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.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
>
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Received on Wed Dec 20 2006 - 06:07:26 PST
