RE: AMBER: What does a crash mean while running a md simulation?

From: Ross Walker <>
Date: Mon, 24 Jan 2005 22:28:32 -0800

Dear Shuli,

> Filesize limit exceeded

Yeap, your mdcrd file has exceeded the 32Bit 2GB file limit (31^2). You have
several options:

1) Use a 64 bit machine these have a 2^63 byte file limit.
2) Split your jobs up into smaller chunks.
3) Write to the mdcrd less frequently (this may have implications on the
analysis you can do).
4) If you don't need the solvent molecule positions skip writing them using
   ntwprt (see manual). Note: you will need a prmtop file without the
solvent molecules for post processing the mdcrd file in ptraj etc.
Experiment with small runs first of all to make sure you can visualise /
analyse the 'truncated' trajectory.
5) Attempt to compile amber8 for large file support.

Concerning option 5:

!!!BEWARE: Files larger than 2GB can be difficult to handle. Many programs
such as vi or gzip (if it hasn't been compiled for 64 bit file pointers) can
corrupt files large than 2GB. Also, be very careful transfering files bigger
than 2GB over NFS shares...!!!

Linux Kernel's later than 2.4.0 support large (64 bit file pointers) files
on 32 bit machines. I have successfully used enabled large files with AMBER
6 using g77 by adding the following option to the compile line:


For amber8 you would add this line to the AMBERBUILDFLAGS line of the
config.h file.

However, I believe this is only for gcc and g77 and so will probably not
work with amber8 which needs a fortran 90 compiler. With Intel's ifc v7.1
there used to be an experimental library that you could link in to get large
file support. I assume there is a similar system for ifort 8.0 and 8.1.
However, a brief google search has not yielded the original help file I used
ages ago.

I suggest you search around on the web and intel's site and see if you can
turn up some information regarding enabling large file support with ifort
v8.0 or 8.1. If you find the information but can't work out what to do email
me the link and I'll take a look at it.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Tue Jan 25 2005 - 06:53:00 PST
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