Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
Ordinarily, I would also point to I/O errors, but not this time. I have had this same version of Mathematica, 5.2, for *years*, on this same machine, over several kernels and several Xorg upgrades, and it was rock-solid. Not one X hang or crash. Ever. No error messages or I/O warnings ever. The only thing I'd ever see in the console would be GTK+ errors from other programs. Something about this latest X upgrade is making Mathematica unhappy, either because some previously supported format that worked fine with it has been altered or something else in that general regard. This version being so outdated - that isn't a surprise. It may not be a bug, so much as an incompatibility, perhaps I think the only thing I can do at this point that probably will fix this is to go to stable arch, but I am not willing to do that because I like my box the way it is now :-) It's great and efficient for all other things. Before I can get a local Mathematica upgrade, I will have to resort to using it via X forwarding off the central server.
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
Denis wrote: Ordinarily, I would also point to I/O errors, but not this time. I have had this same version of Mathematica, 5.2, for *years*, on this same machine, over several kernels and several Xorg upgrades, and it was rock-solid. Not one X hang or crash. Ever. No error messages or I/O warnings ever. The only thing I'd ever see in the console would be GTK+ errors from other programs. Something about this latest X upgrade is making Mathematica unhappy, either because some previously supported format that worked fine with it has been altered or something else in that general regard. This version being so outdated - that isn't a surprise. It may not be a bug, so much as an incompatibility, perhaps I think the only thing I can do at this point that probably will fix this is to go to stable arch, but I am not willing to do that because I like my box the way it is now :-) It's great and efficient for all other things. Before I can get a local Mathematica upgrade, I will have to resort to using it via X forwarding off the central server. I forgot to mention this earlier. The way I found out it was a I/O error for me was this command. hdparm -Tt /dev/hda hdparm -Tt /dev/hda . I kept repeating that until it starting giving me errors. For mine it was after the third pass. Something to keep in mind, it could be something wrong with the driver in the kernel you are using. It could be any number of things like this. It could be that it is a mismatch as you mentioned between Mathematica and some other support program such as gtk, python or any other number of things. Me, I would hop on a mailing list for that software and ask them what strace command you can run and then send them the results. It may be that they can make some sense of the error and recommend a fix or even a downgrade of some other package. You may also want to use the q command to see what was upgraded since it last worked. That might point to something too. I think it is the q command that does that. Dale :-) :-)
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
Alan McKinnon wrote: On Tuesday 13 October 2009 21:04:54 Denis wrote: 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 At a minum you'll need to remove X cairo firefox gtk motif opengl pdf qt3support qt4 truetype scb There will be others, that's just obvious ones from a quick scan through. Also remove similarly obvious stuff from package.use The as Dale said, manually edit your world file to remove everything that is obviously X related. But first, verify that emerge -avuND world want to merge nothing, otherwise --depclean will complain. Then the fun starts: emerge -a --depclean and let it do whatever it wants. emerge -pvuNDt world and look closely at what X stuff it wants to pull in. See if it's a dependency thing or a USE flag thing, and deal with it. Eventually, emerge -pvuND world will not want to remerge anything, only rebuild stuff due to changed USE flags. --depclean again, rinse and repeat as many times as you have to (probably lots). When you have done all this, and it will take a day or three, you will no doubt realise that it was not worth the effort and you should have just reinstalled without X, or fixed the underlying problem. Excising X is like downgrading to stable from unstable - not worth the effort. Sorry, but them's the breaks :-) When world is edited, should I leave make.conf be or do I also need to remove all X-related USE flags from there? Remove the flags from make.conf and also from package.use And if you run into a snag, try this option with emerge: --with-bdeps y I actually have that in make.conf for mine. As mentioned by Alan, I really doubt this is going to do much if any good. After you did a emerge -e world, that is pretty much it. Let us know what blows up. ;-) Dale :-) :-)
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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 :-) :-)
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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 :-) :-)
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
On 14 Oct 2009, at 17:50, Denis wrote: ... 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 don't think this attempt foolish - but I guess you're getting desperate. Having performed `emerge -e world` I would come to the conclusion that the problem is simply Mathematica, with some current libraries. I would probably want to try a fresh install of Gnetoo - on a different box or hard-drive - to prove the point. But I think I would be concluding shortly that it's an upstream bug. Stroller.
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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 :-) :-)
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
On Tuesday 13 October 2009 21:04:54 Denis wrote: 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 At a minum you'll need to remove X cairo firefox gtk motif opengl pdf qt3support qt4 truetype scb There will be others, that's just obvious ones from a quick scan through. Also remove similarly obvious stuff from package.use The as Dale said, manually edit your world file to remove everything that is obviously X related. But first, verify that emerge -avuND world want to merge nothing, otherwise --depclean will complain. Then the fun starts: emerge -a --depclean and let it do whatever it wants. emerge -pvuNDt world and look closely at what X stuff it wants to pull in. See if it's a dependency thing or a USE flag thing, and deal with it. Eventually, emerge -pvuND world will not want to remerge anything, only rebuild stuff due to changed USE flags. --depclean again, rinse and repeat as many times as you have to (probably lots). When you have done all this, and it will take a day or three, you will no doubt realise that it was not worth the effort and you should have just reinstalled without X, or fixed the underlying problem. Excising X is like downgrading to stable from unstable - not worth the effort. Sorry, but them's the breaks :-) When world is edited, should I leave make.conf be or do I also need to remove all X-related USE flags from there? Remove the flags from make.conf and also from package.use -- alan dot mckinnon at gmail dot com
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
On Mon, 2009-10-12 at 01:18 -0400, Denis wrote: libguide.so I don't have this one, and I don't know what it is. libgmp.so.3 This is probably the gmp (GNU Multiple Precision) arithmetic library. libvml.so I don't have this one, but I'm pretty sure it is part of Intel MKL (see below). libmkl.so libmkl_def.so libmkl_lapack32.so libmkl_lapack64.so libmkl_p3.so libmkl_p4.so libmkl_p4p.so libmkl_vml_def.so libmkl_vml_p3.so libmkl_vml_p4.so libmkl_vml_p4p.so These are part of the Intel Math Kernel Library (MKL). My original Mathematica install had the following Qt libraries, in addition to a Qt plugins directory: libQt3Support.so.4 libQtCore.so.4 libQtGui.so.4 libQtNetwork.so.4 libQtSql.so.4 libQtSvg.so.4 libQtXml.so.4 These are all Qt 4 libraries, which did not exist when Mathematica 5 came out. I do not know what toolkit Wolfram used instead, but I was hoping it would be Qt3, GTK, or some other standard toolkit, as that would have potentially solved your issue. Are the files you listed all of the .so files under your Mathematica installation directory? Also, could you post the output of ldd on your main Mathematica executable? The main executable for me is (installdir)/SystemFiles/FrontEnd/Binaries/Linux-x86-64/Mathematica. This will indicate what libraries Mathematica uses. Another thing to try is playing with Java. Mathematica also ships its own bundled version of Java (again, Mathematica 7, I don't know about version 5). I have never tried to have Mathematica use sun-jdk instead of the bundled version, but it may be worth a go. As far as I know, Mathematica only uses Java for J/Link and not for the user interface (unless using custom interfaces with GUIKit - I've never tried that), so this probably is not the culprit, but you might try it. I have had problems with Java and Xlib/XCB in the past, even when there was no GUI. Another place where you might find more information or issues is Help-About-System Information-Devices (or similar). You might also check to see if you have any updates available: http://www.wolfram.com/products/applications/updates/ If none of the above works, I would suggest reverting the upgraded packages individually to figure out which package or packages causes the issue. From there it would be much easier to figure out what is causing the issue. If you post the output of the ldd command above, I might be able to find the source of the issue, or at least narrow down the search for which package is causing the issue, but other than that there's not much more I can do. Sorry, I don't have a copy of Mathematica 5 to play with to see if I can reproduce this; I still used Maple back then, before I made the switch to Mathematica 6. Is there a particular function that seems to trigger the crash when scrolling or does scrolling crash X every time? Good luck. I hope any of this helps. Regards, Brandon Vargo
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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...
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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 :-) :-)
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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.
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
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
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
But X crashing from my use of Mathematica is absolutely unacceptable - I agree, it shouldn't crash. Are you starting Mathematica by clicking on an icon in a menu? If so, I'd suggest starting it from an xterm command prompt because you may see some helpful error messages before the crash. I tried that, actually. There is no warning in the terminal window. And I have been looking at Xorg error logs also, but there is nothing useful at the end of them! All I have is: (WW) Open ACPI failed (/var/run/acpid.socket) (No such file or directory) (EE) Failed to load module dri (module does not exist, 0) (EE) Failed to load module dri2 (module does not exist, 0) One curious thing... (II) Module nvidia: vendor=NVIDIA Corporation compiled for 4.0.2, module version = 1.0.0 Module class: X.Org Video Driver Why does it say compiled for 4.0.2 when all the other X modules say compiled for 1.6.3.901, which is the xorg-server version? I'm sure that's nothing, but I'm just grabbing at straws here.
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
On Sun, 2009-10-11 at 21:46 -0400, Denis wrote: But X crashing from my use of Mathematica is absolutely unacceptable - I agree, it shouldn't crash. Are you starting Mathematica by clicking on an icon in a menu? If so, I'd suggest starting it from an xterm command prompt because you may see some helpful error messages before the crash. I tried that, actually. There is no warning in the terminal window. And I have been looking at Xorg error logs also, but there is nothing useful at the end of them! All I have is: (WW) Open ACPI failed (/var/run/acpid.socket) (No such file or directory) (EE) Failed to load module dri (module does not exist, 0) (EE) Failed to load module dri2 (module does not exist, 0) One curious thing... (II) Module nvidia: vendor=NVIDIA Corporation compiled for 4.0.2, module version = 1.0.0 Module class: X.Org Video Driver Why does it say compiled for 4.0.2 when all the other X modules say compiled for 1.6.3.901, which is the xorg-server version? I'm sure that's nothing, but I'm just grabbing at straws here. I am a Mathematica 7 user on amd64 (gentoo-sources 2.6.30-r5) with an nvidia graphics card, and I just completed the same X upgrade this evening. So far Mathematica has not given me any issues. For what it's worth, I also receive the same compiled for 4.0.2 messages in my logs for the nvidia module, though I have not recompiled my drivers (180.60) since the upgrade. dri and dri2 are not loaded, as you have above. After glancing through your xorg.conf and X logs, I do not see any glaring issues that would cause the problems you are experiencing. Two suggestions (apologies if they have been suggested already): 1) If you haven't already, recompile your xf86* packages. Somehow I missed those when upgrading X, which caused issues for me. 2) Mathematica (at least version 7) ships its own version of Qt, which it will use instead of the system version of Qt. If Mathematica 5 does something similar -- sorry, I have never used that version on Linux, so I do not know -- then it's possible that the old libraries are causing issues. At least in version 7, removing the Mathematica-supplied Qt libraries will cause Mathematica to use the updated system Qt libraries. For me, the Qt libraries shipped with Mathematica are under (install_directory)/SystemFiles/Libraries/Linux-x86-64/. If Mathematica 5 ships libraries that are also installed system-wide, then I would suggest moving the Mathematica files to another location and seeing if using the system libraries helps with your crashing issue. For me, removing the Mathematica Qt libraries made Mathematica faster and look better. Good luck with your issue. Regards, Brandon Vargo
Re: [gentoo-user] Re: my xorg-server 1.6 seems a bit unstable - what am I doing wrong?
Brandon, Thanks very much for all this information about Mathematica - that gives me a glimmer of hope! 1) If you haven't already, recompile your xf86* packages. Somehow I missed those when upgrading X, which caused issues for me. I did recompile all the xf86 packages that qlist came up with. 2) Mathematica (at least version 7) ships its own version of Qt, which it will use instead of the system version of Qt. If Mathematica 5 does something similar -- sorry, I have never used that version on Linux, so I do not know -- then it's possible that the old libraries are causing issues. At least in version 7, removing the Mathematica-supplied Qt libraries will cause Mathematica to use the updated system Qt libraries. For me, the Qt libraries shipped with Mathematica are under (install_directory)/SystemFiles/Libraries/Linux-x86-64/. If Mathematica 5 ships libraries that are also installed system-wide, then I would suggest moving the Mathematica files to another location and seeing if using the system libraries helps with your crashing issue. For me, removing the Mathematica Qt libraries made Mathematica faster and look better. This is very illuminating. I looked in the /usr/local/Wolfram/Mathematica/5.2/SystemFiles/Libraries/Linux directory, and this is what it contains for me: libguide.so libgmp.so.3 libvml.so libmkl.so libmkl_def.so libmkl_lapack32.so libmkl_lapack64.so libmkl_p3.so libmkl_p4.so libmkl_p4p.so libmkl_vml_def.so libmkl_vml_p3.so libmkl_vml_p4.so libmkl_vml_p4p.so Are these names familiar to anyone? Are these Qt libraries or are there others too?
