[OpenSPIM] OpenSPIM 64-bit [0000129]

[Peter Gabriel Pitrone]

Howdy Nikul,

I would love to see this work, and agree with Pavel that this is great!!
May I ask how you plan to handle the data once it is acquired at this
rate?! This is no small feat... I'm also interested in what you will
image.

Have a great evening!
Pete



-- 
Peter Gabriel Pitrone - FRMS TechRMS
Microscopy/Imaging Specialist
Prof. Dr. Pavel Tomancak group
Max Planck Institute for
Molecular Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden

"If a straight line fit is required, obtain only two data points." - Anon.


On Mon, February 3, 2014 21:41, Pavel Tomancak wrote:
<|> Hi Nikul,
<|>
<|> I see, you are really pushing the performance of OpenSPIM to the limit.
<|> That's great!
<|>
<|> When you a re ready, please describe your set-up on the wiki. Are you
<|> working with Brian McCabe? If yes, say hi to him.
<|>
<|> All the best
<|>
<|> PAvel
<|>
<|>
-----------------------------------------------------------------------------------
<|> Pavel Tomancak, Ph.D.
<|>
<|> Group Leader
<|> Max Planck Institute of Molecular Cell Biology and Genetics
<|> Pfotenhauerstr. 108
<|> D-01307 Dresden				Tel.: +49 351 210 2670
<|> Germany						Fax: +49 351 210 2020
<|> email: tomancak at mpi-cbg.de
<|> homepage:
<|> http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html
<|> twitter: @PavelTomancak
<|>
-----------------------------------------------------------------------------------
<|>
<|>
<|>
<|>
<|>
<|> On Feb 3, 2014, at 5:19 PM, Nikul <nikul at ee.columbia.edu> wrote:
<|>
<|>> Hi Luke and Johannes,
<|>>
<|>> I was able to figure out what the problem was. MMCoreJJNI.java lists
<|>> the root directory and mm/Win64 as the search directories for a 64-bit
<|>> build while openspim.build.xml was staging the files to mm/x64.
<|>> Changing
<|>> the staging directory in  openspim.build.xml solved the problem!
<|>>
<|>> On another note, I am trying to interface a 100 fps 5.5mp camera with
<|>> OpenSPIM
<|>> and am using a RAID0 array of four ssd drives. The write speed I get
<|>> through
<|>> OpenSPIM (or micromanager) is at the moment only able to handle about
<|>> 50 fps. Before I dig into the code to see if there is something I can
<|>> optimize for
<|>> the particular setup, I wanted to check if anyone has any tips to
<|>> achieve write speeds
<|>> to get full frame rate capture from the camera.
<|>>
<|>> Thanks,
<|>> ---
<|>> Nikul Ukani
<|>>
<|>> Doctoral Candidate,
<|>> Dept. of Electrical Engineering,
<|>> Columbia University.
<|>> http://www.bionet.ee.columbia.edu/
<|>>
<|>> On Jan 31, 2014, at 4:42 PM, Nikul <nikul at ee.columbia.edu> wrote:
<|>>
<|>>> I'll look into it and get back. If it works, it will be great to have
<|>>> some resource
<|>>> on the OpenSPIM website for compiling it in 64-bit.
<|>>>
<|>>> Thanks,
<|>>> ---
<|>>> Nikul Ukani
<|>>>
<|>>> Doctoral Candidate,
<|>>> Dept. of Electrical Engineering,
<|>>> Columbia University.
<|>>> http://www.bionet.ee.columbia.edu/
<|>>>
<|>>> On Jan 31, 2014, at 4:29 PM, Luke Stuyvenberg <stuyvenberg at wisc.edu>
<|>>> wrote:
<|>>>
<|>>>> Hi Nikul,
<|>>>>
<|>>>> --x64 is supposed to change "mm.architecture" to "x64" before calling
<|>>>> Micro-Manager's build scripts; this should build MM in 64-bit.
<|>>>> However, it's entirely probable that "build.sh" and/or
<|>>>> "openspim.build.xml" do not copy the 64-bit files -- I would check
<|>>>> first to see if the relevant binaries exist in "stage" or "build"
<|>>>> subdirectories. If so, you'll have to look through the build system
<|>>>> to see where we stage this files (I believe the relevant target is
<|>>>> near the end of "openspim.build.xml") and make sure the correct
<|>>>> architecture is copied from.
<|>>>>
<|>>>>
<|>>>> Hope this helps,
<|>>>> Luke
<|>>>>
<|>>>> On 01/31/14, Nikul Ukani  wrote:
<|>>>>> Hi Johannes,
<|>>>>>
<|>>>>> That's possible as all I did was to change the platform to x64 in
<|>>>>> the build script. Can you point me to which project does that
<|>>>>> library correspond to so I can investigate whether the correct flag
<|>>>>> is being passed while compiling it?
<|>>>>>
<|>>>>> Thanks,
<|>>>>> Nikul
<|>>>>>
<|>>>>>> On Jan 31, 2014, at 2:21 PM, Johannes Schindelin
<|>>>>>> <Johannes.Schindelin at gmx.de> wrote:
<|>>>>>>
<|>>>>>> Hi Nikul,
<|>>>>>>
<|>>>>>>> On Fri, 31 Jan 2014, Nikul Ukani wrote:
<|>>>>>>>
<|>>>>>>> I am currently trying to compile OpenSPIM on a 64 bit machine
<|>>>>>>> running
<|>>>>>>> Windows 7. While I was able to get it to compile by modifying some
<|>>>>>>> of
<|>>>>>>> the build scripts; upon trying to open it from Fiji, I get the
<|>>>>>>> following
<|>>>>>>> error
<|>>>>>>>
<|>>>>>>> Error: Failed to open libMMCoreJ_wrap.jnilib
<|>>>>>>> mmcorej.MMCoreJJNI.swig_module_init()V
<|>>>>>>
<|>>>>>> My guess is that the libMMCoreJ_wrap.jnilib is compiled as a 32-bit
<|>>>>>> library. Possible?
<|>>>>>>
<|>>>>>> Ciao,
<|>>>>>> Johannes
<|>>>>>>
<|>>>>>
<|>>>>>
<|>>>>> _______________________________________________
<|>>>>> OpenSPIM mailing list
<|>>>>> OpenSPIM at openspim.org
<|>>>>> http://openspim.org/mailman/listinfo/openspim
<|>>>>
<|>>>
<|>>
<|>> _______________________________________________
<|>> OpenSPIM mailing list
<|>> OpenSPIM at openspim.org
<|>> http://openspim.org/mailman/listinfo/openspim
<|>
<|> _______________________________________________
<|> OpenSPIM mailing list
<|> OpenSPIM at openspim.org
<|> http://openspim.org/mailman/listinfo/openspim
<|>