Re: Fiji/ImageJ on a Windows server

Posted by Gelman, Laurent on Aug 27, 2014; 7:05am
URL: http://imagej.273.s1.nabble.com/Fiji-ImageJ-on-a-Windows-server-tp5009346p5009365.html

Hi Wayne,

I just tested Gaussian Blur. My computer is still twice faster.
As far as I can see on the task manager, those plugins I tested use multi-core processing.

Best regards,

Laurent.

-----Original Message-----
From: Rasband, Wayne (NIH/NIMH) [E] [mailto:[hidden email]]
Sent: mercredi 27 août 2014 02:38
To: Gelman, Laurent
Subject: Re: Fiji/ImageJ on a Windows server


On Aug 26, 2014, at 6:28 AM, Gelman, Laurent wrote:

> Hi everybody,
>
> We recently purchased a server for image processing: 32 Cores (Intel Xeon E5-4627 V2 @ 3.3 GHz, 4 CPUs, no hyperthreading), 518 GB RAM, windows 2012 R2.
> We then compared the speed of this server to that of a desktop machine: iMac, 8 Cores (Intel i7-4771 CPUs @ 3.5 GHz, multithreaded), 32GB RAM, Windows8 (I can explain why we run Windows8 on a iMac if some people are shocked, let's call this computer a "WinMac" :)).
>
> These are results of the speed tests:
> Stitching (Stitching plugin from Fiji): My "WinMac" is twice faster than the server.
> Denoising (with the PureDenoise plugin): My "WinMac" is 3.6 times faster than the server.

Hi Laurent,

Not all commands and plugins are multi-threaded. You should try a command, such as Process>Filters>Gaussian Blur that is known to be multi-threaded.

Best regards,

-wayne

> The server has 32 cores, my WinMac 8 cores. I would not expect the server to be 4 times faster (CPUs are different, some writing to disk might be involved, etc.), but I would not expect it to be more than twice slower as well.
>
> IT tells me, maybe ImageJ or Fiji or Java is not optimized to run on servers.
>
> Is this the case? Is there a problem of configuration of Fiji or Java or Windows on the server? (I checked already "memory and threads" parameters).
>
> Thanks for your help,
>
> Best regards,
>
> Laurent.
>
> NB: When running Matlab, the server outperforms our desktops.
>
> ___________________________
> Laurent Gelman, PhD
> Friedrich Miescher Institut
> Head, Facility for Advanced Imaging and Microscopy Light microscopy
> WRO 1066.2.16 Maulbeerstrasse 66
> CH-4058 Basel
> [phone]
> [phone]
> www.fmi.ch<http://www.fmi.ch/>
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> h/>
>
>
>
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