VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Nov 09 2010 - 10:51:32 CST

On Tue, 2010-11-09 at 17:43 +0100, Prskalo, Alen-Pilip wrote:
> ***************************************
> > important, graphics card. As stated, I'll take SLI, so if one GPU is to
> > little, I'll take the advandage of havind the other one also. I still
>
> not sure, if there actually is a benefit from SLI on linux /w opengl.
> a colleague tried it and didn't see anything.
>
> ***************************************
>
> Does anyone have an opinion onto if two graphics cards connected by SLI would improve the VMD representation, has anyone tried it out?
> As already said, I am buying some workstations now, so if would like to know should I buy one or two Nvidias and I don't want to throw money out of the window if it doesn't help ;-)

google is your friend:

as far as i understand you would need specific support
in the application to benefit from sli, but it looks even
for full screen linux apps that do, it is not worth it.

http://www.nvnews.net/vbulletin/showthread.php?t=153283

axel.

> I agree that a representation of 1M atoms in CPK doenst make sense, I simply wanted to know what I can expect.
>
> Thanks in advance
>
> Alen Prskalo
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Axel Kohlmeyer
> Sent: Montag, 8. November 2010 19:39
> To: Prskalo, Alen-Pilip
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Graphics card for VMD, number of atoms, file format
>
> On Mon, Nov 8, 2010 at 12:38 PM, Prskalo, Alen-Pilip
> <Alen-Pilip.Prskalo_at_mpa.uni-stuttgart.de> wrote:
> > Hi all,
> >
> >
> >
> > i have allready posted a few times here, I got help quite fast, so I'll try
> > it again.
> >
> >
> >
> > Firstly, i indent to by a Nvidia workstation, among other software i
> > especially indend to run VMD on it. Components should be as following: 2
> > Intel 6-Cores, around 32 GB RAM, Nvidia mainboard with SLI, and most
>
> > important, graphics card. As stated, I'll take SLI, so if one GPU is to
> > little, I'll take the advandage of havind the other one also. I still
>
> not sure, if there actually is a benefit from SLI on linux /w opengl.
> a colleague tried it and didn't see anything.
>
> > have some doubts, either to got with Nvidia Quadro FX 5800 4 GB or Nvidia
> > GeForce GTX 480, I must addmit i dont know the difference between the Quadro
> > and GeForce card so I'll take the best one of both models. Quadro is
> > around 2500 Euro and GeForce arround 350 Euro, so the equation seems to be
> > very simple. The reason why i doubt the Quadro card (besides the price ;-)
> > is the fact that a colleaque of mine bought one workstation with a Quadro FX
> > 5800 in it and was dissapointed, so was I, i tried to rotate a a system
> > sonsisting out of 1 000 000 atoms in PDB file format. As long as i stayed in
> > line representation, everything worked fine, but as soon as i used CPK, the
> > PC hanged, i could not move the system as i wished, i had to wait for
>
> this will happen with _any_ card. the Quadro FX5800 is pretty powerful.
> its graphics performance is roughly equivalent to a GTX 280. so the
> GTX 480 should be faster, but also _much_ hotter.
>
> to get better performance on high end graphics cards you should
> enable GLSL. this way, your CPU only needs to compute the centers
> and radii of spheres and GPU does the rest. that being said. for a 1M
> atom system, you will alway have the lines or points rep be much faster.
>
> i regularly visualize systems that are up to 10x larger and always use
> points or lines at point size 5 or larger together with depth cueing rather
> than GLSL as that is the only way to operate smooth enough. rendering
> those systems on the screen with a more detailed rep is more distracting
> than helpful, IMO. that being said, if i look at subsets of the system, i
> certainly use the higher quality visualization reps.
>
> > minutes until a rotation was performed. Or did i expect to much, could
> > someone tryed to to this on their own PC with a good graphics card and tell
> > me if i works.
>
> you are expecting far too much. you should also consider that with
> 1M atoms, you don't have much room for each atom, so what is the
> point to spend a lot of computing effort on a sphere or cylinder if
> that results in only a few pixels.
>
>
> > Secondly: would a a Tesla card accelerate VMD graphics if I used it for
> > visualisation only and dont perform any acctual GPU calculations? So, to
> > have a Tesla and a Quadro for instance.
>
> nope.
>
>
> > Third question: I perform MD calculations on a HPC cluster, the output i get
> > are checkpoint files, basically snapshots of the system for specific time
> > step. The file format is of following: 10 columns (atom number, atom type,
> > mass, x, y, z, v_x, v_y, v_z, E_pot). For a a smooth visualisation with VMD
> > i transform each file into a PDB file format and then glue them together
> > with an "END" inbetween each frame. This is recognized by VMD as a time
> > scale so i can run it as a movie. The problem is offcourse that i have a
> > huge single file, depending on the number of atoms and number of individual
> > frames, so VMD gets very slow. As i was told by Axel Kohlmeyer as a respond
> > on to my previous posts, it is due to the fact that PDB is first of all a
> > text format, having the data into binary format would improve the
> > performance. VMD uses some kind of a start configuration and a trajectory
> > file, both in binary format. Could someone explain me how i get my bunch of
> > files into this binary format(s).
>
> write a converter, or have your MD code output .dcd or .xtc directly,
> or write an interface to the VMD molfile plugin library.
>
> axel.
>
> >
> >
> > I thank you all in advance for any help i get.
> >
> >
> >
> > Regards
> >
> >
> >
> > Alen Prskalo
> >
> >
> >
> >
> >
> > Dipl.-Phys. Alen-Pilip Prskalo
> >
> > Institut für Materialprüfung, Werkstoffkunde und Festigkeitslehre IMWF
> >
> > Universität Stuttgart
> >
> > Pfaffenwaldring 32
> >
> > 70569 Stuttgart
> >
> > Tel: +49 711 685 62579
> >
> > Fax: +49 711 685 62635
> >
> > Email: alen-pilip.prskalo_at_mpa.uni-stuttgart.de
> >
> > Email: alen-pilip.prskalo_at_imwf.uni-stuttgart.de
> >
> >
> >
> >
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.