From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Wed Sep 23 2015 - 17:41:11 CDT

You say that in your machine at home you have SSDs. Do you use the flag
"discard" in fstab or do you run fstrim as a cron job?

I would also appreciate if you could share what brand (and size) you have?
It would help me get an idea and make up my mind.

Thanks,

      Gianluca

On Wed, 23 Sep 2015, John Stone wrote:

> Hi,
> Yes, SSDs are definitely going to be much more epensive, so
> they have to be worth it for your daily use.
>
> Your price for the 1.2TB Intel PCIe SSD was off by a factor of two.
>
> Intel 750 1.2TB PCIe SSD $1052 at Amazon:
> http://www.amazon.com/Intel-Series-1-2TB-Internal-SSDPEDMW012T4R5/dp/B00UHJJQ3Q
>
> Cheers,
> John
>
> On Wed, Sep 23, 2015 at 02:28:07PM -0700, Gianluca Interlandi wrote:
>> The other question in the decision SSD vs HDD is the price tag. A 1 TB
>> Samsung Evo 850 Pro costs 470$, 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.
>> -----------------------------------------------------
>
> --
> 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.
-----------------------------------------------------