AMBER Archive (2006)

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

From: Kailee (kaileeamber_at_googlemail.com)
Date: Tue Dec 19 2006 - 10:13:48 CST

Dear Ross,

Thanks very much for your reply, it is the differences of the architecture
of the nodes I ran interactively and default nodes if I use qsub. Now it is
running now if I specify the queue when I use qsub by:
qsub x86_64 my_script

Thank you all again, and wish you all a merry christmas and very happy new
year!

Kailee

On 12/18/06, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> Dear Kailee,
>
> My suspicion here is that there is some confusion between where you think
> qsub actually runs your job and where it really does. Who setup your system
> and more importantly who set up the various queues etc? It looks to me like
> the system you are compiling and running interactively on is one
> architecture (say x86) while the actual compute nodes that your job gets run
> on through qsub are a different architecture (say x86_64). Unfortunately
> without seeing all the details about how your cluster is setup, how the
> queuing system works etc it is very difficult to help much more. Basically
> the problem you are seeing comes down to two possibilities:
>
> 1) The architecture you are on interactively does not match the compute
> node architecture.
>
> 2) The path/filesystem structure is different on the compute nodes such
> that it cannot locate the file.
>
> The 1st one is more likely as I would expect the second problem to give
> the error "Path not found". Hence you should probably speak to whoever is in
> charge of your cluster and see if they can help some more. And or talk to
> other users of the cluster and see what they do.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> ------------------------------
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Kailee
> *Sent:* Monday, December 18, 2006 09:07
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: sander: cannot execute binary file
>
>
> 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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