emerge output: In file included from init.c:41: modules.h:6: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token In file included from init.c:237: modules.c: In function 'gfs_init': modules.c:6: error: 'gfs_init_' undeclared (first use in this function) modules.c:6: error: (Each undeclared identifier is reported only once modules.c:6: error: for each function it appears in.) modules.c:6: error: expected expression before ')' token make[3]: *** [libgfs2D_la-init.lo] Error 1 make[3]: Leaving directory `/var/tmp/portage/sci-libs/gerris-0.9.2/work/gerris-0.9.2/src' make[2]: *** [all] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-libs/gerris-0.9.2/work/gerris-0.9.2/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-libs/gerris-0.9.2/work/gerris-0.9.2' make: *** [all] Error 2 * * ERROR: sci-libs/gerris-0.9.2 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 189: Called die * The specific snippet of code: * emake -j1 || die "make failed" * The die message: * make failed emerge --info: Portage 2.1.4.4 (default/linux/amd64/2008.0/desktop, gcc-4.1.2, glibc-2.6.1-r0, 2.6.25-gentoo-r7HVLinuxMobile2.5 x86_64) ================================================================= System uname: 2.6.25-gentoo-r7HVLinuxMobile2.5 x86_64 Intel(R) Core(TM)2 Duo CPU T5270 @ 1.40GHz Timestamp of tree: Tue, 30 Sep 2008 20:30:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6 dev-lang/python: 2.5.2-r7 dev-python/pycrypto: 2.0.1-r6 dev-util/ccache: 2.4-r7 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r2 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1-r1 sys-devel/binutils: 2.18-r3 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=nocona -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="ccache collision-protect distlocks metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://mirror.phy.olemiss.edu/mirror/gentoo ftp://ftp.gtlib.gatech.edu/pub/gentoo" LANG="C" LDFLAGS="-Wl,-O1" LINGUAS="en" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" 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" PORTDIR_OVERLAY="/usr/portage/local/layman/pro-audio /usr/portage/local/layman/sunrise /usr/portage/local/layman/desktop-effects /usr/portage/local/layman/gnash-cvs /usr/portage/local/layman/science /usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi aim alsa amd64 bash-completion berkdb bluetooth branding bzip2 cairo caps cdparanoia cdr cli cracklib crypt cups dbus directfb dri dts dv dvd dvdr dvdread eds emacs emboss encode evo fam fbcon ffmpeg flac foomaticdb fortran ftp gdbm gif glut gnome gnome-keyring gphoto2 gpm gstreamer gtk gtk2 hal iconv imagemagick ipod ipv6 isdnlog jack java javascript jpeg kerberos ladspa ldap leim libg++ libnotify mad midi mikmod mime mmap mmx mmxext moznopango mp3 mpeg mplayer msn mudflap multilib ncurses nls nptl nptlonly ogg openal opengl openmp pam pcre pdf perl png ppds pppd python qt3 qt3support qt4 quicktime rdesktop readline reflection samba sdl session smp spell spl sqlite sse sse2 ssl startup-notification svg sysfs tcpd theora threads tiff truetype unicode usb vorbis x264 xml xorg xulrunner xv xvid zlib" ALSA_CARDS="hda-intel" 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 mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en" USERLAND="GNU" VIDEO_CARDS="nvidia" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, FFLAGS, INSTALL_MASK, LC_ALL, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS Reproducible: Always Steps to Reproduce: 1.emerge gerris 2. 3.
Thanks for the report, I'll have a look at this. Best, Markus
I have just added ebuilds for much newer gts and gerris development snapshots which both compile fine for me on x86 and amd64. Please give them a try and let me know if you are still having problems. Thanks, Markus
(In reply to comment #2) > I have just added ebuilds for much newer gts and gerris > development snapshots which both compile fine for me > on x86 and amd64. Please give them a try and let me know > if you are still having problems. > > Thanks, > Markus > utils.c: In function 'compile': utils.c:464: error: expected ',' or ';' before 'MODULES_FLAGS' make[3]: *** [libgfs2D_la-utils.lo] Error 1 make[3]: Leaving directory `/var/tmp/portage/sci-libs/gerris-20080929/work/gerris-snapshot-080929/src' make[2]: *** [all] Error 2 make[2]: Leaving directory `/var/tmp/portage/sci-libs/gerris-20080929/work/gerris-snapshot-080929/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-libs/gerris-20080929/work/gerris-snapshot-080929' make: *** [all] Error 2 * * ERROR: sci-libs/gerris-20080929 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 2609: Called die * The specific snippet of code: * emake -j1 || die "make failed" * The die message: * make failed dx and mpi are enabled
In gerris' build directory in /var/tmp/portage could you please run grep -r 'MODULES_FLAGS' config.h and post the output. Also, please post your complete emerge log. Thanks much, Markus
Created attachment 167382 [details] emerge error log
Comment on attachment 167382 [details] emerge error log $ pwd /var/tmp/portage/sci-libs/gerris-20080929/work/gerris-snapshot-080929 $ grep -r 'MODULES_FLAGS' config.h /* #undef MODULES_FLAGS */
(In reply to comment #6) > (From update of attachment 167382 [details] [edit]) > $ pwd > /var/tmp/portage/sci-libs/gerris-20080929/work/gerris-snapshot-080929 > > $ grep -r 'MODULES_FLAGS' config.h > /* #undef MODULES_FLAGS */ > It looks like configure has trouble detecting gmodule support in glib. Could you please post the config.log file in /var/tmp/portage so I could check why that is? Thanks, Markus
Created attachment 167469 [details] config.log Thanks, Brent
(In reply to comment #8) > Created an attachment (id=167469) [edit] > config.log > > Thanks, > Brent > Hi Brent, Thanks much and your config.log indicates a problem with glib on your machine: ***MEMORY-ERROR***: [20876]: GSlice: failed to allocate 496 bytes (alignment: 512): Cannot allocate memory Unfortunately, I am not quite sure why this happens. Could you please try without the mpi useflag and post your mpi implementation in case this does the trick (gerris compiles fine with openmpi on my machines btw). If that doesn't help maybe try recompiling glib. Best, Markus
Hi Markus, Thank you for taking your time! Gerris compiles fine without mpi. Here's something I noticed: $ emerge -pv openmpi Calculating dependencies... done! [ebuild N ] sys-cluster/openmpi-1.2.6-r1 USE="fortran ipv6 threads -debug -heterogeneous -nocxx -pbs -romio" 3,474 kB [blocks B ] sys-cluster/lam-mpi (is blocking sys-cluster/openmpi-1.2.6-r1) [blocks B ] sys-cluster/openmpi (is blocking sys-cluster/lam-mpi-7.1.2) $ equery depends lam-mpi [ Searching for packages depending on lam-mpi... ] sci-libs/vtk-5.0.4 (mpi? sys-cluster/lam-mpi) virtual/mpi-1.0 (sys-cluster/lam-mpi) $ equery depends vtk [ Searching for packages depending on vtk... ] $ equery depends mpi sci-libs/arpack-96-r2 (mpi? virtual/mpi) sci-libs/gerris-20080929 (mpi? virtual/mpi) sci-mathematics/octave-2.1.73 (mpi? virtual/mpi) So I probably need to clean my system a bit, but also I am not using openmpi as my mpi implementation. I will try recompiling glib when I have time.
In case openmpi works for you with gerris you could try getting rid of lam-mpi and replacing it with openmpi on your system. Eventually, openmpi will become the default mpi implementation. Best, Markus
Is fixed in the recently committed newer version. Thanks.
