Re: [AMBER-Developers] [AMBER] Compiling amber parallel

From: Dickson, Callum <>
Date: Fri, 26 Oct 2012 15:50:17 +0000

Thanks Jason, that first option worked fine (installing Amber without AmberTools).

I did previously try OpenMPI without success, there isn't a version of mpich2 available on the cluster.


From: Jason Swails []
Sent: 26 October 2012 16:28
To: Dickson, Callum; AMBER Developers Mailing List
Subject: Re: [AMBER] Compiling amber parallel

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 <<>> wrote:

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/ undefined reference to `MPIR_Err_return_comm'

/apps/intel/ict/mpi/3.1.038/lib/ undefined reference to `MPIR_Grequest_set_lang_f77'

/apps/intel/ict/mpi/3.1.038/lib/ undefined reference to `b_use_gettimeofday'

/apps/intel/ict/mpi/3.1.038/lib/ undefined reference to `MPID_Wtick'

/apps/intel/ict/mpi/3.1.038/lib/ undefined reference to `MPIR_Err_create_code'

/apps/intel/ict/mpi/3.1.038/lib/ undefined reference to `i_malloc'

/apps/intel/ict/mpi/3.1.038/lib/ undefined reference to `MPIR_Keyval_set_fortran90'

/apps/intel/ict/mpi/3.1.038/lib/ undefined reference to `i_free'

/apps/intel/ict/mpi/3.1.038/lib/ undefined reference to `MPIR_Keyval_set_fortran'

/apps/intel/ict/mpi/3.1.038/lib/ 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 M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Fri Oct 26 2012 - 09:00:04 PDT
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