*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****
I think we will all be using SSD arrays in the near future. The CMOS
cameras from all companies generate about 1.8 gigabytes of data/second
when maxed, you have no choice but to use SSD arrays, we put raid 0 Sata 3
arrays of CMOS drives in all our high speed systems. Normally half a
terabyte suffices, we use 120 gig OCZ drives ($110 ea from amazon) a
Startech 4 drive backplane ($92) and a HighPoint RocketRAID 640 4 SATA
Port PCI-Express 2.0 x4 SATA 6Gb/s RAID Controller ($102). Basically the
whole thing costs about $650, fills a spare Cdrom slot and solves all the
problemsfor us (it does solve our CMOS buffering problem).
S
Simon Watkins Ph.D
Professor and Vice Chair Cell Biology
Professor Immunology
Director Center for Biologic Imaging
University of Pittsburgh
Bsts 225 3550 terrace st
Pittsburgh PA 15261
Www.cbi.pitt.edu <http://Www.cbi.pitt.edu/>
412-352-2277
On 3/11/13 7:11 AM, "Arvydas Matiukas" <[log in to unmask]> wrote:
>*****
>To join, leave or search the confocal microscopy listserv, go to:
>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>*****
>
>I may corroborate regarding recording time series to SSD drive.
>For optical electrophysiology application we needed 500 frames/sec
>at 128x128, 16bit resolution and repeatedly for 10-200 sec duration,
>Only recording to a SSD (or alternatively to RAM which would be
>more expensive and still require later copying to a permanent storage)
>could sustain the required data transfer rate.
>
>Switching back to PCIe SSD cards: does anybody was able to install OS
>and boot
>system from them . Booting should be ultra fast at 1000MB/sec data
>transfer,
>
>Arvydas
>
>
>>>> Craig Brideau 03/10/13 11:54 PM >>>
>*****
>To join, leave or search the confocal microscopy listserv, go to:
>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>*****
>
>In our microscope computers we use SSD's only for immediate experiments.
> The key advantage is that if you are taking volumes over a time series
>the
>drive can save each volume very quickly, allowing your time points to be
>closer together since you don't have to wait for a disk write to complete.
> Since SSD's are still fairly expensive I only put enough space in the
>machine for a few experiments; the users are required to move their data
>over the network to a central storage server rather than leaving it on the
>host computer. This lets us get away with smaller and cheaper SSD's (or
>small but good quality SSDs for reasonable prices) while still having
>secure storage after the fact. I agree with George that you shouldn't
>leave anything on them long term. That said, some high-end servers use
>banks of SSD's rather than hard disks when the data has to be accessed
>frequently. They get around the potential reliability issue by using RAID
>arrays of SSD's. This is pricey, but very efficient for critical
>applications.
>
>Craig
>
>
>On Sun, Mar 10, 2013 at 2:58 PM, George McNamara
>wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy
>> *****
>>
>> I second Craig's comment on SSD PCI-e card speed. I have several such
>> cards in my core's PC's, also some of their SSD SATA drives. One problem
>> with all SSD's is when they die, that's it" everything is lost. Back it
>>up
>> or expect to lose it. Don't count on achieving the specifications
>>provided
>> by OCZ (or any other vendor) - operating system driver performance may
>>be
>> limiting.
>>
>>
>>
>> On 3/10/2013 2:30 PM, Craig Brideau wrote:
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy
>>> *****
>>>
>>> As Oliver says, an SSD can help speed things along. You can get PCI-e
>>> cards which are SSD's rather than relying on the SATA bus for data
>>> transfer. They can be quite speedy depending on what you are doing:
>>>
>>> http://www.ocztechnology.com/**products/solid_state_drives/**
>>> pci-e_solid_state_drives
>>>
>>> I use one of these in our image acquisition computers tied to one of
>>>our
>>> microscopes. It makes file writes for large image stacks go much
>>>faster
>>> than a mechanical drive.
>>>
>>> Craig
>>>
>>>
>>>
>>> On Sun, Mar 10, 2013 at 12:28 AM, Oliver Biehlmaier<
>>> [log in to unmask]> wrote:
>>>
>>>
>>>
>>>> *****
>>>> To join, leave or search the confocal microscopy listserv, go to:
>>>> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy
>>>> *****
>>>>
>>>> Yes, that is the correct order. At least for the software that we are
>>>> using the CPU speed is the most important.
>>>> The SSD for the OS and swapping (eg in Imaris) is also an important
>>>>point
>>>> for speed.
>>>> Cheers,
>>>> Oliver
>>>>
>>>>
>>>>
>>>>>
>>>>> ------------------------------
>>>>>
>>>>> Date: Sat, 9 Mar 2013 05:56:27 -0500
>>>>> From: "Watkins, Simon C"
>>>>> Subject: Re: Subject: Computer for image analysis
>>>>>
>>>>> *****
>>>>> To join, leave or search the confocal microscopy listserv, go to:
>>>>> http://lists.umn.edu/cgi-bin/**wa?A0=3Dconfocalmicroscopy
>>>>> *****
>>>>>
>>>>> So Oliver, what you are saying is that the ultimate bottleneck is the
>>>>> CPU
>>>>> speed, followed by RAM, followed by CPU core count and finally
>>>>>graphics
>>>>> card capabilities?
>>>>>
>>>>> Simon Watkins Ph.D
>>>>>
>>>>> Professor and Vice Chair Cell Biology
>>>>> Professor Immunology
>>>>> Director Center for Biologic Imaging
>>>>> University of Pittsburgh
>>>>> Bsts 225 3550 terrace st
>>>>> Pittsburgh PA 15261
>>>>> Www.cbi.pitt.edu>
>>>>> 412-352-2277
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 3/9/13 3:39 AM, "Oliver Biehlmaier"
>>>>> >
>>>>>
>>>>>
>>>> wrote:
>>>>
>>>>
>>>>>
>>>>>
>>>>>> Dear Arvydas,
>>>>>> I equipped an entire image analysis room with new Image analysis
>>>>>>
>>>>>>
>>>>> machines
>>>>
>>>>
>>>>> about 1.5 years ago. During the evaluation, our main focus was on the
>>>>>> system's performance using software such as Imaris, Volocity,
>>>>>>Huygens,
>>>>>> Fiji, etc.
>>>>>> As already posted in other replies to your email it turns out that
>>>>>>GPU
>>>>>>
>>>>>>
>>>>> is
>>>>
>>>>
>>>>> important, but bottlenecks are CPU, RAM, and the speed of the HDD.
>>>>>> As our institute's IT asked us to go for a Dell-solution, we
>>>>>>evaluated
>>>>>> several possibilities from Dell. We ended up buying 2 Dell Precision
>>>>>>
>>>>>>
>>>>> with
>>>>
>>>>
>>>>> 3GB-GPU, XEON-processors and between 24 to 48GB of RAM, and many
>>>>>>
>>>>>>
>>>>> "pimped"
>>>>
>>>>
>>>>> Optiplex systems where we installed 3GB-GPU, the max. RAM (16GB), an
>>>>>SSD
>>>>>> for the OS and swapping and a fast 500GB-HDD for saving the data.
>>>>>> Price wise the Optiplex systems sum up to a third of the price of
>>>>>>the
>>>>>> precision.
>>>>>> The main reason for the Optiplex was the i7 processor which is
>>>>>>capable
>>>>>>
>>>>>>
>>>>> to
>>>>
>>>>
>>>>> do overclocking which is not possible on the XEON systems. We
>>>>>expected
>>>>>> this to be a key advantage in comparison to our expensive Precision
>>>>>> systems.
>>>>>> Now, after 1,5 years of usage I can confirm that this fully worked
>>>>>>out.
>>>>>> As many programs (especially Imaris) are still mainly relying on
>>>>>>only
>>>>>>
>>>>>>
>>>>> one
>>>>
>>>>
>>>>> but definitely not on all cores, the overclocking feature of the i7
>>>>>> system usually keeps them at the same level or even outperforms the
>>>>>> Precision systems. Only the 48GB-RAM system is a bit faster on the
>>>>>>rare
>>>>>> occasions when it can fully profit from the large RAM (large time
>>>>>>lapse
>>>>>> or stitching tasks). But even then the fast swapping onto the SDDs
>>>>>>on
>>>>>>
>>>>>>
>>>>> the
>>>>
>>>>
>>>>> Optiplex keeps them almost at the same level of performance.
>>>>>> Only recently we ran into some minor problems with our ATI graphics
>>>>>>
>>>>>>
>>>>> cards
>>>>
>>>>
>>>>> which could have been prevented by using NVIDIA cards, thus I would
>>>>>> recommend the latter. There is definitely no need to go for Quadra
>>>>>>
>>>>>>
>>>>> cards,
>>>>
>>>>
>>>>> they are super expensive and receive less updates and patches than
>>>>>the
>>>>>> gaming cards.
>>>>>> I hope this helps you in your decision for your new systems.
>>>>>> Best,
>>>>>> Oliver
>>>>>>
>>>>>>
>>>>>> ------------------------------**------------------------------**----
>>>>>> Oliver Biehlmaier, PhD
>>>>>> Head of Imaging Core Facility
>>>>>> Biozentrum, University of Basel
>>>>>> Klingelbergstrasse 50/70
>>>>>> 4056 Basel
>>>>>> Switzerland
>>>>>>
>>>>>> Tel: +41 (61) 267 20 73
>>>>>> Email: [log in to unmask]<**mailto:
>>>>>>
>>>>>>
>>>>> [log in to unmask]>
>>>>
>>>>
>>>>> http://www.biozentrum.unibas.**ch/imcf
>>>>>> ------------------------------**------------------------------**----
>>>>>>
>>>>>> _________________
>>>>>> From: Arvydas Matiukas>>>>
>>>>>>
>>>>> [log in to unmask]>>
>>>>
>>>>
>>>>> To:=20
>>>>>> [log in to unmask]**EDU
>>>>>> >>>>
>>>>>>
>>>>> [log in to unmask]**EDU >=
>>>>
>>>>
>>>>> =3D
>>>>>
>>>>>
>>>>>> 20
>>>>>> Sent: Friday, March 8, 2013 12:24 PM
>>>>>> Subject: Computer for image analysis
>>>>>>
>>>>>> *****
>>>>>> To join, leave or search the confocal microscopy listserv, go to:
>>>>>> http://lists.umn.edu/cgi-bin/**wa?A0=3D3Dconfocalmicroscopy
>>>>>> *****
>>>>>>
>>>>>> Dear listers/microscopists,
>>>>>>
>>>>>> I assume there is good time to update new trends in
>>>>>> image analysis hardware. The last discussions on image
>>>>>> analysis computer were in 2006-8. Though the basic
>>>>>> principles of CPU, RAM, hard drive, video card, monitor
>>>>>> selection still hold some new types of hardware became
>>>>>> popular/available, e.g. SSD drives, APU, water cooling.
>>>>>> Now a decent gaming computer (~$1k) has the processing power
>>>>>> of a 2006 expensive workstation (~$20K). I was suprised that
>>>>>> I was able to completely overhaul my 8 year old ATX case
>>>>>> to a quad core 2GHz APU, 8GB 1600MHz RAM, 160GB SATA-2
>>>>>> SSD, water cooling, USB3 and SATA3 Gigabyte motherboard,
>>>>>> and 4 monitor 1GB video card.
>>>>>> for under $300 (online, after rebates).
>>>>>>
>>>>>> Now I am wiling to upgrade/overhaul my work computer which
>>>>>> is used to run ImageJ, Fiji, Deconvolution (Autoquant, Huygens),
>>>>>> Matlab, PV-Vawe, Labview, Origin. Please advice/share you thoughts
>>>>>> what best configuration is possible to buy for $2-3k (monitor
>>>>>> excluded).
>>>>>> My first choice would be to go with a fast gaming computer, e.g.
>>>>>> Dell-Alienware Aurora=3D20
>>>>>> Windows* 7 Ultimate, 64Bit, English
>>>>>> 2nd Generation Intel* Core* i7-3820 (10M Cache, Overclocked up to
>>>>>>4.1
>>>>>> GHz)
>>>>>> 16GB (4 X 4GB) Quad Channel DDR3 at 1600MHz
>>>>>> NVIDIA* GeForce* GTX 660 1.5GB GDDR5
>>>>>> 1TB RAID 0 (2x 500GB SATA 6Gb/s) Solid State Hybrid
>>>>>> 19-in-1 Media Card Reader
>>>>>> No Monitor
>>>>>> Integrated 7.1 Channel Audio
>>>>>>
>>>>>> The second choice would be to buy all components online and
>>>>>> build a computer myself (I have done this about 50 times over
>>>>>> 25 years). This option typically saves money or buys better
>>>>>> components,
>>>>>> and provides you full specs of the hardware. The con of this
>>>>>> approach is that it wastes some of your time to debug/make all
>>>>>> the hardware work together and with your software. However,
>>>>>> as the computer is for me not just a box but a tool I am ready
>>>>>> to make this sacrifice.
>>>>>>
>>>>>> BTW, is there any solid preference towards CPU Type (Intel
>>>>>>ix/AMD/Intel
>>>>>> Xeon)
>>>>>>
>>>>>> Thanks for your input/advice/thoughts,
>>>>>> Arvydas
>>>>>> --------------------
>>>>>>
>>>>>>
>>>>>>
>>>>> ------------------------------
>>>>>
>>>>> End of CONFOCALMICROSCOPY Digest - 8 Mar 2013 to 9 Mar 2013
>>>>>(#2013-58)
>>>>> ****************************************************************
>>>>> **********
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
|
