AMBER Archive (2005)

Subject: RE: AMBER: Amber 8 : installation problems : undefined reference to `mpi_allreduce_'

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue May 24 2005 - 10:43:37 CDT

Dear René

> ../lmod/lmod.a -lpbs -lnsl -L/opt/lammpi-7.1.1/lib -llammpio
> -llamf77mpi -lmpi -llam -laio -laio -lutil -ldl \
> ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o
> ../lib/sys.a
> egb.o: In function `genborn_mp_egb_':
> egb.o(.text+0x210b): undefined reference to `mpi_allreduce_'
> egb.o(.text+0x30ff): undefined reference to `mpi_allreduce_'
> sander.o: In function `MAIN__':
> ...
> (many more of this)
>
> Target is a cluster of amd-dual-processor-workstations with
> RedHat 7.3 .
> Fortran compiler : ifc and ifort (intel fortran compiler 8.0)
> C(++) Compiler : gcc 3.4.3
> Configuration : ./configure -lam -athlon ifort

A couple of things to try.

1) Make sure you are building mpich or lam with the exact same compilers as
you are building amber with. Note, for lam and ifort I would use the
following options when running configure. Make sure you do a make clean of
the lam directory before starting. Also make sure you have uninstalled the
default lam that ships with Linux as this is built with gcc and won't work
with the intel compilers. This is for Intel v8.1, for Intel 8.0 you may need
to change export CXX=icpc to CXX=icc:

export CC=icc
export CXX=icpc
export FC=ifort
export F77=ifort
export LDFLAGS -all-static
export FFLAGS -static
export CFLAGS -static
export CXXFLAGS -static
export CXXLDFLAGS -static
./configure --without-romio --prefix=/usr/local/lam/
make
make install
make examples

Make sure you can build the examples before moving onto building amber.

2) In the amber src directory make sure you run configure with the correct
options:

cd $AMBERHOME/src
export LAM_HOME=/usr/local/lam/
./configure -athlon -static -lam ifort
make clean
make parallel
cd $AMBERHOME/test
make clean
make

Let me know how you get on wih this. Note, do NOT skip any make clean
steps...

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu