AMBER: Problem in compiling AMBER8 parallel version

From: <>
Date: Tue, 31 Jan 2006 23:09:09 +0000

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
./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:

     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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Feb 01 2006 - 06:10:06 PST
Custom Search