AMBER Archive (2008)

Subject: Re: AMBER: Install problems

From: Mark Williamson (
Date: Mon Sep 08 2008 - 18:56:35 CDT

Marisa Frechero wrote:
> Hi Ross,
> I am using "Ubuntu 8.04", g95 from

I see you are using Ubuntu 8.04. I've recently been helping a student
with AmberTools and AMBER 10 on such a Linux distro and I've been
writing a mini how-to.

Ubuntu is quite an interesting Linux distro; it has got the robust
package management of Debian, combined with a large friendly support
base which is very active at the moment. The apt package management is
great since if you need package a and that needs package b, which in
turn needs package c, it will get a, b and c and install them all. It
also has this very nice feature whereby one can boot the install CD and
run a live linux session *without* installing to the hard drive. This
enables new users to test wacky things out without any worried from the
fall out :)

Reading the mailing list over the past few years, I think generally new
AMBER users fall down on:

  a) Not having other bits of software that AMBER needs to build installed.
  b) Installation of 3rd party compilers (such as ifort) that support
the Fortran 95 (F95) standard since the "free" GNU compilers do not
support this yet...

Solving problem a) can end up with messy dependency issues which are a
function of their specific Linux distro and solving b) generally
unleashes linking problems as well as random 3rd party compiler issues.

I've worked out all the required packages needed to build AMBER10 and
AmberTools within Ubuntu 8.04 and these can be installed with one
command (command 3, section 1 below). Ubuntu 8.04 ships with gfortran
4.2 which supports F95 and hence it is possible to compile AMBER 10 with
this without having to resort to installing a 3rd party F95 compiler.
There are lots of benefits to this, the linking to other MPI libraries
within the distro should be easy, debugging of the gfortran produced
code can be done with gdb, but there is a downside; gfortran, at this
moment in time, will not produce the fastest binaries, AFIK ifort is
still the king ;)

Anyway... here's the how-to. It's not finished and still WIP, but it's
enough to get you up and running. I still need to check the parallel
building of sander. I hope to put it up online somewhere once I get
settled in a bit more.

How to compile AmberTools 1.2 and AMBER 10 with Ubuntu 8.04
This how to assumes:

a) A fresh install of Ubuntu 8.04 or an instance of it running from the
live CD (the live CD route may require a lot of ram) on a machine that
is connected to the Internet.

b) The presence of AmberTools-1.2.tar.bz2 and Amber10.tar.bz2 in the
user's home directory.

c) A little common sense; this sequence of commands *may* contain bugs
and trash your system; especially if mis wrapped by mail clients. Read
through it and understand what it is doing before blindly executing it.

Section 1: AmberTools 1.2

1) If not already done, enable the Universe Repository by modifying
/etc/apt/sources.list . This can be done graphically via System->
Administration->Software Sources and select the tick box on the 2nd
option (Community-maintained Open Source software (universe) ). OR it
can be done via these commands:

  cd /etc/apt
  sed '/universe$/ s/^.//' sources.list > /tmp/sources.list
  sudo mv sources.list sources.list.backup
  sudo mv /tmp/sources.list sources.list
  cd ~

2) Since you have modified /etc/apt/sources.list you will need to
refresh the apt-get cache
  sudo apt-get update

3) Install the following needed packages:
  sudo apt-get install gcc g++ libxt-dev libxext-dev flex gfortran tcsh
g77 libnetcdf-dev patch

4) Exctract AmberTools:
  cd ~
  tar xfj AmberTools-1.2.tar.bz2

5) Set your environment variable and make it "stick"
  cd amber10
  echo "export AMBERHOME=$PWD" >> ~/.profile
  source ~/.profile

6) Apply bug fixes
  patch -p0 < bugfix.all
  rm bugfix.all

7) Configure and build
  cd $AMBERHOME/src
  ./configure_at gcc
  make -f Makefile_at

8) Make a cup of Tea

9) There is an issue with the MOPAC wrapper script that will cause it to
fail with Ubuntu's default /bin/sh (dash). Fix it by telling it to use bash:

  mv $AMBERHOME/bin/ $AMBERHOME/bin/
  sed s/\\/sh/\\/bash/ $AMBERHOME/bin/ >
  chmod +x $AMBERHOME/bin/

10) Run the tests
  cd $AMBERHOME/test ; make -f Makefile_at

Section 2: Amber 10

The AmberTools bit is now complete. The second phase of this is the
building of AMBER10. It assumes that one has just finished the above.

1) Get to the right place
  cd $AMBERHOME ; cd ..

2) Extract the main files
  tar xfj Amber10.tar.bz2
  cd amber10

3) Get and apply any patches:
  patch -p0 < bugfix.all

4) Configure and build
  cd $AMBERHOME/src
  ./configure_amber gfortran

5) Run the tests
   cd $AMBERHOME/test ; make

I hope you and others find this useful.



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