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AMBER Archive (2009)Subject: [AMBER] Installing AmberTools and Amber10 in Ubuntu - Instructions.
From: David Dubins (d.dubins_at_utoronto.ca)
Hi everyone,
Thanks to your help and resources, I successfully installed AmberTools and
I suspect that many of the libraries I list to install are not required. In
I also don't suspect this script will work for all computers. However, I
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
1) INSTALLING UBUNTU
First, download the Ubuntu installation file by visiting:
www.ubuntu.com
MAKE SURE you download the CORRECT version of Ubuntu for your processor.
Ubuntu is a Linux environment that has been pimped out to work really well
Once you download the .ISO image file, you can burn it to disk by
Or, you can install a virtual drive and mount the image file, using a
http://www.daemon-tools.cc/eng/home
Daemon lite is also free, although they offer an option to pay for it if you
Once Ubuntu is installed, update all the drivers as required. There will be
2) GETTING UBUNTU THE REQUIRED LIBRARIES
Amber Tools is available online here:
http://ambermd.org/AmberTools-get.html
Download Amber Tools to Ubuntu's desktop. Double click the compressed file
(click on your user name on the left pane, then the "Extract" button on the
Now open up a terminal window (Applications on the top bar --> Accessories
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
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
Don't do this: (kept for future records)
# sudo ln -s /usr/bin/gfortran /usr/local/bin/g77
Installing G95:
------------------
Go here:
http://g95.org/downloads.shtml#CS
and download the Debian G95 Binaries (current snapshot) for your system. For
sudo dpkg -i g95-x86.deb
or:
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
cd /etc/apt/
sudo pico sources.list
On the bottom of the file, copy in the following lines: (highlight the
deb http://hu.archive.ubuntu.com/ubuntu/ hardy universe
deb-src http://hu.archive.ubuntu.com/ubuntu/ hardy universe
deb http://hu.archive.ubuntu.com/ubuntu/ hardy-updates
deb-src http://hu.archive.ubuntu.com/ubuntu/ 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
Set the amber10 directory by going into it:
cd~/amber10
and typing:
echo "export AMBERHOME=$PWD" >> ~/.profile
source ~/.profile
3) INSTALLING AMBER TOOLS:
-------------------------------------
Download the bug fixes for ambertools here:
http://ambermd.org/bugfixesat.html
-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 $HOME
sudo apt-get update
pico .bashrc
In PICO, add the following lines to the end of the file: (highlight the
AMBERHOME=$HOME/amber10/
export AMBERHOME
MPI_HOME=/
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:]
PATH="$HOME/amber10/exe:$PATH"
[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:
http://www.open-mpi.org/software/ompi/v1.3/
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
make -f Makefile_at
(less than 2 minute wait time)
If the program output doesn't end in "Completed installation of AmberTools,
----Parallel and Serial Install:
Now type:
cd ../bin/
pico mopac.sh
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
4) INSTALLING AMBER10
------------------------------
Download the bug fixes for amber10 from here:
http://ambermd.org/bugfixes10.html
-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
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
make
(<5 min wait)
cd $AMBERHOME/test
make
(<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 id_dsa.pub > authorized_keys2
chmod 633 authorized_keys2
cd $AMBERHOME/test/
csh
(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)
exit
_________________________________________
That is it! In theory, you should now have a complete and tested Amber10
------------------------------------------------
David Dubins, Ph.D., B.Eng.
Instructor
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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