AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 21 2008 - 13:05:20 CDT

ARRRGHHHH!!!,

So this one worked perfectly. This is similar to what Franesco is seeing.
The segfault is largely random :-(. It appears to be coming from within
dspev somewhere. Can you let me know what the exact specs of the machine you
saw the first problem on are along with exact compiler, mpi and mkl versions
and I will see if I can find an equivalent machine so I can try and
reproduce the failure.

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Cenk (Jenk) Andac
> Sent: Wednesday, May 21, 2008 6:34 AM
> To: amber_at_scripps.edu
> Subject: RE: Fw: RE: AMBER: MKL libraries/Amber10
>
>
> 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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>
>

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