AMBER Archive (2009)

Subject: [AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions.

From: David Dubins (
Date: Mon Sep 21 2009 - 18:02:47 CDT

Hi everyone,


Thanks to your help and resources, I successfully installed AmberTools and
Amber10, and devised scripts for serial and parallel program installation.
For those of you who are new to Amber, this may be very useful.


I suspect that many of the libraries I list to install are not required. In
fact, I'm willing to bet that the majority of them are not. After scouring
the net, these are simply the packages that other people have recommended to
install under various circumstances. I apologize if this misleads anyone.


I also don't suspect this script will work for all computers. However, I
have tested it on a few to get some of the kinks out.


What you will need:


-Set aside at least 2 hours to install Ubuntu, AmberTools, and Amber10 from

-A blank CD or DVD to burn a Ubuntu installation disk




First, download the Ubuntu installation file by visiting:


MAKE SURE you download the CORRECT version of Ubuntu for your processor.
There are both 32 and 64 bit versions of the program. Installing a 32 bit
version will work but may cause problems on a 64 bit system, and will not
use the full capacity of the processor.


Ubuntu is a Linux environment that has been pimped out to work really well
on top of windows, or as its own partition. Select to install Ubuntu on top
of windows, and follow the prompts. Make sure you connect your computer
directly to the network via network cable, rather than wireless. This will
enable you to update it after it is installed.


Once you download the .ISO image file, you can burn it to disk by
downloading the free program, "ImgBurn":


Or, you can install a virtual drive and mount the image file, using a
program like Daemon:


Daemon lite is also free, although they offer an option to pay for it if you
like. Create (or mount) the system disk, and follow the prompts to install
Ubuntu. It is probably best to install it NOT on top of Windows, as it
should be a bit faster that way and molecular dynamics is computer resource
intensive. In this case, just burn a CD and reboot with it in your CD ROM
tray. Set the Ubuntu partition to at least 20 GB.


Once Ubuntu is installed, update all the drivers as required. There will be
an icon in the top status bar for installing proprietary drivers. Click on
this and select the most updated drivers for your system. Ubuntu will also
automatically connect to the web and update itself with whatever add-ons are




Amber Tools is available online here:


Download Amber Tools to Ubuntu's desktop. Double click the compressed file
and expand the contents to the home directory

(click on your user name on the left pane, then the "Extract" button on the
bottom right).


Now open up a terminal window (Applications on the top bar --> Accessories
--> Terminal). This will open up a Unix-like environment where you may find
the following commands useful:


    cd [dirname] (change to a directory)

    cd .. (change to the parent directory)

    ls (list the contents of a directory)

    rm [filename] (delete a file)

    man [command] (look up the manual entry for a command)

    cp [filename1] [filename2] (copy filename1 to filename2)

    locate [filename] (search for what directory filename is in)


Type the following at the prompt: (DO THIS ONE BY ONE!!!). Follow the
prompts as required. Again, most of these are probably not required, but led
me to an error-free install.


                sudo apt-get install build-essential

                sudo apt-get -f install

                sudo apt-get install ssh

                sudo apt-get install libnetcdf-dev

                sudo apt-get install g77

                sudo apt-get install gcc

                sudo apt-get install g++

                sudo apt-get install g++-multilib

                sudo apt-get install g++-4.3-multilib

                sudo apt-get install gcc-4.3-doc

                sudo apt-get install libstdc++6-4.3-dbg

                sudo apt-get install libstdc++6-4.3-doc

                sudo apt-get install bison

                sudo apt-get install fort77

                sudo apt-get install netcdf-bin

                sudo apt-get install gfortran

                sudo apt-get install gfortran-multilib

                sudo apt-get install gfortran-doc

                sudo apt-get install gfortran-4.3-multilib

                sudo apt-get install gfortran-4.3-doc

                sudo apt-get install libgfortran3-dbg

                sudo apt-get install autoconf

                sudo apt-get install autoconf2.13

                sudo apt-get install autobook

                sudo apt-get install autoconf-archive

                sudo apt-get install gnu-standards

                sudo apt-get install autoconf-doc

                sudo apt-get install libtool

                sudo apt-get install gettext

                sudo apt-get install patch

                sudo apt-get install libblas3gf

                sudo apt-get install liblapack3gf

                sudo apt-get install libgfortran2

                sudo apt-get install markdown

                sudo apt-get install csh

                sudo apt-get install libx11-dev

                sudo apt-get install libxt-dev

                sudo apt-get install x-dev

                sudo apt-get install libxext-dev

                sudo apt-get install tcsh

                sudo apt-get install flex

                sudo apt-get upgrade


These lines must be installed one-by-one. After you install them, no matter
what Ubuntu prompts you about upgrading, don't do it until you are finished
this entire script.


Don't do this: (kept for future records)

                # sudo ln -s /usr/bin/gfortran /usr/local/bin/g77


Installing G95:


Go here:



and download the Debian G95 Binaries (current snapshot) for your system. For
ubuntu 32 bit, its Linux86 (Debian). For ubuntu 64 bit, its Linux 86-64
(Debian). Double-click the file when downloaded, and it will install in
Ubuntu. Or you can save the file on the desktop and in the terminal window

                sudo dpkg -i g95-x86.deb


                sudo dpkg -i g95-x86_64.deb

for the 64-bit version.


Installing G77:


Here is the somewhat easier way to install g77. You need to update the
places ubuntu looks to update, by editing the sources.list file:


                cd /etc/apt/

                sudo pico sources.list


On the bottom of the file, copy in the following lines: (highlight the
lines, press Control-C here, and then press Control-Shift-V in the terminal
window in pico)


                deb hardy universe

                deb-src hardy universe

                deb hardy-updates

                deb-src hardy-updates


Now type Control-x, y, then enter to save and quit. To install g77:


                sudo aptitude update

                sudo aptitude install g77


                (answer Y to any prompts)


If ubuntu then prompts you to do a partial upgrade, PRESS CANCEL. It will
want to remove g77, and you need it.


Set the amber10 directory by going into it:



 and typing:

                echo "export AMBERHOME=$PWD" >> ~/.profile

                source ~/.profile




Download the bug fixes for ambertools here:


-right click, save link as, rename the filename to "bugfixtools.all"

-download this file to the amber10 directory, or move it there once


In the terminal window, type:


                cd $AMBERHOME

                patch -p0 -N < bugfixtools.all


                cd $HOME

                sudo apt-get update


                pico .bashrc


In PICO, add the following lines to the end of the file: (highlight the
lines, press Control-C here, and then press Control-Shift-V in the terminal
window in pico)


                export AMBERHOME



                export MPI_HOME


[Type control-X, Y, then enter key to exit]


                source .bashrc

                pico .profile


[In PICO, add the following line to the end of the file:]




[Type control-X, Y, then enter key to exit]


It's time to compile Amber Tools: (fingers crossed)


                cd $HOME/amber10/src


----Serial install (only one processor):

                ./configure_at gcc


----Parallel install (dual core, quad core, multi-core processors):

First, download and install OpenMPI1.3.3:


-Find OpenMPI 1.3.3 here:



Download it into your home directory.


-Open up a terminal window and type:

                cd ~/openmpi-1.3.3

                ./configure -prefix=/


(2 minute wait time here)


                sudo make all install


(5 minute wait time here. Don't you wish terminal windows had status bars?)


Hopefully this install works. Now type:


                cd $HOME/amber10/src

                ./configure_at -mpi


Check that each compiler test ends in "OK". If it doesn't, you will need to
troubleshoot that part of the installation. Now type:


                make -f Makefile_at


(less than 2 minute wait time)


If the program output doesn't end in "Completed installation of AmberTools,
version 1.1" then there was a problem. In one instance, the program was
crashing in the x11 libraries. I went to the "sudo apt-get install" list and
started from libx11-dev, working my way to the end. I re-tried
./configure_at -mpi then make -f Makefile_at, and it worked.


----Parallel and Serial Install:


Now type:


                cd ../bin/



At the top of the file, change sh to bash

On line 12, change "/home/mjw/code/AMBER/amber10/bin/mopac >& FOR006" to:


                /home/mjw/code/AMBER/amber10/bin/mopac > FOR006


(In other words, just delete the "&" key)

[Type control-X, Y, then enter key to exit]


It's time to test whether or not the install worked. Type the following


                cd ../test

                make -f Makefile_at test


(3 minute wait time). Check the output, they should pretty much all say
PASSED, or be within tolerance if they say FAILED. Great work to you if you
get to the end of the test script. It should say "Finished test suite for




Download the bug fixes for amber10 from here:




-right click, save link as, rename the filename to "bugfix10.all"

-download this file to the amber10 directory, or move it there once


In the terminal window, type:


                cd $AMBERHOME

                patch -p0 -N < bugfix10.all



Do I have a 32 or 64 bit processor?



Good question. You should already know the answer though, because at this
point you've either installed Ubuntu 32 or 64 bit. Hopefully you made the
correct choice. To double check, in a terminal window, type:


                sudo lshw -C processor


If the cpu "width" says 32 bits, it's 32. If it says 64 bits, it's 64.


----Serial install:

                cd $AMBERHOME/src

                ./configure_amber gfortran


(<5 min wait)

                cd $AMBERHOME/test


(<5 min wait)


----Parallel Install:

                cd $AMBERHOME/src

                ./configure_amber -openmpi gfortran

                make parallel

(<5 min wait)

The installation should end with:

Installation of Amber10 (parallel) is complete at [then the date and time].

Now type:

                cd /etc/ssh

                ssh-keygen -t dsa

                cd /home/user/.ssh/

                cat > authorized_keys2

                chmod 633 authorized_keys2

                cd $AMBERHOME/test/


(replace N in the following line with the # processors you wish to use:)

                setenv DO_PARALLEL 'mpirun -np N'

                make test.parallel.MM

(<5 minutes wait)




That is it! In theory, you should now have a complete and tested Amber10
and AmberTools 1.2 build sitting in /amber10/exe. Also note that the wait
times I've listed here are from a quad-core 3 GHz processor. If you are
performing your install on a single core processor, they will be much longer
wait times.





David Dubins, Ph.D., B.Eng.


Leslie Dan Faculty of Pharmacy

University of Toronto

144 College Street Toronto, Ontario M5S 3M2

Telephone: 416-946-3840

Mobile: 647-891-8685


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