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From: Hugh Merz (merz_at_[hidden])
Date: 2006-06-07 10:56:48


> However, when I used openmpi to compile a application program( Molecular
> dynamcis code: Amber9), error messages are given:

I think you would be better off using the OpenMPI wrapper compilers rather than trying to link the mpi libraries by hand. For mo
re information read the FAQ, which contains a section on how to compile mpi programs with OpenMPI:

http://www.open-mpi.org/faq/?category=mpi-apps

Likely all that is required is to change the Makefile for Amber9.

> For PMEMD module:

For example, use mpif90 instead of pgf90 here:

> pgf90 -o pmemd gbl_constants.o gbl_datatypes.o state_info.o file_io_dat.o
> ...
> -L/home/ytang/gdata/whli/openmpi/lib -lmpich
> /usr/bin/ld: cannot find -lmpich

This is the error - there is no libmpich in OpenMPI.

> make[1]: *** [pmemd] Error 2
> make[1]: Leaving directory `/gdata/lun8/ytang/whli/amber9/src/pmemd/src'
> make: *** [install] Error 2
>
> For sander module:

Presumably this was not compiled with mpif90 either, but you did not send the command you used to compile it.

> ../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?

Read the FAQ. I also suggest you email the Amber mailing list and read through any documentation on their site, which looks quite extensive.

Hugh