AMBER Archive (2006)

Subject: RE: AMBER: Amber9 failure to compile parallel on Rocks 4.2.1 system

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Dec 06 2006 - 16:48:51 CST

Dear Michael,

The error you are seeing typically arises when the mpi library was compiled
with a different compiler to the one used to compile Amber. Try downloading
the latest copy of mpich (v2) [-mpich2]. Compile this making sure to set
FC=ifort and CC=icc. Then once this is installed in say /usr/local then set
your path so that this mpi (mpirun, mpif90 etc) is used in place of the
system default one. Also set MPI_HOME to point to this installation. You
should then be able to build amber fine.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Michael John Hanby
> Sent: Wednesday, December 06, 2006 13:26
> To: amber_at_scripps.edu
> Subject: AMBER: Amber9 failure to compile parallel on Rocks
> 4.2.1 system
>
> Howdy,
>
> I'm attempting to compile Amber9 on a Rocks 4.2.1 system with
> the Intel
> compilers on a system with dual core 64bit Xeons:
>
> 2.6.9-42.0.2.ELsmp #1 SMP x86_64 GNU/Linux
>
> Compiling serial succeeds, however parallel fails with this error:
>
> force.o(.text+0x5bb4): In function `force_.A':
> : undefined reference to `mpi_bcast_'
> force.o(.text+0x5bdc): more undefined references to
> `mpi_bcast_' follow
> make[1]: *** [sander.MPI] Error 1
> make[1]: Leaving directory `/state/partition1/apps/amber9/src/sander'
> make: *** [parallel] Error 2
>
> I've tried using -mpich -lam and -openmpi. The first 2 fail with the
> error above after several minutes, -openmpi fails immediately with an
> error about a missing mpi header file.
>
> Here are the steps I used for compiling the parallel version:
>
> Compile Amber9 parallel
> # export MPI_HOME=/opt/mpich/gnu
> # export PATH=$MPI_HOME/bin:$PATH
> # export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH
> # cd $AMBERHOME/src
> # make clean
> # ./configure -mpich -p4 ifort_x86_64
> # make parallel
>
> Any suggestions on what I could try differently?
>
> Thanks
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