VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.wroc.pl)
Date: Wed Sep 28 2011 - 04:07:30 CDT

Dear Dean,

If you are happy enough with 2 physical CPU cores, there is a small and
light DELL Alienware M11x with i5, Nvidia graphics and 7 hours battery
life... This will be more than sufficient for VMD, running small NAMD
calculations or setup larger ones for the supercomputers. Maybe other
vendors offer something competitive.

I would not recommend any integrated graphics for serious use with VMD
unless she has access to a remote display server with VMD installed
there. However, relying on the network connection and on software
installed somewhere out of her control may turn out to be a major problem.

There is one more thing to consider which i missed previously: screen
space. My students using nettops with 600 pixel vertical resolution had
hard time using some NAMD-related VMD plugin (Automatic PSF Builder)
because the dialog window was higher than the screen and the "OK" button
was unreachable below the bottom. A detail, but could be annoying :-(. I
believe she will need at least 720p vertical resolution.
For myself screen space is more important than portability and I
wouldn't get anything smaller than 14'' FullHD, but that's personal
preference.

Instead of sightseeing the shelves I would advice you to go to a web
page of any large vendor and to configure a machine, starting from the
requirements you consider the most important ones.
For example, if you go to www.dell.com, then choose "laptops" from the
"For Home" menu, then select "Intel i7 core processor" checkbox on the
left, you will get 17 models with form factors varying from 11'' to
17'', and you can configure the rest of stuff inside like disc, optical
drive, memory, display and graphics (although choices are limited).
BTW, read the specs carefully or check on Intel pages as there are also
two-core i7 processors, e.g 2617M; note also they tend to advertise
"virtual cores" which number is 2x "physical cores" due to hyperthreading.

I see that with 14'' Alienware M14x you could have a quad core i7 and
NVidia GT 555M, but the weight seems similar to 15,6'' XPS which is not
too light.

With a quad-core CPU and dedicated performance graphics, I don't think
you will find a laptop that will last 7 or more hours on battery, but
3-4 hours with office apps and music are possible. The current mobile
hardware has very flexible power management. E.g. this Optimus
technology basically means that the Nvidia graphics is switched off (or
"sleeping") until specifically requested to be used by software which
needs it.

I agree with Axel that Unix tools are indispensable for analysis of such
calculations but this is something for power users with scripting (that
is, programming) skills. If your daughter learns this she may want to
install Linux as a second OS; but it may also run virtualized within
Windows; there also is www.cygwin.org (a package of Unix programs and
tools to be installed on Windows). Therefore it is not a must (for a
Windows user) to consider hardware supported by Linux.

Greetings,
Pawel

W dniu 27.09.2011 23:24, Axel Kohlmeyer pisze:
> 2011/9/27 Dean Thorson<deanthorson_at_hotmail.com>:
>> Thanks for the quick and helpful responses. I am very appreciative. My daughter has asked the few people that she knows who run NAMD / VMD and no one has any recommendations. The super computer people just like to use the super computer. She always likes to setup simulations on her notebook before she uses the super computer. Many times she just uses her notebook (currently very old and slow).
>>
>> I did ask her to consider the laptop / desktop scenario but she does her research at two different schools and she wants to be portable. As you noted, many of the higher end laptops have 17" screens and big bricks, a size and weight that is impractical to lug around the campus on a frequent basis. These are not an option. She will need to balance performance and portability (and cost).
>>
>> As for the type of system, you guessed right, she will be purchasing a Windows 7 notebook. Besides VMD and NAMD she does the standard college stuff: MS Office (lots of MS Word, PowerPoint and very large Excel spreadsheets), iTunes always playing, Netflix, NX client, etc.
> in my opinion, all those requirements are impossible to fit. full stop.
>
> some choices need to be made or your daughter should consider
> changing her workflow. the latter is what i would recommend, and
> it will be _very_ helpful in the long run. most of the NAMD related
> work is text mode and scripts and thus a major PITA on a windows
> machine and much easier to do on a unix/linux PC or the
> corresponding cluster frontend.
>
> the way to tie this together could be to use a "remote desktop"
> setup. i.e. run Xnvc on the machine where the work is done and then
> use a vnc viewer on the laptop (or other machines) and connect to
> the Xvnc server. one of my colleagues uses that to work on his desktop
> from home and on the road (where he uses a small netbook).
>
> check out, e.g., http://www.tightvnc.com/
>
> i personally put extremely high emphasis on portability and
> battery life, since i travel a lot. so decent OpenGL graphics is
> out of the question and i have adapted my laptop usage
> accordingly.
>
> axel.
>
>> When you stop at the various stores you see many manufacturers (15.6" screens) using the Intel i3 or i5 dual core processor with Intel graphics or the new AMD A8-3500m APU quad core processor with on-chip integrated Radeon HD 6620G. The A8 is interesting in that is advertises lower power consumption and is lower priced but displays varied performance results based on what you are doing (good article at http://hothardware.com/Reviews/AMD-Fusion-A83500M-ASeries-Llano-APU-Review/ ). I've never seen the A8-3500M in a VMD benchmark! There are a few 15.6" Intel i7-2630QM machines with nVidia GT 525M, 540M or 555M (Samsung, Dell, Lenovo) or Radeon HD 6670M (HP) on the shelves. More of the off-the-shelf i7's seem to be found in the high end gaming focused hardware that is big and heavy.
>>
>> Your comments lead me to the i7 because of its quad structure and overall performance. I hope that in standard MS Office kind of work that the battery life will be sufficient for her normal around campus activities. For simulations she will need to be plugged in.
>>
>> The comment about VMD / OpenGL and operating system caused me to question the nVidia requirement. I'm not sure how to compare the i7 nVidia 525/540/555M vs the i7 Radeon 6670M.
>>
>> Thanks again for your time and all the information. I remember the first time she got NAMD and VMD to run on her Windows 7 notebook, she was excited and had to show everyone. Whatever choice she makes for a new notebook it will be a welcomed improvement over her current situation.
>>
>> p.s. We need to get the manufacturers or magazines to publish some research tools based benchmarks, not just the many repetitive gaming benchmark sites.
>>
>>
>> -----Original Message-----
>> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
>> Sent: Tuesday, September 27, 2011 10:36 AM
>> To: Paweł Kędzierski
>> Cc: Dean Thorson; vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: Re: Selecting a laptop for VMD and NAMD (was: CUDA cores seen by VMD on GT540M)
>>
>> 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.
>>
>>
>
>