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Bug 926612 - sci-libs/vtk-9.2.6-r1[cuda] fails to configure: ACCESS DENIED: fopen_wr: /proc/self/task/227/comm
Summary: sci-libs/vtk-9.2.6-r1[cuda] fails to configure: ACCESS DENIED: fopen_wr: /pr...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords: PullRequest
Depends on:
Blocks:
 
Reported: 2024-03-09 19:58 UTC by Miroslav Šulc
Modified: 2024-03-30 18:35 UTC (History)
10 users (show)

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


Attachments
build.log (build.log,25.23 KB, text/plain)
2024-03-09 19:58 UTC, Miroslav Šulc
Details

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Description Miroslav Šulc gentoo-dev 2024-03-09 19:58:16 UTC
Created attachment 887190 [details]
build.log

not using the latest vtk because it is blocked by opencascade.

...
-- Detecting CUDA compiler ABI info
-- Detecting CUDA compiler ABI info - done
-- Check for working CUDA compiler: /opt/cuda/bin/nvcc - skipped
 * ACCESS DENIED:  fopen_wr:           /proc/self/task/227/comm
-- Detecting CUDA compile features
-- Detecting CUDA compile features - done
...


emerge -vp =vtk-9.2.6*

[ebuild   R    ] sci-libs/vtk-9.2.6-r1:0/9.2::gentoo  USE="boost cuda ffmpeg logging mpi openmp python qt6 rendering threads tk vtkm -all-modules (-debug) -doc -examples -freetype -gdal -imaging -java -las -mysql -odbc -openvdb -pdal -postgres -qt5* -sdl -tbb -test -views -web" PYTHON_SINGLE_TARGET="python3_11 -python3_10" VIDEO_CARDS="nvidia" 0 KiB



# emerge --info =vtk-9.2.6
Portage 3.0.63 (python 3.12.2-final-0, default/linux/amd64/17.1/hardened, gcc-13, glibc-2.39-r2, 6.7.9-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-6.7.9-gentoo-x86_64-13th_Gen_Intel-R-_Core-TM-_i9-13980HX-with-glibc2.39
KiB Mem:    65452452 total,  12423960 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Sat, 09 Mar 2024 19:34:06 +0000
Head commit of repository gentoo: fc099c1f70af75c6ab853ba5127cf9e0a5cb6e93

Timestamp of repository brave-overlay: Wed, 30 Aug 2023 14:16:44 +0000
Head commit of repository brave-overlay: 6633c093c271deda5b29101a4ed5a611810268e1

Timestamp of repository flavour: Fri, 08 Mar 2024 06:20:26 +0000
Head commit of repository flavour: 47438c383ecf6f5ce8b80287dfe8583fc571b46c

Timestamp of repository fordfrog: Wed, 21 Feb 2024 18:48:28 +0000
Head commit of repository fordfrog: 3a16e1ffacc92a0dbb634780985b883aca8e8f59

Head commit of repository librewolf: 09f2e73504f9247099f8d0d580afbb9237caa2f0

Timestamp of repository pf4public: Sat, 09 Mar 2024 13:33:20 +0000
Head commit of repository pf4public: 26fb5e6c1c1055df1826feec2fbd98c7ca9cab8c

sh bash 5.2_p26
ld GNU ld (Gentoo 2.42 p3) 2.42.0
ccache version 4.9.1 [disabled]
app-misc/pax-utils:        1.3.7::gentoo
app-shells/bash:           5.2_p26::gentoo
dev-build/autoconf:        2.13-r8::gentoo, 2.72-r1::gentoo
dev-build/automake:        1.16.5-r2::gentoo
dev-build/cmake:           3.28.3::gentoo
dev-build/libtool:         2.4.7-r2::gentoo
dev-build/make:            4.4.1-r1::gentoo
dev-build/meson:           1.3.2::gentoo
dev-java/java-config:      2.3.3-r1::gentoo
dev-lang/perl:             5.38.2-r2::gentoo
dev-lang/python:           3.10.13_p3::gentoo, 3.11.8_p1::gentoo, 3.12.2_p1::gentoo
dev-lang/rust-bin:         1.76.0::gentoo
dev-util/ccache:           4.9.1::gentoo
sys-apps/baselayout:       2.14-r2::gentoo
sys-apps/openrc:           0.53::gentoo
sys-apps/sandbox:          2.38::gentoo
sys-devel/binutils:        2.42-r1::gentoo
sys-devel/binutils-config: 5.5::gentoo
sys-devel/clang:           15.0.7-r3::gentoo, 17.0.6::gentoo, 18.1.0::gentoo
sys-devel/gcc:             12.3.1_p20240209::gentoo, 13.2.1_p20240210::gentoo
sys-devel/gcc-config:      2.11::gentoo
sys-devel/lld:             17.0.6::gentoo, 18.1.0::gentoo
sys-devel/llvm:            15.0.7-r3::gentoo, 17.0.6::gentoo, 18.1.0::gentoo
sys-kernel/linux-headers:  6.7::gentoo (virtual/os-headers)
sys-libs/glibc:            2.39-r2::gentoo
Repositories:

gentoo
    location: /var/db/repos/gentoo
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/gentoo.git
    priority: -1000
    volatile: False

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

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

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

librewolf
    location: /var/db/repos/librewolf
    sync-type: git
    sync-uri: https://codeberg.org/librewolf/gentoo.git
    masters: gentoo
    volatile: False

pf4public
    location: /var/db/repos/pf4public
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/pf4public.git
    masters: gentoo
    volatile: False

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA android AnyDesk-TOS NVIDIA-SDK PUEL-11"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=alderlake -mabm -mno-cldemote -mno-kl -mno-pconfig -mno-sgx -mno-widekl -mshstk --param=l1-cache-line-size=64 --param=l1-cache-size=48 --param=l2-cache-size=36864 -O2 -pipe -frecord-gcc-switches"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.9/conf"
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=alderlake -mabm -mno-cldemote -mno-kl -mno-pconfig -mno-sgx -mno-widekl -mshstk --param=l1-cache-line-size=64 --param=l1-cache-size=48 --param=l2-cache-size=36864 -O2 -pipe -frecord-gcc-switches"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--misspell-suggestions n"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE 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 XDG_STATE_HOME"
FCFLAGS="-march=alderlake -mabm -mno-cldemote -mno-kl -mno-pconfig -mno-sgx -mno-widekl -mshstk --param=l1-cache-line-size=64 --param=l1-cache-size=48 --param=l2-cache-size=36864 -O2 -pipe -frecord-gcc-switches"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync merge-wait multilib-strict network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted 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=alderlake -mabm -mno-cldemote -mno-kl -mno-pconfig -mno-sgx -mno-widekl -mshstk --param=l1-cache-line-size=64 --param=l1-cache-size=48 --param=l2-cache-size=36864 -O2 -pipe -frecord-gcc-switches"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="cs_CZ.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LEX="flex"
LINGUAS="cs cs_CZ en en_US en_UK"
MAKEOPTS="-j33"
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 a52 aac aacplus acl alsa amd64 aubio bluetooth bzip2 cdda cddb cdr cet cli color-management colord crypt cuda cups dbus dia dri dssi dvb dvd elogind exif ffmpeg flac fortran gdbm gegl gif gles gles1 gles2 gles3 gphoto2 gsm gtk gtk3 hardened hddtemp http2 iconv icu id3tag ipv6 jack jack-dbus jacksession javafx jpeg keyring kwallet ladspa lastfm latex lcms libass libnotify libproxy libsamplerate libtirpc lilypond lm-sensors lto lv2 mad modplug mp3 mpeg mpi mtp multilib musepack ncurses nls nvme ocr ogg opencl openexr opengl openmp optix opus osc pam pcre pdf pic pie pipewire png policykit pulseaudio qt5 qt6 raw readline rubberband samba scanner screencast seccomp sf2 sndfile soundio speex spell split-usr ssl ssp startup-notification svg svg2 taglib test-rust theora tiff timidity tk tray truetype udev unicode usb vaapi vamp vdpau verify-sig visio vorbis vpx vst vulkan wavpack webp widevine wmf x264 x265 xattr xfce xinerama xmp xtpax xv xvid zlib" ABI_X86="32 64" ADA_TARGET="gnat_2021" APACHE2_MODULES="alias auth_basic authn_core authn_file authz_core authz_host authz_user cgi cgid deflate dir expires filter headers http2 include info log_config mime mime_magic negotiation proxy proxy_ajp rewrite setenvif socache_shmcb status unixd vhost_alias" APACHE2_MPMS="event" 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 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 ntrip navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" INPUT_DEVICES="evdev libinput wacom" KERNEL="linux" L10N="cs cs-CZ en en-US en-UK" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LLVM_TARGETS="NVPTX" LUA_SINGLE_TARGET="luajit lua5-4" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-1" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_10 python3_11 python3_12" RUBY_TARGETS="ruby31 ruby32 ruby33" SANE_BACKENDS="genesys" VIDEO_CARDS="fbdev intel nvidia vesa" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipp2p iface geoip fuzzy condition tarpit sysrq proto 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, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS
Comment 1 Guilherme Amadio gentoo-dev 2024-03-09 21:51:36 UTC
I saw this same problem when compiling sci-physics/root[cuda] today.
Comment 2 caem 2024-03-24 09:32:57 UTC
(In reply to Guilherme Amadio from comment #1)
> I saw this same problem when compiling sci-physics/root[cuda] today.
I've also encountered this while trying to compile media-gfx/openvdb[cuda]
Comment 3 mail 2024-03-26 10:36:19 UTC
Got this same error today when trying to compile dev-libs/cutlass
Comment 4 picarica 2024-03-28 07:48:26 UTC
also hapened to me on hwloc, fixed it by disabling cuda flag
Comment 5 Larry the Git Cow gentoo-dev 2024-03-30 18:35:06 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0e0bdd6727d7ee97d887470c7952862ed933c00a

commit 0e0bdd6727d7ee97d887470c7952862ed933c00a
Author:     Huang Rui <vowstar@gmail.com>
AuthorDate: 2024-03-30 18:34:57 +0000
Commit:     David Seifert <soap@gentoo.org>
CommitDate: 2024-03-30 18:34:57 +0000

    dev-util/nvidia-cuda-toolkit: add 12.4.0
    
    Closes: https://github.com/gentoo/gentoo/pull/35777
    Closes: https://bugs.gentoo.org/926116
    Closes: https://bugs.gentoo.org/926612
    Signed-off-by: Huang Rui <vowstar@gmail.com>
    Signed-off-by: David Seifert <soap@gentoo.org>

 dev-util/nvidia-cuda-toolkit/Manifest              |   1 +
 .../nvidia-cuda-toolkit-12.4.0.ebuild              | 338 +++++++++++++++++++++
 2 files changed, 339 insertions(+)