AMBER Archive (2005)

Subject: RE: Re[2]: AMBER: What does a crash mean while running a md simulation?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Dec 06 2005 - 10:54:11 CST

Dear Yuann

> Is this also suitable for overcoming the memory limit (2GB) on a 32bit
> P4-Xeon machine with 4GB memory while running nmode in AMBER7?
>
> Since there was a memory requirement of 295292922 real words in nmode
> calculation, and nmode can only be compiled when 'MAXMEMX'
> was set to 200000000.
> I tried to change MAXMEMX to 300000000 and add
> " -D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE64" in g77
> MACHINE file, but it still complained about too large array to handle:

These options only deal with file pointer offsets, they have no effect on
memory pointers. If you machine is a 32 bit machine your only option,
without either shrinking your system or seriously re-coding nmode, is to use
a 64 bit machine such as an Opteron or Itanium. You could also get away with
an Intel Em64T or and AMD 64 as long as you compile in 64 bit mode and link
to 64 bit libraries.

> real*8 x (MAXMEMX)
> ^
> Array `x' at (^) is too large to handle
> _nmode_.f: Outside of any program unit:
> _nmode_.f:50: size of variable `store_x__' is too large

Note, I don't think the g77 compiler will compile 64 bit binaries on these
machines, although I might be wrong here.

All the best
Ross

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|\oss Walker

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