AMBER Archive (2008)

Subject: RE: AMBER: Again: Installation problem of AMBER on cluster

From: Ross Walker (
Date: Tue Oct 21 2008 - 11:49:50 CDT

Hi Dmitri,


What compiler are you using and what problems do you encounter? I build
Amber10 all the time with ifort and mpich2-1.07 without any problems on both
Opterons and Intel's.


The procedure I use is as follows:


1) Download mpich2-1.0.7.tar.gz

2) Untar to /usr/local/mpich2-1.0.7

3) cd /usr/local/mpich2-1.0.7

4) export CC=icc

5) export CXX=icc

6) export F90=ifort

7) export F77=ifort

8) export LDFLAGS=-static

9) export F90LAGS=-static

10)export CFLAGS=-static

11)export CXXFLAGS=-static

12)export CXXLDFLAGS=-static

13)./configure --prefix=/usr/local/mpich2-1.0.7-ifort-10.1.008


15)make install

16)make examples

17)edit ~/.bashrc and add

a. export MPI_HOME=/usr/local/mpich2-1.0.7-ifort-10.1.008

b. export PATH=$MPI_HOME/bin:$PATH


d. export AMBERHOME=/usr/local/amber10

18)source ~/.bashrc

19)download ambertools 1.2 and amber10 tar gz files

20)untar both to /usr/local/amber10

21)Download bugfix.all files for both and apply

22)build ambertools as described in the manual - needed for netcdf etc.

23)cd $AMBERHOME/src

24)./configure_amber -mpich2 ifort

25)make clean

26)make parallel

27)cd $AMBERHOME/test

28)mpd &

29)export DO_PARALLEL='mpirun -np 4'

30)make test.parallel

31)make test.parallel.QMMM

32)cd $AMBERHOME/src/pmemd

33)./configure linux_em64t ifort mpich2 bintraj

34)(sometimes it is necessary to edit config.h and change all ifort to
mpif90 and clear the MPI_LIBS line.


36)make install

37)cd $AMBERHOME/test

38)make test.pmemd


This all works flawlessly on a vanilla install of RedHat Enterprise Linux AS
4.0 with ifort 10.1.018.


Good luck,




From: [] On Behalf Of
Dmitri Nilov
Sent: Tuesday, October 21, 2008 9:32 AM
Subject: AMBER: Again: Installation problem of AMBER on cluster


Hi everybody,

I'm currently stuck with installing Amber 10 on a RHEL 4 cluster with
I've found this ( ) in mailing
list, but it seems to me that the problem was not resolved.
Our processors are actually Opterons, and the head node is an Athlon 64.
If this is of any use, the system also has rather old glibc 2.3.4-2.13

Hope for any answer...


Dmitri Nilov

Lomonosov Moscow State University

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)