PyMol and GLX

[alphaace]

Hi Everyone,

I use a piece of software called Pymol (http://www.pymol.org/) to render pdb files (proteins in 3D space). The software is not in the repository, but you don't need to install it. All that needs to be done is download the file, run a script and then the file is executable. It works flawlessly on my pclos box at home. I'm trying to get it working on my pclos box here at the lab and am running into this:


[greg@Ares pymol]$ ./pymol
Xlib:  extension "GLX" missing on display ":0".
freeglut (/home/greg/Software/pymol/pymol.exe): OpenGL GLX extension not supported by display ':0'
 PyMOL: abrupt program termination.

I ran glxinfo | grep rendering and here's what I get:

glxinfo | grep rendering

Can someone give me a hand with this? It's kind of frustrating manipulating these proteins on my laptop!

Thanks!

[djohnston]

cat /etc/X11/xorg.conf | grep GLX

On my nVidia card, I get Option "AddARGBGLXVisuals". On my Ati card I get nothing.

[alphaace]

Hi,

If I run "cat /etc/X11/xorg.conf | grep GLX", I get nothing. However, if I run: "cat /etc/X11/xorg.conf | grep glx",

I get:    Load "glx" # 3D layer

Also, I mistyped the results of a previous command. they are:
[greg@Ares ~]$ glxinfo | grep rendering
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".
Error: couldn't find RGB GLX visual or fbconfig
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".
Xlib:  extension "GLX" missing on display ":0".


Does this mean, it's not supported on my ATI card? That would be a real pain....

[djohnston]

alphaace,

I wouldn't know. I have no idea what ATI card you're using.

[alphaace]

Hi, sorry: ATI Technologies Inc RV380 -- Radeon X600 (PCIE)

[djohnston]

Hmmm. As soon as I saw PCIE, I thought "that's gotta be GLX capable". What driver are you using for the card? Also, have a look at your /etc/X11/xorg.conf file. Easiest way is make a copy of the original to look at. Open a terminal. As regular user, do:

$ cp /etc/X11/xorg.conf xorg.conf

Your copy will be in the root of your home directory. Have a look at this, particularly Section "Module". Bear in mind it's an xorg.conf for FreeBSD, but it should be close. I wouldn't go changing anything yet. Let's see what driver you're using.

[alphaace]

Hi,

I've been playing with xorg.conf for a while now.

Currently, I have the Driver to be "radeon". When I set the Driver to be "ati", the problem is still there.

I also tried the fix documented in this post:
http://www.pclinuxos.com/forum/index.php?PHPSESSID=72ikeaqrmcp0pdfkmju9b0skm7&topic=92281.0

Still nothing. What's worse, now in google chrome when it does the suggestions, all texts are messed up (covered by a black box). When I revert to my original settings, it goes away.

In the Module Section of Xorg.conf, the only 2 items I don't have are:
dri2
record

[djohnston]

Please note my previous post.

I wouldn't go changing anything yet. Let's see what driver you're using.

Changing the driver in the xorg.conf file doesn't actually change the driver. Open the PCLinuxOS Control Center. In the left pane, click Hardware. In the right pane, click Browse and configure hardware. In the left pane, expand the Videocard, then highlight your ATI card. In the right pane, the driver in use will be listed as Module.

What is it?

[alphaace]

Hi,

The module is ATI Radeon X1950 and earlier.

Sorry for going ahead there and trying the other post, xorg changes etc...sometimes it's fun to tinker ;-). Anyway, I've restored to my original changes.

[djohnston]

Hi,

The module is ATI Radeon X1950 and earlier.

Sorry for going ahead there and trying the other post, xorg changes etc...sometimes it's fun to tinker ;-). Anyway, I've restored to my original changes.

No problem. It is, after all, your computer. Or your employer's.

Sometimes I miss details. I missed a couple here. I went back and reread your previous posts. I followed the forum link that you pointed to, and followed those instructions on my own ATI card. After rebooting, I'm getting around 410 fps running glxgears. I was getting about 30. That's a big increase. I still don't get the OpenGL extensions (glx) because my old AGP card isn't OpenGL capable. Yours is.

When you did cat /etc/X11/xorg.conf | grep glx you got Load "glx" # 3D layer. I missed that completely. But, when you do glxinfo | grep rendering, you shouldn't be getting errors. I get direct rendering : Yes, but your results may be different.

Let's start over by setting the driver and re-generating xorg.conf. Open a terminal.

$ su -
# cd /etc/X11
# mv xorg.conf xorg.conf.old
# XFdrake

Xfdrake will run the same video card setup that you would run from PCC. Accept the default highlighted video driver, even if it's the same one you're using now. Save the changes. Next:

# cd /boot/grub
# cp menu.lst menu.lst.backup
# leafpad menu.lst

Leafpad is a text editor. If you're running a KDE desktop, the equivalent is Kwrite. Use whatever text editor you usually do. You are looking for any lines in the file that contains nokmsboot. You want to remove nokmsboot from the line. The line will begin with kernel. Save your changes. Next:

# cd /etc
# cp modprobe.preload modprobe.preload.backup
# leafpad modprobe.preload

You will add the following two lines to the end of the file.

radeon
options radeon modeset=1

Save the file. Close all programs. Reboot. After rebooting, see if modeset is set to 1 by doing cat /sys/module/radeon/parameters/modeset.

[alphaace]

Hi,

Sorry for the delay. I wasn't in the office over the weekend and didn't get a chance to do this.

I followed all your steps and now have both good news and bad news.

Good news: Pymol now works:

Bad News:

1) when I do cat /sys/module/radeon/parameters/modeset , I get a value of 0.

2) I have the same weird thing as before, window corruption (for example the google chrome autocorrect is now becomes see through showing me my desktop)! What's worse is that before everything would go back to normal if I took out the the radeon option in modprobe.preload. Now it does not. The corruption still occurs either way!

What should I do now?

Thanks!


Addendum: By disabling "Enable Translucency (composite extension)", everything seems to work now. Let me finish testing and if all is well, I will mark this as solved.