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><<
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Apr 29 2010 - 08:00:06 PDT
