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Hi Michael,
<div class="">VirtualGL/TurboVNC is what I switched to 5 or 6 years ago. It is actually pretty easy to set up, and provides dramatically better interactivity, particularly over a slower internet connection, but is noticeable even on the same subnet. With a
little tweaking of the settings, you can make this usable even over very slow network links, with a little loss of perceptual quality. Take a look here (bottom section of page):</div>
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<div class=""><a href="http://eman2.org/Remote" class="">http://eman2.org/Remote</a></div>
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<div class="">I'd add that using the remote OpenGL directly via X windows as you described is hit or miss. There are quite a few X clients which seem to have problems with this, producing visual artifacts, and in some cases, inverting 2-D OpenGL displays vertically
(this caused some big issues with particle pickers at one point). So, I strongly recommend VirtualGL!</div>
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<font face="Courier" class=""><span style="font-size: 14px;" class="">--------------------------------------------------------------------------------------<br class="">
Steven Ludtke, Ph.D. <<a href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a>> Baylor College of Medicine <br class="">
Charles C. Bell Jr., Professor of Structural Biology<br class="">
Dept. of Biochemistry and Molecular Biology (<a href="http://www.bcm.edu/biochem" class="">www.bcm.edu/biochem</a>)<br class="">
Academic Director, CryoEM Core (<a href="http://cryoem.bcm.edu" class="">cryoem.bcm.edu</a>)<br class="">
Co-Director CIBR Center (<a href="http://www.bcm.edu/research/cibr" class="">www.bcm.edu/research/cibr</a>)<br class="">
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<blockquote type="cite" class="">
<div class="">On Feb 3, 2019, at 9:27 AM, Michael Elbaum <<a href="mailto:michael.elbaum@weizmann.ac.il" class="">michael.elbaum@weizmann.ac.il</a>> wrote:</div>
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<div class=""><font size="2" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><b class="">***CAUTION:***
This email is not from a BCM Source. Only click links or open attachments you know are safe.</b></font><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span>
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Hi all,<br class="">
<br class="">
I'm normally using a powerful server for image processing, and then I look at the data by remote ssh with X forwarding. Recently I upgraded the linux OS on my laptop (to Ubuntu 18.04) and all sorts of programs stopped working this way, including 3dmod. It turned
out to be a much broader problem having to do with OpenGL. Indirect rendering, which is what we need, is turned off by default in newer versions of X. I assume others have encountered such trouble as well. Since it took quite some digging to find a solution
I'm posting it here.<br class="">
<br class="">
For those who boot into a command line interface with a black screen and start an X session manually, (e.g., startx -- :2) the fix is simple.<span class="Apple-converted-space"> </span><br class="">
Edit the file /usr/bin/startx and change the line defaultclientargs="" to defaultclientargs="+iglx"<br class="">
+iglx allows indirect rendering by OpenGL applications.<br class="">
This is not relevant to most of us.<br class="">
<br class="">
For those who boot the computer and expect to see the graphical display right away it's a bit trickier. Ubuntu uses X or Wayland for the graphical interface, depending on the version. The solution I found is only for X, so we have to revert to that first. It's
done in two steps, as root:<br class="">
1) In the file /etc/gdm3/custom.conf, uncomment (erase the hash) the line #WaylandEnable=false. (In Ubuntu it should be enough to start GNOME in Xorg, which is one of the login options.)<br class="">
2) Create a new file /usr/share/X11/xorg.conf.d/50-iglx.conf:<br class="">
Section "ServerFlags" <span class="Apple-converted-space"> </span><br class="">
Option "AllowIndirectGLX" "on" <span class="Apple-converted-space"> </span><br class="">
Option "IndirectGLX" "on" <span class="Apple-converted-space"> </span><br class="">
EndSection<span class="Apple-converted-space"> </span><br class="">
Reboot and it should work. at your own risk, of course...<br class="">
Other distributions might put these files in different places.<br class="">
<br class="">
Here are some useful resources:<br class="">
<a href="https://www.visitusers.org/index.php?title=Re-enabling_INdirect_glx_on_your_X_server" class="">https://www.visitusers.org/index.php?title=Re-enabling_INdirect_glx_on_your_X_server</a><br class="">
<a href="https://lists.freedesktop.org/archives/xorg/2016-May/058072.html" class="">https://lists.freedesktop.org/archives/xorg/2016-May/058072.html</a><br class="">
<a href="https://askubuntu.com/questions/745135/how-to-enable-indirect-glx-contexts-iglx-in-ubuntu-14-04-lts-with-nvidia-gfx/747088" class="">https://askubuntu.com/questions/745135/how-to-enable-indirect-glx-contexts-iglx-in-ubuntu-14-04-lts-with-nvidia-gfx/747088</a><br class="">
<br class="">
There seems to be a similar issue with XQuartz on the Mac, which is addressed by reverting to the last version that worked.<br class="">
<br class="">
There was another instruction to add in the file /usr/share/lightdm/lightdm.conf.d/50-xserver-command.conf<br class="">
[SeatDefaults]<br class="">
# Dump core<br class="">
xserver-command=X -core +iglx<br class="">
but this didn't work for me.<br class="">
<br class="">
As for Wayland, typing Xwayland -h shows that the options include +iglx, but I wasn't able to find a config file for passing it startup options.<br class="">
<br class="">
A longer term solution seems to be VirtualGL or TurboVNC. Does anyone have those working with 3dem visualization software?<br class="">
<br class="">
regards,<br class="">
Michael<br class="">
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">3dem
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="mailto:3dem@ncmir.ucsd.edu" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">3dem@ncmir.ucsd.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=kXG6BT7EhN-i62A53MTZPKmtfWzusbwlNXLYhaq5bsU&s=NNIidOH0anTASsqL4d5gV1pzxbjZSAHlGJE71Ph7zfQ&e=" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=kXG6BT7EhN-i62A53MTZPKmtfWzusbwlNXLYhaq5bsU&s=NNIidOH0anTASsqL4d5gV1pzxbjZSAHlGJE71Ph7zfQ&e=</a></div>
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