AMBER Archive (2006)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Thu Feb 23 2006 - 01:23:02 CST

This is in reply to Shuli Kang's, German's and Ross
Walker's E-mail messages regarding my question about
the file size of sander outputs.

Splitting sander trajectory outputs into 1 GB file
sizes has worked for me. Thanks for making this issue
clear to me.

best regards,

Jenk.

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Dear JunJun,
>
> Try editing the config.h file produced with your
> configure script and add
> the following to the
> AMBERBUILDFLAGS line:
>
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
>
> Then do a make clean followed by make.
>
> This 'may' depending on your system, compiler etc
> produce an executable that
> can write trajectory files larger than 2GB. That
> said writing such large
> trajectory files is NOT recommended. The reason for
> this is the larger the
> file becomes the more likely it is to be corrupted.
> If a single frame in the
> tajectory gets corrupted then you will have a great
> deal of trouble
> extracting information beyond the corrupted frame.
> If you break your
> simulation up into much smaller parts and one
> trajectory file gets corrupted
> then you can simply re-run this small portion of the
> trajectory from the
> restart file for that portion of the trajectory to
> recreate the mdcrd file.
> Improvements to the trajectory file format in future
> releases of AMBER may
> address this problem but for the moment there is no
> easy fix for corrupted
> trajectories.
>
> Splitting things up is much much much safer... When
> it comes to analysing
> things it also makes things easier. For starters you
> can analyse several
> trajectory files seamlessly in ptraj and VMD will
> allow you to load several
> mdcrd files into a single prmtop (molecule). Havings
> things split up also
> has the advantage that you can easily analyse just a
> small fraction of the
> trajectory without having to load the whole thing.
>
> Add this to the fact that if you copy files bigger
> than 2GB between 32 bit
> and 64 bit machines over NFS shares or try to edit a
> file bigger than 2GB in
> an editor (say vi) that does not have support for
> large files you can end up
> truncating or corrupting the file fairly easily.
>
> Thus unless you have good justification for wanting
> large coordinate files
> you are better off just scripting your simulation
> into smaller pieces...
>
> Just my 2c...
>
> 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.
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> > [mailto:owner-amber_at_scripps.edu] On Behalf Of
> JunJun Liu
> > Sent: Wednesday, February 22, 2006 12:58
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: Problem with file size of
> sander outputs
> >
> > I have little experience about it, not related to
> sander but other
> > program. At first I compiled that program using
> ifort9. The
> > program died
> > with "filesize limit exceeded " displayed when the
> produced
> > file reached
> > 2.1GB. Intel announced that intel compiler
> automatically
> > enable "large
> > file support", but I don't know why my program
> still has the 2GB
> > limitation.
> >
> > Then I use PGI compiler with -Mlfs flag for the
> compiliation. The
> > re-compiled program can now overcome the 2GB
> limitation.
> > Maybe you also
> > can try using PGI compiler with -Mlfs flag to
> re-compile
> > sander. Hope this
> > helps!
> >
> > On Wed, 22 Feb 2006 05:49:49 -0500, german
> > <gsciaini_at_qi.fcen.uba.ar> wrote:
> >
> > > Try to divide your calculation into different
> output files
> > restarting
> > > them with NTX=5, and IREST=1...
> > >
> > > Good look
> > > G.
> > >
> > >
> > >
> > > At 11:54 p.m. 21/02/2006 -0800, you 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)
>
=== message truncated ===

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