[3dem] visualization of data from a remote server

[Michael Elbaum]

Thanks Steve,    those are just the instructions I'd been looking for! VirtualGL looks like the better way. It requires help from the cluster administrators to install on their side. I'll work on that next week.
best,
Michael

________________________________
From: Ludtke, Steven J [sludtke at bcm.edu]
Sent: Sunday, February 03, 2019 19:36
To: Michael Elbaum
Cc: 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] visualization of data from a remote server

Hi Michael,
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):

http://eman2.org/Remote

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!

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <sludtke at bcm.edu<mailto:sludtke at bcm.edu>>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu<http://cryoem.bcm.edu>)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)



On Feb 3, 2019, at 9:27 AM, Michael Elbaum <michael.elbaum at weizmann.ac.il<mailto:michael.elbaum at weizmann.ac.il>> wrote:

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________________________________

Hi all,

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.

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.
Edit the file /usr/bin/startx and change the line defaultclientargs="" to defaultclientargs="+iglx"
+iglx allows indirect rendering by OpenGL applications.
This is not relevant to most of us.

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:
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.)
2) Create a new file /usr/share/X11/xorg.conf.d/50-iglx.conf:
Section "ServerFlags"
Option "AllowIndirectGLX" "on"
    Option "IndirectGLX" "on"
EndSection
Reboot and it should work. at your own risk, of course...
Other distributions might put these files in different places.

Here are some useful resources:
https://www.visitusers.org/index.php?title=Re-enabling_INdirect_glx_on_your_X_server
https://lists.freedesktop.org/archives/xorg/2016-May/058072.html
https://askubuntu.com/questions/745135/how-to-enable-indirect-glx-contexts-iglx-in-ubuntu-14-04-lts-with-nvidia-gfx/747088

There seems to be a similar issue with XQuartz on the Mac, which is addressed by reverting to the last version that worked.

There was another instruction to add in the file /usr/share/lightdm/lightdm.conf.d/50-xserver-command.conf
[SeatDefaults]
# Dump core
xserver-command=X -core +iglx
but this didn't work for me.

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.

A longer term solution seems to be VirtualGL or TurboVNC. Does anyone have those working with 3dem visualization software?

regards,
Michael
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