AMBER Archive (2008)

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

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Mon May 19 2008 - 15:40:37 CDT

Hi Ross,

Thanks for responding. As you suggested I have rerun the 1NLN_dspev test using the "verbosity=4" option in the input file and am sending you the output "mdout.1NLN_dspev.verb4" as an attachment. Just to let you know that I sent a PBS job to the server to assign for 4 CPUs on 4 different nodes to rerun the test.

In addition to this, I ran another 1NLN_dspev test using the 2 CPUs of our server only (that is, no external nodes was used to run the second test). It passed the test this time. Please see the second attachment "mdout.1NLN_dspev.server" for an output for the second test.

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: amber_at_scripps.edu
> Date: Monday, May 19, 2008, 12:19 PM
> 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.
> > > > >
> > >
> -----------------------------------------------------------------------
> > > > > The AMBER Mail Reflector
> > > > > To post, send mail to amber_at_scripps.edu
> > > > > To unsubscribe, send "unsubscribe
> > > amber" (in the
> > > > > *body* of the email)
> > > > > to majordomo_at_scripps.edu
> > > >
> > > >
> > > >
> > > >
> > >
> -----------------------------------------------------------------------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber_at_scripps.edu
> > > > To unsubscribe, send "unsubscribe
> amber" (in
> > > the *body* of the email)
> > > > to majordomo_at_scripps.edu
> > >
> > >
> -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber_at_scripps.edu
> > > To unsubscribe, send "unsubscribe
> amber" (in the
> > > *body* of the email)
> > > to majordomo_at_scripps.edu
> >
> >
> >
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the
> *body* of the email)
> to majordomo_at_scripps.edu

      


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu