AMBER Archive (2004)

Subject: Re: AMBER: make install error

From: Robert Duke (
Date: Sun Sep 12 2004 - 06:52:48 CDT

If you installed and linked against mpich, what is going on here is that a
lot of machines come with lam mpi installed, and that is the stuff you are
finding. Change all your execution paths to point to the mpich versions of
the binaries (make additions to the PATH environment variable such that the
mpich version of mpirun is found first). Do a 'which mpirun' at the command
line; if it is the one that came with the redhat distribution instead of the
one you built and installed, this is the problem. If you were to build
amber with g77, you could do use lam, but otherwise the form of the symbols
in the libraries is probably wrong. IF you intended to use lam and g77,
then you fust need to do a lamboot.
- Bob Duke

----- Original Message -----
From: "Abd Ghani Bin Abd Aziz" <>
To: <>
Sent: Sunday, September 12, 2004 7:25 AM
Subject: RE: AMBER: make install error

> dear amber,
> i already compiled and installed the amber6 to my (redhat)linux cluter
> using mpich with the help of my friend..(thanx also for ross walker for
> your help) but the problem is now when i try to do minimization, it coming
> an error msg.. for your information i'm using mpich-1.2.6.. below is the
> error msg and the minimization script. i hope u all can help me... thanx
> Abd Ghani
> It seems that there is no lamd running on the host alpha.
> This indicates that the LAM/MPI runtime environment is not operating.
> The LAM/MPI runtime environment is necessary for the "mpirun" command.
> Please run the "lamboot" command the start the LAM/MPI runtime
> environment. See the LAM/MPI documentation for how to invoke
> "lamboot" across multiple machines.
> cd /home/leow
> cat <<eof1>
> # minimization in water
> &cntrl
> imin=1, nmropt=0, ncyc=50, maxcyc=10000,
> ntb=1, ntc=2, tol=0.000001, ntr=1,
> cut=10.0, ntpr=25,
> &end
> # Group definition
> 500
> RES 4 37
> RES 43
> RES 49 150
> RES 156 200
> RES 206 214
> RES 220 235
> RES 241 268
> RES 274 388
> eof1
> mpirun -np 4 /usr/local/amber6/exe/sander -O -i -o min.out -p
> tcl.prm -c -ref -r
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