AMBER Archive (2009)

Subject: Re: [AMBER] 60 giga output file .mdcrd file

From: Fernando Martín García (fmgarcia_at_cbm.uam.es)
Date: Tue Nov 03 2009 - 04:35:41 CST

Hello Silvia

I had the same problem. My solution is to make a counter for your crd
files like this:

#!/bin/csh
set i=1
while ($i <= n) #n is the number of your file (my advice is to use an
increase of 15)
echo "yourfile$i.coord >> todas_las_trayectorias" $i
zcat yourfile$i.coord.gz >> fileoutput.crd

@ i++
end

Fer

El mar, 03-11-2009 a las 11:24 +0100, Silvia Carlotto escribió:
> Thanks to all,
>
> I use the command Strip in ptraj and I obtaine a 5 Giga file. But now
>
> the new problem is that vmd open only 2Giga file.
>
> How can I split my mdcrd file in 3 smaller file?
>
>
> I can't understand the command in amber tools
>
> thanks to all
>
> 2009/11/3 Ross Walker <ross_at_rosswalker.co.uk>
>
> > Hi Silvia,
> >
> > This sounds normal to me. Currently ptraj goes through and completely
> > checks
> > the mdcrd file before it processes it. If you figure that your system can
> > do
> > maybe 10MB per second sustained then just to run through a 60GB file
> > without
> > doing any processing will be 1.7 hours. Try just creating a copy of the
> > file
> > and this will give you an idea of the speed of your system, it will
> > probably
> > take > 30 mins just to copy. Then figure at least twice this for ptraj to
> > process it for a basic strip command.
> >
> > Options are to 1) Get yourself a faster system, probably with multiple
> > striped raid disks that will allow you to approach something like 120Meg a
> > second.
> >
> > 2) rerun your simulation and do not save to the mdcrd file as often.
> >
> > 3) break up your mdcrd file into chunks or use ptraj to reduce the number
> > of
> > frames. This of course will still require you to run through it once.
> >
> > AmberTools 1.3 will be released soon and this includes several improvements
> > for ptraj when working with large files, such as removing the initial check
> > etc. It can also do parallel i/o so you can try to take advantage of
> > parallel file systems such as GPFS or Lustre. In short though, if you are
> > running this on your desktop, rather than a well build supercomputer
> > connected by fiber to a true (and well designed) parallel file system then
> > you are unfortunately up against the hardware limitations of your system.
> >
> > If you are using this on some NFS server that you are connecting to
> > remotely
> > then I would just take a weeks vacation while you wait for it to process.
> >
> > Sorry I can't help much more but unfortunately disk speeds have been
> > largely
> > flat for the last 8 years while capacity has ballooned.
> >
> > All the best
> > Ross
> >
> > > -----Original Message-----
> > > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> > > Behalf Of Silvia Carlotto
> > > Sent: Monday, November 02, 2009 9:42 AM
> > > To: amber_at_ambermd.org
> > > Subject: [AMBER] 60 giga output file .mdcrd file
> > >
> > > Dear user,
> > >
> > > I generate a.crd file of 60 Giga (a protein in a water box, 10 ns, n
> > > tot
> > > atom ca. 8000).
> > >
> > > I am using ptraj to strip water but
> > >
> > > the ptraj command is over 30 minutes on
> > >
> > > PTRAJ : trajin XXX.mdcrd
> > >
> > > checking coordinates : XXX.mdcrd
> > > Is it a normal?
> > >
> > > Is it possible to manupulate with ptraj a file of these dimensions?
> > >
> > > I have no other ideas to strip water to generate a movie with vmd.
> > >
> > > thanks to help
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> 

-- 
Fernando Martín García.
Centro de Biología Molecular "Severo Ochoa". 
C/ Nicolás Cabrera, 1. 
Campus UAM. Cantoblanco, 28049 Madrid. Spain.

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