Gentoo Bug 146767 - sci-libs/vtk-5.0.1 fails parallel make

Description:

Opened: 2006-09-07 17:32 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

------- Comment #1 From Matthias Langer 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

------- Comment #2 From Markus Dittrich 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

------- Comment #3 From Markus Dittrich 2006-09-08 13:01:55 0000 -------

What version of cmake are you using?

------- Comment #4 From Matthias Langer 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 ...

------- Comment #5 From Matthias Langer 2006-09-08 19:26:03 0000 -------

well, sorry for the bugspam -- now it also works with python.

------- Comment #6 From Markus Dittrich 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

------- Comment #7 From Matthias Langer 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

------- Comment #8 From Matthias Langer 2006-10-17 19:38:24 0000 -------

reopening because of comment #6 ...

------- Comment #9 From Markus Dittrich 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

------- Comment #10 From Matthias Langer 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

------- Comment #11 From Matthias Langer 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 ...

------- Comment #12 From Markus Dittrich 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.

------- Comment #13 From Matthias Langer 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 ...

------- Comment #14 From Markus Dittrich 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

------- Comment #15 From Jakub Moc (RETIRED) 2006-11-17 03:28:03 0000 -------

*** Bug 155465 has been marked as a duplicate of this bug. ***

------- Comment #16 From Matthias Langer 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 ...

------- Comment #17 From Markus Dittrich 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

Bug 146767 depends on:			Show dependency tree
Bug 146767 blocks:			Show dependency tree

Bugzilla Bug 146767

sci-libs/vtk-5.0.1 fails parallel make

Last modified: 2006-11-18 06:45:21 0000