AMBER Archive (2009)

Subject: Re: [AMBER] compiling amber10 with mac intel, ifort/icc and mpi

From: Alan (
Date: Thu Jun 11 2009 - 06:14:42 CDT

So I did (as following the basic approach as in the manual, with gfortran
instead of g95):make clean
./configure_amber -lamsource gfortran
make parallel

And got:

/Users/alan/Programmes/amber10/bin/mpif77 -ffree-form -o sander.MPI
 constants.o nose_hoover.o [snip] ncsu-smd-hooks.o ncsu-umbrella.o
ncsu-utils.o ncsu-value.o ../netcdf/lib/libnetcdf.a
ld warning: duplicate dylib /sw/lib/gcc4.4/lib/libgcc_s.1.dylib
Undefined symbols:
  "_lam_f77init", referenced from:
      _lam_f77init$non_lazy_ptr in liblamf77mpi.a(init_f.o)
  "_lam_mpi_comm_world", referenced from:
      _mpi_recv_ in liblamf77mpi.a(recv_f.o)
      _mpi_wait_ in liblamf77mpi.a(wait_f.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [sander.MPI] Error 1
make: *** [parallel] Error 2

On Wed, Jun 10, 2009 at 17:54, David A. Case <>wrote:

> On Wed, Jun 10, 2009, Alan wrote:
> > ./configure_amber -nosanderidc -mpi -p4 gfortran
> > Undefined symbols:
> >
> > "_mpi_reduce_", referenced from:
> Your build is not finding the MPI libraries. I have no idea where they are
> on
> your computer. When you use the "-mpi" flag, the configure script assumes
> that the required MPI libraries will be found. If not, you have to edit
> config_amber.h to add the correct paths to the LOADLIB variable.
> As a start, run configure_amber with the -lamsource option instead of -mpi.
> This should(!) compile with gfortran (does on other platforms) and will
> automatically put all the correct paths into the build scripts. (Be sure
> to
> run configure_lam as the script instructs you to do; also, I'd still
> suggest
> leaving off the "-j 2" flag to make..parallel makes have not been tested
> much.
> ...hope this helps....dac
> _______________________________________________
> AMBER mailing list

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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