VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 27 2011 - 10:36:20 CDT

hi,

some comments.

first off, with a laptop one always has to consider the
"second dimension of performance", i.e. how does
absolute performance translate into weight and usability.
i personally consider a fast i/o (= solid state drive)
and lots of RAM, long battery life and tolerable weight
more important for the daily duties of a laptop. it may
be better and more cost efficient to get a moderate
desktop with good graphics _and_ a moderate laptop
than rolling both into one.

2011/9/27 Paweł Kędzierski <pawel.kedzierski_at_pwr.wroc.pl>:
> Dear VMD-users,
> I am cc'ing this answer to the list in case someone might find it useful (or
> would like to add/correct something).
>
> W dniu 27.09.2011 01:05, Dean Thorson pisze:
>
> Let me preface this email by saying that I am the father of a college
> student that uses NAMD and VMD.  I found your exchange on VMD-L as I was
> doing research for my daughter.  I got a call yesterday from her saying that
> her current laptop was failing quickly,  that she needed a new one and could
> I help find one that would be appropriate for normal college activity and be
> better suited to run NAMD and VMD when she is not using the super computer
> center.  I was hoping that the University of Illinois site would have
> recommendations but I couldn’t find anything current.  Talking to people at
> computer stores has proven of no value.  What I tried to find was real
> experience with current laptop hardware configurations and NAMD / VMD.  Your
> VMD-L question was one of the few I found.
>
> Dear Dean,
> Of course everything depends on the money you wish to spend, on the OS you
> use, and on your priorities. I will try to be general, anyway :-)
>
> As for VMD and NAMD, the first one wants good OpenGL support, while the
> second would benefit most from multi-core CPU; but there are CUDA versions
> of NAMD which could use NVidia graphics to speed up calculations.

decent graphics for VMD currently requires good OpenGL, depending
on the operating system choice only Nvidia or AMD graphics may be
acceptable.

> VMD already offers significant support for (some) calculations using CUDA on
> GPU, and support in NAMD appeared recently (I haven't tested it myself yet).

the GPU acceleration in VMD is limited to selected tools and
would be rarely if at all used by somebody using NAMD. apart
from the fact that even high-end mobile GPUs are significantly
slower than desktop models, the speedup in NAMD is also
bounded by memory transfer speed and that always tends to
be lower on laptops, so i would not expect much gain. better
to go for a more powerful (multi-core) CPU. _that_ will help
for _any_ parallel application.

> This kind of calculations is currently only possible with the proprietary
> CUDA libraries from NVidia, and this is the very reason that NVidia cards
> are recommended for VMD and NAMD. With a decent card, such calculations may
> be a few to several tens times quicker than on central processor, but these
> numbers were obtained using desktop setups or even high-end power-hungry
> workstations.
>
> For the info below concerning NVidia please accept my disclaimer as it is
> what I remember from various sources, from the time I did my research on
> this subject a few months ago.
> NVidia offers two lines of GPUs available for laptops: the "professional"
> Quadro cards, and the rest is for mass-market of gamers. Actually they seem
> to be powered by the similar chip architectures but sometimes stripped down
> in hardware (like having some processor cores disabled) or tied to specific
> drivers. The Quadro cards are expensive and their performance is tuned
> against business and scientific applications, while they perform poorly (or
> even don't work) with games. They are also relatively infrequent and may
> limit your choice to relatively few top-of-the-shelf machines.
> The gaming cards might have more memory, more cores and higher clock for
> lower price, but they performance with CUDA is reduced because only some of
> the GPU cores are available for CUDA calculations. I have also read
> somewhere, that some specific OpenGL functions (useful for pro apps and not
> for gaming) are unusually slow with cards other than Quadro or Tesla branded
> ones. I do not know if or how it may affect VMD or NAMD.

OpenGL is mainly require by VMD for stereo display. that is rarely needed
when using a laptop, so quadro would be a waste of money.

> Taking the above into account, I looked for a laptop with NVidia but not
> necessarily something high-end, to be able at least to setup and test GPU
> calculations prior to running them on something better.
>
> Personal experience:
> I am very pleased with my i7 SandyBridge CPU as I already tested
> calculations using 8 cores in parallel (4 physical with HT) and even with
> reported 8x100% CPU usage the machine was still very responsive for
> interactive work, I could even watch fullscreen video without any glitches
> (note this was on Linux).
> The weakest point on the Dell XPS2 seem to be the cooling system, because I
> during such calculations I observed regular (short) drops from 100% to 0%
> CPU usage for a half or all of the cores for no apparent reason. These
> accounted only for some small fraction of time so it wasn't that bad. These
> could be IO related bottlenecks, but I think it is related to inadequate
> cooling since with just two cores on 100%CPU the fan was already working on
> max rpm. It might get worse in case both the Nvidia chip and the CPU are on
> full steam (I have not tested it like this), but I believe that even in this
> case a quad-core should do parallel calculations faster than a two-core
> processor.
>
> From my own experience with VMD on this new laptop, the Intel SandyBridge i7
> integrated graphics is 30-50 times slower with OpenGL display than NVidia
> GT540M (measured with VMD FPS display). I would say that for visualization

FPS measurements are flawed when comparing to intel graphics.
the intel drivers restrict the FPS to the refresh rate of the screen
(typically 60 FPS). however, the performance of the intel chipset
graphics is pretty sad and often OpenGL support is incomplete
and/or being lied about (with the linux drivers).

axel.

> the integrated graphics is not recommendable, as even small proteins with
> high detail settings bog down the performance to 1-5 FPS and the movement
> gets very jerky. That said, it is at least usable with small systems and not
> too demanding graphical representations.
>
> My previous rather old laptop had an AMD Radeon 9000M card with 32MB of RAM
> and it worked quite well with VMD for display with modestly sized structures
> and with default detail settings (up to a few tens of thousands of atoms).
> It was however unable to render surfaces from volumetric data like electron
> density or electrostatic potential, due to insufficient graphics memory.
> Right now it seems that AMD chips offer more performance per dollar than
> NVidia ones when comes to 3D graphics, so if your daughter does not need any
> CUDA support, an AMD card could work well.
>
> Another word of caution:
> Currently it is hard to find a laptop with i3-i7 CPU and NVidia GPU without
> so-called Optimus technology. As you said nothing about the OS, I assume
> Windows 7, and to my knowledge this is the only system where programs can
> use the NVidia GPU with Optimus out of the box.
>
> Since I am mostly Linux user, I hesitated with the purchase until I found a
> successful solution for Linux:
> http://www.martin-juhl.dk/2011/05/optimus-on-linux-problem-solved/
> The offspring of this idea are two independent projects (bumblebee and
> ironhide) but neither one is mature yet so this is something for advanced
> users.
>
> If you are willing, I would be interested in how you selected your hardware
> configuration and any recommendations on what to consider.
>
> I opted for quad-core Intel CPU and modestly priced (that is, gaming level)
> NVidia card with many CUDA cores and large memory. I do not know how large
> calculations your daughter will run but a lot of RAM (6GB or more) and HDD
> space is probably recommendable, too. Having a lot of money to spend you may
> want to get an SDD drive for the sake of speed and robustness on the go, but
> in this case I would say that an external large HDD with fast connection
> (USB 3.0 or at least eSATA) is essential.
> For selection of a specific GPU, you may find this page useful (the
> description is for GT540M but on the left you will find a long list of links
> to other cards, sorted by performance):
> http://www.notebookcheck.net/NVIDIA-GeForce-GT-540M.41715.0.html
>
> Note that the better cards are only mounted in larger laptops due to power
> consumption. My DELL XPS is declared a 15 inch machine (15,6'' actually) but
> it is rather comparable to 16'' ones and seems relatively HUGE in comparison
> with my old 14'' one having good old golden-aspect ratio display. It weighs
> about 3kg itself but its 120W power supply is kind of a brick (probably
> another kg or more) and this together is quite a lot to carry around the
> campus, especially for a girl.
>
> And running calculations on battery is not recommended: with all CPU cores
> running on 100%  the battery life is 30-40min, compared to about 4h without
> load.
>
> Thank you for any information you can provide.
>
> You are welcome.
> Greetings,
> Pawel Kedzierski
>
> 

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