AMBER Archive (2008)

Subject: RE: Fw: RE: AMBER: MKL libraries/Amber10

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon May 19 2008 - 10:41:59 CDT

Hi Francesco,

You only need to apply the bugfixes once to the source tree. So I assume if
you are using the same amber installation (directory structure) to compile
both serial and parallel then you are fine. However, I'd still like to try
and track down what is wrong with the QM/MM in parallel. Can you try running
the test case again and see if it crashes at the same point.

If it does can you then please send me the output file
$AMBERHOME/test/qmmm2/mdout.1NLN_dspev

Thanks,
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Francesco Pietra
> Sent: Monday, May 19, 2008 8:25 AM
> To: amber_at_scripps.edu
> Subject: Re: Fw: RE: AMBER: MKL libraries/Amber10
>
> Hi:
>
> I applied bugfix 1-3 (April 2008) before compiling serial, and all tests
> PASSED, including those for the QMMM part.
>
> Then, I compiled parallel by just commanding
> make parallel
> .?configure ...
> make parallel
>
> I had not imagined that parallel compilation should have been preceded by
> the application of bugfix, as implied in your mail. Perhaps that need
> could be specified in the manual online.
>
> I can't try immediately as the machine is busy with a docking procedure.
>
> Thanks
> francesco pietra
>
> --- On Mon, 5/19/08, Gustavo Seabra <gustavo.seabra_at_gmail.com> wrote:
>
> > From: Gustavo Seabra <gustavo.seabra_at_gmail.com>
> > Subject: Re: Fw: RE: AMBER: MKL libraries/Amber10
> > To: amber_at_scripps.edu
> > Date: Monday, May 19, 2008, 7:18 AM
> > > With immediately subsequent QMMM test, after some tests
> > PASSED, there was some problem with mpirun. Maybe someone is
> > interested in looking at the output of the compilation
> > (attached). To this concern, also the (renamed) config file
> > is attached.
> >
> > You need to apply the bugfixes before compiling.
> > Specifically, your
> > problem with the QM/MM testing should be solved with bugfix
> > 3. See:
> > http://www.ambermd.org/bugfixes10.html
> >
> > Gustavo.
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>
>
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