AMBER Archive (2006)

Subject: AMBER: Problem in compiling AMBER8 parallel version

From: luckyang_at_gmail.com
Date: Tue Jan 31 2006 - 17:09:09 CST

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
rem.in -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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