AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon May 19 2008 - 16:17:25 CDT

Just to note that crash with my system occurred just at the same point as in your case.

Unfortunately I can't provide anything more today as the docking procedure proves very time consuming. If anything, I can provide the (renamed an attached) dspev file related to the crash with my system,

francesco

--- On Mon, 5/19/08, Cenk (Jenk) Andac <cenk_andac_at_yahoo.com> wrote:

> From: Cenk (Jenk) Andac <cenk_andac_at_yahoo.com>
> Subject: RE: Fw: RE: AMBER: MKL libraries/Amber10
> To: amber_at_scripps.edu
> Date: Monday, May 19, 2008, 9:48 AM
> 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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> > >
> > >
> > >
> >
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