VMD-L Mailing List

From: Brett Pemberton (brett_at_vpac.org)
Date: Tue Jun 27 2006 - 22:37:59 CDT

Axel,

That's great, we've got it working fine now.

Thanks for your help.

        / Brett

On Tue, 2006-06-27 at 23:17 -0400, Axel Kohlmeyer wrote:
> On Wed, 28 Jun 2006, Brett Pemberton wrote:
>
> BP> Axel,
> BP>
> BP> That sounds fine, however I can't find the tutorial you talk of.
> BP> Perhaps i'm searching for the wrong terms, would you be able to help in
> BP> finding this ?
>
> try:
>
> http://www.ks.uiuc.edu/Research/vmd/imd/tutorial/
>
> as you can see, you can set the port that NAMD will listen to
> (here 2030), so now you only have to dig the ssh tunnel to connect to it.
>
> axel.
>
> BP>
> BP> / Brett
> BP>
> BP> On Tue, 2006-06-27 at 20:53 -0400, Axel Kohlmeyer wrote:
> BP> > On Wed, 28 Jun 2006, Brett Pemberton wrote:
> BP> >
> BP> > BP> John,
> BP> >
> BP> > brett,
> BP> >
> BP> > BP> The situation (as it has been explained to me by the VMD user) is that
> BP> > BP> he wishes to use vmd to interact with a namd job running on our cluster.
> BP> > BP> Since the compute nodes aren't accessible to his PC, he must ssh to the
> BP> > BP> head node of the cluster, and run VMD there, where it can talk to the
> BP> > BP> namd job.
> BP> >
> BP> > not necessarily. you could also tunnel the IMD (=interactive MD)
> BP> > connection through an ssh tunnel (there should be a tutorial for
> BP> > IMD somewhere on the VMD homepage that should you get you started
> BP> > and then you only need to know the port to forward to the cluster).
> BP> > that connection should be comparatively low throughput compared
> BP> > to the graphics and you (or your 'customer') has the additional
> BP> > benefit of getting the full acceleration of the graphics card.
> BP> >
> BP> > the GLX transport layer on linux is not very reliable and
> BP> > tunneling this through ssh is (currently) asking for trouble.
> BP> > in the rare cases where it worked for me, i had to have the
> BP> > _same_ (i.e. identical to the version number) driver on both
> BP> > sides.
> BP> >
> BP> > cheers,
> BP> > axel.
> BP> >
> BP> > BP>
> BP> > BP> The cluster head node is the machine with the ati card. His (and my)
> BP> > BP> machines both have nvidia cards.
> BP> > BP>
> BP> > BP> VMD tells me
> BP> > BP>
> BP> > BP> Info) Multithreading available, 2 CPUs detected.
> BP> > BP> Info) OpenGL renderer: GeForce FX 5200/AGP/SSE2
> BP> > BP> Info) Features: STENCIL RN MDE MTX PP PS
> BP> > BP> Info) GLSL rendering mode is NOT available.
> BP> > BP> Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
> BP> > BP>
> BP> > BP> This is the same, whether I use ssh X forwarding, or allow VMD to
> BP> > BP> connect to my X server remotely.
> BP> > BP>
> BP> > BP> thanks,
> BP> > BP>
> BP> > BP> / Brett
> BP> > BP>
> BP> > BP> On Tue, 2006-06-27 at 17:15 -0500, John Stone wrote:
> BP> > BP> > Hi,
> BP> > BP> > In general it's not usually a good idea to run VMD through SSH,
> BP> > BP> > as the graphics performance will be terrible (independent of the
> BP> > BP> > other problems you're having). If you want to run remotely, I'd
> BP> > BP> > recommend using a normal X connection instead of tunnelling through
> BP> > BP> > ssh, if you care about speed and must display remotely. In the specific
> BP> > BP> > situation you've got, VMD should be detecting the ATI driver on
> BP> > BP> > the remote display and automatically limiting itself to prevent
> BP> > BP> > problems due to bugs in the ATI driver, but it's possible that
> BP> > BP> > this isn't happening for some reason. Can you send me the startup
> BP> > BP> > messages you get from VMD when it remote displays to the ATI box?
> BP> > BP> > If you're using the MESA ATI driver on the ATI box, that may be
> BP> > BP> > the source of trouble, but I should be able to tell from your
> BP> > BP> > startup messages what's going on there.
> BP> > BP> >
> BP> > BP> > Thanks,
> BP> > BP> > John Stone
> BP> > BP> > vmd_at_ks.uiuc.edu
> BP> > BP> >
> BP> > BP> > On Tue, Jun 27, 2006 at 03:52:41PM +1000, Brett Pemberton wrote:
> BP> > BP> > > Sorry for the semi-repost, but I've subbed to ask more about an email in
> BP> > BP> > > the archives.
> BP> > BP> > >
> BP> > BP> > > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/7239.html
> BP> > BP> > >
> BP> > BP> > > I'm experiencing the exact same problems, running vmd remotely over ssh.
> BP> > BP> > > Machine with VMD is an ibm e326, x86_64, running Fedora Core 5. Host
> BP> > BP> > > machine (fails on many) in my case, is an i386 running FC5 as well.
> BP> > BP> > >
> BP> > BP> > > The host machine has an nvidia card, with the nvidia drivers. The vmd
> BP> > BP> > > machine has an ati card with no 3rd party drivers installed.
> BP> > BP> > >
> BP> > BP> > > setting "VMDSIMPLEGRAPHICS 1" as suggested does work, however I'd like
> BP> > BP> > > to avoid that.
> BP> > BP> > >
> BP> > BP> > > Can you please advise how I can "change drivers", as mentioned in the
> BP> > BP> > > post?
> BP> > BP> > >
> BP> > BP> > > thanks,
> BP> > BP> > >
> BP> > BP> > > / Brett
> BP> > BP> > >
> BP> > BP> > >
> BP> > BP> > > --
> BP> > BP> > > Brett Pemberton - VPAC Systems Programmer
> BP> > BP> > > http://www.vpac.org/ - (03) 9925 4899
> BP> > BP> >
> BP> > BP> >
> BP> > BP> >
> BP> > BP>
> BP> >
> BP> > --
> BP> > =======================================================================
> BP> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> BP> > Center for Molecular Modeling -- University of Pennsylvania
> BP> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> BP> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> BP> > =======================================================================
> BP> > If you make something idiot-proof, the universe creates a better idiot.
> BP>
> 

-- 
Brett Pemberton - VPAC Systems Programmer
http://www.vpac.org/ - (03) 9925 4899