Several different build errors(/warnings) on x86, depending on the USE flag combinations. Type 1: USE=X bash-completion -blas -dmalloc -doc -double-precision ffamber fftw -fkernels gsl lapack mpi single-precision static -static-libs -xml -zsh-completion i686-pc-linux-gnu-gcc -march=prescott -pipe -Wl,-O1 -g -static -o tpbconv tpbconv.o ./.libs/libgmxpreprocess.a ../mdlib/.libs/libmd.a /var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/work/gromacs-4.0.7-single/src/gmxlib/.libs/libgmx.a ../gmxlib/.libs/libgmx.a -lnsl /usr/lib/libfftw3f.a -lm -lblas -llapack -ldmalloc /usr/lib/libSM.a -luuid /usr/lib/libICE.a /usr/lib/libX11.a /usr/lib/libxcb.a /usr/lib/libXau.so /usr/lib/libXdmcp.so -ldl /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/../../../../i686-pc-linux-gnu/bin/ld: attempted static link of dynamic object `/usr/lib/libXau.so' collect2: ld returned 1 exit status /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/../../../../i686-pc-linux-gnu/bin/ld: attempted static link of dynamic object `/usr/lib/libXau.so' collect2: ld returned 1 exit status make[3]: *** [tpbconv] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: *** [mdrun] Error 1 /usr/lib/gcc/i686-pc-linux-gnu/4.4.3/../../../../i686-pc-linux-gnu/bin/ld: attempted static link of dynamic object `/usr/lib/libXau.so' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/work/gromacs-4.0.7-single/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/work/gromacs-4.0.7-single/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/work/gromacs-4.0.7-single/src' make: *** [all-recursive] Error 1 * ERROR: sci-chemistry/gromacs-4.0.7-r3 failed: * emake for single precision failed * * Call stack: * ebuild.sh, line 54: Called src_compile * environment, line 3068: Called die * The specific snippet of code: * emake || die "emake for ${x} precision failed"; * * If you need support, post the output of 'emerge --info =sci-chemistry/gromacs-4.0.7-r3', * the complete build log and the output of 'emerge -pqv =sci-chemistry/gromacs-4.0.7-r3'. * The complete build log is located at '/var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/temp/environment'. * S: '/var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/work/gromacs-4.0.7' However there are at least 3 other sets of use flags that generate this exact same error. I haven't had time to test and sort them all out. Type 2: USE="X -bash-completion -blas dmalloc doc -double-precision -ffamber fftw fkernels -gsl lapack -mpi -single-precision -static -static-libs xml -zsh-completion" Is this expected / normal? I don't think so but I can't be sure. >>> Install gromacs-4.0.7-r3 into /var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/image/ category sci-chemistry sed: can't read /var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/image//usr/bin/GMXRC.bash: No such file or directory rm: cannot remove `/var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/image//usr/bin/completion.*': No such file or directory >>> Completed installing gromacs-4.0.7-r3 into /var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/image/ Again, this is not a specific set of USE flags to generate this. There are a few. Type 3: USE=-X -bash-completion blas dmalloc -doc double-precision -ffamber fftw -fkernels -gsl -lapack -mpi single-precision -static static-libs xml -zsh-completion * QA Notice: The following files contain writable and executable sections * Files with such sections will not work properly (or at all!) on some * architectures/operating systems. A bug should be filed at * http://bugs.gentoo.org/ to make sure the issue is fixed. * For more information, see http://hardened.gentoo.org/gnu-stack.xml * Please include the following list of files in your report: * Note: Bugs should be filed for the respective maintainers * of the package in question and not hardened@g.o. * RWX --- --- usr/lib/libgmx_d.so.5.0.0 * !WX --- --- usr/lib/libgmx_d.a:nb_kernel314_ia32_sse2.o There are a good few combinations that generate that warning with various file names. Is this expected / normal? (And again, other USE flags do this too) I'm going to try to get a specific set of use flags that do each of these, and see if I can figure out why at least the first one is occurring.
Created attachment 237055 [details] Build log for Type 1
Created attachment 237057 [details] Build log for Type 2
emerge --info Portage 2.1.8.3 (default/linux/x86/10.0/desktop, gcc-4.4.3, glibc-2.11.2-r0, 2.6.34-tuxonice i686) ================================================================= System Settings ================================================================= System uname: Linux-2.6.34-tuxonice-i686-Genuine_Intel-R-_CPU_T2500_@_2.00GHz-with-gentoo-1.12.13 Timestamp of tree: Wed, 30 Jun 2010 13:45:01 +0000 distcc 3.1 i686-pc-linux-gnu [disabled] ccache version 2.4 [enabled] app-shells/bash: 4.0_p37 dev-lang/python: 2.6.5-r2, 3.1.2-r3 dev-util/ccache: 2.4-r7 dev-util/cmake: 2.6.4-r3 sys-apps/baselayout: 1.12.13 sys-apps/sandbox: 1.6-r2 sys-devel/autoconf: 2.65 sys-devel/automake: 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.4.3-r2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.2.6b virtual/os-headers: 2.6.30-r1 ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="* -@EULA" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=prescott -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb /usr/share/config" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=prescott -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests ccache collision-protect distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms strict test unmerge-logs unmerge-orphans" GENTOO_MIRRORS="http://gentoo.netnitco.net http://mirror.mcs.anl.gov/pub/gentoo/ http://gentoo.cites.uiuc.edu/pub/gentoo/ http://gentoo.chem.wisc.edu/gentoo/" LDFLAGS="-Wl,-O1" LINGUAS="en_US en" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi alsa berkdb bluetooth branding bzip2 cairo cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gif gnome gpm gtk hal iconv ipv6 jpeg kde lcms ldap libnotify mad mikmod mng modules mp3 mp4 mpeg mudflap ncurses nls nptl nptlonly ogg opengl openmp pam pango pcre pdf perl png ppds pppd python qt3support qt4 readline reflection sdl session spell spl ssl startup-notification svg sysfs tcpd tiff truetype unicode usb vorbis x264 x86 xcb xml xorg xulrunner xv xvid zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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 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" ELIBC="glibc" INPUT_DEVICES="keyboard synaptics evdev mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en_US en" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="vesa radeon fbdev radeonhd" 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, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY Build log for type 3 is too large. If its needed let me know and Ill shrink it some and get it up here.
Type 1: static + X will never work due to the fact libXau misses a static lib (.a) So there is a check missing: use X && use static && die "not possible" Type 2: Strange thing I have: /var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/image//usr/bin/GMXRC.bash and /var/tmp/portage/sci-chemistry/gromacs-4.0.7-r3/image//usr/bin/completion.* I don't see how this is related to bash-comp use flag! Type 3: Gromacs has assembly kernels which contain stacks. So that is fine. We should disable that check, because all binaries are like again libgmx, which contains the kernels. One could add a hardened use flag to disable assembly.
fixes in gromacs-4.0.7-r4
