AMBER Archive (2006)

Subject: Re: AMBER: Problem in compiling AMBER8 parallel version

From: David LeBard (
Date: Tue Jan 31 2006 - 17:23:16 CST

Hi Lu,

I believe you need to make the executable using an additional option for
parallel compilation like -mpich (for MPICH library) or -lam (for the
LAM library). Other parallel options are listed in the configure script

Hope this helps,

David LeBard
Dept. of Chemistry and Biochemistry
Arizona State University

On Tue, 2006-01-31 at 16:09, wrote:
> Dear AMBER users,
> I have a linux (Fedora core 3) cluster with fortran compiler from
> ABSOFT. I can compile serial version of AMBER8 without any problem.
> But I get the following error message for the parallel version:
> /usr/bin/ld: Warning: alignment 32 of symbol `_D_in_DECOMP' in
> decomp.o is smaller than 64 in runmd.o
> egb.o(.text+0x2): undefined reference to `MPI_COMM_DUP_FN'
> egb.o(.text+0x8): undefined reference to `MPI_NULL_COPY_FN'
> egb.o(.text+0xe): undefined reference to `MPI_TYPE_NULL_DELETE_FN'
> egb.o(.text+0x14): undefined reference to `MPI_COMM_NULL_COPY_FN'
> egb.o(.text+0x1a): undefined reference to `MPI_NULL_DELETE_FN'
> egb.o(.text+0x20): undefined reference to `MPI_WIN_DUP_FN'
> egb.o(.text+0x26): undefined reference to `MPI_COMM_NULL_DELETE_FN'
> egb.o(.text+0x2c): undefined reference to `MPI_TYPE_DUP_FN'
> egb.o(.text+0x32): undefined reference to `MPI_WIN_NULL_COPY_FN'
> egb.o(.text+0x38): undefined reference to `MPI_DUP_FN'
> egb.o(.text+0x3e): undefined reference to `MPI_TYPE_NULL_COPY_FN'
> egb.o(.text+0x44): undefined reference to `MPI_WIN_NULL_DELETE_FN'
> egb.o(.text+0x1d73): In function `__EGB_in_GENBORN':
> ......
> I installed lam-7.1.1 with the option "--with-fc=f90" with f90 also
> used to compile amber8.
> What I am trying to do is to run REM. I can enable REM via: make
> clean; make AMBERBUILDFLAGS='-DREM' parallel with the config.h
> generated from the command:
> ./configure -p4 absoft
> But I get the following error message:
> "user: mpirun -np 4 /home/yang/rem_sander -O -ng 4 -rem 1 -remlog
> rem.log -i -p dba8 -c md.r -o rem.out -r rem.r
> mdfil: Error unknown flag:
> -ng
> usage: sander [-O|A] -i mdin -o mdout -p prmtop -c inpcrd -r
> restrt
> [-ref refc -x mdcrd -v mdvel -e mden -idip inpdip
> -rdip rstdip -mdip mddip -ng numgroup -remlog remlog -rem [0|1|2] -inf
> mdinfo -radii radii]
> Consult the manual for additional options."
> I also tried the -DREM in config.h and I get the same error.
> I think I have to make the parallel version compiled first, am I
> right?
> Any suggestion about this problem?
> Thank you very much for your help.
> Lu Yang
> Tulane University

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