AMBER Archive (2009)

Subject: RE: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Sat Aug 15 2009 - 21:45:34 CDT

Thank you Ashish,

 

I did the analysis with single CPU computer. If I cannot add physical memory to the system, are there any other way to solve this problem?

 

Best regards,

 

Cat
 
> Date: Sat, 15 Aug 2009 11:35:53 +0530
> Subject: Re: [AMBER] MM-GBSA nmode error for explicit solvent system only but not for implicit solvent system. Why?
> From: ashish.runthala_at_gmail.com
> To: amber_at_ambermd.org
>
> Total memory required : 1604498119 real words
> > Total memory required : 60129519 real words
> > ASSERTion 'ier ==0' failed in nmode.f at line 105.
>
> Amber's nmode is not a parallel program, so it cannot make use of any memory
> except that available to the cpu that is running the code.
> You have not mentioned the number of nodes you are accessing for it. But
> they are definitely not sufficient for your calculation.
>
> Don't worry. This is a common problem to a parallel systems.
> Although nodes are allocated to share CPUs, random access memories are
> somewhat not shared or not allowed to share high amount of memory. I advise
> you to ask the computer facility guide there, to allocate physical memories
> among different nodes.
> So
>
> Ashish Runthala,
> Faculty Division III,
> Assistant Lecturer, Biological Sciences,
> Birla Institute of Technology and Science,
> Pilani, Rajasthan- 333031
> INDIA
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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