AMBER Archive (2006)

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

From: Kailee (kaileeamber_at_googlemail.com)
Date: Mon Dec 18 2006 - 11:06:36 CST

Hi, all,

Sorry for the unfinished email I just sent out, and looking forward to your
suggestions.

Best regards,
Kailee

On 12/18/06, Kailee <kaileeamber_at_googlemail.com> wrote:
>
> 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
> Run.test):
>
>
> ----------------------------------------------------------------------------------------
>
> #!/bin/bash
>
> cat << eof > in.md
> test
> &cntrl
> 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
> /
> eof
>
> $DO_PARALLEL $AMBERHOME/exe/sander -O -i in.md -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 <case_at_scripps.edu> 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
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>

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