VMD-L Mailing List

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Sep 23 2015 - 16:28:07 CDT

The other question in the decision SSD vs HDD is the price tag. A 1 TB
Samsung Evo 850 Pro costs 470$, a 1 TB Intel costs ~ 600$ and a PCIe Intel
1 TB is over 2000$. On the other hand, a 4 TB WD 7200RPM is under 200$.

Gianluca

On Wed, 23 Sep 2015, John Stone wrote:

> Hi,
> I would echo Axel's comments about using mirroring, particularly
> for individual usage. For large systems using RAID-6 is okay, but
> it's definitely more work than mirroring. We have a few petabytes of
> storage here, and we lose a hard drive about once per two or three
> weeks. Every time there's a drive failure the RAID-6 rebuild takes
> about 2 days, during which that particular RAID partition runs really slow...
>
> For our large storage system we couldn't afford to use mirroring, but
> for smaller systems, that's definitely what I would recommend.
>
> One thing that mirroring doesn't save you from is user errors....
> On filesystems like Solaris/Linux ZFS, you can use filesystem snapshotting
> to deal with that. On more primitive filesystems like ext2/3/4 or xfs,
> you are left using backups as the main mechanism of recovery.
>
> On my machine at home I have SSDs w/ ext4 as my main storage, but I do
> complete dumps of the SSDs to magnetic mechanical drives on a
> regular basis. If the SSD fails, I have a recovery path, and if
> I did 'rm -rf' in the wrong place, I could also recover from a previous
> dump.
>
> I would be using ZFS on my linux box at home, but I wanted the linux
> version to settle a bit before I really start using it. We use ZFS
> here on Solaris file servers and it's awesome with the commercial
> implementation...
>
> Cheers,
> John Stone
>
>
> On Wed, Sep 23, 2015 at 03:52:43PM -0400, Axel Kohlmeyer wrote:
>> On Wed, Sep 23, 2015 at 3:11 PM, John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>>
>> Hi,
>> A 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.A The margin of improvement is greater with
>> faster storage systems.A 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.A 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.A We have been playing around with
>> the Intel 750 series PCIe SSDs and they have been working quite well
>> so far.A 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.
>>
>> a**even with backups, the size of current storage systems (regardless
>> whether spinning disk or solid state) makesa** 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.
>> A
>>
>> 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,
>> A John Stone
>> A [2]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,
>> >
>> >A A A 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:
>> >> [3]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.,
>> >>>
>> >
>> >>[4]https://www.reddit.com/r/buildapc/comments/3a58s0/dont_use_linux_on_samsung_ssds/
>> >>>
>> >>>Thanks,
>> >>>
>> >>>A A A Gianluca
>> >>>
>> >>>-----------------------------------------------------
>> >>>Gianluca Interlandi, PhD [5]gianluca_at_u.washington.edu
>> >>>A A A A A A A A A A +1 (206) 685 4435
>> >>>A A A A A A A A A A
>> [6]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
>> >>[7]http://www.ks.uiuc.edu/~johns/A A A A A A Phone: 217-244-3349
>> >>[8]http://www.ks.uiuc.edu/Research/vmd/
>> >>
>> >
>> > -----------------------------------------------------
>> > Gianluca Interlandi, PhD [9]gianluca_at_u.washington.edu
>> >A A A A A A A A A A A +1 (206) 685 4435
>> >A A A A A A A A A A
>> A [10]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
>> [11]http://www.ks.uiuc.edu/~johns/A A A A A A Phone: 217-244-3349
>> [12]http://www.ks.uiuc.edu/Research/vmd/
>>
>> --
>> Dr. Axel Kohlmeyer A [13]akohlmey_at_gmail.com A [14]http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>> References
>>
>> Visible links
>> 1. mailto:johns_at_ks.uiuc.edu
>> 2. mailto:johns_at_ks.uiuc.edu
>> 3. http://dx.doi.org/10.1007/978-3-642-24031-7_1
>> 4. https://www.reddit.com/r/buildapc/comments/3a58s0/dont_use_linux_on_samsung_ssds/
>> 5. mailto:gianluca_at_u.washington.edu
>> 6. http://artemide.bioeng.washington.edu/
>> 7. http://www.ks.uiuc.edu/~johns/
>> 8. http://www.ks.uiuc.edu/Research/vmd/
>> 9. mailto:gianluca_at_u.washington.edu
>> 10. http://artemide.bioeng.washington.edu/
>> 11. http://www.ks.uiuc.edu/~johns/
>> 12. http://www.ks.uiuc.edu/Research/vmd/
>> 13. mailto:akohlmey_at_gmail.com
>> 14. http://goo.gl/1wk0
>
> --
> 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.
-----------------------------------------------------