AMBER Archive (2006)

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

From: luckyang_at_gmail.com
Date: Tue Jan 31 2006 - 17:51:06 CST

Dear David,

Thanks for your reply. I did the following to compile the parallel version:

cd $AMBERHOME/src
make clean
./configure -lam absoft
make parallel

And I have defined the LAM_HOME.

All the best.

Lu Yang
Tulane University

On 1/31/06, David LeBard <david.lebard_at_asu.edu> wrote:
>
> 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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