Ross's observation is exactly what I would guess, as well. However, your
email suggests that you're trying to use pmemd, not sander. In that case,
it would appear as though pmemd was compiled without parallel support. What
does the config.h file in $AMBERHOME/src/pmemd/ look like? Do you see a
"-DMPI" in the MPI_DEFINES variable?
Better yet, do you know the configure command used to configure pmemd?
Also, remember that if you first build pmemd in parallel followed by a
serial build, both executables are named pmemd, so the serial version will
overwrite the parallel version. This has been changed in amber11, where the
default build installs both pmemd and pmemd.MPI, similar to what is done
with sander.
All the best,
Jason
On Fri, Oct 29, 2010 at 12:21 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Seren,
>
> It definitely looks to me like you are running the serial version of sander
> but with mpirun. Make sure you are using a parallel version of the code.
> Make sure the executable given to mpirun is sander.MPI and NOT just sander.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Seren Soner [mailto:seren.soner.gmail.com]
> > Sent: Friday, October 29, 2010 9:10 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Output problem on Amber 9
> >
> > Thanks for the reply Adrian.
> >
> > But I'm afraid that isnt the case. In fact, I just reinstalled AMBER on a
> > clean and fresh server using MPICH2.
> >
> > The tests all seem just fine, and the run keeps going, but the coordinate
> > file is corrupt (according to ptraj), and the .out file from the pmemd is
> as
> > following:
> >
> > NSTEP = 5005 TIME(PS) = 10.010 TEMP(K) = 293
> > NSTEP = 5020 TIME(PS) = 10.040 TEMP(K) = 292.63 PRESS =
> > 274.9
> > Etot = -206080.1422 EKtot = 50018.8412 EPtot =
> > -256098.9834
> > BOND = 1158.7574 ANGLE = 3226.4692 DIHED =
> > 4959.5549
> > 1-4 NB = 1696.6991 1-4 EEL = 21230.7542 VDWAALS =
> > 32958.6284
> > EELEC = -321329.8466 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 22722.9567 VIRIAL = 17729.8009 VOLUME =
> > 841143.0522
> > Density =
> > 1.0138
> > Ewald error estimate: 0.5244E-04
> > --------------------
> > NSTEP = 5010 TIME(PS) = 10.020 TEMP(K) = 293
> > NSTEP = 5025 TIME(PS) = 10.050 TEMP(K) = 293.83 PRESS =
> > 220.5
> > Etot = -206067.1820 EKtot = 50223.4622 EPtot =
> > -256290.6442
> > BOND = 1143.5592 ANGLE = 3270.5782 DIHED =
> > 4942.4778
> > 1-4 NB = 1674.3206 1-4 EEL = 21252.6748 VDWAALS =
> > 32893.7176
> > EELEC = -321467.9724 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 22820.5212 VIRIAL = 18815.7936 VOLUME =
> > 841238.7879
> > Density =
> > 1.0137
> > Ewald error estimate: 0.4236E-04
> > --------------------
> > NSTEP = 5015 TIME(PS) = 10.030 TEMP(K) = 292
> > NSTEP = 5030 TIME(PS) = 10.060 TEMP(K) = 293.63 PRESS =
> > 162.4
> > Etot = -206054.1128 EKtot = 50189.3052 EPtot =
> > -256243.4180
> > BOND = 1095.1010 ANGLE = 3234.5279 DIHED =
> > 4948.3120
> > 1-4 NB = 1664.1808 1-4 EEL = 21271.6600 VDWAALS =
> > 32890.3861
> > EELEC = -321347.5860 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 22884.4044 VIRIAL = 19934.3426 VOLUME =
> > 841311.4130
> > Density =
> > 1.0136
> > Ewald error estimate: 0.6402E-04
> > --------------------
> > NSTEP = 5020 TIME(PS) = 10.040 TEMP(K) = 292
> > NSTEP = 5035 TIME(PS) = 10.070 TEMP(K) = 292.97 PRESS =
> > 108.3
> > Etot = -206041.0229 EKtot = 50075.8387 EPtot =
> > -256116.8616
> > BOND = 1188.6496 ANGLE = 3253.7780 DIHED =
> > 4958.3474
> > 1-4 NB = 1657.4676 1-4 EEL = 21231.7085 VDWAALS =
> > 32913.2619
> > EELEC = -321320.0746 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 22908.5928 VIRIAL = 20940.4972 VOLUME =
> > 841363.6741
> > Density =
> > 1.0136
> > Ewald error estimate: 0.9973E-04
> > --------------------
> >
> >
> > There seems to be a problem of synchronization, but I don't have any idea
> > what causes it, or what can solve it.
> >
> > Thanks,
> > Seren Soner
> >
> > On Mon, Oct 18, 2010 at 1:40 PM, Adrian Roitberg
> > <roitberg.qtp.ufl.edu>wrote:
> >
> > > I have seen this before, and it is usually due to more than one
> instance
> > > of amber trying to write to the same files. Check that there is only
> one
> > > set of amber runs active in that directory.
> > >
> > > Adrian
> > >
> > >
> > > On 10/18/10 11:16 AM, Seren Soner wrote:
> > > > Hello there,
> > > >
> > > > I've been using AMBER in our server for some time, and after the
> > > > server crash a few weeks back, my output files have been acting
> weird.
> > > > My computer administrator tells me nothing has been changed after the
> > > > server crash, and the output file becomes as follows:
> > > >
> > > >
> > > > NSTEP = 219965 TIME(PS) = 12939.930 TEMP(K) = 299
> > > > NSTEP = 220080 TIME(PS) = 12940.160 TEMP(K) = 299.63 PRESS = 79.6
> > > > Etot = -203606.8511 EKtot = 51214.7469 EPtot = -254821.5980
> > > > BOND = 1362.7033 ANGLE = 3547.3148 DIHED = 4862.2996
> > > > 1-4 NB = 1683.6634 1-4 EEL = 21484.6416 VDWAALS = 32232.8437
> > > > EELEC = -319995.0644 EHBOND = 0.0000 RESTRAINT = 0.0000
> > > > EKCMT = 23099.5614 VIRIAL = 21648.8530 VOLUME = 844163.5532
> > > >
> > > > Or, sometimes I may see NSTEP = 219000 information at one line, and
> > > > then NSTEP = 218990, NSTEP = 218995, and NSTEP = 219000 again.
> > > >
> > > > Does anyone have any idea what may cause this problem ?
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > > --
> > > Dr. Adrian E. Roitberg
> > > Associate Professor
> > > Quantum Theory Project, Department of Chemistry
> > > University of Florida
> > >
> > > Senior Editor. Journal of Physical Chemistry.
> > >
> > > on Sabbatical in Barcelona until August 2011.
> > > Email roitberg.ufl.edu
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Oct 29 2010 - 09:30:07 PDT
