VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 23 2015 - 14:11:51 CDT

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/