AMBER Archive (2006)

Subject: AMBER: compiler error for Amber9

From: Weihua Li (
Date: Wed Jun 07 2006 - 09:34:49 CDT

Dear all,
        CPU: AMD opeteron Linux86-64
         I used the following command to configure the open-mpi-1.0.2.
        ./configure --prefix=/home/ytang/gdata/whli/openmpi CC=pgcc CXX=pgCC
F90=pgf90 --with-openib
       and set environment variables in .bashrc as follows:
           export MPI_HOME=/home/ytang/gdata/whli/openmpi
          export PATH=$MPI_HOME/bin:$PATH

In the ~openmpi/lib directory: libmpi_f90.a mpi_kinds.mod mpi.mod openmpi

For PMEMD module:

pgf90 -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o
parallel_dat.o mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd
_dat.o dynamics_dat.o img.o parallel.o pme_direct.o pme_recip.o pme_fft.o
fft1d.o bspline.o pme_force.o pbc.o nb_pairlist.o cit.o dynamics.o b
onds.o angles.o dihedrals.o runmd.o loadbal.o shake.o runmin.o
constraints.oaxis_optimize.o gb_ene.o
veclib.o gb_force.o timers.o pmemd_lib.o
 runfiles.o file_io.o bintraj.o pmemd_clib.o pmemd.o random.o degcnt.o
erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o master_setup.o alltasks_s
etup.o pme_setup.o ene_frc_splines.o nextprmtop_section.o
-L/home/ytang/gdata/whli/openmpi/lib -lmpich
/usr/bin/ld: cannot find -lmpich
make[1]: *** [pmemd] Error 2
make[1]: Leaving directory `/gdata/lun8/ytang/whli/amber9/src/pmemd/src'
make: *** [install] Error 2

For sander module:

 ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
../lib/nxtsec.o ../lib/sys.a -L/home/ytang/gdata/whli/openmpi/lib -lmpi_f90
-lmpi -lorte -lopal -lutil -lnsl -lpthread -ldl -Wl,--export-dynamic -lm
-lutil -lnsl -lpthread -ldl
/usr/bin/ld: skipping incompatible
/home/ytang/gdata/whli/openmpi/lib/libmpi_f90.a when searching for -lmpi_f90
/usr/bin/ld: cannot find -lmpi_f90
make[1]: *** [sander.MPI] Error 2
make[1]: Leaving directory `/gdata/lun8/ytang/whli/amber9/src/sander'
make: *** [parallel] Error 2

I know it must be something wrong with the installation of open-mpi, but I
don't know where it is.

Could you please give me some advice?

Best regards,

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to