AMBER Archive (2006)

Subject: Re: AMBER: <kein Betreff>

From: Gustavo Seabra (
Date: Mon Nov 13 2006 - 11:52:55 CST

Hi Michel,

Just a guess here... I don't know if this is the case here, but some
systems copy all your files to a temporary location during the
calculation, and then copy the output back to the original
directories. (I believe this can be controlled by the -D and -wd
options in the 'mpirun' command.)


On 11/13/06, Michel Becker <> wrote:
> Dear Amber Users,
> recently we have compiled the multiprocessorversion of Amber8 but unfortunately a rather strange problem has occured. As I am accustumed to know with Amber 7 the .out and .inf files are written and readable during a job.
> Surley you can influence this with ntpr and ntwx.
> But with that multiprocessorversion of Amber8, the .out and .inf files are written not until the job is finished. It's a little trouble not to know what's going on during the run; our boss ment, it could be a problem of a wrong adjustment of the buffer; perhaps files are first written until they are large enough to overcome the buffer capacity (because the .rst and .trj files are written during the jobs)
> Thanks a lot in advance.
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