AMBER Archive (2002)

Subject: Re: cannot deal with large trajectory?

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Mon Dec 30 2002 - 20:55:41 CST

On Mon, 30 Dec 2002, Thomas Cheatham wrote:
> Is this a 3 gigabyte file? I do not know of specific limitations within
yes

> ptraj with file size other than those that are standard to the system.
> ptraj uses the C system command fopen() to open a file (or popen if it is
> compressed).
> Are you sure the file is named correctly? (the full name, i.e. include
> the .gz or .Z if present).
  I compress it (.Z format) and its size is down to no more than 2gb, and
ptraj can read this compressed file into buffer.

> I have read in trajectories that are near a gigabyte in size but not tried
> anything larger than 2 GB (file size limits on linux) that I can
> remember. This is because I never create files this large; normally I
> break up a run to produce smaller files. Also, I almost never dump the
> files at such a high resolution (i.e. every frame).
I just dump it every 0.1ps. Maybe it is due to buffer limit, I think.
I've no idea about file size limits on linux, but it seems to be okay
on AIX51(IBM P690) where I've stored gaussian98' single I/O file more than
27gb.

> Let me know if I can be of further help in tracking down your problem.
I guess it is maybe due to the limit of C compiler.

Happy Holidays!

sychen