AMBER Archive (2006)

Subject: Re: AMBER: sander: cannot execute binary file

From: David A. Case (
Date: Fri Dec 15 2006 - 11:48:49 CST

On Fri, Dec 15, 2006, Kailee wrote:
> Thanks for your reply, as Ross has suggested, I have checked the location of
> sander, it was correct, and also I can see this file using my account. As to
> the architecture, the node I was trying to run was the one I compiled the
> amber.

I know that this may not be much help, but (as I understand it)
this is a situation where the test cases all pass, but your attempt to run
your own job never even gets far enough to look at your input, but just
reports that it cannot execute the binary. You need to look for *anything*
that is different between what you are doing and what the test cases are
doing. For example, try running the test cases "by hand" in the same way
your run your job. I didn't see anything in what you reported that looks
wrong, so you will probably have to poke around yourself. The good thing is
that the test cases indicate that you do have a working installation.

My best guess is that you used "qsub" for your job, but that the
test cases didn't use the queuing system. If this is in fact the cause of the
problem, then at least you will have narrowed it down.


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