Bug 904973 – sci-libs/cholmod-3.0.14 cholmod_gpu.h: No such file or directory

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Andrea Postiglione 2023-04-24 18:13:25 UTC]

Created attachment 860712 [details]
build.log

make[2]: Entering directory '/var/tmp/portage/sci-libs/cholmod-3.0.14/work/cholmod-3.0.14/GPU'
/bin/sh ../libtool --tag=CC --mode=compile /opt/cuda/bin/nvcc -c cholmod_gpu_kernels.cu
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../Include  -I../Include    -march=native -mtune=native -O3 -pipe -c -o cholmod_gpu.lo cholmod_gpu.c
/bin/sh ../libtool  --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../Include  -I../Include  -DDLONG   -march=native -mtune=native -O3 -pipe -c -o libcholmodl_gpu_la-cholmod_gpu.lo `test -f 'cholmod_gpu.c' || echo './'`cholmod_gpu.c
libtool: compile:  /opt/cuda/bin/nvcc -c cholmod_gpu_kernels.cu  -fPIC -DPIC -o .libs/cholmod_gpu_kernels.o
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../Include -I../Include -march=native -mtune=native -O3 -pipe -c cholmod_gpu.c  -fPIC -DPIC -o .libs/cholmod_gpu.o
libtool: compile:  x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../Include -I../Include -DDLONG -march=native -mtune=native -O3 -pipe -c cholmod_gpu.c  -fPIC -DPIC -o .libs/libcholmodl_gpu_la-cholmod_gpu.o
nvcc fatal   : Unknown option '-fPIC'
make[2]: *** [Makefile:675: cholmod_gpu_kernels.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
cholmod_gpu.c:20:10: fatal error: cholmod_gpu.h: No such file or directory
   20 | #include "cholmod_gpu.h"
      |          ^~~~~~~~~~~~~~~
compilation terminated.
cholmod_gpu.c:20:10: fatal error: cholmod_gpu.h: No such file or directory
   20 | #include "cholmod_gpu.h"
      |          ^~~~~~~~~~~~~~~
compilation terminated.
make[2]: *** [Makefile:448: cholmod_gpu.lo] Error 1
make[2]: *** [Makefile:455: libcholmodl_gpu_la-cholmod_gpu.lo] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-libs/cholmod-3.0.14/work/cholmod-3.0.14/GPU'
make[1]: *** [Makefile:643: all-recursive] Error 1
make[1]: Leaving directory '/var/tmp/portage/sci-libs/cholmod-3.0.14/work/cholmod-3.0.14'
make: *** [Makefile:507: all] Error 2


isabella ~ # emerge --info cholmod
Portage 3.0.46 (python 3.10.11-final-0, default/linux/amd64/17.1/desktop/plasma, gcc-12, glibc-2.37-r2, 6.2.12-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-6.2.12-gentoo-x86_64-12th_Gen_Intel-R-_Core-TM-_i7-12700H-with-glibc2.37
KiB Mem:    32650364 total,   7645636 free
KiB Swap:    8388604 total,   8388604 free
Timestamp of repository gentoo: Mon, 24 Apr 2023 16:30:01 +0000
Head commit of repository gentoo: 50729f0a454142f0b34c1f4748fd9592e889d08f
sh bash 5.2_p15-r2
ld GNU ld (Gentoo 2.40 p4) 2.40.0
app-misc/pax-utils:        1.3.7::gentoo
app-shells/bash:           5.2_p15-r2::gentoo
dev-java/java-config:      2.3.1::gentoo
dev-lang/perl:             5.36.0-r2::gentoo
dev-lang/python:           3.10.11::gentoo
dev-lang/rust:             1.69.0::local
dev-util/cmake:            3.26.3::gentoo
dev-util/meson:            1.1.0::gentoo
sys-apps/baselayout:       2.13-r1::gentoo
sys-apps/openrc:           0.47.1::gentoo
sys-apps/sandbox:          2.30-r1::gentoo
sys-devel/autoconf:        2.13-r8::gentoo, 2.71-r6::gentoo
sys-devel/automake:        1.16.5-r1::gentoo
sys-devel/binutils:        2.40-r4::gentoo
sys-devel/binutils-config: 5.5::gentoo
sys-devel/clang:           16.0.2::gentoo
sys-devel/gcc:             12.2.1_p20230304::gentoo
sys-devel/gcc-config:      2.10::gentoo
sys-devel/libtool:         2.4.7-r1::gentoo
sys-devel/lld:             16.0.2::gentoo
sys-devel/llvm:            16.0.2::gentoo
sys-devel/make:            4.4.1::gentoo
sys-kernel/linux-headers:  6.2::gentoo (virtual/os-headers)
sys-libs/glibc:            2.37-r2::gentoo
Repositories:

gentoo
    location: /var/db/repos/gentoo
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage/
    priority: 10
    volatile: True
    sync-rsync-extra-opts: 
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-metamanifest: no
    sync-rsync-verify-max-age: 24

local
    location: /var/db/repos/local
    masters: gentoo
    priority: 100
    volatile: True

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -mtune=native -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=native -mtune=native -O3 -pipe"
DISTDIR="/var/cache/distfiles"
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=native -mtune=native -O3 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync metadata-transfer 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 -mtune=native -O3 -pipe"
GENTOO_MIRRORS="http://distfiles.gentoo.org/"
LANG="it_IT.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LEX="flex"
MAKEOPTS="-j20"
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 acl acpi activities alsa amd64 bluetooth branding bzip2 cairo cdda cdr cli crypt cups dbus declarative dri dts dvd dvdr elogind encode exif flac fortran gdbm gif gpm gtk gui iconv icu ipv6 jpeg kde kwallet lcms libglvnd libnotify libtirpc mad mng mp3 mp4 mpeg multilib ncurses nls nptl ogg opengl openmp pam pango pcre pdf plasma png policykit ppds qml qt5 readline sdl seccomp semantic-desktop sound spell split-usr ssl startup-notification svg test-rust tiff truetype udev udisks unicode upower usb vorbis widgets wxwidgets x264 xattr xcb xft xml xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2021" 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="fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx mmxext fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sse3 sdbg fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust sgx bmi1 avx2 smep bmi2 erms invpcid mpx rdseed adx smap clflushopt intel_pt xsaveopt xsavec xgetbv1 xsaves dtherm ida arat pln pts hwp hwp_notify hwp_act_window hwp_epp pku ospke sgx_lc md_clear flush_l1d arch_capabilities" 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="efi-64" INPUT_DEVICES="libinput evdev mouse synaptics" KERNEL="linux" L10N="it" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="NVPTX" LUA_SINGLE_TARGET="lua5-4" LUA_TARGETS="lua5-4" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-4 php8-0" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_10" PYTHON_TARGETS="python3_10" QEMU_SOFTMMU_TARGETS="x86_64 hppa i386 arm sparc64" RUBY_TARGETS="ruby32" USERLAND="GNU" VIDEO_CARDS="intel nvidia nouveau 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:  ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, 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

[Comment 1 Todd Walter 2023-08-21 17:09:54 UTC]

AFAICT, nvcc is choking on -fPIC as it's not being called with -Xcompiler.

m4/libtool.m4 needs a patch

[Comment 2 Larry the Git Cow 2023-12-16 09:21:13 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6c0474cc8a08172cdc244af680edba8be5ada95b

commit 6c0474cc8a08172cdc244af680edba8be5ada95b
Author:     Paul Zander <[e-mail]>
AuthorDate: 2023-11-27 19:58:40 +0000
Commit:     Pacho Ramos <[e-mail]>
CommitDate: 2023-12-16 09:20:20 +0000

    sci-libs/cholmod: fix cuda build
    
    - include cuda patch from https://bugs.gentoo.org/715610#c16
    - make use of cuda.eclass for nvcc
    
    Closes: https://bugs.gentoo.org/913921
    Closes: https://bugs.gentoo.org/904973
    Closes: https://bugs.gentoo.org/715610
    Signed-off-by: Paul Zander <[e-mail]>
    Closes: https://github.com/gentoo/gentoo/pull/34020
    Signed-off-by: Pacho Ramos <[e-mail]>

 sci-libs/cholmod/cholmod-3.0.13.ebuild             |  14 ++-
 sci-libs/cholmod/cholmod-3.0.14.ebuild             |  14 ++-
 .../cholmod/files/cholmod-3.0.14-fix-CUDA.patch    | 109 +++++++++++++++++++++
 3 files changed, 133 insertions(+), 4 deletions(-)