[gentoo-user] my xorg-server 1.6 seems a bit unstable - wh..

Brandon,

Thank you for helping me along here!

Here is the output of "ldd Mathematica":

linux-gate.so.1 => (0xb8042000)
libm.so.6 => /lib/libm.so.6 (0xb800c000)
libpthread.so.0 => /lib/libpthread.so.0 (0xb7ff4000)
librt.so.1 => /lib/librt.so.1 (0xb7feb000)
libXt.so.6 => /usr/lib/libXt.so.6 (0xb7f9a000)
libXext.so.6 => /usr/lib/libXext.so.6 (0xb7f8b000)
libXmu.so.6 => /usr/lib/libXmu.so.6 (0xb7f74000)
libSM.so.6 => /usr/lib/libSM.so.6 (0xb7f6a000)
libICE.so.6 => /usr/lib/libICE.so.6 (0xb7f51000)
libX11.so.6 => /usr/lib/libX11.so.6 (0xb7e3a000)
libc.so.6 => /lib/libc.so.6 (0xb7cf7000)
/lib/ld-linux.so.2 (0xb8043000)
libuuid.so.1 => /lib/libuuid.so.1 (0xb7cf2000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb7cd7000)
libXau.so.6 => /usr/lib/libXau.so.6 (0xb7cd3000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb7ccd000)
libdl.so.2 => /lib/libdl.so.2 (0xb7cc9000)

So far, I see a bunch of references Java directories in the
installation and a few .jar files. I haven't seen any reference to
Qt. I did see the GUI-Kit and JLink in the AddOns directory.

Basically, the only thing that triggers the crash is if I hold down
the mouse button and drag the scrollbar UP right after I drag it DOWN.
Dragging it down doesn't seem to make any difference by itself and
hasn't crashed the program until I reverse and drag UP. Sometimes
going up slowly will be OK too, but if I drag UP rapidly, it will
crash. I can use the scroll arrows on top and bottom of the
scrollbar, and it will scroll without incident, albeit slowly.

Can the integrity of the above library links be checked, or would
rebuilding all of them again make any difference? What is the command
to determine which package the given .so.* file belongs to?

Many thanks,
Denis

Denis wrote:
>> He may also want to ask the question "Do I *really* need acroread?" and get
>> the full complete answer. In my experience very few people actually need all
>> the features in acroread, and okular|evince are quite adequate
>>
>
> I am flexible on acroread, but acroread doesn't crash X - just gets a
> little backed up. I am OK with that.
>
> But X crashing from my use of Mathematica is absolutely unacceptable -
> this is what I need for my work. Before I upgraded to xorg-1.6 and
> libxcb-1.4, this *never* happened, not once, *in several years*, under
> extensive use, and I have been using the same Mathematica version all
> this time, 5.2. So if downgrading X and libxcb is what I have to do
> to restore reliable operation of my machine with Mathematica, then
> this is what I am doing next.
>
> Let me ask this next: is the downgrade of libxcb and xorg-server possible?
>
>
>

I have downgraded xorg-server before and it is not to bad. Just mask
the current version and do a emerge -uvDNa world. You may have to mask
a couple more packages but the error will tell you which ones they are.
I was able to just mask the one tho.

If you are using hal, you may have to reemerge the mouse and keyboard
drivers. I find them using this: equery list xf86-input That should
list the drivers that need to be reemerged. I have three.

Dale

On Mon, 2009-10-12 at 03:18 -0400, Denis wrote:
> Brandon,
>
> Thank you for helping me along here!
>
> Here is the output of "ldd Mathematica":
>
> linux-gate.so.1 => (0xb8042000)
> libm.so.6 => /lib/libm.so.6 (0xb800c000)
> libpthread.so.0 => /lib/libpthread.so.0 (0xb7ff4000)
> librt.so.1 => /lib/librt.so.1 (0xb7feb000)
> libXt.so.6 => /usr/lib/libXt.so.6 (0xb7f9a000)
> libXext.so.6 => /usr/lib/libXext.so.6 (0xb7f8b000)
> libXmu.so.6 => /usr/lib/libXmu.so.6 (0xb7f74000)
> libSM.so.6 => /usr/lib/libSM.so.6 (0xb7f6a000)
> libICE.so.6 => /usr/lib/libICE.so.6 (0xb7f51000)
> libX11.so.6 => /usr/lib/libX11.so.6 (0xb7e3a000)
> libc.so.6 => /lib/libc.so.6 (0xb7cf7000)
> /lib/ld-linux.so.2 (0xb8043000)
> libuuid.so.1 => /lib/libuuid.so.1 (0xb7cf2000)
> libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb7cd7000)
> libXau.so.6 => /usr/lib/libXau.so.6 (0xb7cd3000)
> libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb7ccd000)
> libdl.so.2 => /lib/libdl.so.2 (0xb7cc9000)
>
> So far, I see a bunch of references Java directories in the
> installation and a few .jar files. I haven't seen any reference to
> Qt. I did see the GUI-Kit and JLink in the AddOns directory.
>
> Basically, the only thing that triggers the crash is if I hold down
> the mouse button and drag the scrollbar UP right after I drag it DOWN.
> Dragging it down doesn't seem to make any difference by itself and
> hasn't crashed the program until I reverse and drag UP. Sometimes
> going up slowly will be OK too, but if I drag UP rapidly, it will
> crash. I can use the scroll arrows on top and bottom of the
> scrollbar, and it will scroll without incident, albeit slowly.

That sounds really bizarre. I have no idea what would be causing that.

> Can the integrity of the above library links be checked, or would
> rebuilding all of them again make any difference? What is the command
> to determine which package the given .so.* file belongs to?

equery (from app-portage/gentoolkit) can tell you which package a
particular file belongs to. `equery belongs /path/to/filename` should do
the trick. You could try downgrading those packages to see if it fixes
your issue. I have not tried downgrading just one or two X libraries,
though I have heard that it can break pretty badly (especially with
respect to libxcb), so I would make a backup first. Another option could
be trying an updated version of X from the x11 overlay. Maybe someone
else on this list has experience with either case and can offer some
pointers; I unfortunately have none.

Packages with the above-listed libraries: x11-libs/libXt,
x11-libs/libXmu x11-libs/libSM, x11-libs/libICE, x11-libs/libX11,
x11-libs/libxcb, x11-libs/libXau.

Good luck; I cannot think of anything else to suggest.

Regards,

Brandon Vargo

On Tuesday 13 October 2009 00:33:02 Brandon Vargo wrote:
> > Basically, the only thing that triggers the crash is if I hold down
> > the mouse button and drag the scrollbar UP right after I drag it DOWN.
> > Dragging it down doesn't seem to make any difference by itself and
> > hasn't crashed the program until I reverse and drag UP. Sometimes
> > going up slowly will be OK too, but if I drag UP rapidly, it will
> > crash. I can use the scroll arrows on top and bottom of the
> > scrollbar, and it will scroll without incident, albeit slowly.
>
> That sounds really bizarre. I have no idea what would be causing that.
>

sounds like a segfault

For example, data gets moved around in memory as the display is scrolled and
somewhere there is a pointer to that memory. It gets updated somehow but when
the scrolling is rapid the pointer gets used after the data is moved and
before the pointer is updated.

If it's something along these lines it's a) horrible to find and fix and b)
horrible code

--
alan dot mckinnon at gmail dot com

I tried a few things today:

1) rebuilt all x11-libs, media-libs, and anything I could think of
that would be related to x11-libs (such as gtk+, qt...)

2) downgraded to xorg-server-1.5

Neither of these things helped. Alan's hypothesis sounds plausible,
but I don't even know which package to point fingers at! Probably
it's the Mathematica interface itself, which is horribly old by now,
but I cannot upgrade it at this time. As I said, dragging the
scrollbar down works fine, but you drag the scroll bar up, and in a
few seconds X gets zapped. I tried instead clicking above or below
the scroll bar to avoid dragging. That is a tad better, but after a
few times, it goes down again...

The weird thing is that I never had this problem before doing the
massive lib-xcb upgrade, and obviously the xorg-server doesn't seem to
be helping or hurting anything, so I went back to xorg-server 1.6.

Is there any procedure out there about de-Xifying your system? I
don't have the time right now to do all this, but I am just wondering
if some people have removed everything X-related from their system and
started anew without completely wrecking the box...

Denis wrote:
> I tried a few things today:
>
> 1) rebuilt all x11-libs, media-libs, and anything I could think of
> that would be related to x11-libs (such as gtk+, qt...)
>
> 2) downgraded to xorg-server-1.5
>
> Neither of these things helped. Alan's hypothesis sounds plausible,
> but I don't even know which package to point fingers at! Probably
> it's the Mathematica interface itself, which is horribly old by now,
> but I cannot upgrade it at this time. As I said, dragging the
> scrollbar down works fine, but you drag the scroll bar up, and in a
> few seconds X gets zapped. I tried instead clicking above or below
> the scroll bar to avoid dragging. That is a tad better, but after a
> few times, it goes down again...
>
> The weird thing is that I never had this problem before doing the
> massive lib-xcb upgrade, and obviously the xorg-server doesn't seem to
> be helping or hurting anything, so I went back to xorg-server 1.6.
>
> Is there any procedure out there about de-Xifying your system? I
> don't have the time right now to do all this, but I am just wondering
> if some people have removed everything X-related from their system and
> started anew without completely wrecking the box...
>
>
>

I would take a look at the world file and remove everything X related.
A --depclean should then remove everything X related.

Keep in mind, that could be a huge amount of stuff to re-install. I
would make binaries of *some* things that you know would not affect the
programs you are having issues with. Say for example OOo or some other
large packages that take a while to compile. You can then use the -k
option to reinstall them. Naturally, I wouldn't save anything related
to X itself. I would recompile them from scratch.

I wish I had better ideas or a quick fix.

Dale

On 13 Oct 2009, at 01:25, Denis wrote:

> I tried a few things today:
> ...
>
> Neither of these things helped. Alan's hypothesis sounds plausible,
> but I don't even know which package to point fingers at!

Have you `emerge -e world` yet?

Stroller.

> Have you `emerge -e world` yet?
>
> Stroller.

I have that going now. I offloaded OpenOffice to shorten the duration
of the rebuild, and I don't have KDE or Gnome - just fluxbox. So it
should finish by sometime tomorrow, probably. There are 604 packages
total. Instead of trying to rebuild X-related stuff in parts, I
should have just done that from the beginning.

Dale - thanks for the advices also. That's the route I thought about
taking. Doing 'emerge -e world' first seems like a reasonable thing
to do. It could be that whatever is causing this cannot be resolved
by a simple rebuild. Whatever went into the lib-xcb upgrade probably
is either incompatible with the Mathematica frontend or has a bug
that's being exploited in this situation. Keeping my fingers crossed
for the rebuild for now.

-Denis

Denis wrote:
>> Let us know what blows up.
>>
>> Dale
>>
>
> Nothing blew up I was successful removing X, downgrading, and
> getting X working again with xorg-server-1.5.3 and libxcb-1.1
>
> FYI, the working package.mask file for this operation is:
>
>
>> =x11-libs/libXext-1.0.5
>> =x11-libs/libX11-1.2
>> =x11-libs/libxcb-1.4
>> =x11-base/xorg-server-1.6
>> =x11-base/xorg-x11-7.4
>> =x11-proto/xproto-7.0.15
>> =x11-proto/xextproto-7.0.5
>> =x11-libs/xcb-util-0.3.5
>> =x11-proto/xcb-proto-1.2
>>
>
> However, this must not have restored my previous X configuration fully
> because Mathematica still crashes. So I've decided to abandon this
> attempt, remove all masks, and allow the full X upgrade because I
> reinstall all the X packages back onto my system. While some folks
> here probably think this attempt foolish, I still think it was worth a
> try, and I learned some new things, which is always good.
>
> I appreciate everyone's help and support with this.
> Denis
>
>
>

Well, I do foolish things sometimes myself. Once every few months for
example, I run a emerge -ev world. Then I reboot and make my back ups.
At least I know it is a sane build and it will boot if restored from. I
don't back up as much as I used to since I got DSL. I guess we all try
something just to satisfy our curiosity if nothing else.

I do wish it would have fixed your problem tho. I would travel upstream
and see if you can help them by providing information on the crash.

Dale

On Wed, 2009-10-14 at 12:50 -0400, Denis wrote:
> > Let us know what blows up.
> >
> > Dale
>
> Nothing blew up I was successful removing X, downgrading, and
> getting X working again with xorg-server-1.5.3 and libxcb-1.1
>

Have you tried "strace'ing" mathematica to see why it dies?

BillK

Denis wrote:
> Ok, "emerge -e world" completed successfully.
>
> Bad news: X still crashes when scrolling in Mathematica...
>
> On to the downgrade of xcb then, as much as I'd rather not do that.
> As suggested, I would edit the world file to remove main X packages
> and then use emerge --depclean to prune out the danglers. As someone
> who has never done this before, I got two questions:
>
> 1. The easy one: where is the world file located these days?
>
> 2. The hard one: which packages do I remove from the world file to
> clean out anything X-related? I read of a suggestion to remove
> "x11-base/xorg-x11" and the rest would follow from depclean... Is
> that too optimistic?
>
> Thanks,
> Denis
>
>
>

1: /var/lib/portage/world

2: The file is in alphabetical order nowadays. The X stuff should be
at the bottom of the file. Keep in mind tho, if you have a GUI such as
KDE installed, that will pull the X stuff as a dependency. Things like
Seamonkey may even pull in some X stuff. After all, don't you have to
have a GUI for things like Seamonkey to work?

Not on your list but if you have done a emerge -e world, I'm not real
sure what this will accomplish. That should have recompiled EVERYTHING
on your system already. I would be looking for a mailing list for the
software to see if they know about this issue and have a fix or if they
can give some ideas or even commands to run to help them fix it. I'm
not real sure that this is going to help any at all.

That help?

Dale

Perhaps I should try this procedure on my home gentoo box first.

Here are my USE flags:

X aac aim alsa ao bash-completion bdf branding bzip2 cairo cdda cddb
cdparanoia cdr cpudetection djvu emacs encode exif firefox flac
foomaticdb gif glut graphics gs gtk ieee1394 imagemagick imlib java
javascript jbig jpeg jpeg2k kpathsea lame latex ldap libnotify libwww
lm_sensors mad mmx mmxext mng motif mp3 mpeg mplayer msn openal opengl
oss pdf plotutils png ppds preview-latex pstricks qt3support qt4
quicktime rtc samba science sdl sensord smp sndfile spell sse sse2 svga
swat tcl tetex tiff tk truetype tta usb wavpack winbind wmp xcb xine xml
yahoo -dri -isdnlog -pppd

When "world" is edited, should I leave make.conf be or do I also need
to remove all X-related USE flags from there?

Here is my world file. I did not include anything under x11-* for brewity.

I marked everything I am planning to remove with a preceding "- "
Could someone look this over, please, to make sure I didn't select
anything critical? I did use "equery depends" and some common sense,
but I could use a sanity check!

- app-admin/emacs-updater
app-admin/syslog-ng
- app-editors/emacs
- app-emacs/emacs-common-gentoo
- app-office/abiword
- app-office/abiword-plugins
app-portage/gentoolkit
app-portage/mirrorselect
app-portage/portage-utils
app-portage/ufed
app-shells/bash-completion
- app-text/acroread
- app-text/djvu
- app-text/enchant
- app-text/ghostscript-gpl
- app-text/gnome-doc-utils
- app-text/gtkspell
- app-text/gv
- app-text/hunspell
- app-text/iso-codes
- app-text/libpaper
- app-text/libwpd
app-text/poppler-data
app-text/poppler-utils
- app-text/ps2eps
- app-text/psutils
- app-text/rarian
- app-text/rman
- app-text/scrollkeeper
- app-text/scrollkeeper-dtd
app-text/sgml-common
- app-text/t1utils
- app-text/texi2html
- app-text/texlive
- app-text/wv
- app-vim/fluxbox-syntax
dev-java/javatoolkit
dev-java/sun-jdk
dev-lang/tcl
dev-libs/dbus-glib
dev-libs/libtasn1
dev-libs/mpfr
dev-perl/XML-Parser
dev-python/pygobject
dev-python/pygtk
- dev-tex/latex-beamer
- dev-tex/mh
- dev-texlive/texlive-bibtexextra
- dev-texlive/texlive-latexextra
dev-util/pkgconfig
- gnome-base/gdm
- gnome-base/libgnomecanvas
- media-fonts/corefonts
- media-fonts/dejavu
- media-fonts/encodings
- media-fonts/font-adobe-100dpi
- media-fonts/font-adobe-75dpi
- media-fonts/font-adobe-utopia-100dpi
- media-fonts/font-adobe-utopia-75dpi
- media-fonts/font-adobe-utopia-type1
- media-fonts/font-alias
- media-fonts/font-arabic-misc
- media-fonts/font-bh-100dpi
- media-fonts/font-bh-75dpi
- media-fonts/font-bh-lucidatypewriter-100dpi
- media-fonts/font-bh-lucidatypewriter-75dpi
- media-fonts/font-bh-ttf
- media-fonts/font-bh-type1
- media-fonts/font-bitstream-100dpi
- media-fonts/font-bitstream-75dpi
- media-fonts/font-bitstream-speedo
- media-fonts/font-bitstream-type1
- media-fonts/font-cronyx-cyrillic
- media-fonts/font-cursor-misc
- media-fonts/font-daewoo-misc
- media-fonts/font-dec-misc
- media-fonts/font-ibm-type1
- media-fonts/font-isas-misc
- media-fonts/font-jis-misc
- media-fonts/font-micro-misc
- media-fonts/font-misc-cyrillic
- media-fonts/font-misc-ethiopic
- media-fonts/font-misc-meltho
- media-fonts/font-misc-misc
- media-fonts/font-mutt-misc
- media-fonts/font-schumacher-misc
- media-fonts/font-screen-cyrillic
- media-fonts/font-sony-misc
- media-fonts/font-sun-misc
- media-fonts/font-util
- media-fonts/font-winitzki-cyrillic
- media-fonts/font-xfree86-type1
- media-fonts/freefonts
- media-fonts/gnu-gs-fonts-std
- media-fonts/intlfonts
- media-fonts/terminus-font
- media-fonts/ttf-bitstream-vera
- media-fonts/unifont
- media-gfx/gimp
- media-gfx/gqview
- media-gfx/imagemagick
- media-gfx/jpeg2ps
- media-gfx/sam2p
- media-gfx/transfig
- media-gfx/xfig
- media-gfx/xv
media-libs/alsa-lib
media-libs/audiofile
- media-libs/babl
media-libs/flac
- media-libs/fontconfig
- media-libs/freeglut
- media-libs/freetype
- media-libs/ftgl
- media-libs/gd
- media-libs/gegl
- media-libs/giflib
- media-libs/glew
- media-libs/gst-plugins-base
- media-libs/gst-plugins-good
- media-libs/gstreamer
- media-libs/imlib2
- media-libs/jasper
- media-libs/jbigkit
- media-libs/jpeg
- media-libs/lcms
media-libs/libart_lgpl
media-libs/libcddb
- media-libs/libexif
media-libs/libid3tag
media-libs/libmad
- media-libs/libmng
media-libs/libogg
media-libs/libpng
media-libs/libsdl
media-libs/libsndfile
media-libs/libvorbis
- media-libs/mesa
- media-libs/netpbm
media-libs/openjpeg
- media-libs/pdflib
- media-libs/plotutils
media-libs/raptor
media-libs/svgalib
-media-libs/t1lib
media-libs/tiff
- media-libs/vigra
media-plugins/alsa-plugins
media-sound/alsa-utils
media-sound/asunder
media-sound/audacious
media-sound/cdparanoia
media-sound/cdplay
media-sound/wavpack
- media-video/nvidia-settings
net-analyzer/netselect
net-fs/samba
- net-im/pidgin
- net-irc/xchat
net-misc/dhcpcd
- net-print/cups
perl-core/IO-Compress
- sci-misc/qcad
- sci-visualization/gnuplot
sys-apps/dbus
sys-apps/groff
sys-apps/lm_sensors
sys-apps/pciutils
sys-boot/grub
sys-devel/gcc
sys-devel/gcc:4.1
sys-devel/gettext
sys-devel/libtool
sys-fs/e2fsprogs
sys-kernel/gentoo-sources
sys-kernel/gentoo-sources:2.6.27-r8
sys-kernel/module-rebuild
sys-libs/timezone-data
sys-process/vixie-cron
virtual/perl-ExtUtils-CBuilder
www-client/links
- www-client/mozilla-firefox
- www-plugins/adobe-flash

Denis wrote:
>> Have you tried "strace'ing" mathematica to see why it dies?
>>
>> BillK
>>
>
> I ran an strace, but I can't make sense out of it. There's a bunch of
> polling and trying to access unavailable resources, from what I can
> see... The file is huge, but here is the tail end of it:
>
> << SNIP >>
>
> Does this make any sense to anyone?
>
>
>

OK, first off. I have no clue what this program does. I'm shooting in
the dark here. I found this:

http://forums.wolfram.com/mathgroup/archive/2001/Dec/msg00034.html

It seems you are not alone. I browsed though a couple other places and
saw people mentioning python a bit. Does this software use python by
any chance?

I also noticed a lot of talking about I/O issues. Are you sure and for
certain that you have the right chip set compiled for your hard drive?
I ran into a lot of errors once and I had the wrong chip set selected in
my kernel and although it was trying to work, it didn't work very well
when there was a lot of I/O activity. Programs would crash and in the
Konsole I would get all sorts of errors including the plan old seg fault
type.

Again, read the first three sentences. Just thinking and typing and
that is dangerous for me.

Dale