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 - 23:12:42 CDT

Thank you Ashish,

 

I am using red hat linux, with 2-5G free hard disk in running directory but less than 1 G in the partition where I installed the OS. I may have ~1G RAM, but i am not sure. Please kindly instruct.

 

Best regards,

Cat
 
> Date: Sun, 16 Aug 2009 12:59:11 +0900
> 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
>
> Ya there are there catherine. Tell me which OS you are working on?
> Also tell me the size of your RAM and the available free hard disk
> space in the partition where you have installed your OS.
>
> 2009/8/16 Catein Catherine <askamber23_at_hotmail.com>:
> >
> > 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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>
>
>
> --
> 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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