AMBER Archive (2008)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon May 19 2008 - 12:19:37 CDT

Hi Cenk,

I need to see if I can reproduce this problem myself to work out what is
going on and fix the bug. I believe it likely stems from a variable
somewhere not being correctly copied to all of the nodes.

In the meantime it would really help if you could try to get some more
debugging info out of the run for me.

In a scratch directory can you try manually running the dspev job for me.
The commands are effectively:

cd ~/
mkdir foo
cd foo
cp $AMBERHOME/test/qmmm2/1NLN_test_diagonalizers/1NLN_15A_solv.prmtop
./prmtop
cp $AMBERHOME/test/qmmm2/1NLN_test_diagonalizers/1NLN_15A_solv_min.rst
./inpcrd

Then create a mdin file with the following contents:

foo
 &cntrl
  imin=0, irest=0, ntx=1,
  nstlim=4,dt=0.002,
  temp0=300.0,tempi=300.0,
  ntc=2, ntf=2,
  ntb=1,
  cut=8.0,
  ntt=1,
  ntpr=1,
  ifqnt=1
 /
 &ewald use_pme=1 /
 &qmmm
        iqmatoms=1585,1586,1587,1588,1589,1590,
        1591,1592,1593,1594,1595,1596,1597,1598,1599,1600,1601,1602,
        1603,1604,1605,1606,1607,1608,1609,1610,1611,1612,1613,1614,
        1615,1616,1617,1618,
        3348,3349,3350,3351,3352,3353,3354,3355,
        3356,3357,3358,3359,3360,3361,3362,3363,3364,3365,3366,3367,
        3368,3369,3370,3371,3372,3373,3374,3375,3376,
        qm_theory='AM1', qmcharge=0,
        verbosity=0, qmshake=1,
        qmcut=8.0, qm_ewald=1, qm_pme=1,
        verbosity=4,writepdb=0,adjust_q=2, diag_routine=2,
 /

Then can you try running this as you would in parallel. I.e. something like:

mpirun -np 2 $AMBERHOME/exe/sander.MPI -O

Then please send me the mdout file so I can see exactly where it crashes.

Thanks,

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: Monday, May 19, 2008 9:48 AM
> To: amber_at_scripps.edu
> Subject: RE: Fw: RE: AMBER: MKL libraries/Amber10
>
> 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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