AMBER Archive (2009)

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

From: oguz gurbulak (gurbulakoguz_at_gmail.com)
Date: Tue Sep 22 2009 - 01:46:27 CDT


Dear David,
Thank you very much for your valuable effort and the detailed info about
installing Amber 10 to Ubuntu. This will definitely useful for me and other
Amber users that want to use Ubuntu.

All the Best,

Oguz GURBULAK

Ege University Faculty of Science

Department of Physics

Bornova, Izmir/Turkey

e-mail: oguzgurbulak_at_mail.ege.edu.tr

2009/9/22 David Dubins <d.dubins_at_utoronto.ca>

> 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
> scratch.
>
> -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.
> 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":
>
> http://www.imgburn.com/
>
>
>
> Or, you can install a virtual drive and mount the image file, using a
> program like Daemon:
>
> http://www.daemon-tools.cc/eng/home
>
>
>
> 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
> available.
>
>
>
> 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
> 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:
>
> http://g95.org/downloads.shtml#CS
>
>
>
> 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
> type:
>
> 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
> 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 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
> universe
>
> deb-src http://hu.archive.ubuntu.com/ubuntu/ hardy-updates
> universe
>
>
>
> 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:
>
> 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
> downloaded
>
>
>
> In the terminal window, type:
>
>
>
> cd $AMBERHOME
>
> patch -p0 -N < bugfixtools.all
>
>
>
> cd $HOME
>
> sudo apt-get update
>
>
>
> pico .bashrc
>
>
>
> In PICO, add the following lines to the end of the file: (highlight the
> lines, press Control-C here, and then press Control-Shift-V in the terminal
> window in pico)
>
> AMBERHOME=$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
> 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/
>
> 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
> commands:
>
>
>
> 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
> AmberTools".
>
>
>
> 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
> downloaded
>
>
>
> 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
>
> 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 <http://test.parallel.mm/>
>
> (<5 minutes wait)
>
> exit
>
> _________________________________________
>
>
>
> 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.
>
> Instructor
>
> Leslie Dan Faculty of Pharmacy
>
> University of Toronto
>
> 144 College Street Toronto, Ontario M5S 3M2
>
> Telephone: 416-946-3840
>
> Mobile: 647-891-8685
>
> d.dubins_at_utoronto.ca
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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