AMBER Archive (2006)

Subject: Re: AMBER: Nmode memory allocation problem

From: JunJun Liu (ljjlp03_at_gmail.com)
Date: Tue Jun 13 2006 - 10:08:25 CDT

Hi Dr.Walker,

Thanks a lot! I added a option forcing 64 compiliation in config.h and the
memory problem is gone, thanks!

Liu

On Mon, 12 Jun 2006 22:34:24 -0300, Ross Walker <ross_at_rosswalker.co.uk>
wrote:

> 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
>
> /\
> \/
> |\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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-- 
JunJun Liu

College of Chemistry
Central China Normal University
WuHan   430079
P.R. China
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