AMBER Archive (2005)

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

From: shuli kang (mmv_at_whu.edu.cn)
Date: Tue Jan 25 2005 - 01:35:45 CST

Thank you very much for your reply.

I think splitting the jobs up into chunks , at least for me, is the most
convenient way to overcome the difficulty.

Ross Walker wrote:

>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:
>
>-D_GNU_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE64
>
>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
>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 |
>
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