AMBER Archive (2008)

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

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Wed May 21 2008 - 08:33:35 CDT

Hi Ross,

I ran the 1NLN_15A_auto test using a total of 4 CPUs from 4 different nodes. Attached is an output file of the test you were asking for.

regards,

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: chiendarret_at_yahoo.com, cenk_andac_at_yahoo.com
> Date: Monday, May 19, 2008, 10:46 PM
> Hi Francesco and Cenk,
>
> I have a guess for what might be causing the problem here
> but need some more
> info in order to make sure if this is the problem or not.
> Could you both try
> running the 1NLN_auto test case in parallel and let me know
> what happens /
> also send me the resulting output files. It would be really
> great if you
> could up verbosity to 4 for this test but if you can't
> work out how to do
> that don't worry.
>
> All the best
> 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 2:17 PM
> > To: amber_at_scripps.edu
> > Subject: RE: Fw: RE: AMBER: MKL libraries/Amber10
> >
> > 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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