata.xml                     |   4 +
 media-gfx/openvdb/openvdb-9.1.0.ebuild             | 173 +++++++++++++++++++++
 4 files changed, 289 insertions(+)