We have slowly introduced OnDemand here at CWRU, and had another intro session today. Some of the attendees wanted to use Gaussview, which is installed as a cluster module. After starting a desktop session, ‘gview’ launches, but the display window content is black/empty. All the menu functionality is supported.
We have binaries purchased from the kind folks who develop Gaussian and GaussView. The software executes and generates output as expected on the same nodes with x2go used for the graphical ssh connections. This leads to a gray background with a very simple render of Carbon tetrasomethingorother – not, to the unaided eye, a particularly challenge scene.
I see that VMD is implemented as a standalone application in OnDemand. Does anyone have insight into whether Gaussian requires additional packages perhaps not available in our standard Xfce and Mate desktop builds?
Thanks in advance
~ Em
I’m not sure because I can’t test that app here (our gview is gui vim).
Looking online though, it may not be a library thing, just an optimization thing. That said I can’t say for sure. I’d been looking for a way to even see what the problem may be, or how you (or I) could even debug and try to find out what the issue may be.
I’d imagine if you didn’t have the GUI libraries it would just crash? But since you can load it, it’s just not being displayed properly so maybe it’s an optimization problem (especially given that the menu is still working)? The fact that it works in x2go may also corroborate this, like it’s a problem of throughput and vncserver isn’t up to the task.
You may want to play around with some configs in $HOME/.vnc/config. We use turbovnc so there are docs here. Really quickly you may want to lower the DPI, though that’s going to give you a lower resolution - it’ll only be for yourself and it’ll just be for a test.
Hi, Jeff – I don’t know very much about how gview creates the images. I thought I would test a few other packages. I tried VMD, and encountered basically the same issue: all the mechanisms seem to succeed within OnDemand, but the view itself is just black screen.
Then I look again at the OOD interactive apps, and find VMD there. It calls for VIrtualGL 2.3, which seems consistent with the VMD viewer header phrase including “VMD 1.9.3 OpenGL Display”. So our cluster VMD is built with OpenGL, and the OnDemand app implements VIrtualGL.
Does Gaussview also have an OpenGL requirement? Gaussian and Gaussview documentation isn’t immediately clear on this point.
Clearly, VMD shouldn’t actually work through the Desktop app, since there is an interactive app dedicated to it. If there is a discussion about how to know what applications would be supported through the desktop that would be great.
Thanks
OK let’s work on VMD, because that’s something we can both test. I think you’re onto something looking at OpenGL libraries.
Probably, I saw this note here from UGA about users may needing to export a mesa flag.
Here are the opengl libs and versions we’re running and VMD is working for us. I don’t think you’ll need all of them (devel libraries for example) but it’s just to illustrate the versions we run. Looks like solidly 18.0.5-4.
[johrstrom@host d9ab453d-b6f3-49a4-9dca-64034d65021c]$ rpm -qa | grep mesa
mesa-libGL-devel-18.0.5-4.el7_6.x86_64
mesa-libxatracker-18.0.5-4.el7_6.x86_64
mesa-libEGL-devel-18.0.5-4.el7_6.x86_64
mesa-libEGL-18.0.5-4.el7_6.i686
mesa-libGL-18.0.5-4.el7_6.x86_64
mesa-private-llvm-3.9.1-3.el7.x86_64
mesa-libGLU-devel-9.0.0-4.el7.x86_64
mesa-libGL-18.0.5-4.el7_6.i686
mesa-libGLES-18.0.5-4.el7_6.x86_64
mesa-libGLU-9.0.0-4.el7.x86_64
mesa-libglapi-18.0.5-4.el7_6.i686
mesa-libglapi-18.0.5-4.el7_6.x86_64
mesa-filesystem-18.0.5-4.el7_6.x86_64
mesa-libgbm-18.0.5-4.el7_6.i686
mesa-libEGL-18.0.5-4.el7_6.x86_64
mesa-libgbm-18.0.5-4.el7_6.x86_64
mesa-dri-drivers-18.0.5-4.el7_6.x86_64
I don’t think there was a technical reason other than we wanted to make it easier for users to use it. Looks like we have to load some modules and have some env setup beforehand which maybe tedious to do in a desktop. Plus it’s a BC application, so fairly cheap to implement. Other folks may have a different (better) historical perspective on it, but that’s the way it looks to me.
I completely agree, I don’t think there is a discussion or documentation on how we need X11 or GL libraries.
Hi, Jeff –
Thanks for the nudge to try loading our mesa module (v17.1.6). It bundles together a variety of other resources (updated X11, system libs, numa, libdrm). With this infrastructure in place, gview is able to render the default molecule (carbon tetrahedral). I’ll push this out to my researchers and let them explore the capabilities and limitations. I’ll also work to understand a little better this ecosystem to support OpenGL.
Thanks again
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