AMBER Archive (2008)

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

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Thu May 22 2008 - 17:24:33 CDT

Hi Ross,

I use TR-GRID, the supercomputer-facility of Turkey, to run AMBER10. As far as I know, the nodes were purchased from HP and each one of them has 4 AMD-em64T CPUs. The servr CPU info is attached. We use 4 X INTEL XEON DUALCORE CPUs @1.6 GHz (cache size 4 MB, cpu family 6, model 15) on the server.

We have Red Hat Linux x86_64 with
gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)
ifort version 10.1
intel-mkl version 10.0
lam7.1.4
running on the facility

regards,

jenk

 

--- On Wed, 5/21/08, 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: Wednesday, May 21, 2008, 1:05 PM
> 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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