AMBER Archive (2008)

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

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Mon May 19 2008 - 11:48:21 CDT

Hi Ross,

I think I have a similar problem. Although the parallel static installation of AMBER10 went well (with all bugfixes applied) and it passed MM tests, it failed in QMMM tests at step 1NLN_dspev. Attached are my output files reqarding the QMMM tests. I would appreciate it if you let me know if there is a workaround for the fail messages.

cheers,

jenk.

--- On Mon, 5/19/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> From: Ross Walker <ross_at_rosswalker.co.uk>
> Subject: RE: Fw: RE: AMBER: MKL libraries/Amber10
> To: amber_at_scripps.edu
> Date: Monday, May 19, 2008, 10:41 AM
> 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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