AMBER Archive (2006)

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

From: David LeBard (david.lebard_at_asu.edu)
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
itself.

Hope this helps,

David LeBard
Dept. of Chemistry and Biochemistry
Arizona State University

On Tue, 2006-01-31 at 16:09, luckyang_at_gmail.com 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 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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