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Bitplane Imaris multi threading
 

Concurrent Processing of Multiple Imaris windows  (run code including  ImarisXT in an un-conventional way to process ims file list) was accomplished via Matlab under the "SuperColoc" : A Matlab-based smart, self-rescuable and utility extensible job-queueing framework for robust and unattended batch processing of images using Imaris.

The number of windows could be specified from 1 to infinity, as long as the hardware could cope with,

For a pilot test, 12 Imaris windows runs fluently on PC with 64GB memory and E5-1620 8-core CPU. The optimal number of concurrent Imaris windows was depend on the memory, CPU, imaris file size and computational workload of processing an image.

On a single machine (personal PC, image workstation, HPC…), the maximum number of Imaris windows was limited to 512.

On distributed computing server, there will be no limiting of number of Imaris windows.

 Imaris files could even be concurrently processed in the Continental distributed computing server.

 
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video snapshot at
https://www.youtube.com/watch?v=uzlIIhqi3As
 
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There is still one last problem:

For each imaris window, after processing files one-by-one, the memory usage always increased and gradually use up the memory, and may be finally crushed(although I have not seen it. What I see is that memory usage keeps at ~100% but imaris still runs without problem). The reason may be that datasets or objects that was created by Matlab command but not loaded to surpass scene will hold place somewhere in memory even after imaris application opens the next file, unless the current imaris application quit. A reasonable property of Imarisapplication should be that once ImarisAplication.FileOpen() was executed it should clear all the memory related to previous file. However, this was not the case by now.

Another video at:
https://www.youtube.com/watch?v=8Al7JoZrYlQ
 
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The virtual memory take space from C drive. Just now I see that C drive usable space drops from 82GB to 68GB.
My memory has 60GB, plus 60GB virtual memory.
The commit(GB) a while ago was 104/127, but now it truns to 136/148. So the system is always increasing the virtual memory to accomodate the memory need of imaris.
 
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a new problem:

The first processing of 354 ims files. After processing 241 files, all the windows seems sleeping. Although memory usage is 106GB/165GB, the CPU dropped to 0. Althogh all imaris windows shows images, no activity appeared on imaris windows, and matlab also in normal waiting as usual. This last for 20 minutes untill I noticed them. I just click the imaris windows on the task bar, then these windows wake up one-by-one, and the processing resumed as normal. .So weired.

 
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I have just enabled SuperColoc to detect the total commit memory before processing each file in case the total commit memory is close to upperlimit and automatically re-start imaris.exe. Also enabled the auto-click to activate all Imaris windows one-by-one in case that all these windows show no CPU usage.
 
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SuperColoc also has an interface to ImarisXT so that any single ImarisXT step or a series of ImarisXT steps could be run at multiple imaris windows.
 
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Four mode of automation:


Mode 1: Tandem, interrupted thread 
--Slowest, but most robust and stable. 
--Preferable on low-performance PC/laptop/low-level office computer.
        --Thread is monitored real-time to rescue any catastrophy in memory.




Mode 2: Tandem, streamed thread
--Faster than mode 1.
--Preferable on medium-performance PC/laptop.
        --Thread is monitored real-time to rescue any catastrophy in memory.


Mode 3: Parallel streamed threads
--customizable threads (≤ 512 threads/local cluster).
--Preferable on Workstation/HPC cluster.
        --All threads are monitored real-time to rescue any catastrophy in memory.


Mode 4: Distributed Computing Servers
--Multiplication of mode 3.
        --Rescue disabled.

 
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