AMBER Archive (2003)

Subject: upper limited of memory for nmode

From: wentaofu (wentaofu_at_uic.edu)
Date: Fri May 02 2003 - 19:06:06 CDT

Dear Amber user;

I would like to do nmode for a system about 4000 atoms too. I was asked for
about 270,000,000 words by nmode. We only have a system with 1G memory. Can
I use swap memory(about 2.5G) to do that? I tried to recompile nmode using
280,000,000 words. But, the amber said "array too large". Is there a upper
limited for how many words you have to use in nmode?

Thanks,

Wentao Fu
Ctr for Pharm Biotech
UIC

>===== Original Message From amber_at_heimdal.compchem.ucsf.edu =====
>On Thu, May 01, 2003, Masaki Tomimoto wrote:
>>
>> I have a question about a simle mathematics to calculate how much memory I
>> need. I found the following comments from Dr. Case in Amber Mailing
>> Archive.
>>
>>
>> My system contains about 4000 atoms. According to the above math, I should
>> need (4000x3)x(4000x3)/2 = 144,000,000 words, or 1.15 GB. However, when I
>> execute nmode, it says that it require almost double, 208,497,233. Even
>> Hessian is a symmetric matrix which requires only triangle part (that
>> denotes "/2" is the above math), nmode requires memory space which hold
>> entire hessian matrix?
>>
>
>The current version of nmode actually requires about 3*(3n)**2/2 words of
>memory for the matrices. This would be 216 million words, or 1.7 Gbytes for
a
>4000 atom system; some smaller amounts of memory are needed for other tasks.
>You can follow the allocation by looking at the "ntrun.eq.1" sections of
>alloc.f.
>
>This is a tradeoff of memory usage for faster computational time. I would be
>possible to use less than half this amount of memory, and that may be an
>important consideration for clusters that have limited amounts of physical
>memory. I can work off-line with you to put together such a code if that
>seems necessary.
>
>.dave case
>
>--
>
>==================================================================
>David A. Case | e-mail: case_at_scripps.edu
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA | http://www.scripps.edu/case
>==================================================================