Memory Requirements

[I.Ramadaan]

I am encountering out of memory messages in the MATLAB command window,
followed by the progress bar freezing and I would then have to close
dirart and start again. This maybe encountered at any point during the
loading of structures, and while it occurs most frequently with large
structure sets like body and spinal cord contours, it can occur with
smaller structures like CTV. For interest, the message is similar to:

Loading planC from W:\IR\CERR plans\Booth1.mat
Generating meshRep for structure: Spinal Cord
Out of memory. Type HELP MEMORY for your options.
Unexpected error status flag encountered. Resetting to proper state.

I guess the problem is apparent - I need a bigger memory. But my
question is whether anyone can please give me an indication of the
memory size that is equal to the job?

[Yang, Deshan]

Out off memory is a very general problem for MATLAB because MATLAB needs to allocate continuous memory blocks for large matrix. There are already many efforts in DIRART to avoid this problem, for example, calculation is carried out in multiple but smaller piece of data instead of the whole large image data.

To get around this problem for you, you can do a few things:
1. Use a 64-bit windows instead of 32-bit one.
2. For 32-bit windows, enable the 3GB option (google search)
3. Buy more RAM for 64-bit windows.
4. Delete unnecessary and very large structures from your CERR plans
5. Crop your images before DIR computation
6. Do some computation outside DIRART if you know how to do so
7. Use LINUX instead windows

 

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[I.Ramadaan]

Thank you for your reply. The current memory problems I'm having were
encountered on the PC at work which is indeed a windows 32-bit. In
fact your suggestion for enabling the 3 GB option gives me a good ball-
park figure for the memory needed, this particular PC only has 1GB of
memory - I suppose the solution would be to expand this. Due to
administrative issues this may take a while, I did try to overcome
this problem by installing DIRART on my Windows 7 64-bit personal
computer (which has 4GB memory). Unfortunately, I encountered a
problem of a different kind:

When I try to load structures from CERR plans I get the error along
the lines "Microsoft Visual C++ 2005 components are not found" while
in fact I have the 2008 and 2010 versions installed. After some
investigation it seems that the MATLAB loadlibrary.m file that gives
rise to the error looks for a tools folder that provides the
'VS80COMNTOOLS' environment. This folder however is only available in
the x86 (32-bit) directory and not the x64. All downloadable versions
from the Microsoft Download Center don't have 64-bit compatible tools.
My personal copy of MATLAB is 2008b version. Is there a simple way to
overcome this problem?

Thank you.

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[Yang, Deshan]

As I remember, the loadLibrary.m error is just a warning and won't stop you from running dirart. In fact, the latest CERR version has stopped to support the mesh library which DIRART is using to manipulate the structures. My current solution is to install both 32-bit and 64-bit MATLAB on a windows-64 PC. I use the 32-bit MATLAB with older version of CERR to load everything into DIRART (CT, structures and dose), save DIRART projects, and then use DIRART in 64-bit MATLAB to have more memory.

For the MS VC++ problem, you should ask questions in the CERR googlegroup.

Please do pay attention to my other general suggestions about memory footprint reduction.

Deshan

[I.Ramadaan]

Thanks Deshan. Unfortunately, the MS VC++ problem that causes the
loadlibrary.m error does stop me by kicking up errors from files down
the chain so I am not able to go past the stage where I get prompted
to select the structures to load for the first image. I will attempt
your solution. Also, I will definietly keep in mind the memory
footprint reduction techniques you suggested.

If I may make a suggestion of my own, could you please consider adding
those suggestions to the DIRART User Manual when you update it; I
found the User Manual extremely helpful when using DIRART, especially
the table of algorithms and the suggestions on how best to use them.

Thanks,
Ihab

[Yang, Deshan]

Sounds good. I will definitely add your suggestions into the manual.

I haven't seriously used DIRART with CERR for a while. I need to fix the structure loading problems. In fact, DIRART could manipulate the structures without using the mesh library, even though it won't be as nice.

Please blame Microsoft and MATLAB to mess up the 32-bit and 64-bit configurations.