AMBER Archive (2006)

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

From: Kailee (
Date: Mon Dec 18 2006 - 10:41:11 CST

Hi, all,

Thanks for your help, I looked at the run script for the tests and wrote a
similar script according to the test script, which looks like (named as



cat << eof >
  imin = 0, irest = 1, ntx =7,
  ntb = 2, pres0 = 1.0, ntp =1,
  taup = 2.0,
  cut = 10, ntr =0,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 1.0,
  nstlim = 10000, dt = 0.001,
  ntpr = 200, ntwx = 200, ntwr = 2000

$DO_PARALLEL $AMBERHOME/exe/sander -O -i -o test3.out -c
model_mass_md2.rst -p model_mass.prmtop -r test3.rst -x test3.mdcrd

and then I used nohup to run this job as:

nohup ./Run.test &

And it ran OK without any errors, gave me same outputs as I ran on other
machines, therefore, I think it is as David suggested, it is because of the
qsub I used to submit my job. And I tried to change the shell script i used,
still no luck,

On 12/15/06, David A. Case <> wrote:
> 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.
> ...regards...dac
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