VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Nov 02 2023 - 16:54:02 CDT

If I *have* to use VMD on a remote machine, repeatedly (or have to support
people that need/want to do that), I download the Mesa sources and compile
a software-rendering only version (so no DRI drivers and any of the other
fancy stuff) and then use LD_PRELOAD to substitute the local OpenGL library
on the remote machine with it. Of course, this is agonizingly slow, but it
is completely independent from GLX support since it used plain X11
primitives only. On our HPC clusters we have such a feature for people that
need to use OpenGL accelerated software from remote. There were times (20+
years ago) when this was the only option to run VMD and it was linked to
Mesa directly, but fortunately, those times are long gone.

On Thu, Nov 2, 2023 at 5:46 PM Gianluca Interlandi <
gianluca_at_u.washington.edu> wrote:

> Hi Axel!
>
> Thanks for your reply.
>
> > This rarely works unless you have identical OS, X11, and OpenGL software
> > on both sides.
>
> So you are saying that having the same GPU with proprietary drivers may
> not help if everything else is different.
>
> > It most often breaks when the remote machine has more recent libraries
> > than the local one.
>
> In my situation it's the other way around, the local machine has more
> recent libraries.
>
> > So moving the data and running VMD locally is often the best solution.
>
> I found `sshfs` to be practical. Only caveat is that sshfs truncates the
> time stamp to the seconds, i.e.,
>
> Folder mounted with sshfs:
> > ls -lt --full-time test.trj
> 14:00:25.000000000 -0700 test.trj
>
> ssh to the remore machine:
> > ls -lt --full-time test.trj
> 14:00:25.720541063 -0700
>
> So I only use sshfs to read the trajectories locally with VMD but if I
> need to write new files I do it on the remote machine after logging in
> with ssh. Running VMD remotely is useful for example when performing an
> analysis that can only be done when VMD is in graphics mode. This used to
> be the case for example with parseFEP, but newer implementations of VMD
> allow parseFEP to be run through a script in text mode.
>
> Best,
>
> Gianluca
>
> On Thu, 2 Nov 2023, Axel Kohlmeyer wrote:
>
> > When using a remote desktop solution the OpenGL processing is done
> remotely and then
> > the resulting graphics captured and then "streamed" to the remote
> desktop client.
> > With GLX (i.e. OpenGL over X11) the situation is much more complex: the
> OpenGL
> > directives are encapsulated into X11 protocol and then unpacked on the
> local machine
> > and processed by the local graphics card. This is very fragile since the
> OpenGL
> > implementations on both ends of the connection need to be compatible.
> This rarely
> > works unless you have identical OS, X11, and OpenGL software on both
> sides. It most
> > often breaks when the remote machine has more recent libraries than the
> local one.
> >
> > So moving the data and running VMD locally is often the best solution.
> >
> > On Thu, Nov 2, 2023 at 4:41?PM Gianluca Interlandi <
> gianluca_at_u.washington.edu> wrote:
> > Hi Diego,
> >
> > Thanks for the reply. My question is also about the clients. Do the
> > clients from which you connect also have NVIDIA with proprietary
> drivers
> > installed? What I'm trying to figure out is whether remote openGL
> (VMD)
> > works if both server and client have NVIDIA GPUs both with the
> > proprietary
> > drivers installed.
> >
> > I am using VMD 1.8.7 and 1.9.2b21, both with the same result.
> >
> > > Have you considered using a remote desktop solution instead
> of ssh?
> > Over
> > > here we use Nice DCV.
> >
> > I am considering such an option. My understanding is that rdesktop
> works
> > only to connect to a windows server. Is Nice DCV included in major
> > distributions? Right now I am using `sshfs` to mount the remote
> directory
> > and then start VMD locally.
> >
> > Thanks!
> >
> > Gianluca
> >
> > On Thu, 2 Nov 2023, Diego Gomes wrote:
> >
> > > Hi Gianluca, although I can't help with the X error, I can
> confirm the
> > issue
> > > with VMD.Can you please share which VMD version you are using?
> > >
> > > For me it works very well when I ssh -X to our head-node, which
> does
> > not contain a
> > > dedicated GPU, while using vmd 1.9.3 and 1.9.4a55. It fails with
> vmd
> > 1.9.4a58.
> > > For any other machine the OpenGl windows fails either using "ssh
> -X" or
> > "ssh -Y", vmd
> > > 1.9.3, 1.9.4a55, and 1.9.4a58.
> > > XRequest.130: BadRequest (invalid request code or no such
> operation)
> > 0x3600090
> > >
> > > Machines are Ubuntu 2022.04.2, the ones with GPU have Nvidia
> Driver
> > Version:
> > > 530.30.02 CUDA Version: 12.1.
> > >
> > > Have you considered using a remote desktop solution instead
> of ssh?
> > Over here we use
> > > Nice DCV.
> > >
> > > Friendly regards,
> > > Diego.
> > >
> > >
> >
> > -----------------------------------------------------
> > Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> > +1 (206) 685 4435
> >
> https://urldefense.com/v3/__http://gianluca.today/__;!!DZ3fjg!9dM36IdGRdmFnQn3PC8kw
> >
> CuiFnDlXnfxOoFtpV827RN1u-glDiSMsPpDwciy4mJV-EBmLoJs4veR78k8SzpAuMU3FOU$
> >
> > Department of Bioengineering
> > University of Washington, Seattle WA U.S.A.
> > -----------------------------------------------------
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!9tiyRnO0t1MGUYrVsaXVwBcctfDrQOMoonHxAN9yZ-d8sUUhdUDsbc1RCR-Wk9C4cdbCnxzXLNKUKbvm8g$
> > College of Science & Technology, Temple University, Philadelphia PA, USA
> >
> >
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> https://urldefense.com/v3/__http://gianluca.today/__;!!DZ3fjg!9tiyRnO0t1MGUYrVsaXVwBcctfDrQOMoonHxAN9yZ-d8sUUhdUDsbc1RCR-Wk9C4cdbCnxzXLNIVN_Rt8g$
>
> Department of Bioengineering
> University of Washington, Seattle WA U.S.A.
> ----------------------------------------------------- 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!9tiyRnO0t1MGUYrVsaXVwBcctfDrQOMoonHxAN9yZ-d8sUUhdUDsbc1RCR-Wk9C4cdbCnxzXLNKUKbvm8g$ 
College of Science & Technology, Temple University, Philadelphia PA, USA