From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Sep 23 2015 - 13:57:22 CDT

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.
-----------------------------------------------------