AMBER: nmode calculation

From: mingche Pan <>
Date: Mon, 24 Jan 2005 07:34:18 -0800 (PST)

Dear amber users,

I posted this email two days ago, but my last email has been messed up, and I didn't get any response yet. So I post again.


I'd like to do some nmode calculations. My system is rather big, having 6660 atoms (need ~1.7 G memory with amber6, and ~3.2G memory with amber8). I have tried different ways on different machines to test nmode compilation and execution, but no luck. I summarized the testing results as below.


On Dell PowerEdge 1750, 3.2G dual Intel Xeon (32 bits system), 4G memory


MAXMEMX= 110,000,000

Compilation: OK

Execution: OK for small system

MAXMEMX= 120,000,000 - 260,000,000

Compilation: OK

Execution: Segment fault, core dumped by only typing 'nmode' command

MAXMEMX >= 270,000,000
Compilation: failed, "x" is too large to handle, "store_x_" is too large.

Execution: -----


MEMDRV = 400,000,000, MAXATOM = 7000, etc.

Compilation: OK

Execution: failed due to insufficient memory (ASSERTion 'ier == 0' failed in nmode.f at line 105.)


On SGI, 64bit, 64G memory

Amber6: MAXMEMX= 500,000,000

Compilation: using '-64' instead of '-n32', succeeded!

Execution: works for small system, but core dumped after running my job, but no Segment fault error by typing 'nmode' command

Amber8: MEMDRV = 400,000,000, MAXATOM = 7000

Compilation: using '-64' instead of '-n32', OK

Execution: works for small system; core dumped again for my system!!!! Different error message, it says memory available is only 260,000,000 (2G), asking to increase the memory!!!


My questions are:

Is it possible to get nmode to work with my system on Dell machine?

What is the problem with nmode calculations on SGI machine? How can I get it to work? (on both machines, I have no limitations of disk and memory usage)

Can anyone give me a hand? Thanks for any suggestion!!



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Received on Mon Jan 24 2005 - 15:52:59 PST
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