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    (No real need to involve the list, we'll figure this out and report
    back)<br>
    <div class="moz-forward-container"><br>
      <br>
      -------- Original Message --------
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            <th nowrap="nowrap" valign="BASELINE" align="RIGHT">Subject:
            </th>
            <td>Re: [Chimera-users] Chimera on a virtualbox</td>
          </tr>
          <tr>
            <th nowrap="nowrap" valign="BASELINE" align="RIGHT">Date: </th>
            <td>Tue, 05 Feb 2013 17:22:51 -0800</td>
          </tr>
          <tr>
            <th nowrap="nowrap" valign="BASELINE" align="RIGHT">From: </th>
            <td>Greg Couch <a class="moz-txt-link-rfc2396E" href="mailto:gregc@cgl.ucsf.edu">&lt;gregc@cgl.ucsf.edu&gt;</a></td>
          </tr>
          <tr>
            <th nowrap="nowrap" valign="BASELINE" align="RIGHT">To: </th>
            <td><a class="moz-txt-link-abbreviated" href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a></td>
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      <div class="moz-cite-prefix">It appears as if you missed the:<br>
        <br>
        &nbsp;&nbsp;&nbsp; export LD_LIBRARY_PATH=$CHIMERA/lib<br>
        <br>
        before running gdb because the import of libgfxinfo.so failed.&nbsp;
        And there should be a space between "break" and "_exit" in the
        gdb command.<br>
        <br>
        &nbsp;&nbsp;&nbsp; -- Greg<br>
        <br>
        On 02/05/2013 04:38 PM, <a moz-do-not-send="true"
          class="moz-txt-link-abbreviated"
          href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a>
        wrote:<br>
      </div>
      <blockquote
cite="mid:7BF0C7F486F2F04EACD95EF31F284100161144AF@EXCHMBX01.fed.cclrc.ac.uk"
        type="cite">
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          <p class="MsoNormal"><span style="color:windowtext">Hi Greg,<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">I know
              that doing anything with graphics within virtual machines
              is not always a brilliant idea, but I have seen Chimera
              work in VirtualBox and I wanted to get to the bottom of
              why mine doesn&#8217;t&#8230;<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">I&#8217;ve got
              the latest graphics driver on my host (and I run Chimera
              successfully on it anyway).&nbsp; I&#8217;ve run the commands you
              suggested, with the following output<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">$ gdb
              $CHIMERA/bin/python2.7<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">GNU gdb
              (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">Copyright
              (C) 2012 Free Software Foundation, Inc.<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">License
              GPLv3+: GNU GPL version 3 or later <a
                moz-do-not-send="true" class="moz-txt-link-rfc2396E"
                href="http://gnu.org/licenses/gpl.html">&lt;http://gnu.org/licenses/gpl.html&gt;</a><o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">This is
              free software: you are free to change and redistribute it.<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">There is
              NO WARRANTY, to the extent permitted by law.&nbsp; Type "show
              copying"<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">and "show
              warranty" for details.<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">This GDB
              was configured as "x86_64-linux-gnu".<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">For bug
              reporting instructions, please see:<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext"><a
                moz-do-not-send="true" class="moz-txt-link-rfc2396E"
                href="http://bugs.launchpad.net/gdb-linaro/">&lt;http://bugs.launchpad.net/gdb-linaro/&gt;</a>...<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">Reading
              symbols from
              /home/ccw/.local/chimera-1.7/bin/python2.7...done.<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">(gdb)
              break_exit<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">Undefined
              command: "break_exit".&nbsp; Try "help".<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">(gdb) run
              $CHIMERA/share/__main__.py --debug<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">Starting
              program: /home/ccw/.local/chimera-1.7/bin/python2.7
              $CHIMERA/share/__main__.py --debug<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">[Thread
              debugging using libthread_db enabled]<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">Using host
              libthread_db library
              "/lib/x86_64-linux-gnu/libthread_db.so.1".<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">Traceback
              (most recent call last):<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">&nbsp; File
              "/home/ccw/.local/chimera-1.7/share/__main__.py", line 69,
              in &lt;module&gt;<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">&nbsp;&nbsp;&nbsp; value
              = chimeraInit.init(sys.argv)<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">&nbsp; File
              "/home/ccw/.local/chimera-1.7/share/chimeraInit.py", line
              594, in init<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">&nbsp;&nbsp;&nbsp; import
              chimera<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">&nbsp; File
              "/home/ccw/.local/chimera-1.7/share/chimera/__init__.py",
              line 16, in &lt;module&gt;<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">&nbsp;&nbsp;&nbsp; from
              _chimera import BBox, Camera, Color, ColorGroup,
              DirectionalLight, LODControl, Lens, LensViewer, Light,
              Material, MaterialColor, Model, NoGuiViewer, OGLFont,
              OSLAbbreviation, OpenModels, OpenState, PathFinder,
              PixelMap, Plane, Point, PositionalLight, Selectable,
              SharedState, SpotLight, Sphere, Texture, TextureColor,
              TrackChanges, Vector, Viewer, X3DScene, Xform<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">ImportError:

              libgfxinfo.so: cannot open shared object file: No such
              file or directory<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">[Inferior
              1 (process 4025) exited with code 01]<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">(gdb) bt<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">No stack.<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">I guess
              the lack of libgfxinfo.so is fairly significant, and I
              assume that the result from bt is all part of the problem?<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext"><o:p>&nbsp;</o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">Thanks,<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext">Chris<o:p></o:p></span></p>
          <p class="MsoNormal"><span style="color:windowtext"><o:p>&nbsp;</o:p></span></p>
          <div>
            <div style="border:none;border-top:solid #B5C4DF
              1.0pt;padding:3.0pt 0cm 0cm 0cm">
              <p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:windowtext;mso-fareast-language:EN-GB"
                    lang="EN-US">From:</span></b><span
style="font-size:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;;color:windowtext;mso-fareast-language:EN-GB"
                  lang="EN-US"> <a moz-do-not-send="true"
                    class="moz-txt-link-abbreviated"
                    href="mailto:chimera-users-bounces@cgl.ucsf.edu">chimera-users-bounces@cgl.ucsf.edu</a>
                  [<a moz-do-not-send="true"
                    class="moz-txt-link-freetext"
                    href="mailto:chimera-users-bounces@cgl.ucsf.edu">mailto:chimera-users-bounces@cgl.ucsf.edu</a>]
                  <b> On Behalf Of </b>Greg Couch<br>
                  <b>Sent:</b> 05 February 2013 23:26<br>
                  <b>To:</b> <a moz-do-not-send="true"
                    class="moz-txt-link-abbreviated"
                    href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>
                  <b>Subject:</b> Re: [Chimera-users] Chimera on a
                  virtualbox<o:p></o:p></span></p>
            </div>
          </div>
          <p class="MsoNormal"><o:p>&nbsp;</o:p></p>
          <p class="MsoNormal">(Forgot to send reply to whole list)<o:p></o:p></p>
          <div>
            <p class="MsoNormal">-------- Original Message -------- <o:p></o:p></p>
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              cellspacing="0">
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                  <td style="padding:0cm 0cm 0cm 0cm" nowrap="nowrap"
                    valign="top">
                    <p class="MsoNormal" style="text-align:right"
                      align="right"><b>Subject: </b><b><span
                          style="font-size:12.0pt"><o:p></o:p></span></b></p>
                  </td>
                  <td style="padding:0cm 0cm 0cm 0cm">
                    <p class="MsoNormal">Re: [Chimera-users] Chimera on
                      a virtualbox<span style="font-size:12.0pt"><o:p></o:p></span></p>
                  </td>
                </tr>
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                    valign="top">
                    <p class="MsoNormal" style="text-align:right"
                      align="right"><b>Date: </b><b><span
                          style="font-size:12.0pt"><o:p></o:p></span></b></p>
                  </td>
                  <td style="padding:0cm 0cm 0cm 0cm">
                    <p class="MsoNormal">Tue, 05 Feb 2013 13:51:47 -0800<span
                        style="font-size:12.0pt"><o:p></o:p></span></p>
                  </td>
                </tr>
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                  <td style="padding:0cm 0cm 0cm 0cm" nowrap="nowrap"
                    valign="top">
                    <p class="MsoNormal" style="text-align:right"
                      align="right"><b>From: </b><b><span
                          style="font-size:12.0pt"><o:p></o:p></span></b></p>
                  </td>
                  <td style="padding:0cm 0cm 0cm 0cm">
                    <p class="MsoNormal">Greg Couch <a
                        moz-do-not-send="true"
                        href="mailto:gregc@cgl.ucsf.edu">&lt;gregc@cgl.ucsf.edu&gt;</a><span
                        style="font-size:12.0pt"><o:p></o:p></span></p>
                  </td>
                </tr>
                <tr>
                  <td style="padding:0cm 0cm 0cm 0cm" nowrap="nowrap"
                    valign="top">
                    <p class="MsoNormal" style="text-align:right"
                      align="right"><b>To: </b><b><span
                          style="font-size:12.0pt"><o:p></o:p></span></b></p>
                  </td>
                  <td style="padding:0cm 0cm 0cm 0cm">
                    <p class="MsoNormal"><a moz-do-not-send="true"
                        href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a><span
                        style="font-size:12.0pt"><o:p></o:p></span></p>
                  </td>
                </tr>
              </tbody>
            </table>
            <p class="MsoNormal" style="margin-bottom:12.0pt"><o:p>&nbsp;</o:p></p>
            <div>
              <p class="MsoNormal">Hi Chris,<br>
                <br>
                So what are you trying to do with Chimera inside a
                virtual machine?&nbsp; Presumably, you're not trying to use
                it graphically because virtualized graphics performance
                is usually abysmal.&nbsp; Chimera benefits immensely from
                direct access to the graphics hardware.&nbsp; So that leaves
                using Chimera as a server, and for that the headless
                version of Chimera is usually better -- the headless
                version uses a software implementation of OpenGL and
                thus avoids any driver issues.<br>
                <br>
                That said, this bug is still likely to be related to
                OpenGL support in VirtualBox.&nbsp; Make sure the computer
                that VirtualBox is running on has an up-to-date OpenGL
                graphics driver.&nbsp; It doesn't matter what VirtualBox does
                if the underlying system has a bad graphics driver.<br>
                <br>
                To confirm that the bug is in the graphics driver, get a
                backtrace of where the error occurs by using gdb as
                follows in a Terminal window (and assuming there is a
                symbolic link to the chimera binary on your path):<br>
                <br>
                &nbsp;&nbsp;&nbsp; % export CHIMERA=`chimera --root`<br>
                &nbsp;&nbsp;&nbsp; % export LD_LIBRARY_PATH=$CHIMERA/lib<br>
                &nbsp;&nbsp;&nbsp; % gdb $CHIMERA/bin/python2.7<br>
                &nbsp;&nbsp;&nbsp; (gdb) break_exit<br>
                &nbsp;&nbsp;&nbsp; (gdb) run $CHIMERA/share/__main__.py --debug<br>
                &nbsp;&nbsp;&nbsp; (gdb) bt<br>
                <br>
                The '%' and '(gdb)' parts are the shell and gdb prompts,
                respectively.&nbsp; The output from the bt command will
                probably be in Chimera's molecular drawing code (as
                opposed to drawing the UI).&nbsp; If you need help
                interpreting the chimera backtrace, you can send it to
                me. <br>
                <br>
                &nbsp;&nbsp;&nbsp; HTH,<br>
                <br>
                &nbsp;&nbsp;&nbsp; Greg<br>
                <br>
                On 02/05/2013 12:48 PM, <a moz-do-not-send="true"
                  href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a>
                wrote:<o:p></o:p></p>
            </div>
            <blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
              <p class="MsoNormal">Hello all,<o:p></o:p></p>
              <p class="MsoNormal">&nbsp;<o:p></o:p></p>
              <p class="MsoNormal">I'm trying to run Chimera on
                VirtualBox. The installation completes fine, but when I
                try and run the program (<code><span
style="font-size:10.0pt;font-family:&quot;Calibri&quot;,&quot;sans-serif&quot;">cd</span></code>
                to the bin directory and run <code><span
                    style="font-size:10.0pt">./chimera</span></code>) I
                see<o:p></o:p></p>
              <p class="MsoNormal">&nbsp;<o:p></o:p></p>
              <p class="MsoNormal"><span style="font-size:10.0pt">X
                  Error of failed request:&nbsp; BadDrawable (invalid Pixmap
                  or Window parameter)</span><o:p></o:p></p>
              <p class="MsoNormal"><span style="font-size:10.0pt">Major
                  opcode of failed request:&nbsp; 72 (X_PutImage)</span><o:p></o:p></p>
              <p class="MsoNormal"><span style="font-size:10.0pt">Resource

                  id in failed request:&nbsp; 0x480006a</span><o:p></o:p></p>
              <p class="MsoNormal"><span style="font-size:10.0pt">Serial
                  number of failed request:&nbsp; 1382</span><o:p></o:p></p>
              <p class="MsoNormal"><span style="font-size:10.0pt">Current

                  serial number in output stream:&nbsp; 1388</span><o:p></o:p></p>
              <p class="MsoNormal">&nbsp;<o:p></o:p></p>
              <p class="MsoNormal">I've tried enabling / disabling
                hardware virtualization &amp; 3D acceleration, but to no
                avail. Although people do seem to have problems with
                chimera on a virtualbox, it normally seems to be a
                problem with OpenGL, which this doesn't seem to be.<o:p></o:p></p>
              <p class="MsoNormal">&nbsp;<o:p></o:p></p>
              <p class="MsoNormal">Has anyone seen this error before? Is
                there anything else I'm missing? I can&#8217;t even work out
                if it's a hardware, VirtualBox, or OS problem&#8230;<o:p></o:p></p>
              <p class="MsoNormal"><strong><span
style="font-size:10.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;">&nbsp;</span></strong><o:p></o:p></p>
              <p class="MsoNormal"><strong><span
style="font-size:10.0pt;font-family:&quot;Verdana&quot;,&quot;sans-serif&quot;">System:</span></strong><o:p></o:p></p>
              <p class="MsoNormal">VirtualBox 4.2.4<br>
                Guest additions 4.2.4<o:p></o:p></p>
              <p class="MsoNormal">Guest OS: Ubuntu 12.04<br>
                Host OS: Windows 7 professional<o:p></o:p></p>
              <p class="MsoNormal">&nbsp;<o:p></o:p></p>
              <p class="MsoNormal">Thanks in advance!<o:p></o:p></p>
              <p class="MsoNormal">Chris<o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="mso-fareast-language:EN-GB">-------------------</span><o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="mso-fareast-language:EN-GB">Dr Chris Wood</span><o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="mso-fareast-language:EN-GB">STFC Rutherford
                  Appleton Laboratory</span><o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="mso-fareast-language:EN-GB">Didcot</span><o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="mso-fareast-language:EN-GB">OX11 0QX</span><o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="mso-fareast-language:EN-GB">&nbsp;</span><o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="mso-fareast-language:EN-GB"><a
                    moz-do-not-send="true"
                    href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a><br>
                  <a moz-do-not-send="true"
                    href="http://www.ccpem.ac.uk">www.ccpem.ac.uk</a></span><o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="mso-fareast-language:EN-GB"><br>
                  Tel: +44(0)1235 567864</span><o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="mso-fareast-language:EN-GB">Tel: +44(0)7909
                  586624<br>
                  Fax: +44(0)1235 567801</span><o:p></o:p></p>
              <p class="MsoNormal">&nbsp;<o:p></o:p></p>
              <p class="MsoNormal"><span
                  style="font-size:12.0pt;font-family:&quot;Times New
                  Roman&quot;,&quot;serif&quot;;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
              <p>-- <br>
                Scanned by iCritical.<o:p></o:p></p>
            </blockquote>
            <p class="MsoNormal" style="margin-bottom:12.0pt"><span
                style="font-size:12.0pt;font-family:&quot;Times New
                Roman&quot;,&quot;serif&quot;;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
          </div>
          <p class="MsoNormal"><span
              style="font-size:12.0pt;font-family:&quot;Times New
              Roman&quot;,&quot;serif&quot;;mso-fareast-language:EN-GB"><o:p>&nbsp;</o:p></span></p>
        </div>
        <br>
        <p>-- <br>
          Scanned by iCritical. </p>
        <br>
      </blockquote>
      <br>
      <br>
    </div>
    <br>
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