AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Aug 15 2009 - 23:40:26 CDT

Hi Cat,

Sometimes it helps just to take a careful look at the error message rather
than going to all the trouble of specifying your system specs etc. In your
case you will see that nmode is asking for:

Total memory required : 1604498119 real words

In Fortran 1 word = 8 bytes so in your case this is 12835984952 bytes. This
is equivalent to 11.95GB. Thus you need at least 16GB available to you - so
you are not swapping. Unless you have some high end workstation it is
unlikely your machine can be upgraded for this much ram. You could check on
using some large shared memory machines such as are available on the US
teragrid system. E.g. Pople the SGI Altix at PSC. Of course this is still a
very expensive simulation so you might want to see if you can cut down the
size of your system or look for alternative approaches such as principle
component analysis techniques. Maybe others on the list can comment more.

Good luck,
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Catein Catherine
> Sent: Saturday, August 15, 2009 9:13 PM
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] MM-GBSA nmode error for explicit solvent system
> only but not for implicit solvent system. Why?
>
>
> 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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