Re: CONFOCALMICROSCOPY Digest - 7 May 2018 to 8 May 2018 (#2018-106)

[Jared K. Buks]

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We have two 12 bay NAS systems from Synology.  We like the 12 bay because we can have 2 redundant drives so data loss is a minimal issue with a RAID configuration as we would have to have 3 drive failures to lose the NAS.  This gives us the capacity of 10 drives for storage and with the 8-10TB drives gives a considerable amount of data storage.  These are also very economical storage from our perspective.  The other commenters have covered most of the other specifics.

Jared

Jared K. Burks, PhD
Assistant Professor
Co-Director, Flow Cytometry & Cellular Imaging Core Facility
Department of Leukemia
M.D. Anderson Cancer Center Unit 0425
1515 Holcombe Blvd. Y8.5311a
Houston, TX  77030
713-792-6592

-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of CONFOCALMICROSCOPY automatic digest system
Sent: Wednesday, May 9, 2018 12:02 AM
To: [hidden email]
Subject: CONFOCALMICROSCOPY Digest - 7 May 2018 to 8 May 2018 (#2018-106)

There are 3 messages totaling 226 lines in this issue.

Topics of the day:

  1. Data storage - NAS servers (3)

----------------------------------------------------------------------

Date:    Tue, 8 May 2018 15:41:29 -0500
From:    Adam Glaser <[hidden email]>
Subject: Data storage - NAS servers

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Hello everyone,

We are currently exploring in lab data storage options for storing the large amounts of data our light-sheet microscopes are producing (while simultaneously providing shared access from multiple PCs for processing and/or visualization).  Given these needs, we have tentatively arrived at purchasing a NAS server.  I was wondering if anyone had suggestions or recommendations on the best companies/options available.  In preliminary searching I have seen FreeNAS pop up several times, but am quite a novice when it comes to data storage - so any input from the listserv would be greatly appreciated!

Thanks!
Adam

------------------------------

Date:    Tue, 8 May 2018 17:07:27 -0400
From:    Michael Giacomelli <[hidden email]>
Subject: Re: Data storage - NAS servers

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*****

Hi Adam,

We use 12 bay Synology NAS devices.  Currently the RS2416RP+ model.
Each rack mount device can further support an expansion bay, for a total of 24 disks per device.  Cost for the base device is about 2300, then when that fills up, another 1200 for an expansion bay.  That works out to be about 3500 worth of server per 24 disks, or $150 of server per disk.

Setup and management is easy, the software automatically updates itself, emails you if there is a problem or disk failure.  We run two disk redundancy per 12 disk set.  Performance is acceptable for what we do (dump a few hundred GB of images at a time into long term
storage) but you could do better if you needed, the CPUs are quite slow.

We have bought them from SimplyNAS before.  They are ok, although they did mess up one order in the past and we had to exchange the hardware they sent, but we like that they will bundle the disks in with the unit, which is helpful for us for accounting reasons.  There are many other vendors (Amazon, etc). BackBlaze publishes disk reliability, so we typically buy what they say is reliable:
https://www.backblaze.com/b2/hard-drive-test-data.html

You can do cheaper using PC hardware and storage optimized linux distros, but we typically run the racks for ~7 years before retiring them, which means you need to make sure someone will be around that knows how to rebuild a RAID array when a disk fails, which happens from time to time.  We were concerned about this since students leave over time and we don't necessarily have someone available any given year who knows older linux systems.

Mike

On Tue, May 8, 2018 at 4:41 PM, Adam Glaser <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hello everyone,
>
> We are currently exploring in lab data storage options for storing the large amounts of data our light-sheet microscopes are producing (while simultaneously providing shared access from multiple PCs for processing and/or visualization).  Given these needs, we have tentatively arrived at purchasing a NAS server.  I was wondering if anyone had suggestions or recommendations on the best companies/options available.  In preliminary searching I have seen FreeNAS pop up several times, but am quite a novice when it comes to data storage - so any input from the listserv would be greatly appreciated!
>
> Thanks!
> Adam

------------------------------

Date:    Tue, 8 May 2018 23:56:11 -0400
From:    Menelaos Symeonides <[hidden email]>
Subject: Re: Data storage - NAS servers

*****
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*****

Hi Adam,

(warning: long email ahead)

For our iSPIM we have the 8-bay Synology DS1817+ (about $900-$1000) loaded with 8 x Western Digital Gold WD101KRYZ 10 TB hard drives (about
$400 each), and set up in SHR-2 mode (which is basically RAID-6, i.e.
2-disk redundancy) which leaves about 60 TB of usable space. I also installed an Intel X520-DA2 10GbE adapter as the integrated Gigabit Ethernet connection would bottleneck the speed of the drive array, I was able to find one of those for $150 but it was a refurb. You'll also need a 10GbE adapter for your PC and the appropriate SFP+ cable(s).

Once this fills up, and we have exhausted all possibilities of compressing or discarding data, I think we will just buy another one as opposed to buying an expansion bay for this one, as the expansion bay runs on the eSATA connector and is therefore limited in speed, so you get no speed gains from any RAID array that's in the expansion bay.

Just be aware that, with regular SATA 7.2K pm HDDs (i.e. not SSDs or 15K rpm SAS drives), the best real-world performance you will ever get (with an 8-drive RAID-6 array over 10GbE) is about 160-170 MB/s read (that's bytes, not bits) and 270 MB/s write. Teaming two 10 GbE connections by link aggregation does nothing for real-world performance, it's just for failover redundancy in case one port or one cable dies mid-transfer - for speed benefits you need to optimize your operations to split up your packet stream across each link, which is not trivial. These speeds are way lower than what you get with a benchmarking tool like CrystalDiskMark - always pays to do real-world work to figure out how something performs.

This kind of performance means that you can pretty much forget any multi-user applications with this kind of NAS for large imaging datasets. You will just not be able to provide access for anything more than someone copying their data off to their own system to then process and analyze off a local drive/array, and you should only allow one user to be logged in at a time or they will all complain that it's taking ages. Also, if you'll be using your building's built-in Ethernet wiring, it's unlikely that it will be capable of 10GbE performance, so really you'll end up asking people to bring their portable drive down to you and copy the data right off as it'll end up being 2-3x faster (of course, that also presumes that their portable drive isn't bottlenecking either). I also have a 6 TB RAID-0 SSD array in my workstation PC, so whenever I need to process/analyze data, I copy it off the NAS to the SSD RAID over the 10GbE connection, do all the work on the SSD RAID, and then copy it back to the NAS for storage.

If you want to actually serve large datasets directly to multiple simultaneous users, these Synology units will just not cut it. You'll need an enterprise solution, e.g. something from Dell, HP, or NetApp, which will cost somewhere in the tens of thousands USD for anything close to the 60 TB I mentioned. These will run large arrays of either SSDs (super expensive) or at least fast SAS HDDs (only very expensive), and will run on a multi-CPU Xeon platform with tons of RAM that is capable of handling multiple users. The Synology units have really awful CPUs and very low RAM, which can just barely handle a single user.
You'll also need the necessary infrastructure in your building to allow remote users to connect at 10GbE speeds (and have them install 10GbE adapters in their computers), or it will totally defeat the point of having spent all that money on the enterprise server.

If you're really nuts you can try to build your own and could conceivably get performance close to what these enterprise units get for somewhat less money, but you really need to know what you're doing. Plus you will be entirely responsible for servicing it. You'll need to have a drive failure plan because server performance will tank for several days if you have to replace a failed drive and have to rebuild the array - your users will be very unhappy during the rebuild, and the larger the array/the slower the drives, the longer the rebuild will take.

Honestly, institutions that host big data labs will sooner or later need to start taking responsibility for the data if they are going to expect their labs to continue doing their work and bringing in grant money for the institution. It makes much more sense for there to be an institutional "data core facility" to maximize cost efficiency in purchasing these servers, buildings will need to be rewired with fiber, and personnel will need to be hired to maintain these servers and provide user support, all of which costs institutions $$$, so good luck with that.

No commercial interest for anything I mentioned.

Mel


On 5/8/2018 4:41 PM, Adam Glaser wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hello everyone,
>
> We are currently exploring in lab data storage options for storing the large amounts of data our light-sheet microscopes are producing (while simultaneously providing shared access from multiple PCs for processing and/or visualization).  Given these needs, we have tentatively arrived at purchasing a NAS server.  I was wondering if anyone had suggestions or recommendations on the best companies/options available.  In preliminary searching I have seen FreeNAS pop up several times, but am quite a novice when it comes to data storage - so any input from the listserv would be greatly appreciated!
>
> Thanks!
> Adam
>

--
Menelaos Symeonides
Post-Doctoral Associate, Thali Lab
Department of Microbiology and Molecular Genetics University of Vermont
318 Stafford Hall
95 Carrigan Dr
Burlington, VT 05405
[hidden email]
Phone: [phone]

------------------------------

End of CONFOCALMICROSCOPY Digest - 7 May 2018 to 8 May 2018 (#2018-106)
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[mcammer]

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*****

We recommend a direct fiber connection from light sheet to any server & analysis computers.

Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
[hidden email]  http://nyulmc.org/micros  http://microscopynotes.com/ 
Cell: 1-914-309-3270  --  Office direct (do not leave voicemail):  1-646-501-0567



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Burks,Jared K
Sent: Wednesday, May 9, 2018 9:05 AM
To: [hidden email]
Subject: Re: CONFOCALMICROSCOPY Digest - 7 May 2018 to 8 May 2018 (#2018-106)

*****

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Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=M5FeCeiMzIQ5-iETJRr9Yj1K04gsumnZfd8V-zDvMMA&s=9y-bhsVji368bT0ErLLVvtIbUhQR7K4K41C401H7D1g&e= and include the link in your posting.

*****



We have two 12 bay NAS systems from Synology.  We like the 12 bay because we can have 2 redundant drives so data loss is a minimal issue with a RAID configuration as we would have to have 3 drive failures to lose the NAS.  This gives us the capacity of 10 drives for storage and with the 8-10TB drives gives a considerable amount of data storage.  These are also very economical storage from our perspective.  The other commenters have covered most of the other specifics.



Jared



Jared K. Burks, PhD

Assistant Professor

Co-Director, Flow Cytometry & Cellular Imaging Core Facility

Department of Leukemia

M.D. Anderson Cancer Center Unit 0425

1515 Holcombe Blvd. Y8.5311a

Houston, TX  77030

713-792-6592



-----Original Message-----

From: Confocal Microscopy List <[hidden email]> On Behalf Of CONFOCALMICROSCOPY automatic digest system

Sent: Wednesday, May 9, 2018 12:02 AM

To: [hidden email]

Subject: CONFOCALMICROSCOPY Digest - 7 May 2018 to 8 May 2018 (#2018-106)



There are 3 messages totaling 226 lines in this issue.



Topics of the day:



  1. Data storage - NAS servers (3)



----------------------------------------------------------------------



Date:    Tue, 8 May 2018 15:41:29 -0500

From:    Adam Glaser <[hidden email]>

Subject: Data storage - NAS servers



*****

To join, leave or search the confocal microscopy listserv, go to:

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Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=M5FeCeiMzIQ5-iETJRr9Yj1K04gsumnZfd8V-zDvMMA&s=9y-bhsVji368bT0ErLLVvtIbUhQR7K4K41C401H7D1g&e= and include the link in your posting.

*****



Hello everyone,



We are currently exploring in lab data storage options for storing the large amounts of data our light-sheet microscopes are producing (while simultaneously providing shared access from multiple PCs for processing and/or visualization).  Given these needs, we have tentatively arrived at purchasing a NAS server.  I was wondering if anyone had suggestions or recommendations on the best companies/options available.  In preliminary searching I have seen FreeNAS pop up several times, but am quite a novice when it comes to data storage - so any input from the listserv would be greatly appreciated!



Thanks!

Adam



------------------------------



Date:    Tue, 8 May 2018 17:07:27 -0400

From:    Michael Giacomelli <[hidden email]>

Subject: Re: Data storage - NAS servers



*****

To join, leave or search the confocal microscopy listserv, go to:

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Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=M5FeCeiMzIQ5-iETJRr9Yj1K04gsumnZfd8V-zDvMMA&s=9y-bhsVji368bT0ErLLVvtIbUhQR7K4K41C401H7D1g&e= and include the link in your posting.

*****



Hi Adam,



We use 12 bay Synology NAS devices.  Currently the RS2416RP+ model.

Each rack mount device can further support an expansion bay, for a total of 24 disks per device.  Cost for the base device is about 2300, then when that fills up, another 1200 for an expansion bay.  That works out to be about 3500 worth of server per 24 disks, or $150 of server per disk.



Setup and management is easy, the software automatically updates itself, emails you if there is a problem or disk failure.  We run two disk redundancy per 12 disk set.  Performance is acceptable for what we do (dump a few hundred GB of images at a time into long term

storage) but you could do better if you needed, the CPUs are quite slow.



We have bought them from SimplyNAS before.  They are ok, although they did mess up one order in the past and we had to exchange the hardware they sent, but we like that they will bundle the disks in with the unit, which is helpful for us for accounting reasons.  There are many other vendors (Amazon, etc). BackBlaze publishes disk reliability, so we typically buy what they say is reliable:

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.backblaze.com_b2_hard-2Ddrive-2Dtest-2Ddata.html&d=DwIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=M5FeCeiMzIQ5-iETJRr9Yj1K04gsumnZfd8V-zDvMMA&s=TRZ20lW8v-z4QJEq5ubpw68nzlZSdUSoFw365289_cU&e=



You can do cheaper using PC hardware and storage optimized linux distros, but we typically run the racks for ~7 years before retiring them, which means you need to make sure someone will be around that knows how to rebuild a RAID array when a disk fails, which happens from time to time.  We were concerned about this since students leave over time and we don't necessarily have someone available any given year who knows older linux systems.



Mike



On Tue, May 8, 2018 at 4:41 PM, Adam Glaser <[hidden email]> wrote:

> *****

> To join, leave or search the confocal microscopy listserv, go to:

> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.umn.edu_cgi-2Dbin_wa-3FA0-3Dconfocalmicroscopy&d=DwIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=M5FeCeiMzIQ5-iETJRr9Yj1K04gsumnZfd8V-zDvMMA&s=HisXrg0ILaPaBaMk8RGG3mixND9UJAxvaGxId0cNwfQ&e=

> Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=M5FeCeiMzIQ5-iETJRr9Yj1K04gsumnZfd8V-zDvMMA&s=9y-bhsVji368bT0ErLLVvtIbUhQR7K4K41C401H7D1g&e= and include the link in your posting.

> *****

>

> Hello everyone,

>

> We are currently exploring in lab data storage options for storing the large amounts of data our light-sheet microscopes are producing (while simultaneously providing shared access from multiple PCs for processing and/or visualization).  Given these needs, we have tentatively arrived at purchasing a NAS server.  I was wondering if anyone had suggestions or recommendations on the best companies/options available.  In preliminary searching I have seen FreeNAS pop up several times, but am quite a novice when it comes to data storage - so any input from the listserv would be greatly appreciated!

>

> Thanks!

> Adam



------------------------------



Date:    Tue, 8 May 2018 23:56:11 -0400

From:    Menelaos Symeonides <[hidden email]>

Subject: Re: Data storage - NAS servers



*****

To join, leave or search the confocal microscopy listserv, go to:

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Post images on https://urldefense.proofpoint.com/v2/url?u=http-3A__www.imgur.com&d=DwIGaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=M5FeCeiMzIQ5-iETJRr9Yj1K04gsumnZfd8V-zDvMMA&s=9y-bhsVji368bT0ErLLVvtIbUhQR7K4K41C401H7D1g&e= and include the link in your posting.

*****



Hi Adam,



(warning: long email ahead)



For our iSPIM we have the 8-bay Synology DS1817+ (about $900-$1000) loaded with 8 x Western Digital Gold WD101KRYZ 10 TB hard drives (about

$400 each), and set up in SHR-2 mode (which is basically RAID-6, i.e.

2-disk redundancy) which leaves about 60 TB of usable space. I also installed an Intel X520-DA2 10GbE adapter as the integrated Gigabit Ethernet connection would bottleneck the speed of the drive array, I was able to find one of those for $150 but it was a refurb. You'll also need a 10GbE adapter for your PC and the appropriate SFP+ cable(s).



Once this fills up, and we have exhausted all possibilities of compressing or discarding data, I think we will just buy another one as opposed to buying an expansion bay for this one, as the expansion bay runs on the eSATA connector and is therefore limited in speed, so you get no speed gains from any RAID array that's in the expansion bay.



Just be aware that, with regular SATA 7.2K pm HDDs (i.e. not SSDs or 15K rpm SAS drives), the best real-world performance you will ever get (with an 8-drive RAID-6 array over 10GbE) is about 160-170 MB/s read (that's bytes, not bits) and 270 MB/s write. Teaming two 10 GbE connections by link aggregation does nothing for real-world performance, it's just for failover redundancy in case one port or one cable dies mid-transfer - for speed benefits you need to optimize your operations to split up your packet stream across each link, which is not trivial. These speeds are way lower than what you get with a benchmarking tool like CrystalDiskMark - always pays to do real-world work to figure out how something performs.



This kind of performance means that you can pretty much forget any multi-user applications with this kind of NAS for large imaging datasets. You will just not be able to provide access for anything more than someone copying their data off to their own system to then process and analyze off a local drive/array, and you should only allow one user to be logged in at a time or they will all complain that it's taking ages. Also, if you'll be using your building's built-in Ethernet wiring, it's unlikely that it will be capable of 10GbE performance, so really you'll end up asking people to bring their portable drive down to you and copy the data right off as it'll end up being 2-3x faster (of course, that also presumes that their portable drive isn't bottlenecking either). I also have a 6 TB RAID-0 SSD array in my workstation PC, so whenever I need to process/analyze data, I copy it off the NAS to the SSD RAID over the 10GbE connection, do all the work on the SSD RAID, and then copy it back to the NAS for storage.



If you want to actually serve large datasets directly to multiple simultaneous users, these Synology units will just not cut it. You'll need an enterprise solution, e.g. something from Dell, HP, or NetApp, which will cost somewhere in the tens of thousands USD for anything close to the 60 TB I mentioned. These will run large arrays of either SSDs (super expensive) or at least fast SAS HDDs (only very expensive), and will run on a multi-CPU Xeon platform with tons of RAM that is capable of handling multiple users. The Synology units have really awful CPUs and very low RAM, which can just barely handle a single user.

You'll also need the necessary infrastructure in your building to allow remote users to connect at 10GbE speeds (and have them install 10GbE adapters in their computers), or it will totally defeat the point of having spent all that money on the enterprise server.



If you're really nuts you can try to build your own and could conceivably get performance close to what these enterprise units get for somewhat less money, but you really need to know what you're doing. Plus you will be entirely responsible for servicing it. You'll need to have a drive failure plan because server performance will tank for several days if you have to replace a failed drive and have to rebuild the array - your users will be very unhappy during the rebuild, and the larger the array/the slower the drives, the longer the rebuild will take.



Honestly, institutions that host big data labs will sooner or later need to start taking responsibility for the data if they are going to expect their labs to continue doing their work and bringing in grant money for the institution. It makes much more sense for there to be an institutional "data core facility" to maximize cost efficiency in purchasing these servers, buildings will need to be rewired with fiber, and personnel will need to be hired to maintain these servers and provide user support, all of which costs institutions $$$, so good luck with that.



No commercial interest for anything I mentioned.



Mel





On 5/8/2018 4:41 PM, Adam Glaser wrote:

> *****

> To join, leave or search the confocal microscopy listserv, go to:

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>

> Hello everyone,

>

> We are currently exploring in lab data storage options for storing the large amounts of data our light-sheet microscopes are producing (while simultaneously providing shared access from multiple PCs for processing and/or visualization).  Given these needs, we have tentatively arrived at purchasing a NAS server.  I was wondering if anyone had suggestions or recommendations on the best companies/options available.  In preliminary searching I have seen FreeNAS pop up several times, but am quite a novice when it comes to data storage - so any input from the listserv would be greatly appreciated!

>

> Thanks!

> Adam

>



--

Menelaos Symeonides

Post-Doctoral Associate, Thali Lab

Department of Microbiology and Molecular Genetics University of Vermont

318 Stafford Hall

95 Carrigan Dr

Burlington, VT 05405

[hidden email]

Phone: [phone]



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End of CONFOCALMICROSCOPY Digest - 7 May 2018 to 8 May 2018 (#2018-106)

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