AMBER Archive (2004)


From: Cenk Andac (
Date: Tue Nov 16 2004 - 08:19:03 CST

I am sending you my personal guide flines for installation of ifort and amber8
in Linux Suse 9.1. Let me know it works for you. ***********************************************************************************
Installation of ifort in Linux Suse 9.1
jenk directory can be your personal home directory

Installation requirements:

make sure you have pre-installed kernel and glibc libraries

fromSuse Linux installation disks



# now untar fortran compiler

cd /home/jenk

tar -zxvf l_fc_p_8.0.034.tar.gz


# create licenses directory in home/jenk/opt/ifort/ (if not available there!)

mkdir home/jenk/opt/ifort/licenses


#copy intel evaluation license file (xxx.lic) to ../ifort/licenses directory as ifort.lic

#become a root user

cd home/jenk/l_fc_p_8.0.034

cp intel-ifort8-8.0-40.i386.rpm /home/jenk/opt/ifort/intel-ifort8-8.0-40.i386.rpm

# using SuSe File manager open home/jenk/opt/ifort

# click on the rpm file and allow Suse handle installation as root (enter root password).

# source ifort

cd /home/jenk/opt/ifort/bin


#or better yet

# become a root user

#add path lines in /etc/profile

#to eliminate sourcing ifort each time system is restarted

# (see the following /etc/profile file)

cd /etc

# you may want to use vi or other editors (kate , emacs, etc.) to edit /etc/profile

# say you use vi. then

vi profile

# add the following red path lines in /etc/profile and save and quit

# here are some quick tips on using vi for beginners:

# hit insert on your keyboard to make additions

# Backspace has never worked for me, so use delete instead when necessary

# hit ESC on your keybord to quit insert mode

# type " :wq " to save and quit

# here is the red path lines you should add in /etc/profile

Make path more comfortable


if test -z "$PROFILEREAD" ; then


if test "$HOME" != "/" ; then

for dir in $HOME/bin/$CPU $HOME/bin ; do

test -d $dir && PATH=$dir:$PATH



test "$UID" = 0 && PATH=/sbin:/usr/sbin:/usr/local/sbin:/home/jenk/opt/ifort/bin:$PATH

for dir in /var/lib/dosemu \

/usr/games \


/opt/bin \

/opt/gnome/bin \

/opt/kde3/bin \

/opt/kde2/bin \

/opt/kde/bin \

/usr/openwin/bin \



test -d $dir && PATH=$PATH:$dir


unset dir

export PATH



#You may now proceed to install amber8



Installation of Amber 8 in Linux Suse 9.1
jenk directory can be your personal home directory

Installation requirements:

1) make sure that files involving gcc, cc, c, c++, mpich are all installed from Suse-Linux disks

2) make sure that g77 that is installed from Suse-Linux disks

3) make sure that ifort (f90) is properly installed and sourced

4) make sure that yacc is installed from Suse-Linux disks

    suggested files involving yacc are

    bison, global, gob2,pccts

5) Before installing amber8, you need to source ifort (see the guide above for

   sourcing ifort)



#DO NOT run any other application while amber8 installs

# untar amber 8 in /home/jenk directory

tar -zxvf amber8.tar.gz

# configure amber8

cd /home/jenk/amber8/src

./configure ifort

# ignore warning message of unset path for MKL_HOME

make serial

#make sure instalation is complete

#update amber8

#download the most recent bugfix.all patch from Amber website

#into $AMBERHOME (/home/jenk/amber8

#then patch bugfix.all

cd /home/jenk/amber8

patch -p0 -N -r patch_rejects <bugfix.all


#test amber

cd /home/jenk/amber8/test

make test

#make sure amber8 passes all tests

#some failure messages regarding xxx.dif files may be listed

#while testing SANDER and ANTECHAMBER

#They do not however seem to affect amber functionality!

#So amber should be fine with the xxx.dif files.

#other failure messages could be problematic and

#hence the installation must be revised.


#set AMBERHOME environment and path in cshell (csh)

#so that $AMBERHOME/exe/.. commands work in csh with no requirement for path definition

#for instance; xleap executes xleap in any directory in csh


#become a root user

#create or open /etc/csh.cshrc.local and /etc/csh.login.local

#add and save following red path lines in /etc/csh.cshrc.local and /etc/csh.login.local

# using any available editor


setenv AMBERHOME /home/jenk/amber8

set path=($path $AMBERHOME/exe)

#set AMBERHOME environment in bash


#so that $AMBERHOME/exe/.. commands work in bash but requires path definition

#for instance; $AMBERHOME/exe/xleap executes xleap in any directory in bash


#become a root user

#create or open /etc/bash.bashrc.local

#add and save the following line in /etc/bash.bashrc.local


#setenv AMBERHOME /home/jenk/amber8

That is about all from me. Let me know if things work out allright for you.
Cenk Andac
M.S., Ph.D. candidate
Faculty candiate in Turkey
Ilyas Yildirim <> wrote:

Dear Amber members,
Did anyone install AMBER 8 to a SUSE 9.1 Personal system? If yes, can you
give me the address of the compiler u have used? I have tried Intel
Fortran Compiler 8.1, and pgf90, but they did not work. There were a lot
of other problems, which I could not solve using internet. Thanks in

Ilyas Yildirim
- Department of Chemisty - -
- University of Rochester - -
- Hutchison Hall, Office B10 - Ph.:(585) 503 44 00 (Cell) -
- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- -

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