bfast-0.6.5a, MUMmer-3.22, and Amos-3.0.0 Installs In Ubuntu 10.04 LTS (And Related)

Taking care of a DNA/RNA fragment alignment installation triple-threat with this post. These Ubuntu installs for largely problem-free, but one little trick is needed for Amos (this because of my use of “/opt” for my usual installation and compilation attempts and, more so, my not being interested in modifying the root PATH statement despite the constant use of sudo when building in “/opt”).

So, with the downloads of

bfast-0.6.5a (currently: sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page)
MUMmer-3.22 (currently: mummer.sourceforge.net)
Amos-3.0.0 (currently: sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS)

taken care of, the following process is performed.

user@machine:~sudo aptitude update
user@machine:~sudo aptitude upgrade

[POSSIBLE RESTART REQUIRED after this. You don’t need-need to update/upgrade, but I do it before all builds regardless.]

user@machine:~sudo apt-get install bison build-essential cmake csh doxygen flex fort77 freeglut3-dev g++ g++-multilib gcc gcc-multilib gettext gfortran gnuplot ia32-libs lib32asound2 lib32gcc1 lib32gcc1-dbg lib32gfortran3 lib32gomp1 lib32mudflap0 lib32ncurses5 lib32nss-mdns lib32z1 libavdevice52 libbz2-dev libc6-dev-i386 libc6-i386 libfreeimage-dev libglew1.5-dev libnetcdf-dev libopenal1 libopenexr-dev libopenmpi-dev libpng12-dev libqt4-dev libssl-dev libstdc++6-4.3-dbg libstdc++6-4.3-dev libstdc++6-4.3-doc libxext-dev libxi-dev libxml-simple-perl libxmu-dev libxt-dev mercurial nfs-common nfs-kernel-server openmpi-bin patch portmap python2.6-dev rpm ssh tcsh xorg-dev zlib1g-dev

The large apt-get above is my “default” additional install for a variety of programs, including Amber, Abinit, GAMESS, GROMAC, etc. Many of these may not be needed but hard drives are cheap and figuring out the minimum list is more work than simply installing everything. Do check the list, however, to make sure something won’t confuse any other installs on your machine (if you’re new to this, likely not. If you’ve done builds a few times, you may already know the difference).

user@machine:~$ sudo mv bfast-0.6.5a.tar.gz /opt
user@machine:~$ sudo mv MUMmer3.22.tar.gz /opt
user@machine:~$ sudo mv amos-3.0.0.tar.gz /opt
user@machine:~$ cd /opt

Move the three programs to /opt (or not). Specifically for bfast, two additional apt-get’s are required.

user@machine:/opt$ sudo apt-get install libstatistics-descriptive-perl libdbd-pg-perl

The build for bfast is straightforward.

user@machine:/opt$ sudo tar xvfz bfast-0.6.5a.tar.gz 
user@machine:/opt$ cd bfast-0.6.5a/
user@machine:/opt/bfast-0.6.5a$ sudo ./configure 
user@machine:/opt/bfast-0.6.5a$ sudo make
user@machine:/opt/bfast-0.6.5a$ sudo make install
user@machine:/opt/bfast-0.6.5a$ cd ..

bfast is officially built and you’ve returned to your “/opt” directory. MUMmer is also straightforward.

user@machine:/opt$ sudo tar xvfz MUMmer3.22.tar.gz 
user@machine:/opt$ cd MUMmer3.22/
user@machine:/opt/MUMmer3.22$ sudo make check
user@machine:/opt/MUMmer3.22$ sudo make install

MUMmer is officially built. If you intend to build Amos, you will need some of what you built in MUMmer. Specifically, nucmer, delta-filter, and show-coords are used by Amos and must be present in your PATH during the Amos build. As I am building in “/opt,” I’m using sudo. As I do not want to deal with setting a new PATH for root, the solution is simply to move these three programs to a universally accessible place.

user@machine:/opt/MUMmer3.22$ sudo cp nucmer /usr/local/bin/
user@machine:/opt/MUMmer3.22$ sudo cp delta-filter /usr/local/bin/
user@machine:/opt/MUMmer3.22$ sudo cp show-coords /usr/local/bin/
user@machine:/opt/MUMmer3.22$ cd ..

And, with that, you are ready for the Amos build procedure. You will need two more apt-get installs to complete the Amos build.

user@machine:/opt/amos-3.0.0$ sudo apt-get install libboost-all-dev libqt3-headers

To build Amos with no errors and all of the listed components, note the ./configure settings and run the list below.

user@machine:/opt$ sudo tar xvfz amos-3.0.0.tar.gz 
user@machine:/opt$ cd amos-3.0.0/
user@machine:/opt/amos-3.0.0$ sudo ./configure --with-Qt-dir=/usr/share/qt3 --prefix=/opt/amos-3.0.0
user@machine:/opt/amos-3.0.0$ sudo make
user@machine:/opt/amos-3.0.0$ sudo make check
user@machine:/opt/amos-3.0.0$ sudo make install

If nucmer, delta-filter, show-coords, and the qt3 libraries are not present, you’ll see the following error list after running ./configure:

-- AMOS Assembler 2.0.8 Configuration Results --
  C compiler:          gcc -g -O2
  C++ compiler:        g++ -g -O2
  GCC version:         gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /opt/amos-3.0.0
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email  with questions and bug reports.

WARNING! nucmer was not found but is required to run AMOScmp
   install nucmer if planning on using AMOScmp
WARNING! delta-filter was not found but is required to run AMOScmp-shortReads-alignmentTrimmed
   install delta-filter if planning on using AMOScmp-shortReads-alignmentTrimmed
WARNING! show-coords was not found but is required to run minimus2
   install show-coords if planning on using minimus2
WARNING! Qt3 toolkit was not found but is required to run AMOS GUIs
   install Qt3 or locate Qt3 with configure to build GUIs
   see config.log for more information on what went wrong
WARNING! Boost graph toolkit was not found but is required to run parts of the AMOS Scaffolder (Bambus 2)
   install Boost or locate Boost with configure to build Scaffolder
   see config.log for more information on what went wrong

And, finally, add these directories to your PATH.

user@machine:~$ cd
user@machine:~$ pico .profile

Add the following to your PATH statement:

/opt/amos-3.0.0/bin/:/opt/MUMmer3.22/:/opt/bfast-0.6.5a/butil/:

Crtl-X, “Y”, and quit.

UNAFold 3.8, MFold Utilities 4.5/4.6 And Additional Component Installation (Using XCode Tools 3 And Fink 0.29.21) For OSX 10.6.x

NOTE: The version numbers for everything are given specifically because aspects of the installation process may change with different versions and, in the event, I will not necessarily know the answer to subsequent problems if major version changes include major changes to the below (and that should clear up the “qualifications” section).

The UNAFold (UNified Nucleic Acid Fold(ing)) nucleic acid folding and hybridization prediction program set (here using version 3.8) can by itself be built with few (and not important) errors in OSX with Xcode Tools 3. The actual running of UNAFold.pl produces several errors that do not affect the run but do affect the amount/format of the output. It is my assumption that any OS running a less-than “kitchen sink” installation of Linux/Unix (Ubuntu, gentoo and Damn Small Linux come to mind) will have these errors and will require subsequent installations of programs/libraries that pieces of UNAFold rely on for processing output into, specifically, images and PDF files. OSX has the same issue that is easy to handle using Fink (and less so trying to install otherwise completely unrelated programs to make these “dependencies” (programs and libraries) available to UNAFold). Once Fink is installed, it is a few-step process to build UNAFold, move the Mfold Utilities contents to their proper folders (and there is a small trick here as well), and generate a UNAFold-complete install for all your DNA/RNA needs.

1. UNAFold 3.8 Installation

To begin, download (currently at mfold.rna.albany.edu/?q=DINAMelt/software), extract, open a terminal, cd into the unafold_3.8 directory (likely ~/Downloads/unafold_3.8), and run ./configure.

[prompt]$ cd ~/Downloads/unafold_3.8
[prompt]$ ./configure

On my machine (MacBook Pro, 10.6.x OSX + XCode Tools 3), this produces the output found in the local file 2011june_unafold_configure_output.txt.

You will likely note two sets of errors in the ./configure output:

./configure: line 8579: sort: No such file or directory
./configure: line 8576: sed: No such file or directory
./configure: line 10077: sort: No such file or directory
./configure: line 10074: sed: No such file or directory

The 10077 and 10074 errors are a bit odd because there are only 10039 lines in the configure file.

Are these errors important? No, you can build UNAFold just fine. I have run into these two “sort” and “sed” problems with a few other build attempts in OSX but have no good answer as to how to get around them (in case you’re wondering, sort and sed are most certainly installed on the machine. The “sort” error can be removed by specifying the path explicitly in the configure file (in line 8579, change “sort” the “/usr/bin/sort”), but the sed error persists in the few attempts I tried to work around it. It doesn’t appear to be a simple PATH issue. I’m not yet interested enough in finding a proper solution but, if you know, please post a comment or send a message. Is it just a character issue as discussed at itmercenary.livejournal.com/1585.html?).

running “make” produces the output found in the local file 2011june_unafold_make_output.txt.

[prompt]$ make

No issues. To install UNAFold, which will default to putting components into /usr/local/bin and /usr/local/share/, run sudo make install, which produces the output found in the local file 2011june_unafold_sudo_make_install_output.txt.

[prompt]$ sudo make install

Again, no issues. You will now have a populated /usr/local/bin folder.

2. MFold Utilities 4.5 (and, currently, the source for 4.6)

The next (optional) step is the inclusion of the mfold_util-4.5-Mac binaries (currently available at mfold.rna.albany.edu/?q=mfold/download-mfold), which I’ve also placed into the /usr/local/bin folder by extracting the contents of this file, them performing a cp * /usr/local/bin from within the MacBin directory.

[prompt]$ cd ~/Downloads/MacBin/
[prompt]$ sudo cp * /usr/local/bin

The processing of the data into plots with these programs requires that a set of *.col files be placed in the folder /usr/local/shared/mfold_util. Furthermore, these *.col are NOT provided in the mfold_util-4.5-Mac binary package. To get these files, you need only download the mfold_util-4.6.tar.gz file (currently at mfold.rna.albany.edu/?q=mfold/download-mfold), cd your way into src, make the /usr/local/shared/mfold_util folder, and copy the *.col files to /usr/local/shared/mfold_util.

[prompt]$ sudo mkdir /usr/local/shared/mfold_util
[prompt]$ cd Downloads/mfold_util-4.6/src
[prompt]$ sudo cp *.col /usr/local/shared/mfold_util

3. Fink 0.29.21 Install From Scratch

The first indication that other work was required came from trying to run mutplot randomly, which produced the following error:

dyld: Library not loaded: /sw/lib/libpng12.0.dylib
  Referenced from: /usr/local/bin/mutplot
  Reason: image not found
Trace/BPT trap

As digging around for libraries is not as straightforward as it would be for a Linux distro, I chose instead to solve the many problems by installing dependencies through the Fink program (currently fink-0.29.21). As 10.6.x users will find that there is no available Fink binary, you must build this from the source (which, with Xcode Tools 3 installed, occurs without error. If you don’t have Xcode Tools 3 installed, the new mechanism for buying a copy of XCode Tools 4 is less than ideal (to me, anyway. $4.99?) but now occurs through the App Store).

Download the fink source (fink 0.29.21), extract, cd into the fink-0.29.21 directory, and run bootstrap. Upon completion, you run pathsetup.sh, source your .profile, and update fink.

[prompt]$ cd ~/Downloads/fink-0.29.21
[prompt]$ ./bootstrap
[prompt]$ . /sw/bin/pathsetup.sh 
[prompt]$ cd ~/
[prompt]$ source .profile
[prompt]$ fink selfupdate-rsync
[prompt]$ fink update-all

The output for my installation can be found in 2011june_fink_install_output.txt. The rsync output can be found in 2011june_fink_selfupdate_rsync_output.txt. NOTE: You will be asked several questions about the installation process. Be prepared to blindly select the default settings with [enter], but don’t just walk away from the screen.

This completes the UNAFold install, MacBin install, and Fink install, meaning now we can walk through the dependencies.

4. Installing UNAFold (well, MFold Utils) Dependencies

First dependency-free UNAFold.pl run attempt produces the following error:

[prompt]$ UNAFold.pl seqtest.txt 
Checking for boxplot_ng... dyld: Library not loaded: /sw/lib/libpng12.0.dylib
  Referenced from: /usr/local/bin/boxplot_ng
  Reason: image not found
found, supports Postscript
Checking for hybrid-plot-ng... found, supports Postscript
Checking for sir_graph_ng or sir_graph... dyld: Library not loaded: /sw/lib/libpng12.0.dylib
  Referenced from: /usr/local/bin/sir_graph
  Reason: image not found
found, supports Postscript
Checking for ps2pdfwr... not found
Calculating for seqtest.txt, t = 37

As the UNAFold install page states, you need glut, the GD library, and gnuplot installed (and all of the many libraries therein).

[prompt]$ fink install libjpeg tetex gd2 gnuplot

For gnuplot, you will be required to make a few selections during the build process (blindly hitting the enter key at these questions will do, but this is not just a “type and go” install process. And it took about two hours on a MBP).

A final working error-free run looks as below, leaving you to process the data with the MFold Utilities as you like:

[prompt]$ UNAFold.pl seqtest.txt 
Checking for boxplot_ng... found, supports Postscript
Checking for hybrid-plot-ng... found, supports Postscript
Checking for sir_graph_ng or sir_graph... found, supports Postscript
Checking for ps2pdfwr... found
Calculating for seqtest.txt, t = 37

Amber And Ubuntu Part 1. Amber10 (Serial Execution) Installation In Ubuntu 8.10 (Intrepid Ibex)

[15 March 2009: In case you miss it while searching, the MPI build of Amber is provided in a future link.  Check out www.somewhereville.com/?p=437 for installation and commentary.]

Ubuntu continues to be a pleasantly stable and very, very clean Linux distribution (although my last Ubuntu post about a minor glitch was only a few weeks ago).  That said, for the typical research user perhaps not used to dealing with either Linux distributions or code compilation, it may appear to be a little too clean.  In my previous learning endeavors with Fedora and OpenSuse, I often found myself installing the entire DVD for fear of missing an important library or some random program (almost entirely unnecessary after you learn your way around a distribution, but when your hard drives break the 200 GB point, what’s a waste of 5 GB when you don’t have to dig up the DVD again?).  With the standard Ubuntu installation and an internet connection, your only problem becomes determining which programs and libraries are needed to complete a compilation from source.

Posted here is a procedure for building a serial execution (not parallel, that is en route as part of an upcoming post) version of Amber10 under Ubuntu 8.10 (Server or Desktop, makes no difference), completed on all 15 of the Dell quad-core boxes that make up the contents of the Chemistry Department Learning Center in the new Life Sciences Building at Syracuse (the transition from Windows to Ubuntu is shown above because it looks neat).  Like a number of oft-employed computational chemistry programs, pre-compiled binaries can be hard to come by and, if you’ve never had to compile a program before, even more difficult to build on your own.  My hope is that, with only an Ubuntu 8.10 installation and an internet connection, the procedure below will walk you from download to execution.

About the procedure

The content below assumes a limited knowledge of Linux and is written in such a manner that people in the Chemistry Department at S.U. can, if they have to after I spontaneously combust, reinstall Amber10 and AmberTools.  If you find yourself asking “why is he spending so much time on such a trivial point?“, then consider yourself a 1334 hax0r or something and ignore everything in black.

This procedure is very likely general to Amber and AmberTools, but is specifically addressing the installation of Amber10 and AmberTools 1.2 in Ubuntu 8.10 with g95.  One never knows what may change in one or assorted programs.

LEGEND

Text in black – my ramblings.

Text in bold preformatted red - things you will type in the Terminal

Text in green – text you will either see or will type into files (using pico, my preference)

Step 0: Coming To Grips With sudo

The one aspect of Ubuntu that differs from most other Linux distributions is the differentiation between root, Administrator, and user right from the installation.  Whereas you set up the root user in Suse and Fedora as part of  the installation process, you set up an Administrator account during Ubuntu installation that is distinct from root.  As a result, if you do not set up the root account to perform installations and system-level modifications, you are left in the Administrator account to use the sudo (super-user do…) command to allow you, the Administrator, to build and install programs outside your home ($HOME) directory.

“Do I have to constantly sudo everything?”  No.  Accessing a pure “root” terminal for installations is straightforward after the root password is assigned, it is simply argued by many (including the Ubuntu wiki) that it is safer to use sudo.  If you want to go the root route, check out help.ubuntu.com/community/RootSudo.

Step 1. Install Ubuntu 8.10 Desktop or Server

Default installation, simply walk through the entire installation process.  If your machine requires DNS registering to dive into your subnet’s IP pool (as is the case at S.U.), this will be accomplished by simply opening a browser in most instances (and the standard install is set up for DHCP) after install. With the internet connection established, you’ll likely get a message in the upper right-hand corner (wait a few minutes if you need to) mentioning that updates are available.  Not necessary for the Amber build, but it never hurts to be current.

Step 2. Terminal

There’s no use in driving through the Applications drop box to get to a program you’ll be using as often as Terminal.  If you didn’t know it yet, go to Applications -> Accessories -> left-click-and-hold on the Terminal icon, then drag the icon to the panel (next to your handy Firefox icon, for instance) or right-click and “Add this launcher to panel.”

Step 3. apt-get

It is at this point that your internet connection becomes vital in Ubuntu.  In the words of Bruce Byfield

If any single program defines the Debian Linux project, that program is apt-get.

If you’re a research scientist hoping to build software from source, it’s about as an important an interface between Ubuntu and your programs as your neck is between your head and your body.  For building Amber10, you will need to install several programs (and associated libraries.  One required program, g95, is not get available by apt-get, but we’ll get to that later).  apt-get makes this process (nearly) painless.

At the Terminal window:

sudo apt-get update

This updates the package list in the apt-get database (and it is recommended that you run this regularly, as it is your connection to newly available and updated programs).

sudo apt-get install fort77 g++ flex csh patch

This installs four base programs and many additional programs and libraries. The fort77 (fortran) compiler is required for the compilation of AmberTools (1.2).  Installing g++, the GNU Compiler Collection, takes care of your C and C++ compiling requirements.  flex is a fast lexical analyzer generator.  As of this writing (and, admittedly, with little research under my belt), I do not know exactly how this is used in Amber, but I know it will not compile without it.  Finally, csh.  Yes, you need to install csh (I was stunned at first that it wasn’t already present).

NOTE 1: If you get an error related to hplip, see my previous post about fixing it.

NOTE 2: In my google travels, I discovered a page (that now I can’t find.  How sad is that?) that used gfortran in a previous version of AmberTools (1.0, I think).  I started with gfortran out of ignorance of the apt-get for g77 and, because I did not want to deal with modifying installation scripts, simply placed a link from gfortran to g77 in the /usr/bin folder.  This compiles AmberTools 1.2 just fine, but g77 is specifically required to pass all of the tests for AmberTools (in the flags), so my seemly crafty ln -s trick failed me miserably.  Your life is made much easier by apt-get’ing g77 and it is my expectation that I’m the only person on the planet that tried to use gfortran for compiling AmberTools 1.2 in Ubuntu in such a cavalier manner.

Step 4: .bashrc and .profile Modifications

These next two steps (1) define the location of AMBERHOME (specifying for those programs that call “$AMBERHOME” to “look in … directory”) and (2) add the amber10 directory to your path (so you need only type “antechamber” and not “/opt/amber10/bin/antechamber“, etc.).  Both .bashrc and .profile (yes, I’m a bash user) are in your $HOME directory (simply typing “cd” will return you to $HOME and it is where the Terminal window starts you).

pico .bashrc

Into .bashrc, place the following (at bottom, just to keep track of the changes you make)

AMBERHOME=/location/to/amber10
export AMBERHOME

Crtl-X, The Enter Key twice, and done.

To make these changes to your account,

source .bashrc

In the interest of keeping track of where I install programs on a machine, I tend to use the /opt directory, which Perry thinks is crazy.  You may see /usr/local, /usr/local/bin, or various combinations thereof in your web searching travels.  If you’re new to Linux, you’ll blindly do what I did because you’re concerned that something below will rely on something being in /opt.

pico .profile

Into .profile, place the following (at bottom, just to keep track of the changes you make)

PATH=”/location/to/amber10/exe:$PATH”

Again, mine would be /opt/amber10/exe

Crtl-X, The Enter Key twice, and done.

To make these changes to your account,

source .profile

Step 5. Installing g95

The g95 program is an open source fortran compiler with support for f90 and f95.  I found myself NOT using CPMD a few years ago because I could not find a free f90 compiler (this was before the Intel Fortran Compiler became available for Linux) and am very happy that g95 has matured as of late.  That said, there is no apt-get for it yet, so you need to install this the olde-fashioned way.  With its Debian underpinnings, the Ubuntu g95 installation is trivial.  You need only be cognizant of whether you installed the 32-bit or 64-bit versions of Ubuntu.  If you don’t know, it will be obvious when you go to build Amber10 (and you can simply install the other flavor over the old one).

At g95.org/downloads.shtml#CS, you will find the current snapshots for various flavors and installation formats for g95.  You either want to download the Linux x86 (Debian) or the Linux x86-64 (Debian) packages.  If you’re using Firefox in Ubuntu, your download folder should be your Desktop.  Sticking to the Terminal, simply type the following:

cd ~/Desktop

to go to the Desktop Folder in your $HOME directory

sudo dpkg -i g95-x86.deb

if you downloaded with the intent of installing the 32-bit version, or

sudo dpkg -i g95-x86_64.deb

if you downloaded with the intent of installing the 64-bit version

The dpkg program is Debian’s equivalent of Redhat’s rpm (and vice versa).  It will extract the contents of a .deb file and place all of the executables and libraries in their proper folders PROVIDED you remember the sudo.  If you do not use the .deb package and decide to install from the .tgz file, you may find yourself having to copy libraries and executables into relevant directories.  If possible, stick with dpkg.

Ignorable Aside:

I did not use dpkg on my first pass of installations on the Learning Center machines above and had to go through the following steps to properly use g95 (which will fail with far harsher error messages than shown below).  The steps below extract the .tgz g95 file you download from the website (g95-x86-linux.tgz), move the executable f951 to a directory already in your path and copies all of the associated libraries into path libraries (the “1:30 am frustration” fix).  Do you see the benefit of dpkg!?

sudo mkdir /usr/local/bin/g95

makes the base g95 directory

sudo mv ~/Desktop/g95-x86-linux.tgz /usr/local/bin/g95

moves the downloaded g95-x86-linux.tgz to /usr/local/bin/g95

cd /usr/local/bin/g95
sudo tar xvjf g95-x86-linux.tgz

extracts g95-x86-linux.tgz, makes the directory g95-install

sudo mv g95-install/* /usr/local/bin/g95

moves all of the g95 files out of the g95-install directory (not mandatory)

sudo ln -s /usr/local/bin/g95/bin/*g95* /bin/g95

creates a link to the g95 executable that is placed into /bin (in the PATH)

sudo cp lib/gcc-lib/i686-suse-linux-gnu/4.0.3/f951 /bin

places a copy of f951 into /bin

sudo cp lib/gcc-lib/i686-suse-linux-gnu/4.0.3/*.o /usr/lib

places a copy of all files *.o into /usr/lib

sudo cp lib/gcc-lib/i686-suse-linux-gnu/4.0.3/*.a /usr/lib

places a copy of all files *.a into /usr/lib

NOTE: You do not need to type all of lib/gcc-lib/i686-suse-linux-gnu/4.0.3/.  Simply start the name and hit the TAB key to fill in the rest.  You’re welcome.

Now, if you install the wrong build of g95 for your version of Ubuntu (32 instead of 64, 64 instead of 32), you will likely see an error at the Amber10 compilation stage (down below) that looks like:

Testing the Fortran compiler:
g95 -O0  -fsecond-underscore -o testp testp.f
/tmp/ccUG0LYy.s: Assembler messages:
/tmp/ccUG0LYy.s:11: Error: suffix or operands invalid for `push’
./configure_amber: 1169: ./testp: not found
Unable to compile a Fortran program using g95 -O0  -fsecond-underscore
Please check your compiler settings or configure flags.

At this point, simply download the OTHER version of g95 and dpkg -i it.

Step 6. Extract Amber and AmberTools

You should have already downloaded Amber10.tar.bz2 and AmberTools-1.2.tar.bz2 with your confirmation-of-purchase email.  I will assume that you’ve downloaded a fresh copy in Ubuntu so that both files are sitting on your Desktop.

sudo cp ~/Desktop/Amber* /opt
cd /opt
sudo tar xvjf Amber10.tar.bz2

will make a folder amber10 in opt/

sudo tar xvjf AmberTools-1.2.tar.bz2

will extract AmberTools-1.2 into the previously created amber10 folder

Step 7. Build and Test AmberTools 1.2

My 7th grade math teacher and one-time musical director Mr. Marshall Nye used to tell us that “Fools rush in where angels fear to tread,” this obviously in reference to the manifold ways in which 7th graders had previously attempted to short-cut polynomial expansion in homework assignments.  I’d say a good 2 hours were spent dealing with foolish issues to streamline what is provided below and it is by no means guaranteed that the below will work flawlessly for you (unless you start with a pristine Ubuntu 8.10 install and do everything above exactly as typed, in which case you should be good to go).

cd $AMBERHOME

This takes you to /opt/amber10 or wherever else you defined the AMBERHOME directory to be

cd amber10/src

Enter the source directory for AmberTools

sudo ./configure_at gcc

This runs the configure script for AmberTools and specifies to use gcc flags (the compilers we installed with g77 and g++).  If you’re using other compilers, you probably don’t need this blog post anyway.  Your output should look as follows:

Setting AMBERHOME to /opt/amber10

Warning: the X11 libraries are not in the usual location !
To search for them try the command: locate libXt
On Fedora Core 5 install an xorg-x11-devel package.
On RedHat8 install an XFree86-devel package.
For the moment Amber will be configured not to build XLEaP.

Testing the C compiler:
gcc  -m64 -o testp testp.c
OK

Obtaining the C++ compiler version:
g++ -v
The version is 4.2.3
OK

Testing the g77 compiler:
g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
OK

Testing flex:
OK

Configuring netcdf; (may be time-consuming)

NETCDF configure succeeded.

The configuration file, config.h, was successfully created.

The next step is to type ‘make -f Makefile_at’

sudo make -f Makefile_at

This builds the AmberTools programs.  This may take some time but provides plently of on-screen feedback.  To see what an otherwise flawless installation looks like, you can view my output HERE.

After the build is complete, we run the tests.  This was a MAJOR hassle for me for three reasons.

FIRST, sudo make test would fail instantaneously because it decided that AMBERHOME had not been defined, despite it being defined above.  I remedied this by not fully diagnosing the problem but instead simply adding two lines to the top of Makefile_at (see below).

SECOND, a linked gfortran is NOT the same thing as g77 to the test scripts and I spent a considerable amount of time re-writing and commenting out scripts before doing the obvious and looking-for-and-installing g77. This is fixed with proper g77 installation.

THIRD, the test sequence would come to a screeching halt at the ./Run.tp section of the script.  After much searching, I found a page that described the fix and am grateful to Mark Williamson for posting this on the Amber listserve at structbio.vanderbilt.edu/archives/amber-archive/2008/3476.php.

We’ll deal with FIRST:

cd $AMBERHOME/test
sudo pico Makefile_at

To the almost-top of this file, I added two lines to re-define AMBERHOME, getting around my initial error.  My top 6 lines then looked like the following:

include ../src/config.h

AMBERHOME=/opt/amber10
export AMBERHOME

test: is_amberhome_defined \

Crtl-X, The Enter Key twice, and done.

Now the THIRD:

The file mopac.sh is written into /location/of/amber10/bin/.  We take care of all of the test issues associated with this file by changing the shell called at the top of the file.

sudo pico /opt/amber10/bin/mopac.sh

Change

#!/bin/sh

to

#!/bin/bash

Crtl-X, The Enter Key twice, and done.

If you want to know much more, have a read of structbio.vanderbilt.edu/archives/amber-archive/2008/3476.php.  I understand what’s at issue, but my only concern is that it worked.

You should still be in $AMBERHOME/test at this point (you can cd $AMBERHOME/test if you’re not).  Run those tests!

sudo make -f Makefile_at test

If you tried the gfortran trick for g77, you will notice the error at the cd antechamber/tp && ./Run.tp portion of the script (expectedly, at the first instance of .hasG77:).  These will take a while but confirm that nothing got butchered in the AmberTools build.  To see what an otherwise flawless installation looks like, you can view my output HERE.

Step 8. bugfix.all

I’m making this its own step so that you don’t forget to do it.

download bugfix.all from ambermd.org/bugfixes10.html

sudo cp ~/Desktop/bugfix.all $AMBERHOME
sudo patch -p0 -N -r patch-rejects < bugfix.all

This will result in a small amount of on-screen output.  To compare and contrast with mine, see HERE.

Step 9. Build and Test Amber10

Finally!  Nearing completion with only one problem discovered in the test sequence.

cd $AMBERHOME/src
sudo ./configure_amber -gnucompat g95

You may or may not find considerable discussions about how much faster Amber10 execution is by using other compilers instead of the gcc variety.  As you should be spending money on hardware and minimizing your software costs, I say go with gcc all the way (unless you’re offering).  Your output for this step should look like the following:

Setting AMBERHOME to /opt/amber10

Setting up Amber configuration file for architecture: g95
Using parallel communications library: none
The MKL_HOME environment variable is not defined.

Testing the C compiler:
gcc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m64 -o testp testp.c
OK

Testing the Fortran compiler:
g95 -O0  -fsecond-underscore -o testp testp.f
OK

——   Configuring the netCDF libraries:   ——–

Configuring netcdf; (may be time-consuming)
NETCDF configure succeeded.

The configuration file, config_amber.h, was successfully created.

sudo make serial

Again, making a serial (one processor) set of executables.  This will take a while and provide plenty of on-screen feedback.  To see what an otherwise flawless installation looks like, you can view my output HERE.

cd $AMBERHOME/test
sudo make test

I ran into failures of script (not of testing, but of the actual script) at Run.pbpgb. The output is as below.

cd pb_pgb && ./Run.pbpgb
./Run.pbpgb: line 3: syntax error near unexpected token `set’
./Run.pbpgb: line 3: `if( ! $?TESTsander ) set TESTsander = “http://www.somewhereville.com/exe/sander”‘
make: *** [test.sander.BASIC] Error 2

I’ve found nothing about it online and have not yet found out what the problem is so, in the interest of getting the rest of this instruction set posted, I simply commented out the problematic lines and ran the rest of the tests otherwise flawlessly.  The commented Makefile will look like the following (simply not running anything related to pb_).

cd $AMBERHOME/test
sudo pico Makefile

Search down the file and add three # such that the lines look like the following:

cd trajene && ./Run.trajene
cd alp && ./Run.alp
#    cd pb_pgb && ./Run.pbpgb
#    cd pb_ivcap1 && ./Run.pb_ivcap1
#    cd pb_ivcap5 && ./Run.pb_ivcap5
cd umbrella && ./Run.umbrella
cd noesy && ./Run.noesy

Crtl-X, The Enter Key twice, and done.

You can see the results of my otherwise flawless tests HERE.

Final thoughts…

The parallel version is en route as I complete the installation of a new cluster and install mpi.  It will not differ much from the above, save the inclusion of an additional flag or two in the two ./configure scripts for AmberTools and Amber10.  If questions are raised, comments are thought of, speed-ups identified, etc., please either send me an email or post them here.  Our concern as computational chemists should be making predictions and interpreting data, not making compilation errors and interpreting error messages.

www.ubuntu.com
www.linux.org
www.somewhereville.com/?p=149
fedoraproject.org
www.opensuse.org/en/
ambermd.org
www.dell.com
chemistry.syr.edu
thecollege.syr.edu/lifesciences/about.html
www.syr.edu
www.microsoft.com
en.wikipedia.org/wiki/Spontaneous_human_combustion
en.wikipedia.org/wiki/Sudo
help.ubuntu.com/community/RootSudo
en.wikipedia.org/wiki/Domain_name_system
en.wikipedia.org/wiki/Dhcp
help.ubuntu.com/community/UsingTheTerminal
www.mozilla.com/en-US/firefox
members.axion.net/~bbyfield
www.linux.com/feature/113879
www.g95.org
www.debian.org/doc/manuals/apt-howto
www.gnu.org/software/fortran/fortran.html
gcc.gnu.org
flex.sourceforge.net
en.wikipedia.org/wiki/C_shell
hplipopensource.com/hplip-web/index.html
www.google.com
en.wikipedia.org/wiki/Bash
www.piermont.com
www.cpmd.org
www.intel.com/cd/software/products/asmo-na/eng/282048.htm
www.us.debian.org
g95.org/downloads.shtml#CS
en.wikipedia.org/wiki/Dpkg
en.wikipedia.org/wiki/RPM_Package_Manager
en.wikipedia.org/wiki/Fools_Rush_In_(Where_Angels_Fear_to_Tread)
en.wikipedia.org/wiki/Polynomial_expansion
structbio.vanderbilt.edu/archives/amber-archive/2008/3476.php
ambermd.org/bugfixes10.html