Do you keep all steps of your iteration - that means, do you end up with 200 matrices? Unless you really need all steps it should be possible to do the same with just two matrices, maybe even just one.
Is the iteration done in a function? The memory of matrices created locally in a function is deallocated when the routine finishes. Memory of matrices defined (globally) in the sheet never is deallocoated - not even when the matrix (variable) is completely deleted.
I am using Mathcad 14.
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I am running Matchcad on a Windows 7. I have no experience with the newer version of Mathcad.
Prime is a rather useless program in my opinion - missing a lot of the features available in MC15 or 14, is extremely slow and very uncomfortable.
But ... its available in 64bit flavor and so should be able to benefit from more memory in the machine. Furthermore there is a switch to make use of multiple processor cores, so it may speedup calculation in some cases. But Prime is generally slower - there was a thread here a while ago (http://communities.ptc.com/message/198425#198425) with the facit, that the speed of Prime with multicore on was approximately the speed of MC15 - but that sure depends much on the specific calculations done.
So despite in my opinion Prime is not a software to work with - because of the ability to use more memory it may be an option for you to testdrive Prime. The trial version is fully functional for 30 days and then falls back in a crippled "Express" mode.
You most likely would have to recreate you sheet from scratch for two reason:
1) Prime cannot read MC14 or MC15 files (and it cannot save back in older formats, too)
2) There is a converter to turn older files in Prime format, but it ever so often produces unuseable results. Furthermore this converter needs that the current MC15 is installed. If you install the MC15 trial it will deinstall your MC14 - you will have to save your license file first. When the MC15 trial period is over you will have to deinstall MC15, reinstall MC14 and provide the saved license file.