Created attachment 554792 [details] build log emerge gromacs fails in configure phase: -- Found blas, version 3.8.0 CMake Error at cmake/gmxManageLinearAlgebraLibraries.cmake:141 (message): You have set GMX_EXTERNAL_BLAS=ON to instruct GROMACS to use an external BLAS library, but no external library could be detected. Call Stack (most recent call first): cmake/gmxManageLinearAlgebraLibraries.cmake:193 (manage_linear_algebra_library ) cmake/gmxManageLinearAlgebraLibraries.cmake:201 (gmxManageLinearAlgebraLibrari es) CMakeLists.txt:750 (include) I'm using BLAS from openblas and lapack-reference (both from science overlay). pkg-config --libs blas: -lblas pkg-config --libs lapack: -lreflapack and, as the message suggests, BLAS is actually found. Package compiles fine with "-blas -lapack". emerge --info gromacs Portage 2.3.51 (python 3.6.6-final-0, default/linux/amd64/17.1, gcc-8.2.0, glibc-2.27-r6, 4.19.1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.19.1-x86_64-AMD_A8-3870_APU_with_Radeon-tm-_HD_Graphics-with-gentoo-2.6 KiB Mem: 15881300 total, 4582808 free KiB Swap: 16777212 total, 16777212 free Head commit of repository gentoo: 9e9ae4ca9dbdcb6eea0f79a0701958f502debb43 sh bash 4.4_p23 ld GNU gold (Gentoo 2.31.1 p3 2.31.1) 1.16 app-shells/bash: 4.4_p23::gentoo dev-java/java-config: 2.2.0-r4::gentoo dev-lang/perl: 5.26.2::gentoo dev-lang/python: 2.7.15::gentoo, 3.6.6::gentoo, 3.7.0::gentoo dev-util/cmake: 3.12.3::gentoo sys-apps/baselayout: 2.6-r1::gentoo sys-apps/openrc: 0.39.2::gentoo sys-apps/sandbox: 2.13::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.16.1-r1::gentoo sys-devel/binutils: 2.31.1-r1::gentoo sys-devel/gcc: 8.2.0-r4::gentoo sys-devel/gcc-config: 2.0::gentoo sys-devel/libtool: 2.4.6-r5::gentoo sys-devel/make: 4.2.1-r4::gentoo sys-kernel/linux-headers: 4.19::gentoo (virtual/os-headers) sys-libs/glibc: 2.27-r6::gentoo Repositories: gentoo location: /usr/portage sync-type: git sync-uri: https://github.com/gentoo/gentoo.git priority: -1000 kernelpanic location: /usr/local/portage/kernelpanic masters: gentoo priority: 0 libressl location: /var/lib/layman/libressl sync-type: laymansync sync-uri: https://github.com/gentoo/libressl.git masters: gentoo priority: 50 science location: /var/lib/layman/science sync-type: laymansync sync-uri: https://anongit.gentoo.org/git/proj/sci.git masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA @EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -mtune=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /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 -O2 -pipe" DISTDIR="/var/portage/distfiles" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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 -mtune=native -O2 -pipe" FEATURES="assume-digests binpkg-logs cgroup clean-logs compress-build-logs config-protect-if-modified distlocks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch preserve-libs protect-owned sandbox sfperms split-elog split-log strict unknown-features-warn unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-march=native -mtune=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" INSTALL_MASK=" activity-stream@mozilla.org.xpi followonsearch@mozilla.com.xpi" LDFLAGS="-Wl,-O2 -Wl,--as-needed" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" 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 a52 aac acl acpi alsa amd64 ao berkdb blas bluetooth branding bzip2 cairo cdda cdparanoia cdr cjk cli crypt cups curl cxx dbus djvu dri dts dv dvb dvd encode exif ffmpeg fftw flac fontconfig fortran gdbm gif gimp gmp gsm gstreamer gtk iconv icu imlib inotify ipv6 jbig jemalloc jpeg jpeg2k lame lapack latex lcms libass libnotify libressl libtirpc lzma lzo mad matroska mms mng mp3 mpeg mtp multilib musepack musicbrainz ncurses nls nptl offensive ogg openal openexr opengl openmp pam pcre pdf png postscript qt5 raw readline scanner seccomp smp sndfile sound sox speex spell sqlite ssl startup-notification svg taglib theora threads tiff truetype udev unicode usb v4l vaapi vdpau vim-syntax vorbis wavpack webp wmf wxwidgets x264 xattr xcb xml xmp xpm xv xvid zlib" ABI_X86="64 32" 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 plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext popcnt sse sse2 sse3 sse4a" CURL_SSL="libressl" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="pc" INPUT_DEVICES="libinput" KERNEL="linux" L10N="it en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="AMDGPU BPF" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-1" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_6" PYTHON_TARGETS="python2_7 python3_6 python3_7" QEMU_SOFTMMU_TARGETS="x86_64 i386 arm" QEMU_USER_TARGETS="x86_64 i386 arm" RUBY_TARGETS="ruby25" SANE_BACKENDS="xerox_mfp" USERLAND="GNU" VIDEO_CARDS="radeon r600" 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, EMERGE_DEFAULT_OPTS, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS ================================================================= Package Settings ================================================================= sci-chemistry/gromacs-2019_beta1::gentoo was built with the following: USE="X fftw gmxapi lmfit offensive openmp single-precision threads tng -blas -cuda -doc -double-precision -hwloc -lapack -mkl -mpi -opencl -test" ABI_X86="(64)" CPU_FLAGS_X86="sse2 -avx -avx2 -fma4 -sse4_1"
sci-chemistry/gromacs-2019_beta1 is no more in portage. sci-chemistry/gromacs-2019 does not show this issue; what about closing as obsolete?
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3815b25d5f2b4606ad17095b3f8591e827f0a876 commit 3815b25d5f2b4606ad17095b3f8591e827f0a876 Author: Alexey Shvetsov <alexxy@gentoo.org> AuthorDate: 2019-02-18 11:54:28 +0000 Commit: Alexey Shvetsov <alexxy@gentoo.org> CommitDate: 2019-02-18 11:55:10 +0000 sci-chemistry/gromacs: Version bump Closes: https://bugs.gentoo.org/673350 Closes: https://bugs.gentoo.org/673340 Closes: https://bugs.gentoo.org/670846 Closes: https://bugs.gentoo.org/669460 Closes: https://bugs.gentoo.org/591952 Package-Manager: Portage-2.3.61, Repoman-2.3.12 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> sci-chemistry/gromacs/Manifest | 2 + sci-chemistry/gromacs/gromacs-2019.1.ebuild | 307 ++++++++++++++++++++++++++++ 2 files changed, 309 insertions(+)
