Re: Lightsheet imaging analysis Workstation Specs

Posted by PAVAK SHAH on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Lightsheet-imaging-analysis-Workstation-Specs-tp7590391p7590400.html

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Hi Francesco,

I should clarify that it depends a lot on the software pipeline being used.
The ones I am most familiar with for diSPIM data (MIPAV, Shroff lab
software, and Stephan Preibisch's Multiview Reconstruction) don't
inherently support parallel processing of a single dataset on multiple
GPU's but multiple instances can be run separately on different datasets
(or different segments of the same dataset). I have not kept up as closely
with what folks use for fusing data from Z1, openSPIM, MuVi SPIM, or
bespoke multiview systems.

With enough memory, multiple fusions can also be performed on the same GPU,
albeit with sub-linear gains in performance. In the case of MVR, my
understanding is that GPU support may have become deprecated (at least I
haven't succeeded in running the CUDA libraries it depends on in several
years) and most users run it on CPU clusters now. I've been meaning to take
a stab at recompiling the CUDA libraries to see if they'll run as is on
10.1, but haven't found the time to do so.

Best,
Pavak

On Wed, Jan 15, 2020, 12:33 AM Francesco Pasqualini <
[hidden email]> wrote:

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> *****
>
> Hi Pavak et al,
> This is very interesting and helpful.
>
> Do I understand you correctly that multiple GPU won't help with multiview
> deconvolution?
>
> If there is a reference for deconvolution performances as a function of
> various hardware options can anyone point it out?
>
> Thanks
> Francesco
>
>
>
> On Wed, Jan 15, 2020, 12:57 AM PAVAK SHAH <[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.
> > *****
> >
> > Hi Niyanta,
> >
> > What lightsheet instrument and what is the size of your typical dataset?
> Is
> > your processing pipeline primarily for segmentation or multiview
> > deconvolution? This will dictate, to a large extent, the kind of memory
> and
> > CPU you need.
> >
> > An RTX 2080ti or Titan RTX will be competitively performant but much
> > cheaper than a Quadro card, which offers no benefits for an image
> analysis
> > workflow unless you're running virtual machines. If your workflow is
> > primarily single view deconvolution, multiple GPUs can also be a huge
> boon
> > in terms of processing throughput, especially if individual volumes can
> fit
> > in 11 GB of VRAM since you can fill a large workstation to bursting with
> > 2080ti's for the price of 1 Quadro card. Even 2x Titan RTX can be had for
> > less than the price of 1x Quadro 6000.
> >
> > Depending on the specific piece of software, many will not scale
> > efficiently to >16 cores and a faster clocked CPU with fewer cores may be
> > advantageous. If you can benchmark it on a high core count system, that
> > should show whether your pipelines are able to keep that many cores fed
> > before running into algorithmic, disk access or memory throughput
> > bottlenecks.
> >
> > Best,
> > Pavak
> >
> > On Tue, Jan 14, 2020, 1:27 PM Niyanta Kumar <
> > [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.
> > > *****
> > >
> > > Hi all,
> > > I plan to get a workstation that can handle confocal and lightsheet
> data
> > > analysis using Imaris and/or Arivis. Lightsheet data clearly has the
> > higher
> > > bar/needs in terms of specs. Below are the specs I am considering. Can
> > you
> > > please let me know if you have any recommendations?
> > >
> > > Lenovo Think Station P920
> > > 3.7 GHz CPUs (Intel) 48 cores
> > > Graphics: NVIDIA Quadro RTX 6000 or 8000
> > > 4 X 3 TB of local SSD (multiple drives - one for the OS, one for
> writing,
> > > one for reading)
> > > RAM: 500 GB
> > > Monitor: dual 1920 x 1200
> > > 300 TB NAS via 10 GB ethernet – file sharing
> > > Mouse: 3 button wheel
> > >
> > > Monitor: thinking of a dual Lenovo Think Vision P32u-10 but it doesn’t
> > > have a full array LED. Any suggestions? I hear the curved monitors can
> > > cause issues with display when sharing screens over Webex etc.
> > > Thanks,
> > > Niyanta
> > >
> >
>