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Avo does no longer start #90

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cryos opened this issue Jul 25, 2007 · 13 comments
Closed

Avo does no longer start #90

cryos opened this issue Jul 25, 2007 · 13 comments
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@cryos
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cryos commented Jul 25, 2007

Since the threading-branch was merged into trunk Avogadro no longer starts.

I already reported this by mail:

http://sourceforge.net/mailarchive/forum.php?thread_name=c048b1c20707210441s144e9d3bg9443a3d12e93b852%40mail.gmail.com&forum_name=avogadro-devel

I am using OpenBabel 2.1.1, tested this with both CMake 2.4.6 and 2.4.7, using a patched Qt 4.3.0 (patches from the snapshorts to 4.3.1 as provided by OpenSUSE). All other applications (also those using threads in Qt) work without issues.

Here is what strace tells me:

chdir("/home/kde4/build/avo") = 0
stat64("/usr/lib/qt4/plugins/inputmethods/libqimsw-multi.so", {st_mode=S_IFREG|0755, st_size=27444, ...}) = 0
stat64("/usr/lib/qt4/plugins/inputmethods/libqimsw-multi.so", {st_mode=S_IFREG|0755, st_size=27444, ...}) = 0
stat64("/home/kde4/.config/Trolltech.conf", {st_mode=S_IFREG|0600, st_size=27856, ...}) = 0
open("/home/kde4/.config/Trolltech.conf", O_RDONLY|O_LARGEFILE) = 8
close(8) = 0
stat64("/home/kde4/.config/Trolltech.conf", {st_mode=S_IFREG|0600, st_size=27856, ...}) = 0
stat64("/home/kde4/.config/Trolltech.conf", {st_mode=S_IFREG|0600, st_size=27856, ...}) = 0
stat64("/etc/settings/Trolltech.conf", 0xbffdd350) = -1 ENOENT (No such file or directory)
stat64("/etc/settings/Trolltech.conf", 0x80e3878) = -1 ENOENT (No such file or directory)
stat64("/home/kde4/build/avo/avogadro/src/inputmethods/.", 0x80e3740) = -1 ENOENT (No such file or directory)
lstat64("/home/kde4/build/avo/avogadro/src/inputmethods/.", 0xbffdd730) = -1 ENOENT (No such file or directory)
stat64("/home/kde4/kde/lib/kde4/plugins/inputmethods/.", 0x80e3740) = -1 ENOENT (No such file or directory)
lstat64("/home/kde4/kde/lib/kde4/plugins/inputmethods/.", 0xbffdd730) = -1 ENOENT (No such file or directory)
write(7, "\24\0\6\0D\0\0\0\27\0\0\0\0\0\0\0\0\0\0\0\0 \0\0", 24) = 24
read(7, "\1\10z\0G\20\0\0\37\0\0\0\0\0\0\0\33A\0\0\0\0\0\0\0\0\0"..., 32) = 32
readv(7, [{"*AxeText.Translations:\t#override"..., 16667}, {"\0", 1}], 2) = 16668
writev(7, [{"b\0\6\0\17\0\0\0", 8}, {"XInputExtension", 15}, {"\0", 1}], 3) = 24
read(7, "\1\322{\0\0\0\0\0\1\221_\250\0\20\0\0\0\0\0\0\0\0\0\0\0"..., 32) = 32
futex(0x80cb468, FUTEX_WAIT, 2, NULL

I have no idea how to debug this any further so please guide me.

Reported by: @cniehaus
@cryos
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cryos commented Jul 25, 2007

Logged In: YES
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  1. kde4@moinmoin:~/build/avo/avogadro/src> ldd -v avogadro

  2.     linux-gate.so.1 =>  (0xffffe000)

  3.     libopenbabel.so.2 => /usr//lib/libopenbabel.so.2 (0xb7de5000)

  4.     libQtOpenGL.so.4 => /usr//lib/libQtOpenGL.so.4 (0xb7d80000)

  5.     libQtGui.so.4 => /usr//lib/libQtGui.so.4 (0xb76fb000)

  6.     libpng12.so.0 => /usr//lib/libpng12.so.0 (0xb76d7000)

  7.     libSM.so.6 => /usr//lib/libSM.so.6 (0xb76cd000)

  8.     libICE.so.6 => /usr//lib/libICE.so.6 (0xb76b3000)

  9.     libXi.so.6 => /usr//lib/libXi.so.6 (0xb76aa000)

  10.     libXrender.so.1 => /usr//lib/libXrender.so.1 (0xb76a1000)

  11.     libXrandr.so.2 => /usr//lib/libXrandr.so.2 (0xb769c000)

  12.     libXcursor.so.1 => /usr//lib/libXcursor.so.1 (0xb7692000)

  13.     libXinerama.so.1 => /usr//lib/libXinerama.so.1 (0xb768d000)

  14.     libfreetype.so.6 => /usr//lib/libfreetype.so.6 (0xb7621000)

  15.     libfontconfig.so.1 => /usr//lib/libfontconfig.so.1 (0xb75f6000)

  16.     libXext.so.6 => /usr//lib/libXext.so.6 (0xb75e7000)

  17.     libX11.so.6 => /usr//lib/libX11.so.6 (0xb74ca000)

  18.     libQtCore.so.4 => /usr//lib/libQtCore.so.4 (0xb7375000)

  19.     libz.so.1 => /usr//lib/libz.so.1 (0xb7361000)

  20.     libpthread.so.0 => /lib/libpthread.so.0 (0xb7324000)

  21.     libdl.so.2 => /lib/libdl.so.2 (0xb7320000)

  22.     libavogadro.so.0 => /home/kde4/build/avo/libavogadro/src/libavogadro.so.0 (0xb72c5000)

  23.     libm.so.6 => /lib/libm.so.6 (0xb729f000)

  24.     libGLU.so.1 => /usr//lib/libGLU.so.1 (0xb7227000)

  25.     libGL.so.1 => /usr//lib/libGL.so.1 (0xb71cb000)

  26.     libstdc++.so.6 => /usr//lib/libstdc++.so.6 (0xb70e7000)

  27.     libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb70db000)

  28.     libc.so.6 => /lib/libc.so.6 (0xb6fad000)

  29.     libXfixes.so.3 => /usr//lib/libXfixes.so.3 (0xb6fa7000)

  30.     librt.so.1 => /lib/librt.so.1 (0xb6f9d000)

  31.     libXdmcp.so.6 => /usr//lib/libXdmcp.so.6 (0xb6f97000)

  32.     libXau.so.6 => /usr//lib/libXau.so.6 (0xb6f93000)

  33.     libexpat.so.1 => /usr//lib/libexpat.so.1 (0xb6f72000)

  34.     /lib/ld-linux.so.2 (0xb7f12000)

  35.     libXxf86vm.so.1 => /usr//lib/libXxf86vm.so.1 (0xb6f6b000)

  36.     libdrm.so.2 => /usr//lib/libdrm.so.2 (0xb6f63000)

  38.     Version information:

  39.     ./avogadro:

  40.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  41.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  42.             libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6

  43.             libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6

  44.     /usr//lib/libopenbabel.so.2:

  45.             libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1

  46.             libdl.so.2 (GLIBC_2.1) => /lib/libdl.so.2

  47.             libm.so.6 (GLIBC_2.0) => /lib/libm.so.6

  48.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  49.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  50.             libstdc++.so.6 (GLIBCXX_3.4.6) => /usr//lib/libstdc++.so.6

  51.             libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6

  52.             libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6

  53.     /usr//lib/libQtOpenGL.so.4:

  54.             libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1

  55.             libm.so.6 (GLIBC_2.0) => /lib/libm.so.6

  56.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  57.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  58.             libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6

  59.             libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6

  60.     /usr//lib/libQtGui.so.4:

  61.             libgcc_s.so.1 (GLIBC_2.0) => /lib/libgcc_s.so.1

  62.             libm.so.6 (GLIBC_2.0) => /lib/libm.so.6

  63.             libpng12.so.0 (PNG12_0) => /usr//lib/libpng12.so.0

  64.             libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6

  65.             libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6

  66.             libpthread.so.0 (GLIBC_2.0) => /lib/libpthread.so.0

  67.             libc.so.6 (GLIBC_2.1.2) => /lib/libc.so.6

  68.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  69.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  70.     /usr//lib/libpng12.so.0:

  71.             libm.so.6 (GLIBC_2.0) => /lib/libm.so.6

  72.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  73.             libc.so.6 (GLIBC_2.4) => /lib/libc.so.6

  74.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  75.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  76.     /usr//lib/libSM.so.6:

  77.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  78.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  79.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  80.     /usr//lib/libICE.so.6:

  81.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  82.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  83.             libc.so.6 (GLIBC_2.3) => /lib/libc.so.6

  84.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  85.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  86.     /usr//lib/libXi.so.6:

  87.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  88.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  89.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  90.     /usr//lib/libXrender.so.1:

  91.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  92.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  93.     /usr//lib/libXrandr.so.2:

  94.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  95.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  96.     /usr//lib/libXcursor.so.1:

  97.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  98.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  99.             libc.so.6 (GLIBC_2.3) => /lib/libc.so.6

  100.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  101.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  102.     /usr//lib/libXinerama.so.1:

  103.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  104.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  105.     /usr//lib/libfreetype.so.6:

  106.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  107.             libc.so.6 (GLIBC_2.3) => /lib/libc.so.6

  108.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  109.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  110.     /usr//lib/libfontconfig.so.1:

  111.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  112.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  113.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  114.             libc.so.6 (GLIBC_2.2) => /lib/libc.so.6

  115.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  116.     /usr//lib/libXext.so.6:

  117.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  118.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  119.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  120.     /usr//lib/libX11.so.6:

  121.             libdl.so.2 (GLIBC_2.1) => /lib/libdl.so.2

  122.             libdl.so.2 (GLIBC_2.0) => /lib/libdl.so.2

  123.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  124.             libc.so.6 (GLIBC_2.1.2) => /lib/libc.so.6

  125.             libc.so.6 (GLIBC_2.2) => /lib/libc.so.6

  126.             libc.so.6 (GLIBC_2.3) => /lib/libc.so.6

  127.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  128.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  129.             libc.so.6 (GLIBC_2.3.2) => /lib/libc.so.6

  130.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  131.     /usr//lib/libQtCore.so.4:

  132.             librt.so.1 (GLIBC_2.2) => /lib/librt.so.1

  133.             libm.so.6 (GLIBC_2.2) => /lib/libm.so.6

  134.             libm.so.6 (GLIBC_2.1) => /lib/libm.so.6

  135.             libm.so.6 (GLIBC_2.0) => /lib/libm.so.6

  136.             libdl.so.2 (GLIBC_2.1) => /lib/libdl.so.2

  137.             libdl.so.2 (GLIBC_2.0) => /lib/libdl.so.2

  138.             libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6

  139.             libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6

  140.             libgcc_s.so.1 (GLIBC_2.0) => /lib/libgcc_s.so.1

  141.             libpthread.so.0 (GLIBC_2.1) => /lib/libpthread.so.0

  142.             libpthread.so.0 (GLIBC_2.2) => /lib/libpthread.so.0

  143.             libpthread.so.0 (GLIBC_2.3.3) => /lib/libpthread.so.0

  144.             libpthread.so.0 (GLIBC_2.3.2) => /lib/libpthread.so.0

  145.             libpthread.so.0 (GLIBC_2.0) => /lib/libpthread.so.0

  146.             libc.so.6 (GLIBC_2.4) => /lib/libc.so.6

  147.             libc.so.6 (GLIBC_2.1.2) => /lib/libc.so.6

  148.             libc.so.6 (GLIBC_2.3) => /lib/libc.so.6

  149.             libc.so.6 (GLIBC_2.2) => /lib/libc.so.6

  150.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  151.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  152.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  153.     /usr//lib/libz.so.1:

  154.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  155.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  156.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  157.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  158.     /lib/libpthread.so.0:

  159.             ld-linux.so.2 (GLIBC_2.3) => /lib/ld-linux.so.2

  160.             ld-linux.so.2 (GLIBC_2.1) => /lib/ld-linux.so.2

  161.             ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2

  162.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  163.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  164.             libc.so.6 (GLIBC_2.3.2) => /lib/libc.so.6

  165.             libc.so.6 (GLIBC_2.2) => /lib/libc.so.6

  166.             libc.so.6 (GLIBC_PRIVATE) => /lib/libc.so.6

  167.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  168.     /lib/libdl.so.2:

  169.             ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2

  170.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  171.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  172.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  173.             libc.so.6 (GLIBC_PRIVATE) => /lib/libc.so.6

  174.     /home/kde4/build/avo/libavogadro/src/libavogadro.so.0:

  175.             libm.so.6 (GLIBC_2.0) => /lib/libm.so.6

  176.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  177.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  178.             libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6

  179.             libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6

  180.     /lib/libm.so.6:

  181.             ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2

  182.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  183.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  184.     /usr//lib/libGLU.so.1:

  185.             libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1

  186.             libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6

  187.             libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6

  188.             libm.so.6 (GLIBC_2.0) => /lib/libm.so.6

  189.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  190.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  191.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  192.     /usr//lib/libGL.so.1:

  193.             libdl.so.2 (GLIBC_2.1) => /lib/libdl.so.2

  194.             libdl.so.2 (GLIBC_2.0) => /lib/libdl.so.2

  195.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  196.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  197.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  198.             libpthread.so.0 (GLIBC_2.0) => /lib/libpthread.so.0

  199.     /usr//lib/libstdc++.so.6:

  200.             ld-linux.so.2 (GLIBC_2.3) => /lib/ld-linux.so.2

  201.             libgcc_s.so.1 (GCC_4.2.0) => /lib/libgcc_s.so.1

  202.             libgcc_s.so.1 (GLIBC_2.0) => /lib/libgcc_s.so.1

  203.             libgcc_s.so.1 (GCC_3.3) => /lib/libgcc_s.so.1

  204.             libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1

  205.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  206.             libc.so.6 (GLIBC_2.3) => /lib/libc.so.6

  207.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  208.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  209.             libc.so.6 (GLIBC_2.2) => /lib/libc.so.6

  210.     /lib/libgcc_s.so.1:

  211.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  212.             libc.so.6 (GLIBC_2.2.4) => /lib/libc.so.6

  213.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  214.     /lib/libc.so.6:

  215.             ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2

  216.             ld-linux.so.2 (GLIBC_2.3) => /lib/ld-linux.so.2

  217.             ld-linux.so.2 (GLIBC_2.1) => /lib/ld-linux.so.2

  218.     /usr//lib/libXfixes.so.3:

  219.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  220.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  221.     /lib/librt.so.1:

  222.             ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2

  223.             libpthread.so.0 (GLIBC_2.1) => /lib/libpthread.so.0

  224.             libpthread.so.0 (GLIBC_2.2) => /lib/libpthread.so.0

  225.             libpthread.so.0 (GLIBC_PRIVATE) => /lib/libpthread.so.0

  226.             libpthread.so.0 (GLIBC_2.0) => /lib/libpthread.so.0

  227.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  228.             libc.so.6 (GLIBC_2.3.2) => /lib/libc.so.6

  229.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  230.             libc.so.6 (GLIBC_2.2) => /lib/libc.so.6

  231.             libc.so.6 (GLIBC_PRIVATE) => /lib/libc.so.6

  232.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  233.     /usr//lib/libXdmcp.so.6:

  234.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  235.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  236.     /usr//lib/libXau.so.6:

  237.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  238.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  239.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  240.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  241.     /usr//lib/libexpat.so.1:

  242.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  243.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  244.     /usr//lib/libXxf86vm.so.1:

  245.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  246.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

  247.     /usr//lib/libdrm.so.2:

  248.             libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6

  249.             libc.so.6 (GLIBC_2.1) => /lib/libc.so.6

  250.             libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6

  251.             libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

Original comment by: @milkypostman

@cryos
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cryos commented Jul 25, 2007

Logged In: YES
user_id=684210
Originator: YES

kde4@moinmoin:~/build/avo/avogadro/src> ldd -v avogadro
linux-gate.so.1 => (0xffffe000)
libopenbabel.so.2 => /usr//lib/libopenbabel.so.2 (0xb7de5000)
libQtOpenGL.so.4 => /usr//lib/libQtOpenGL.so.4 (0xb7d80000)
libQtGui.so.4 => /usr//lib/libQtGui.so.4 (0xb76fb000)
libpng12.so.0 => /usr//lib/libpng12.so.0 (0xb76d7000)
libSM.so.6 => /usr//lib/libSM.so.6 (0xb76cd000)
libICE.so.6 => /usr//lib/libICE.so.6 (0xb76b3000)
libXi.so.6 => /usr//lib/libXi.so.6 (0xb76aa000)
libXrender.so.1 => /usr//lib/libXrender.so.1 (0xb76a1000)
libXrandr.so.2 => /usr//lib/libXrandr.so.2 (0xb769c000)
libXcursor.so.1 => /usr//lib/libXcursor.so.1 (0xb7692000)
libXinerama.so.1 => /usr//lib/libXinerama.so.1 (0xb768d000)
libfreetype.so.6 => /usr//lib/libfreetype.so.6 (0xb7621000)
libfontconfig.so.1 => /usr//lib/libfontconfig.so.1 (0xb75f6000)
libXext.so.6 => /usr//lib/libXext.so.6 (0xb75e7000)
libX11.so.6 => /usr//lib/libX11.so.6 (0xb74ca000)
libQtCore.so.4 => /usr//lib/libQtCore.so.4 (0xb7375000)
libz.so.1 => /usr//lib/libz.so.1 (0xb7361000)
libpthread.so.0 => /lib/libpthread.so.0 (0xb7324000)
libdl.so.2 => /lib/libdl.so.2 (0xb7320000)
libavogadro.so.0 => /home/kde4/build/avo/libavogadro/src/libavogadro.so.0 (0xb72c5000)
libm.so.6 => /lib/libm.so.6 (0xb729f000)
libGLU.so.1 => /usr//lib/libGLU.so.1 (0xb7227000)
libGL.so.1 => /usr//lib/libGL.so.1 (0xb71cb000)
libstdc++.so.6 => /usr//lib/libstdc++.so.6 (0xb70e7000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb70db000)
libc.so.6 => /lib/libc.so.6 (0xb6fad000)
libXfixes.so.3 => /usr//lib/libXfixes.so.3 (0xb6fa7000)
librt.so.1 => /lib/librt.so.1 (0xb6f9d000)
libXdmcp.so.6 => /usr//lib/libXdmcp.so.6 (0xb6f97000)
libXau.so.6 => /usr//lib/libXau.so.6 (0xb6f93000)
libexpat.so.1 => /usr//lib/libexpat.so.1 (0xb6f72000)
/lib/ld-linux.so.2 (0xb7f12000)
libXxf86vm.so.1 => /usr//lib/libXxf86vm.so.1 (0xb6f6b000)
libdrm.so.2 => /usr//lib/libdrm.so.2 (0xb6f63000)

    Version information:
    ./avogadro:
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6
            libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6
    /usr//lib/libopenbabel.so.2:
            libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
            libdl.so.2 (GLIBC_2.1) => /lib/libdl.so.2
            libm.so.6 (GLIBC_2.0) => /lib/libm.so.6
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
            libstdc++.so.6 (GLIBCXX_3.4.6) => /usr//lib/libstdc++.so.6
            libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6
            libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6
    /usr//lib/libQtOpenGL.so.4:
            libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
            libm.so.6 (GLIBC_2.0) => /lib/libm.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6
            libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6
    /usr//lib/libQtGui.so.4:
            libgcc_s.so.1 (GLIBC_2.0) => /lib/libgcc_s.so.1
            libm.so.6 (GLIBC_2.0) => /lib/libm.so.6
            libpng12.so.0 (PNG12_0) => /usr//lib/libpng12.so.0
            libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6
            libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6
            libpthread.so.0 (GLIBC_2.0) => /lib/libpthread.so.0
            libc.so.6 (GLIBC_2.1.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libpng12.so.0:
            libm.so.6 (GLIBC_2.0) => /lib/libm.so.6
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libSM.so.6:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libICE.so.6:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libXi.so.6:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
    /usr//lib/libXrender.so.1:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libXrandr.so.2:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libXcursor.so.1:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libXinerama.so.1:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libfreetype.so.6:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libfontconfig.so.1:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libXext.so.6:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
    /usr//lib/libX11.so.6:
            libdl.so.2 (GLIBC_2.1) => /lib/libdl.so.2
            libdl.so.2 (GLIBC_2.0) => /lib/libdl.so.2
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libQtCore.so.4:
            librt.so.1 (GLIBC_2.2) => /lib/librt.so.1
            libm.so.6 (GLIBC_2.2) => /lib/libm.so.6
            libm.so.6 (GLIBC_2.1) => /lib/libm.so.6
            libm.so.6 (GLIBC_2.0) => /lib/libm.so.6
            libdl.so.2 (GLIBC_2.1) => /lib/libdl.so.2
            libdl.so.2 (GLIBC_2.0) => /lib/libdl.so.2
            libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6
            libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6
            libgcc_s.so.1 (GLIBC_2.0) => /lib/libgcc_s.so.1
            libpthread.so.0 (GLIBC_2.1) => /lib/libpthread.so.0
            libpthread.so.0 (GLIBC_2.2) => /lib/libpthread.so.0
            libpthread.so.0 (GLIBC_2.3.3) => /lib/libpthread.so.0
            libpthread.so.0 (GLIBC_2.3.2) => /lib/libpthread.so.0
            libpthread.so.0 (GLIBC_2.0) => /lib/libpthread.so.0
            libc.so.6 (GLIBC_2.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libz.so.1:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /lib/libpthread.so.0:
            ld-linux.so.2 (GLIBC_2.3) => /lib/ld-linux.so.2
            ld-linux.so.2 (GLIBC_2.1) => /lib/ld-linux.so.2
            ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_PRIVATE) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /lib/libdl.so.2:
            ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
            libc.so.6 (GLIBC_PRIVATE) => /lib/libc.so.6
    /home/kde4/build/avo/libavogadro/src/libavogadro.so.0:
            libm.so.6 (GLIBC_2.0) => /lib/libm.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6
            libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6
    /lib/libm.so.6:
            ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libGLU.so.1:
            libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
            libstdc++.so.6 (CXXABI_1.3) => /usr//lib/libstdc++.so.6
            libstdc++.so.6 (GLIBCXX_3.4) => /usr//lib/libstdc++.so.6
            libm.so.6 (GLIBC_2.0) => /lib/libm.so.6
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libGL.so.1:
            libdl.so.2 (GLIBC_2.1) => /lib/libdl.so.2
            libdl.so.2 (GLIBC_2.0) => /lib/libdl.so.2
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
            libpthread.so.0 (GLIBC_2.0) => /lib/libpthread.so.0
    /usr//lib/libstdc++.so.6:
            ld-linux.so.2 (GLIBC_2.3) => /lib/ld-linux.so.2
            libgcc_s.so.1 (GCC_4.2.0) => /lib/libgcc_s.so.1
            libgcc_s.so.1 (GLIBC_2.0) => /lib/libgcc_s.so.1
            libgcc_s.so.1 (GCC_3.3) => /lib/libgcc_s.so.1
            libgcc_s.so.1 (GCC_3.0) => /lib/libgcc_s.so.1
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.2) => /lib/libc.so.6
    /lib/libgcc_s.so.1:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.2.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /lib/libc.so.6:
            ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2
            ld-linux.so.2 (GLIBC_2.3) => /lib/ld-linux.so.2
            ld-linux.so.2 (GLIBC_2.1) => /lib/ld-linux.so.2
    /usr//lib/libXfixes.so.3:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /lib/librt.so.1:
            ld-linux.so.2 (GLIBC_PRIVATE) => /lib/ld-linux.so.2
            libpthread.so.0 (GLIBC_2.1) => /lib/libpthread.so.0
            libpthread.so.0 (GLIBC_2.2) => /lib/libpthread.so.0
            libpthread.so.0 (GLIBC_PRIVATE) => /lib/libpthread.so.0
            libpthread.so.0 (GLIBC_2.0) => /lib/libpthread.so.0
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.2) => /lib/libc.so.6
            libc.so.6 (GLIBC_PRIVATE) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libXdmcp.so.6:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libXau.so.6:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libexpat.so.1:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libXxf86vm.so.1:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6
    /usr//lib/libdrm.so.2:
            libc.so.6 (GLIBC_2.1.3) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.1) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.3.4) => /lib/libc.so.6
            libc.so.6 (GLIBC_2.0) => /lib/libc.so.6

Original comment by: @cniehaus

@cryos
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Owner Author

cryos commented Jul 25, 2007

Logged In: YES
user_id=684210
Originator: YES

Ok, I have no idea if this helps or not, but it also crashes (or whatever it does) in Valgrind 3.2.3.

kde4@moinmoin:~/build/avo> valgrind -v avogadro/src/avogadro
==10501== Memcheck, a memory error detector.
==10501== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.
==10501== Using LibVEX rev 1732, a library for dynamic binary translation.
==10501== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
==10501== Using valgrind-3.2.3, a dynamic binary instrumentation framework.
==10501== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.
==10501==
--10501-- Command line
--10501-- avogadro/src/avogadro
--10501-- Startup, with flags:
--10501-- -v
--10501-- Contents of /proc/version:
--10501-- Linux version 2.6.18.8-0.5-default (geeko@buildhost) (gcc version 4.1.2 20061115 (prerelease) (SUSE Linux)) #1 SMP Fri Jun 22 12:17:53 UTC 2007
--10501-- Arch and hwcaps: X86, x86-sse1
--10501-- Page sizes: currently 4096, max supported 4096
--10501-- Valgrind library directory: /usr/lib/valgrind
--10501-- Reading syms from /lib/ld-2.5.so (0x4000000)
--10501-- Reading syms from /home/kde4/build/avo/avogadro/src/avogadro (0x8048000)
--10501-- Reading syms from /usr/lib/valgrind/x86-linux/memcheck (0x38000000)
--10501-- object doesn't have a symbol table
--10501-- object doesn't have a dynamic symbol table
--10501-- Reading suppressions file: /usr/lib/valgrind/default.supp
--10501-- REDIR: 0x4015970 (index) redirected to 0x38027EDB (???)
--10501-- Reading syms from /usr/lib/valgrind/x86-linux/vgpreload_core.so (0x401E000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/valgrind/x86-linux/vgpreload_memcheck.so (0x4021000)
--10501-- object doesn't have a symbol table
==10501== WARNING: new redirection conflicts with existing -- ignoring it
--10501-- new: 0x04015970 (index ) R-> 0x040242C0 index
--10501-- REDIR: 0x4015B10 (strlen) redirected to 0x4024370 (strlen)
--10501-- Reading syms from /usr/lib/libopenbabel.so.2.1.1 (0x4028000)
--10501-- Reading debug info from /usr/lib/debug/usr/lib/libopenbabel.so.2.1.1.debug...
--10501-- Reading syms from /usr/lib/libQtOpenGL.so.4.3.0 (0x4153000)
--10501-- Reading syms from /usr/lib/libQtGui.so.4.3.0 (0x41B8000)
--10501-- Reading syms from /usr/lib/libpng12.so.0.12.0 (0x483D000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libSM.so.6.0.0 (0x4862000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libICE.so.6.3.0 (0x486C000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libXi.so.6.0.0 (0x4885000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libXrender.so.1.3.0 (0x488E000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libXrandr.so.2.0.0 (0x4897000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libXcursor.so.1.0.2 (0x489D000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libXinerama.so.1.0.0 (0x48A7000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libfreetype.so.6.3.10 (0x48AB000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libfontconfig.so.1.1.0 (0x4917000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libXext.so.6.4.0 (0x4942000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libX11.so.6.2.0 (0x4951000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libQtCore.so.4.3.0 (0x4A6F000)
--10501-- Reading syms from /lib/libz.so.1.2.3 (0x4BC4000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /lib/libpthread-2.5.so (0x4BFC000)
--10501-- Reading syms from /lib/libdl-2.5.so (0x4C14000)
--10501-- Reading syms from /home/kde4/build/avo/libavogadro/src/libavogadro.so.0.0.1 (0x4C18000)
--10501-- Reading syms from /lib/libm-2.5.so (0x4C74000)
--10501-- Reading syms from /usr/lib/libGLU.so.1.3.060501 (0x4C9A000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libGL.so.1.2 (0x4D12000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libstdc++.so.6.0.8 (0x4D6D000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /lib/libgcc_s.so.1 (0x4E51000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /lib/libc-2.5.so (0x4E5D000)
--10501-- Reading syms from /usr/lib/libXfixes.so.3.1.0 (0x4F8C000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /lib/librt-2.5.so (0x4F92000)
--10501-- Reading syms from /usr/lib/libXdmcp.so.6.0.0 (0x4F9B000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libXau.so.6.0.0 (0x4FA1000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libexpat.so.1.5.0 (0x4FA6000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libXxf86vm.so.1.0.0 (0x4FC7000)
--10501-- object doesn't have a symbol table
--10501-- Reading syms from /usr/lib/libdrm.so.2.0.0 (0x4FCD000)
--10501-- object doesn't have a symbol table
--10501-- REDIR: 0x4EC8FB0 (memset) redirected to 0x40246D0 (memset)
--10501-- REDIR: 0x4EC94B0 (memcpy) redirected to 0x40252E0 (memcpy)
--10501-- REDIR: 0x4EC8130 (rindex) redirected to 0x40241A0 (rindex)
--10501-- REDIR: 0x4EC7D80 (strlen) redirected to 0x4024350 (strlen)
--10501-- REDIR: 0x4E1D450 (operator new(unsigned)) redirected to 0x4023CD0 (operator new(unsigned))
--10501-- REDIR: 0x4EC5040 (malloc) redirected to 0x4023530 (malloc)
--10501-- REDIR: 0x4EC5470 (realloc) redirected to 0x40235DF (realloc)
--10501-- REDIR: 0x4EC8F40 (memmove) redirected to 0x4024700 (memmove)
--10501-- REDIR: 0x4E1D590 (operator new) redirected to 0x4023960 (operator new)
--10501-- REDIR: 0x4EC2CF0 (free) redirected to 0x402314A (free)
--10501-- REDIR: 0x4E1BF60 (operator delete(void_)) redirected to 0x4022E61 (operator delete(void_))
--10501-- REDIR: 0x4EC8AB0 (memchr) redirected to 0x4024540 (memchr)
--10501-- REDIR: 0x4E1BFC0 (operator delete) redirected to 0x4022AE3 (operator delete)
--10501-- REDIR: 0x4EC4B20 (calloc) redirected to 0x402285D (calloc)
--10501-- REDIR: 0x4EC8080 (strncpy) redirected to 0x4024B50 (strncpy)
--10501-- REDIR: 0x4EC7800 (strcmp) redirected to 0x4024420 (strcmp)
--10501-- REDIR: 0x4EC7F80 (strncmp) redirected to 0x40243B0 (strncmp)
--10501-- REDIR: 0x4EC7690 (index) redirected to 0x4024290 (index)
--10501-- REDIR: 0x4EC9E30 (strchrnul) redirected to 0x4024770 (strchrnul)
--10501-- REDIR: 0x4EC9010 (mempcpy) redirected to 0x4024DB0 (mempcpy)
--10501-- REDIR: 0x4EC7E30 (strnlen) redirected to 0x4024320 (strnlen)
--10501-- REDIR: 0x4EC91B0 (stpcpy) redirected to 0x4024A70 (stpcpy)
--10501-- REDIR: 0x4EC7870 (strcpy) redirected to 0x4025540 (strcpy)
--10501-- REDIR: 0x4EC9D60 (rawmemchr) redirected to 0x40247A0 (rawmemchr)
--10501-- Reading syms from /usr/lib/gconv/UTF-16.so (0x4BE8000)
--10501-- REDIR: 0x4EC74E0 (strcat) redirected to 0x4025620 (strcat)
--10501-- REDIR: 0x4F2DA10 (__strcpy_chk) redirected to 0x4024A10 (__strcpy_chk)
--10501-- memcheck GC: 1024 nodes, 1024 survivors (100.0%)
--10501-- memcheck GC: increase table size to 2048
--10501-- memcheck GC: 2048 nodes, 2048 survivors (100.0%)
--10501-- memcheck GC: increase table size to 4096

==10501==
==10501== Process terminating with default action of signal 2 (SIGINT)
==10501== at 0x4C07C4E: lll_mutex_lock_wait (in /lib/libpthread-2.5.so)
==10501== by 0x497A429: (within /usr/lib/libX11.so.6.2.0)
==10501== by 0x49821F5: XQueryExtension (in /usr/lib/libX11.so.6.2.0)
==10501== by 0x4976B0A: XInitExtension (in /usr/lib/libX11.so.6.2.0)
==10501== by 0x494E0F2: XextAddDisplay (in /usr/lib/libXext.so.6.4.0)
==10501== by 0x488A6FD: XInput_find_display (in /usr/lib/libXi.so.6.0.0)
==10501== by 0x4888524: XiGetExtensionVersion (in /usr/lib/libXi.so.6.0.0)
==10501== by 0x488867A: XGetExtensionVersion (in /usr/lib/libXi.so.6.0.0)
==10501== by 0x431B131: qt_init(QApplicationPrivate, int, XDisplay, unsigned long, unsigned long) (in /usr/lib/libQtGui.so.4.3.0)
==10501== by 0x42C7158: QApplicationPrivate::construct(XDisplay, unsigned long, unsigned long) (in /usr/lib/libQtGui.so.4.3.0)
==10501== by 0x42C7D42: QApplication::QApplication(int&, char, int) (in /usr/lib/libQtGui.so.4.3.0)
==10501== by 0x8065970: Avogadro::Application::Application(int&, char_*) (in /home/kde4/build/avo/avogadro/src/avogadro)
--10501-- Discarding syms at 0x4BE8000-0x4BEC000 in /usr/lib/gconv/UTF-16.so due to munmap()
==10501==
==10501== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 3 from 1)
--10501--
--10501-- supp: 3 dl-hack3
==10501== malloc/free: in use at exit: 364,963 bytes in 7,793 blocks.
==10501== malloc/free: 19,569 allocs, 11,776 frees, 4,890,382 bytes allocated.
==10501==
==10501== searching for pointers to 7,793 not-freed blocks.
==10501== checked 840,360 bytes.
==10501==
==10501== LEAK SUMMARY:
==10501== definitely lost: 1,853 bytes in 32 blocks.
==10501== possibly lost: 22,863 bytes in 1,243 blocks.
==10501== still reachable: 340,247 bytes in 6,518 blocks.
==10501== suppressed: 0 bytes in 0 blocks.
==10501== Rerun with --leak-check=full to see details of leaked memory.
--10501-- memcheck: sanity checks: 100 cheap, 5 expensive
--10501-- memcheck: auxmaps: 0 auxmap entries (0k, 0M) in use
--10501-- memcheck: auxmaps: 0 searches, 0 comparisons
--10501-- memcheck: SMs: n_issued = 140 (2240k, 2M)
--10501-- memcheck: SMs: n_deissued = 0 (0k, 0M)
--10501-- memcheck: SMs: max_noaccess = 65535 (1048560k, 1023M)
--10501-- memcheck: SMs: max_undefined = 0 (0k, 0M)
--10501-- memcheck: SMs: max_defined = 246 (3936k, 3M)
--10501-- memcheck: SMs: max_non_DSM = 140 (2240k, 2M)
--10501-- memcheck: max sec V bit nodes: 2672 (135k, 0M)
--10501-- memcheck: set_sec_vbits8 calls: 8482 (new: 2672, updates: 5810)
--10501-- memcheck: max shadow mem size: 2679k, 2M
--10501-- translate: fast SP updates identified: 24,975 ( 88.9%)
--10501-- translate: generic_known SP updates identified: 1,909 ( 6.8%)
--10501-- translate: generic_unknown SP updates identified: 1,180 ( 4.2%)
--10501-- tt/tc: 51,009 tt lookups requiring 62,380 probes
--10501-- tt/tc: 51,009 fast-cache updates, 4 flushes
--10501-- transtab: new 19,729 (437,473 -> 7,028,039; ratio 160:10) [0 scs]
--10501-- transtab: dumped 0 (0 -> ??)
--10501-- transtab: discarded 89 (1,741 -> ??)
--10501-- scheduler: 10,075,943 jumps (bb entries).
--10501-- scheduler: 100/63,329 major/minor sched events.
--10501-- sanity: 101 cheap, 5 expensive checks.
--10501-- exectx: 30,011 lists, 4,251 contexts (avg 0 per list)
--10501-- exectx: 31,217 searches, 27,354 full compares (876 per 1000)
--10501-- exectx: 0 cmp2, 3 cmp4, 0 cmpAll

Original comment by: @cniehaus

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cryos commented Jul 25, 2007

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As you can see in my previous post these are the important information we need to debug this:

==10501== at 0x4C07C4E: __lll_mutex_lock_wait (in /lib/libpthread-2.5.so)
==10501== by 0x497A429: (within /usr/lib/libX11.so.6.2.0)

Please note that I don't know what this means, but at least we know where it happens...

Original comment by: @cniehaus

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cryos commented Jul 30, 2007

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I tried to debug this further. In latest trunk I changed one line in avogadro/src/main.cpp:

qDebug() << "0"; Application app(argc, argv); qDebug() << "1";

On the CLI I see the 0 but not the 1. So this is somehow in the "Application app(argc, argv);"

I just also tried the current branch of the bondcentric tool. It starts just fine.

Original comment by: @cniehaus

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cryos commented Aug 9, 2007

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As Qt 4.3.1 is out now I removed all of KDE4 and Qt4 from my system, removed almost all of my development-user, removed the $BUILDDIR, installed Qt 4.3.1 and started from scratch. The issue remains.

Original comment by: @cniehaus

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cryos commented Aug 15, 2007

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With that diff it "work". Works means: it starts and I can see a rendered molecule before Avo crashes. Marcus says the crash makes sense. I am now investigating further.

carsten@moinmoin:~/svn/avogadro/trunk> svn diff

Index: avogadro/src/main.cpp

--- avogadro/src/main.cpp (Revision 631)
+++ avogadro/src/main.cpp (Arbeitskopie)
@@ -46,7 +46,7 @@
QCoreApplication::setApplicationName("Avogadro");

#ifdef Q_WS_X11

  • XInitThreads();
    +//X XInitThreads();
    #endif

    Application app(argc, argv);

Original comment by: @cniehaus

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cryos commented Aug 20, 2007

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I have found some similar problems as of late (deadlock) and I am almost positive it's an Xlibs issue. Which makes me think that the problem we are having here is related to XLibs and the threading support. As far as i know we need this XLib threading support for the GL stuff, but I could be wrong and i'll have to check up on it more later (ie look back at the QT documenatation).

Original comment by: @milkypostman

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cryos commented Aug 20, 2007

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The problem I have been having is related to XCB (http://xcb.freedesktop.org/) which is a new X protocol C language binding (...) so anyways, in Gentoo you can get libX11 that uses XCB or one that doesn't. The one that uses XCB causes me all kinds of problems with the pthread mutex deadlock. So my question to Carsten is if he knows if OpenSuSE is using the XCB version of libX11?

Original comment by: @milkypostman

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cryos commented Aug 30, 2007

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Moin

I just managed to crash Gwenview on the same machine. The backtrace looks very similar, so I guess this is definetly outside Avogadros scope? Note the pthread_mutex_lock ()

#9 0xb72403f0 in pthread_mutex_lock () from /lib/libpthread.so.0
#10 0xb714447f in XInitThreads () from /usr/lib/libX11.so.6
#11 0xb715f03e in XrmQGetResource () from /usr/lib/libX11.so.6
#12 0xb715215a in XStringToKeysym () from /usr/lib/libX11.so.6
#13 0xb7a793f7 in KKeyServer::Sym::init () from /opt/kde3/lib/libkdecore.so.4
#14 0xb7ab64b6 in KKey::init () from /opt/kde3/lib/libkdecore.so.4
#15 0xb7ab67d4 in KKey::KKey () from /opt/kde3/lib/libkdecore.so.4
#16 0xb7ab68e6 in KKeySequence::init () from /opt/kde3/lib/libkdecore.so.4
#17 0xb7ab6a23 in KShortcut::init () from /opt/kde3/lib/libkdecore.so.4
#18 0xb7ab6fc6 in KShortcut::KShortcut () from /opt/kde3/lib/libkdecore.so.4
#19 0xb4c4a601 in KSVGPlugin::KSVGPlugin ()
from /opt/kde3/lib/kde3/libksvgplugin.so
#20 0xb4c4ba70 in KSVGPluginFactory::createPartObject ()
from /opt/kde3/lib/kde3/libksvgplugin.so

Original comment by: @cniehaus

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cryos commented Sep 16, 2007

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Still working with XCB guys and other stuff to track down this error. In the meantime I have disabled the threaded OpenGL widget but you can enable it with a compile-time flag. To enable do 'cmake -DENABLE_THREADED_GL ..'

posted fix in svn head revision 650

Original comment by: @milkypostman

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cryos commented Sep 17, 2007

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As I already stated on the mailinglist: Donalds commit (I think a later one, 651) fixed it for me. The interesting thing is that I don't even use XCB!

ldd /usr/lib/libX11.so
linux-gate.so.1 => (0xffffe000)
libXau.so.6 => /usr/lib/libXau.so.6 (0xb7e36000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb7e30000)
libdl.so.2 => /lib/libdl.so.2 (0xb7e2c000)
libc.so.6 => /lib/libc.so.6 (0xb7cfe000)
/lib/ld-linux.so.2 (0x80000000)

Original comment by: @cniehaus

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cryos commented Sep 24, 2007

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As Carsten said below, this is now fixed. Marking the bug closed.

Original comment by: @ghutchis

@cryos cryos closed this as completed Apr 27, 2016
psavery pushed a commit to psavery/avogadro that referenced this issue Feb 20, 2017
@cryos
Merge pull request cryos#90 from psavery/crystal-undo-added
29c7184 
Added undo features for all crystal operations
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