VMD-L Mailing List

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Sep 23 2015 - 14:24:18 CDT

Hi John,

Sorry, I need to ask for some help. How do I tell NAMD to write a .js
trajectory instead of .dcd? I cannot find this under "File formats" in the
NAMD manual.

Thanks,

      Gianluca

On Wed, 23 Sep 2015, John Stone wrote:

> Hi,
> If you want peak performance from an SSD, you would want to use
> the "js" trajectory format with VMD and NAMD rather than DCD, as
> shown in that paper, it outruns DCD (and all others I'm aware of)
> by a significant margin. The margin of improvement is greater with
> faster storage systems. The 'js' file is also faster than DCD files
> even on magnetic mechanical drives/RAIDs, etc.
>
> An SSD with a proper TRIM implementation, when used on an
> OS that has correctly working TRIM support, should not exhibit decreasing
> write performance over time. That said, I've used SSDs under very suboptimal
> conditions with hardware that didn't use TRIM (some RAIDS) and with OS
> kernels and filesystem drivers that didn't support TRIM, and even there,
> they still greatly outperform mechanical drives.
>
> If want both speed and reliability, you might look at the new
> PCIe based SSDs Intel makes. We have been playing around with
> the Intel 750 series PCIe SSDs and they have been working quite well
> so far. They are very fast (faster than some RAIDS I built previously)
> and they are simple to install and use.
>
> I think reliability is primarily an issue with the choice of vendor,
> but my own advice is that you should never store ANY data you care
> about without also having backups on a second storage device.
>
> I've never had an SSD fail on me thus far, but I've had a large number
> of mechanical hard drives fail on me over the years.
>
> Cheers,
> John Stone
> johns_at_ks.uiuc.edu
>
> On Wed, Sep 23, 2015 at 11:57:22AM -0700, Gianluca Interlandi wrote:
>> Thanks for the reply. I read from Table 2 that for a 1-3 million atoms
>> system you get a 2.5 to 2.6 speed up using a SSD vs HDD while reading a
>> DCD file. I do not plan to build a RAID with it and I want to use it in a
>> desktop PC. What about reliability of consumer's SSDs? I'm leaning towards
>> stability and reliability vs speed. Also, does write performance decrease
>> over time even when using TRIM in linux?
>>
>> Thanks,
>>
>> Gianluca
>>
>> On Wed, 23 Sep 2015, John Stone wrote:
>>
>>> Hi,
>>> SSDs can give a huge performance benefit to MD trajectory processing.
>>> I wrote a paper in 2011 that describes this in some detail, where I
>>> got VMD to read trajectories at several gigabytes per second using
>>> multiple SSDs in a RAID:
>>> http://dx.doi.org/10.1007/978-3-642-24031-7_1
>>>
>>> The performance does depend somewhat on the trajectory file format,
>>> and my paper describes those issues in some detail also.
>>>
>>> Cheers,
>>> John
>>>
>>> On Wed, Sep 23, 2015 at 11:22:06AM -0700, Gianluca Interlandi wrote:
>>>> Dear all,
>>>>
>>>> Does anybody have experience using a SSD or combined mechanical/SSD drive
>>>> for reading large trajectories into VMD? Do any of the two provide a speed
>>>> up compared to conventional hard disks? Also, how well are SSD/SSHD
>>>> supported in Linux?
>>>>
>>>> I was considering ordering a Samsung Evo 850 Pro until I read some
>>>> negative reports, e.g.,
>>>>
>>>> https://www.reddit.com/r/buildapc/comments/3a58s0/dont_use_linux_on_samsung_ssds/
>>>>
>>>> Thanks,
>>>>
>>>> Gianluca
>>>>
>>>> -----------------------------------------------------
>>>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>>>> +1 (206) 685 4435
>>>> http://artemide.bioeng.washington.edu/
>>>>
>>>> Research Assistant Professor at the Department of Bioengineering
>>>> at the University of Washington, Seattle WA U.S.A.
>>>> -----------------------------------------------------
>>>
>>> --
>>> NIH Center for Macromolecular Modeling and Bioinformatics
>>> Beckman Institute for Advanced Science and Technology
>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/
>>>
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> http://artemide.bioeng.washington.edu/
>>
>> Research Assistant Professor at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------