From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Sep 23 2015 - 14:52:43 CDT

On Wed, Sep 23, 2015 at 3:11 PM, John Stone <johns_at_ks.uiuc.edu> 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.
>

‚Äčeven with backups, the size of current storage systems (regardless whether
spinning disk or solid state) makes‚Äč a drive failure a major PITA. also,
murphy's law dictates that a failure will come at the most inconvenient
moment. thus for any serious use, i always use and recommend to use RAID-1
or RAID-0 over RAID-1 setups. that will give you increased resilience
without loss of performance (unlike RAID-5/6). the cost of storage devices
has come down so much, that it doesn't really make that much of a
difference unless you need to store/archive a very large amount of data.
always consider the cost of your time that you have to spend on restoring
from a backup. that said, backups (or rotating/redundant media!) and
reasonably structured archival are an absolute necessity as well.

axel.

>
> 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/
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.