146767 2006-09-07 17:32 0000 sci-libs/vtk-5.0.1 fails parallel make 2006-11-18 06:45:21 0000 1 1 1 Unclassified Gentoo Linux Library 2006.1 All Linux RESOLVED FIXED P2 normal --- 1 mlangc@gmx.at markusle@gentoo.org s.breedveld@erasmusmc.nl sci@gentoo.org mlangc@gmx.at 2006-09-07 17:32:44 0000 when trying to merge vtk-5.0.1 USE="doc examples java python threads -mpi -patented -qt3 -qt4 -tcl -tk" i get: Building CXX object Rendering/CMakeFiles/vtkRendering.dir/vtkOpenGLExtensionManager.o /var/tmp/portage/vtk-5.0.1/work/VTK/Rendering/vtkOpenGLExtensionManager.cxx: In member function mlangc@gmx.at 2006-09-07 17:32:44 0000 when trying to merge vtk-5.0.1 USE="doc examples java python threads -mpi -patented -qt3 -qt4 -tcl -tk" i get: Building CXX object Rendering/CMakeFiles/vtkRendering.dir/vtkOpenGLExtensionManager.o /var/tmp/portage/vtk-5.0.1/work/VTK/Rendering/vtkOpenGLExtensionManager.cxx: In member function ‘virtual void (* vtkOpenGLExtensionManager::GetProcAddress(const char*))()’: /var/tmp/portage/vtk-5.0.1/work/VTK/Rendering/vtkOpenGLExtensionManager.cxx:195: error: ‘glXGetProcAddressARB’ was not declared in this scope make[2]: *** [Rendering/CMakeFiles/vtkRendering.dir/vtkOpenGLExtensionManager.o] Error 1 make[2]: *** Waiting for unfinished jobs.... make[1]: *** [Rendering/CMakeFiles/vtkRendering.dir/all] Error 2 make: *** [all] Error 2 !!! ERROR: sci-libs/vtk-5.0.1 failed. ... ... ... !!! When you file a bug report, please include the following information: GENTOO_VM=sun-jdk-1.4 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.4.2.12" JAVACFLAGS="-source 1.4 -target 1.4" COMPILER="" Portage 2.1-r2 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.4-r3, 2.6.16-gentoo-r13 i686) ================================================================= System uname: 2.6.16-gentoo-r13 i686 AMD Athlon(tm) XP 2400+ Gentoo Base System version 1.12.4 app-admin/eselect-compiler: [Not Present] dev-lang/python: 2.4.3-r1 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: [Not Present] dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r3 sys-devel/gcc-config: 1.3.13-r3 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.11-r5 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=athlon-xp -O2 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-march=athlon-xp -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig collision-protect distlocks metadata-transfer sandbox sfperms strict test" GENTOO_MIRRORS="http://gentoo.ynet.sk/pub " LANG="en_US.utf8" LC_ALL="en_US.utf8" LINGUAS="en de" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://192.168.0.1/gentoo-portage" USE="x86 3dnow 3dnowext X a52 aac acpi alsa audiofile avi beagle berkdb bitmap-fonts bzip2 cairo cdr cli crypt css cups dbus dlloader dri dvd dvdr dvdread eds emboss encode evo exif fam fbcon ffmpeg firefox flac fortran gdbm gif ginac gmp gnome gphoto2 gpm gstreamer gtk gtk2 hal howl icq ipv6 isdnlog java javascript jpeg jpeg2k lcms ldap libg++ mad mikmod mime mmx mmxext mozsvg mp3 mpeg msn nautilus ncurses nfs nls nptl nptlonly nsplugin nvidia offensive ogg oggvorbis opengl pam pcre pdflib perl plotutils png posix ppds pppd python qt3 qt4 quicktime readline real reflection ruby sdl session sockets spell spl sqlite3 sse ssl subtitles svg tcpd tetex theora tiff truetype truetype-fonts type1-fonts udev unicode usb vcd vorbis win32codecs wma xine xml xorg xv xvid zlib elibc_glibc input_devices_keyboard input_devices_mouse kernel_linux linguas_en linguas_de userland_GNU video_cards_nvidia" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS markusle@gentoo.org 2006-09-08 10:57:04 0000 Hi Matthias, Thanks for your report. Unfortunately, I can't reproduce this error on my machine and I'll have to look at the source to figure out what is going wrong. Best, Markus markusle@gentoo.org 2006-09-08 13:01:55 0000 What version of cmake are you using? mlangc@gmx.at 2006-09-08 16:17:31 0000 well, i'm almost sure that i was using cmake-2.4.2-r1 when i experienced the bug described above ... however, the strange thing is, that when i tried to remerge vtk-5.0.1 USE="doc examples java threads -mpi -patented -python -qt3 -qt4 -tcl -tk" (notice -python this time) i got Scanning dependencies of target vtkCommon /var/tmp/portage/vtk-5.0.1/work/VTK/java/vtk/../vtk/vtkVTKJavaCommonDriver.java:11: cannot resolve symbol symbol : class vtkAbstractArray location: class vtk.vtkVTKJavaCommonDriver dummy = new vtkAbstractArray(); ^ /var/tmp/portage/vtk-5.0.1/work/VTK/java/vtk/../vtk/vtkVTKJavaCommonDriver.java:12: cannot resolve symbol symbol : class vtkAbstractTransform location: class vtk.vtkVTKJavaCommonDriver dummy = new vtkAbstractTransform(); ^ ... ... ... /var/tmp/portage/vtk-5.0.1/work/VTK/java/vtk/../vtk/vtkVTKJavaCommonDriver.java:110: cannot resolve symbol symbol : class vtkStructuredVisibilityConstraint location: class vtk.vtkVTKJavaCommonDriver dummy = new vtkStructuredVisibilityConstraint(); ^ 100 errors make[2]: *** [java/vtk/vtkBuildAllDriver.class] Error 1 make[1]: *** [Wrapping/Java/CMakeFiles/VTKBuildAll.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... Building CXX object Common/CMakeFiles/vtkCommon.dir/vtkAbstractArray.o ... ... ... Building CXX object Common/CMakeFiles/vtkCommon.dir/vtkCommonInstantiator.o Linking CXX shared library ../bin/libvtkCommon.so make: *** [all] Error 2 !!! ERROR: sci-libs/vtk-5.0.1 failed. when i tried doing so a second time, it suddenly worked without any issues. i'm now going check what happens if i add "python" again ... mlangc@gmx.at 2006-09-08 19:26:03 0000 well, sorry for the bugspam -- now it also works with python. markusle@gentoo.org 2006-09-09 07:00:45 0000 Hi Matthias, No problem and I am glad it works. I am almost certain that your first issue was due to cmake, since one of the macros wasn't exported properly. Please don't hesitate to reopen this bug should things like that crop up again. Best, Markus mlangc@gmx.at 2006-10-17 19:36:47 0000 when trying to emerge vtk-5.0.1 (tried 5 times to be sure) on $BOX1 vtk-5.0.1 USE="doc java threads -examples -mpi -patented -python -qt3 -qt4 -tcl -tk" with cmake-2.4.3, cmake-2.2.3 or cmake-2.4.2-r1 i get: [...] Scanning dependencies of target vtkCommon /var/tmp/portage/vtk-5.0.1/work/VTK/java/vtk/../vtk/vtkVTKJavaCommonDriver.java:11: cannot resolve symbol symbol : class vtkAbstractArray location: class vtk.vtkVTKJavaCommonDriver dummy = new vtkAbstractArray(); ^ /var/tmp/portage/vtk-5.0.1/work/VTK/java/vtk/../vtk/vtkVTKJavaCommonDriver.java:12: cannot resolve symbol symbol : class vtkAbstractTransform location: class vtk.vtkVTKJavaCommonDriver dummy = new vtkAbstractTransform(); ^ /var/tmp/portage/vtk-5.0.1/work/VTK/java/vtk/../vtk/vtkVTKJavaCommonDriver.java:13: cannot resolve symbol symbol : class vtkAmoebaMinimizer location: class vtk.vtkVTKJavaCommonDriver dummy = new vtkAmoebaMinimizer(); ^ [...] 100 errors Java Wrappings make[2]: *** [java/vtk/vtkBuildAllDriver.class] Error 1 make[1]: *** [Wrapping/Java/CMakeFiles/VTKBuildAll.dir/all] Error 2 [...] [ 10%] Building CXX object Common/CMakeFiles/vtkCommon.dir/vtkCommonInstantiator.o Linking CXX shared library ../bin/libvtkCommon.so [ 10%] Built target vtkCommon make: *** [all] Error 2 !!! ERROR: sci-libs/vtk-5.0.1 failed. [...] !!! When you file a bug report, please include the following information: GENTOO_VM=sun-jdk-1.4 CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.4.2.12" JAVACFLAGS="-source 1.4 -target 1.4" COMPILER="" the strange thing, is that it works without any issues in $BOX2 ... BOX1: Portage 2.1.1 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.4-r3, 2.6.17-gentoo-r8 i686) ================================================================= System uname: 2.6.17-gentoo-r8 i686 Intel(R) Pentium(R) 4 CPU 3.40GHz Gentoo Base System version 1.12.5 Last Sync: Tue, 17 Oct 2006 12:50:01 +0000 app-admin/eselect-compiler: [Not Present] dev-java/java-config: 1.3.7, 2.0.30 dev-lang/python: 2.3.5-r2, 2.4.3-r4 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: [Not Present] dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r3 sys-devel/gcc-config: 1.3.13-r4 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.17-r1 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -march=prescott" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/X11/xkb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-O2 -march=prescott" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig distlocks metadata-transfer sandbox sfperms strict" GENTOO_MIRRORS="http://gentoo.ynet.sk/pub " LC_ALL="en_US.utf8" LINGUAS="" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.europe.gentoo.org/gentoo-portage" USE="x86 X acpi aiglx alsa berkdb bitmap-fonts browserplugin bzip2 cairo cli crypt cups dbus dlloader dri dvd elibc_glibc emboss encode fam firefox fortran gdbm gif gnome gpm gstreamer gtk hal input_devices_keyboard input_devices_mouse ipv6 isdnlog java jpeg kernel_linux ldap libg++ mad mikmod mmx mp3 mpeg ncurses nls nptl nptlonly nsplugin nvidia ogg opengl pam pcre perl png ppds pppd python quicktime readline reflection ruby sdl session spell spl sse sse2 ssl tcpd threads tiff truetype truetype-fonts type1-fonts udev unicode usb userland_GNU video_cards_nvidia vorbis win32codecs xinerama xml xorg xv zlib" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS BOX2: Portage 2.1.1 (default-linux/x86/2006.1/desktop, gcc-4.1.1, glibc-2.4-r3, 2.6.16-gentoo-r13 i686) ================================================================= System uname: 2.6.16-gentoo-r13 i686 AMD Athlon(tm) XP 2400+ Gentoo Base System version 1.12.5 Last Sync: Tue, 17 Oct 2006 09:50:01 +0000 distcc 2.18.3 i686-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] app-admin/eselect-compiler: [Not Present] dev-java/java-config: 1.3.7, 2.0.30 dev-lang/python: 2.4.3-r4 dev-python/pycrypto: 2.0.1-r5 dev-util/ccache: [Not Present] dev-util/confcache: [Not Present] sys-apps/sandbox: 1.2.17 sys-devel/autoconf: 2.13, 2.59-r7 sys-devel/automake: 1.4_p6, 1.5, 1.6.3, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2 sys-devel/binutils: 2.16.1-r3 sys-devel/gcc-config: 1.3.13-r4 sys-devel/libtool: 1.5.22 virtual/os-headers: 2.6.17-r1 ACCEPT_KEYWORDS="x86" AUTOCLEAN="yes" CBUILD="i686-pc-linux-gnu" CFLAGS="-march=athlon-xp -O2 -pipe" CHOST="i686-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/X11/xkb /usr/share/config /usr/share/texmf/dvipdfm/config/ /usr/share/texmf/dvips/config/ /usr/share/texmf/tex/generic/config/ /usr/share/texmf/tex/platex/config/ /usr/share/texmf/xdvi/" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/gconf /etc/java-config/vms/ /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-march=athlon-xp -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="autoconfig collision-protect distlocks metadata-transfer sandbox sfperms strict test" GENTOO_MIRRORS="http://gentoo.ynet.sk/pub " LANG="en_US.utf8" LC_ALL="en_US.utf8" LINGUAS="en de" MAKEOPTS="-j2" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude='/distfiles' --exclude='/local' --exclude='/packages'" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://192.168.0.1/gentoo-portage" USE="x86 3dnow 3dnowext X a52 aac acpi alsa audiofile beagle berkdb bitmap-fonts bzip2 cairo cdr cli crypt css cups dbus dlloader dri dvd dvdr dvdread eds elibc_glibc emboss encode evo exif fam fbcon ffmpeg firefox flac fortran gdbm gif ginac gmp gnome gphoto2 gpm gstreamer gtk gtk2 hal howl icq input_devices_keyboard input_devices_mouse ipv6 isdnlog java javascript jpeg jpeg2k kernel_linux lcms ldap libg++ linguas_de linguas_en mad mikmod mime mmx mmxext mono mozsvg mp3 mpeg msn nautilus ncurses nfs nls nptl nptlonly nsplugin nvidia offensive ogg oggvorbis opengl pam pcre perl plotutils png posix ppds pppd python qt3 qt4 quicktime readline real reflection ruby sdl session sockets spell spl sqlite3 sse ssl subtitles svg tcpd tetex theora threads tiff truetype truetype-fonts type1-fonts udev unicode usb userland_GNU vcd video_cards_nvidia vorbis win32codecs wma xine xml xorg xv xvid zlib" Unset: CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LDFLAGS, PORTAGE_RSYNC_EXTRA_OPTS mlangc@gmx.at 2006-10-17 19:38:24 0000 reopening because of comment #6 ... markusle@gentoo.org 2006-10-18 05:43:43 0000 (In reply to comment #7) > reopening because of comment #6 ... > Do both boxes have the same java? If yes, does java work properly on box 1 with other applications? Could you try with blackdown-java and see if that works please! Thanks, Markus mlangc@gmx.at 2006-10-18 08:56:33 0000 (In reply to comment #8) > Do both boxes have the same java? Yes, they have ... > If yes, does java work > properly on box 1 with other applications? I think so, but i'll verify that tomorrow (at the moment i've no access to box2) ... > Could you try > with blackdown-java and see if that works please! i'll do that tomorrow (see above) ... thanks for your quick reply, matthias mlangc@gmx.at 2006-10-19 08:40:27 0000 (In reply to comment #8) > ... does java work > properly on box 1 with other applications? well, i was able to emerge and start azureus-2.5.0.0-r3 - thus i think java should be ok; besides, i'm also able to emerge vtk-5.0.0 USE="doc examples java threads -mpi -patented -python -qt3 -qt4 -tcltk" > Could you try > with blackdown-java and see if that works please! i'm getting exactly the same errors with blackdown-jdk-1.4.2.03 set as my generation-1 jdk ... markusle@gentoo.org 2006-10-19 18:25:02 0000 (In reply to comment #10) Hmm, unfortunately I am not quite sure what the problem could be. Possibly, one of the libraries failed to build at some point and now you get linking errors. You could try dropping the -march=prescott to -march=pentium4 and MAKEOPTS down to -j1. mlangc@gmx.at 2006-10-20 03:05:03 0000 you are right: dropping to "-j1" solved this issue; now also comment #3 seems to make some sense again ... markusle@gentoo.org 2006-10-20 05:49:07 0000 (In reply to comment #12) > you are right: dropping to "-j1" solved this issue; now also comment #3 seems > to make some sense again ... > Good :) I think the ebuild forced this at some point but I removed it since it seemed to work. I'll probably stick it back in next time I'll update the ebuild. I'll close this bug then. Please re-open if this comes up again (and is non MAKEOPTS related). Thanks, Markus jakub@gentoo.org 2006-11-17 03:28:03 0000 *** Bug 155465 has been marked as a duplicate of this bug. *** mlangc@gmx.at 2006-11-18 05:14:22 0000 [from bug bug 155465] > From the changelog for VTK, emake works fine with -j2. This is correct, but the > build fails at -j4 or higher. I have tested this on a computer with 4 physical > cores. it may (not always) even fail on a single-core box with -j2 ... markusle@gentoo.org 2006-11-18 06:45:21 0000 (In reply to comment #15) > [from bug bug 155465] > > From the changelog for VTK, emake works fine with -j2. This is correct, but the > > build fails at -j4 or higher. I have tested this on a computer with 4 physical > > cores. > > it may (not always) even fail on a single-core box with -j2 ... > I've personally never had any problems with -j2 but it looks like the cmake generated makefiles are kind of unpredictable (possibly also depending on the specifiv cmake version installed). I will stick the -j1 back into ebuild later today. Thanks, Markus