I'm moving this discussion over to the developers list since it's a
developer version issue.
On Fri, Oct 26, 2012 at 11:11 AM, Dickson, Callum <
callum.dickson09.imperial.ac.uk> wrote:
> Hi,
>
> I am having some issues trying to compile the development version of
> amber12 parallel on the cluster at my university. I am able to compile the
> serial version, however I get an MPI related error when I then try to
> compile the parallel version. The configuration of amber12 parallel seems
> to proceed without a problem.
>
> I am using intel compilers and intel MPI. Here is the exit output error
> when I try to compile:
>
>
> FILE_SOURCE -DBINTRAJ -I/home/cd709/include -DMPI
> -I/apps/intel/2013/mkl/include -shared-intel \
> -o mdgx.MPI CompFrc.o BSpline.o Grid.o Random.o mdgxVector.o Matrix.o
> ChargeMap.o pmeRecip.o mleRecip.o pmeDirect.o CrdManip.o CellManip.o
> Topology.o Trajectory.o SpecialMath.o Nonbonded.o Bonded.o Parse.o
> Command.o Constraints.o Thermostats.o Barostats.o Integrator.o Timings.o
> Manual.o VirtualSites.o Buckingham.o ThermoDyn.o ChargeFit.o ParamFit.o
> Debug.o BroadcastCommand.o MPIMap.o MPITypeCast.o ptrajmask.o
> ../sff/AmberNetcdf.o mdgx.o -lfftw3 -L/home/cd709/amber12/lib
> -L/home/cd709/amber12/lib -lnetcdf -lm
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `MPIR_Err_return_comm'
>
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `MPIR_Grequest_set_lang_f77'
>
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `b_use_gettimeofday'
>
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `MPID_Wtick'
>
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `MPIR_Err_create_code'
>
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `i_malloc'
>
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `MPIR_Keyval_set_fortran90'
>
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `i_free'
>
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `MPIR_Keyval_set_fortran'
>
> /apps/intel/ict/mpi/3.1.038/lib/libmpigf.so: undefined reference to
> `MPID_Wtime_todouble'
>
> make[2]: *** [mdgx.MPI] Error 1
>
> make[2]: Leaving directory
> `/export71/home/cd709/amber12/AmberTools/src/mdgx'
>
> make[1]: *** [parallel] Error 2
>
> make[1]: Leaving directory `/export71/home/cd709/amber12/AmberTools/src'
>
> make: *** [install] Error 2
>
Yikes. Looks like the MPI is borked. Maybe mdgx is not strictly adhering
to some standard. Or maybe MDGX is using some MPI-2 standard features that
Intel has not implemented in their MPI. (Dave C. can weigh in on this if
he knows any of them to be true).
In any case, I don't know of many devs that regularly test Intel's MPI, so
you have a couple options (and if you try them, we'd appreciate hearing
back):
1) compile the Amber programs (sander.MPI and pmemd.MPI) without doing any
of the AmberTools installs: cd $AMBERHOME/src && make install) and see if
that works.
2) try mpich2 instead of intel MPI (or OpenMPI, either one).
Also, I don't know of any devs that have been using Intel 13 compilers yet,
so you could also try downgrading to an older (more-tested) version if the
2 options above don't work.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Fri Oct 26 2012 - 08:30:03 PDT
