Thanks Jason,
I am using openmpi from Fink, so I am not building one myself.
The problem is that openmpi in Fink has one problem (mpicc is calling system
gcc instead of Fink gcc, known as gcc-4).
But I found a solution for this problem and it requires changing config.h,
and forgot to check that the same config.h has to be in AmberTools/src and
Amber11/src.
On Thu, Apr 29, 2010 at 15:51, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> On Thu, Apr 29, 2010 at 10:41 AM, Alan <alanwilter.gmail.com> wrote:
>
> > Hi there,
> >
> > It's not clear on the manuals which version of openmpi is required. I
> > have openmpi-1.3.3 from Fink on my Mac, and I managed to compile pjtraj
> and
> > nab with mpi.
> >
> > Then I try to install amber11. Serial was smooth, test (although long)
> went
> > all fine. So parallel...
> >
> > Using the same successful config.h from AmbertTools with mpi, my attempt
> > fails with:
> >
> > [snip]
> > mpif90 -c -O3 -mtune=generic -ffree-form -o ips.o _ips.f
> > cpp -traditional -P -DBINTRAJ -DMPI sander.f > _sander.f
> > mpif90 -c -O0 -ffree-form -o sander.o _sander.f
> > _sander.f:95.75:
> >
> > use qmmm_module, only : qmmm_nml,qmmm_struct, deallocate_qmmm,
> qmmm_mpi,
> > &
> >
> 1
> > Error: Symbol 'qmmm_mpi_setup' referenced at (1) not found in module
> > 'qmmm_module'
> > make[1]: *** [sander.o] Error 1
> > make: *** [parallel] Error 2
> >
>
> This smells like an incompletely cleaned sander. Did you make clean before
> make parallel in $AMBERHOME/src? The clean target in
> $AMBERHOME/AmberTools/src does NOT trigger the clean target in the amber
> source directory.
>
>
> >
> > I see that in configure_openmpi is mentioned openmpi 1.4, but should be
> > 1.3.3 OK?
> >
>
> OpenMPI 1.3.3 will work just fine as long as it was properly built I'm
> assuming. The configure_openmpi is provided for those that want to build
> an
> MPI as part of their Amber/AmberTools build. If you want to use this
> script, you'll have to download OpenMPI 1.4 (or 1.4.1). You can always
> hack
> the configure script to cd into openmpi-1.3.3 instead of openmpi-1.4(.1),
> but if you have to build an MPI anyway, why not just build the latest one?
>
> Good luck!
> Jason
>
>
> > Any ideas about the error above?
> >
> > Many thanks,
> >
> > Alan
> > --
> > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> > Department of Biochemistry, University of Cambridge.
> > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> > >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Thu Apr 29 2010 - 08:00:09 PDT
