[21/89] cd /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual && /usr/bin/ps2pdf14 -dEPSCrop\ /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4/docs/manual/plots/lincs.eps /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual/plots/lincs.pdf FAILED: cd /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual && /usr/bin/ps2pdf14 -dEPSCrop\ /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4/docs/manual/plots/softcore.eps /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual/plots/softcore.pdf Error: /invalidfont in /findfont Operand stack: Times-Roman Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1900 1 3 %oparray_pop 1899 1 3 %oparray_pop --nostringval-- 1883 1 3 %oparray_pop 1771 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- 1852 1 4 %oparray_pop Dictionary stack: --dict:1176/1684(ro)(G)-- --dict:0/20(G)-- --dict:81/200(L)-- --dict:58/80(L)-- Current allocation mode is local Last OS error: No such file or directory Current file position is 9152 GPL Ghostscript 9.10: Unrecoverable error, exit code 1 FAILED: cd /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual && /usr/bin/ps2pdf14 -dEPSCrop\ /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4/docs/manual/plots/subst-im.eps /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual/plots/subst-im.pdf Error: /invalidfont in /findfont Operand stack: Times-BoldItalic Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1900 1 3 %oparray_pop 1899 1 3 %oparray_pop --nostringval-- 1883 1 3 %oparray_pop 1771 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- 1852 1 4 %oparray_pop Dictionary stack: --dict:1176/1684(ro)(G)-- --dict:0/20(G)-- --dict:84/200(L)-- --dict:27/200(L)-- Current allocation mode is local Last OS error: No such file or directory Current file position is 2115 GPL Ghostscript 9.10: Unrecoverable error, exit code 1 FAILED: cd /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual && /usr/bin/ps2pdf14 -dEPSCrop\ /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4/docs/manual/plots/maxwell.eps /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual/plots/maxwell.pdf Error: /invalidfont in /findfont Operand stack: Helvetica Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1900 1 3 %oparray_pop 1899 1 3 %oparray_pop --nostringval-- 1883 1 3 %oparray_pop 1771 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- 1852 1 3 %oparray_pop Dictionary stack: --dict:1176/1684(ro)(G)-- --dict:0/20(G)-- --dict:158/200(L)-- Current allocation mode is local Last OS error: No such file or directory Current file position is 10952 GPL Ghostscript 9.10: Unrecoverable error, exit code 1 FAILED: cd /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual && /usr/bin/ps2pdf14 -dEPSCrop\ /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4/docs/manual/plots/lincs.eps /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float/docs/manual/plots/lincs.pdf Error: /invalidfont in /findfont Operand stack: --nostringval-- Helvetica Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push 1900 1 3 %oparray_pop 1899 1 3 %oparray_pop --nostringval-- 1883 1 3 %oparray_pop 1771 1 3 %oparray_pop --nostringval-- %errorexec_pop .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- 1852 2 4 %oparray_pop Dictionary stack: --dict:1176/1684(ro)(G)-- --dict:0/20(G)-- --dict:135/200(L)-- --dict:43/200(L)-- Current allocation mode is local Last OS error: No such file or directory Current file position is 19145 GPL Ghostscript 9.10: Unrecoverable error, exit code 1 CMake Warning at cmake/gmxManageFFTLibraries.cmake:94 (message): The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation. Call Stack (most recent call first): CMakeLists.txt:738 (include) -- <<< Gentoo configuration >>> Build type Gentoo Install path /usr Compiler flags: C -mavx -O2 -pipe -march=native -fno-stack-protector -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter C++ -mavx -std=c++0x -O2 -pipe -march=native -fno-stack-protector -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function Linker flags: Executable -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu Module -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu Shared -Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -- Configuring done -- Generating done -- Build files have been written to: /var/tmp/portage/sci-chemistry/gromacs-5.0.4-r1/work/gromacs-5.0.4_float ninja: build stopped: subcommand failed.
Created attachment 401268 [details] build.log.bz2 # emerge --info Portage 2.2.18 (python 3.4.1-final-0, default/linux/amd64/13.0/desktop/gnome/systemd, gcc-4.8.4, glibc-2.20-r2, 3.18.9-gentoo x86_64) ================================================================= System uname: Linux-3.18.9-gentoo-x86_64-Intel-R-_Core-TM-_i7-3537U_CPU_@_2.00GHz-with-gentoo-2.2 KiB Mem: 8052332 total, 593280 free KiB Swap: 4607996 total, 4055640 free Timestamp of repository gentoo: Tue, 14 Apr 2015 18:00:01 +0000 sh bash 4.2_p53 ld GNU ld (Gentoo 2.24 p1.4) 2.24 ccache version 3.1.9 [enabled] app-shells/bash: 4.2_p53::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.9-r1::gentoo, 3.4.1::gentoo dev-util/ccache: 3.1.9-r4::gentoo dev-util/cmake: 2.8.12.2-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.13.11::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.10.3-r1::gentoo, 1.11.6-r1::gentoo, 1.13.4::gentoo sys-devel/binutils: 2.24-r3::gentoo sys-devel/gcc: 4.8.4::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 3.18::gentoo (virtual/os-headers) sys-libs/glibc: 2.20-r2::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 ago location: /usr/portage/local/layman/ago masters: gentoo priority: 0 x-portage location: /usr/local/portage masters: gentoo priority: 1 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=native -fno-stack-protector" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/fax /usr/lib64/libreoffice/program/sofficerc /usr/share/gnupg/qualified.txt /var/lib/hsqldb /var/spool/fax/etc" 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=native -fno-stack-protector" DISTDIR="/usr/distfiles" EMERGE_DEFAULT_OPTS="--quiet-build=n --autounmask-write --keep-going" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs ccache config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms sign split-log strict test test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.heanet.ie/pub/gentoo/" LANG="es_ES.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu" MAKEOPTS="-j5" PKGDIR="/usr/local/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" PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac acl acpi alsa amd64 applet avahi avx avx256 bash-completion berkdb bluetooth branding bzip2 cairo ccache cdda cddb cdr cli colord cracklib crypt cups cvs cxx dbus djvu dri dts dvd dvdr dvi eds emboss enchant encode evo exif fam fat ffmpeg firefox flac fortran fuse gdbm gif glamor gnome gnome-keyring gnome-online-accounts gphoto2 gpm gromacs gstreamer gtk gtk3 gtkstyle http iconv infinality introspection irc jabber jpeg kpathsea latex lcms ldap libnotify libsecret libvisual lyx mad mms mmx mmxext mng modules monolithic-build mp3 mp4 mpeg multilib musicbrainz nautilus ncurses network-cron networkmanager nls nptl ntfs ntp numa nvidia ogg opengl openmp optimized-qmake pam pango pch pdf png policykit ppds pulseaudio qt3support qt4 readline reiserfs scanner sdl session smp sna socialweb spell sse sse2 sse3 sse4 sse4_1 ssl ssse3 startup-notification svg systemd t1lib tcpd test theora threads tiff truetype udev udisks unicode upnp upnp-av upower usb v4l vaapi vala vcd vdpau vorbis wifi wxwidgets x264 xattr xcb xfs xml xv xvid youtube zeroconf zlib" ABI_X86="64" 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="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="es es_ES en_US" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="fbdev vesa intel i915 i965" 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: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
*** This bug has been marked as a duplicate of bug 436500 ***
