AMBER Archive (2006)

Subject: Re: AMBER: Problem with file size of sander outputs

From: shuli kang (kangshuli_at_gmail.com)
Date: Wed Feb 22 2006 - 02:45:21 CST

Dear cenk,

This problem is due to the limit of your filesystem.
You can simply divide your simulation into several portions to avoid it.

Best,
Shuli.

On 2/22/06, Cenk Andac <cenk_andac_at_yahoo.com> wrote:
>
> Dear amber community,
>
> I have been running a PME explicit solvent molecular
> dynamics for a 20 KDa protein and its ligand using the
> sander module of AMBER8.
> I set nstlim=40000 and ntpr=10. After a couple of
> hours , my MD run stopped at nstep =9970 giving me the
> following error message:
>
> Filesize limit exceeded
>
> My trajectory file size has reached to 2 GB, the MD
> output is 666 Kb and the coordinate output is 6.6 MB.
>
> I believe I will have to recompile sander changing
> some codes to increase the file size in sander. Could
> someone please let me know what codes in sander should
> be modified?
>
> cheers,
>
> jenk.
>
>
>
>
>
>
> --- Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> >
> > > ./configure -mpi ifort
> > > make parallel
> >
> > -mpi means native MPI libraries as provided by the
> > operating system. This is
> > the option to use for things like an SGI altix. For
> > a regular PC running
> > redhat you need to provide an mpi installation
> > either MPICH or LAM. This MPI
> > installation needs to be compiled with the same
> > compiler as you are using
> > for compiling Amber. Hence the lam that is often
> > installed by default with
> > redhat will not work as it is compiled with GCC.
> >
> > So, download either Lam or MPICH, compile it with
> > ifort and chech your PATH
> > is correct so that the correct installation is being
> > used.
> >
> > E.g. which lamboot
> >
> > should return /usr/local/lam/lamboot (or similar)
> > rather than /usr/bin/lamboot
> >
> > Once this is done create a config.h for the lam or
> > mpich:
> >
> > export LAM_HOME=/usr/local/lam..... (or where you
> > installed it)
> > ./configure -p4 -lam ifort
> > or
> > export MPICH_HOME=/usr/local/mpich.....
> > ./configure -p4 -mpich ifort
> >
> > Then:
> >
> > make clean
> > make parallel
> >
> > You should then not get the undefined references you
> > are seeing.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Department of Molecular Biology TPC15 |
> > | The Scripps Research Institute |
> > | Tel: +1 858 784 8889 | EMail:-
> > ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on
> > request |
> >
> > Note: Electronic Mail is not secure, has no
> > guarantee of delivery, may not
> > be read every day, and should not be used for urgent
> > or sensitive issues.
> >
> >
> >
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>
>
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--
Modern Virology Research Center
College of Life Sciences,
Wuhan University
Wuhan, P. R. China, 430072

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