VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 23 2015 - 15:44:15 CDT

At present I don't think NAMD will let you write a js
format trajectory yet, and you would need to use 'catdcd'
to convert from dcd to js format. This is something we're working
on going forward. I'll ask my NAMD developer colleagues if there's
a flag that I don't know about to allow them to be written using
js files from the outset...

Cheers,
  John

On Wed, Sep 23, 2015 at 12:24:18PM -0700, Gianluca Interlandi wrote:
> 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.
> ----------------------------------------------------- 

-- 
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/