[AMBER-Developers] cygwin memory limit (was Re: near-final testing)

From: Mengjuei Hsieh <mengjueh.uci.edu>
Date: Thu, 15 Apr 2010 18:38:57 -0700


I've tested the April14 RC on cygwin with larger memory available and
I can confirm that default cygwin installation can only allocate far
less than the physical memory at a time. Take a windows xp with 1 GB
physical ram for example, you have to at least give it 1GB swap in
order to be able to allocate 1536 MB. And 1536M is large enough for
*pbsa_delphi but not so much for *pbsa_tsr. However *pbsa_tsr can
be run with the modification of maxarcdot=8000.

Here I attached a patch for this maxarcdot thing just in case you are

Before today I was using 2GB physical memory but 256MB virtual memory
for this windows, I could not even run pbsa_delphi, which is kinda odd.
So for these test cases, adequate virtual memory is required, but I'm
not sure how many mega byte is enough.

For some allocations much larger, you are out of luck for a default
cygwin environment. In order to make it work one might need to use
this command to increase the limit:
        $ regtool -i set /HKLM/Software/Cygwin/heap_chunk_in_mb 2048
        (2048 be a large number of mega byte, also remember to exit
         everything cygwin to make the setting effective)

    Cygwin, "Changing Cygwin's Maximum Memory",
Mengjuei Hsieh, Luo Research Group, Molecular Biology & Biochemistry,
University of California Irvine.
On Thu, Apr 15, 2010 at 03:39:46PM -0700, MengJuei Hsieh wrote:
> Hi,
> I just got a chance to test the April 14 RC on cygwin and found out
> *pbsa_tsr and *pbsa_delphi still have the problem of allocating memory. It
> would be nice if anyone can help us to test this on the system with larger
> memory, since I only have access to some a virtualbox with small memory. In
> the meantime, I can only say that we are aware of the problem and I am
> working on the fix this, but that's probably going to be patches (if any)
> after the release.

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Received on Thu Apr 15 2010 - 19:00:02 PDT
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