Re: [AMBER] compiling failure on ibm

From: Jason Swails <>
Date: Mon, 26 Mar 2012 15:51:48 -0400

On Mon, 2012-03-26 at 13:44 -0500, Yubo Fan wrote:

> ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
> ../lib/nxtsec.o ../lib/sys.a ../netcdf/lib/libnetcdf.a
> -L/users/yf4/UTILS/OPENMPI/1.4.3/lib -lmpi_f90 -lmpi_f77 -lmpi
> -lopen-rte -lopen-pal -libverbs -ltorque -lnuma -ldl
> -Wl,--export-dynamic -lnsl -lutil -lpthread
> /usr/bin/ld: cannot find -lrdmacm
> make: *** [sander.MPI] Error 1

One thing that confuses me here is that I don't see where -lrdmacm is
actually linked in from anywhere (that is, it must be hidden somewhere).
The problem is that the linker can't find the or
librdmacm.a files. Are these files anywhere on your system? If so,

To help, what is the output of:

mpif90 -show


Try changing this line to:

LOADCC= /users/yf4/UTILS/OPENMPI/1.4.3/bin/mpicc $(LOCALFLAGS)

> LOADLIB= -L/users/yf4/UTILS/OPENMPI/1.4.3/lib -lmpi_f90 -lmpi_f77
> -lmpi -lopen-rte -lopen-pal -lrdmacm -libverbs -ltorque -lnuma -ldl
> -Wl,--export-dynamic -lnsl -lutil -lpthread

Try changing this line to:

LOADLIB= -Wl,--export-dynamic -lnsl -lutil -lpthread

The MPI compiler wrapper (mpif90) should pull in the actual MPI
libraries and include headers without having to specify them here.

> #NETCDF=/users/yf4/APPS/AMBER10/NETCDF/include/netcdf.mod
> #NETCDFLIB=/users/yf4/APPS/AMBER10/NETCDF/lib/libnetcdf.a

Yikes! Where did this come from?? I thought you said you were
compiling Amber 9 (and indeed, other references in your message indicate
you're working with AMBER9) -- but these NetCDF variables appear to
point to an Amber 10 installation. While I realize these lines are
commented out, it makes me suspect that you took many non-standard steps
when you attempted to configure and build Amber 9...

> xlf and xlc has been loaded and OpenMPI/NetCDF have been precompiled correctly.

Are you sure? One thing you could try is to download AmberTools 1.5 and
use the "configure_openmpi" or "configure_mpich2" scripts in there to
make sure you build a compatible MPI, and use that to build Amber 9.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Mar 26 2012 - 13:00:02 PDT
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