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Bug 738274 - media-gfx/hugin-2019.2.0 USE=lapack - ../hugin_base/libhuginbase.so.0.0: error: undefined reference to 'dgemm_'
Summary: media-gfx/hugin-2019.2.0 USE=lapack - ../hugin_base/libhuginbase.so.0.0: erro...
Status: UNCONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Andreas K. Hüttel
URL:
Whiteboard:
Keywords: PATCH
Depends on:
Blocks:
 
Reported: 2020-08-20 21:11 UTC by Dennis Schridde
Modified: 2020-08-22 18:33 UTC (History)
1 user (show)

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


Attachments
hugin-2019.2-lapack-blas.patch (hugin-2019.2-lapack-blas.patch,1.42 KB, patch)
2020-08-20 21:11 UTC, Dennis Schridde
Details | Diff
build.log (build.log,127.02 KB, text/x-log)
2020-08-22 07:03 UTC, Dennis Schridde
Details

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Description Dennis Schridde 2020-08-20 21:11:59 UTC
Created attachment 655810 [details, diff]
hugin-2019.2-lapack-blas.patch

cd /tmp/portage/media-gfx/hugin-2019.2.0/work/hugin-2019.2.0_build/src/tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/cpclean.dir/link.txt --verbose=1
/usr/sbin/x86_64-pc-linux-gnu-g++ -pipe -O2 -march=znver1 -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -fopenmp CMakeFiles/cpclean.dir/cpclean.cpp.o -o cpclean  -Wl,-rpath,/tmp/portage/media-gfx/hugin-2019.2.0/work/hugin-2019.2.0_build/src/hugin_base: ../hugin_base/libhuginbase.so.0.0 /usr/lib64/libpano13.so ../foreign/levmar/libhuginlevmar.a /usr/lib64/libGLEW.so /usr/lib64/libboost_filesystem-mt.so /usr/lib64/libboost_system-mt.so /usr/lib64/liblapack.so /usr/lib64/libfftw3.so /usr/lib64/libvigraimpex.so /usr/lib64/libImath.so /usr/lib64/libIlmImf.so /usr/lib64/libIex.so /usr/lib64/libHalf.so /usr/lib64/libIlmThread.so /usr/lib64/libz.so /usr/lib64/libjpeg.so /usr/lib64/libtiff.so /usr/lib64/libpng.so /usr/lib64/libz.so /usr/lib64/libz.so /usr/lib64/libexiv2.so /usr/lib64/liblcms2.so -pthread /usr/lib64/libX11.so /usr/lib64/libpano13.so /usr/lib64/libboost_filesystem-mt.so /usr/lib64/libboost_system-mt.so /usr/lib64/liblapack.so /usr/lib64/libGL.so /usr/lib64/libGLU.so /usr/lib64/libGLEW.so /usr/lib64/libsqlite3.so /usr/lib64/libvigraimpex.so /usr/lib64/libjpeg.so /usr/lib64/libpng.so /usr/lib64/libtiff.so /usr/lib64/libexiv2.so /usr/lib64/liblcms2.so 
../hugin_base/libhuginbase.so.0.0: error: undefined reference to 'dgemm_'
collect2: error: ld returned 1 exit status


```
hugin-2019.2.0/src/foreign/levmar/misc_core.c:45:#define GEMM LM_MK_BLAS_NAME(gemm)
```

This function is a BLAS function: https://en.wikipedia.org/wiki/Basic_Linear_Algebra_Subprograms#Level_3

Thus, since levmar is built as a static library, Hugin itself should call `find_package(BLAS)` and `huginbase` should link against `BLAS_LIBRARIES`.

Attached patch fixes this (in an admittedly slightly crude way) for me.

Upstream report: https://bugs.launchpad.net/hugin/+bug/1892420


Portage 3.0.4 (python 3.6.9-final-0, default/linux/amd64/17.1/desktop/plasma/systemd, gcc-10.2.0, glibc-2.32, 5.8.1 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.8.1-x86_64-AMD_Ryzen_5_2400G_with_Radeon_Vega_Graphics-with-gentoo-2.7
KiB Mem:    14194336 total,   1928084 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Thu, 20 Aug 2020 18:45:01 +0000
Head commit of repository gentoo: ff03def29006e7148fdf3efbe1ccd8f2ff2c646d
Head commit of repository flatpak-overlay: 26c396aef4d2f8908eea9b3ad2ccf7dc843a0887

Head commit of repository local: 8e22343ec3e3332f91a6a171a891407c95a0d44d

sh bash 5.0_p18
ld GNU gold (Gentoo 2.34 p6 2.34.0) 1.16
ccache version 3.7.11 [disabled]
app-shells/bash:          5.0_p18::gentoo
dev-java/java-config:     2.3.1::gentoo
dev-lang/perl:            5.30.3-r1::gentoo
dev-lang/python:          2.7.18-r1::gentoo, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.5::gentoo, 3.9.0_rc1::gentoo
dev-util/ccache:          3.7.11::gentoo
dev-util/cmake:           3.18.1::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.7::gentoo
sys-apps/sandbox:         2.20::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.13.4-r2::gentoo, 1.16.2::gentoo
sys-devel/binutils:       2.34-r2::gentoo
sys-devel/gcc:            10.2.0::gentoo
sys-devel/gcc-config:     2.3.1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.8::gentoo (virtual/os-headers)
sys-libs/glibc:           2.32::gentoo
Repositories:

gentoo
    location: /var/cache/portage/gentoo
    sync-type: rsync
    sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-extra-opts: --new-compress
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-metamanifest: yes

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

crossdev
    location: /var/cache/portage/crossdev
    masters: gentoo
    priority: 100

local
    location: /var/cache/portage/local
    sync-type: git
    sync-uri: https://github.com/devurandom/gentoo-overlay.git
    masters: gentoo
    priority: 1000

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-pipe -O2 -march=znver1"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /etc/grs/systems.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.6/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="-pipe -O2 -march=znver1"
DISTDIR="/var/cache/portage/distfiles"
EMERGE_DEFAULT_OPTS="--nospinner"
ENV_UNSET="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"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildsyspkg cgroup compressdebug config-protect-if-modified distlocks ebuild-locks fakeroot fixlafiles ipc-sandbox merge-sync mount-sandbox multilib-strict network-sandbox news parallel-fetch parallel-install 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="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.spline.inf.fu-berlin.de/mirrors/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://distfiles.gentoo.org"
LANG="en_GB.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu"
MAKEOPTS="-j6 -l4"
PKGDIR="/var/cache/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_EXTRA_OPTS="--new-compress"
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="/tmp"
USE="7z 7zip X a52 aac aacplus aacs acl acpi activities aio alsa amd64 appindicator appstream archive audit avahi ayatana bdplus berkdb blake2 blas bluetooth bluray bpf branding brotli bs2b btrfs bzip2 cairo caps cdda cddb cdio cdr celt chromaprint cjk clang cli clipboard color-management colord conntrack crypt cups d3d9 dav1d dbus declarative device-mapper dirac djvu dri drm dts dvb dvd dvdr ed25519 editorconfig egl elf emboss encode epub evdev exif faudio fax fbcon fdk ffmpeg fftw filecaps firefox firewalld fish-completion fits flac fontconfig fontforge fortran fribidi gamepad gbm gdal gdbm geoclue geolocation gif git gles2 gles3 gmp gnome-online-accounts gnupg google googledrive gpg gps graphicsmagick gstreamer gtk gtk3 gzip harfbuzz hdf5 heif http2 ibus iconv icu idn imlib inotify introspection ipv6 iwd jemalloc jpeg jpeg2k json kde kipi kms kwallet ladspa lapack latex lcms libatomic libglvnd libidn2 libinput libnotify libproxy libsecret libsoxr libtirpc libvirt lm-sensors lrz lv2 lvm lz4 lzma lzo mad mariadb markdown mbim mercurial mjpeg mng mobi modemmanager modplug mp3 mp4 mpeg mplayer mpris mtp multilib mysql ncurses netlink networkmanager nftables nls nptl numa office ofono ofx ogg openal opencl opencv openexr opengl openh264 openmax openmp opus pam pango pcap pch pcre pcre2 pdf pgo phonon pixman pkcs11 pkcs7 plasma pm-utils png policykit postscript ppds prison pulseaudio pwquality python qml qrcode qt5 raw rdp readline redfish samba sasl scanner schroedinger screencast sctp sdl sdl2 seccomp semantic-desktop share smartcard snappy sparse speech speex spell spice ssl startup-notification steamruntime stemmer svg systemd systemtap tbb tcpd teamd telemetry telepathy tga theora threads thunderbolt tiff timezone tmux truetype tslib udev udisks uinput unicode unwind upnp upnp-av upower usb utempter v4l v4l2 vaapi vdpau vkd3d vorbis vpx vulkan wasm wavpack wayland webchannel webengine webp widgets wireguard wmf woff2 wps x264 x265 xattr xcb xinerama xkb xml xmp xrandr xscreensaver xv xvid xwayland xxhash xz yaml zeroconf zeromq zimg zlib zstd" ABI_X86="64" ADA_TARGET="gnat_2018" ALSA_CARDS="hda-intel" 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" CAMERAS="ptp2" 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" ENLIGHTENMENT_MODULES="*" 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="efi-64" INPUT_DEVICES="joystick libinput" KERNEL="linux" L10N="de de-DE en en-GB ar fa tr ja ko zh zh-CN zh-TW" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver scripting-javascript wiki-publisher" LIRC_DEVICES="devinput" LLVM_TARGETS="AMDGPU BPF RISCV WebAssembly" LUA_TARGET="lua5-2" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2 php7-3" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7 pypy pypy3" QEMU_SOFTMMU_TARGETS="riscv32 riscv64 x86_64" QEMU_USER_TARGETS="riscv32 riscv64" RUBY_TARGETS="ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu virgl" 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, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS

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

media-gfx/hugin-2019.2.0::gentoo was built with the following:
USE="lapack python raw sift -debug" ABI_X86="(64)" L10N="de en-GB ja zh-CN zh-TW -ca -ca-valencia -cs -da -es -eu -fi -fr -hu -it -nl -pl -pt-BR -ro -ru -sk -sv" PYTHON_SINGLE_TARGET="python3_7 -python3_6 -python3_8"


sci-libs/lapack-3.8.0-r1::gentoo was built with the following:
USE="-deprecated -doc -eselect-ldso -lapacke" ABI_X86="(64)"
Comment 1 Dennis Schridde 2020-08-22 07:03:24 UTC
Created attachment 656058 [details]
build.log
Comment 2 Dennis Schridde 2020-08-22 11:43:47 UTC
Upstream played the ball back into our court:

> I checked the build system. Our FindPackage(LAPACK) does already search
> for the blas libraries. So maybe you are using a slightly different name
> of the BLAS library (other implementation) so that CMake does not pick
> up this variant. So the easiest way to fix would be to update
> CMakeModules/FindLAPACK.cmake for this BLAS variant.

Gentoo removes that FindLAPACK.cmake file during src_prepare, probably because a file of the same name is provided by CMake itself.
Comment 3 Dennis Schridde 2020-08-22 18:33:33 UTC
Upstream further explained that /usr/share/cmake/Modules/FindLAPACK.cmake should actually search (and make the application link against) both LAPACK and BLAS.  For some reason this does not happen on my system / Gentoo.  I am investigating.