AMBER Archive (2006)

Subject: RE: AMBER: Nmode memory allocation problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jun 12 2006 - 20:34:24 CDT

Hi JunJun,

> I have a system containing 10,000 atoms which would need
> about 4GB memory
> if want to do nmode calculation with ismem=1 specified. In our
> supercomputer, there's 100GB free shared memory when I submit
> a nmode
> calculation, but I'm still getting the following error messages:
>
> ====
> Total memory required : 538254755 real words
>
> Total memory required : 60406787 integer words
>
> Maximum nonbond pairs 59737914
> ASSERTion 'ier == 0' failed in nmode.f at line 105.

This means the allocation failed. Did you definately compile the code to be
completely 64 bit? You need 64 bit code to be able to allocate more than 2GB
of memory as a single block. Also, try writing a short piece of code that
simply allocates a 5GB array, checks it was allocated okay and then
deallocates it. Make sure you can get this to compile and work on your
machine. If you can get this to work then you should be able to get nmode to
work. If you can't get a simple code to work then you likely have issues
with the compiler, machine architecture etc.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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