Amber And Ubuntu Part 2. Amber10 (Parallel Execution) Installation In Ubuntu 8.10 (Intrepid Ibex) With OpenMPI 1.3… And Commentary

After considerable trial and building/testing errors, what follows is as simplified a complete installation and (non-X11/QM) testing of Amber10 and OpenMPI 1.3 as I think can be procedure'd in Ubuntu 8.10 (and likely previous and subsequent Ubuntu versions), dealing specifically with assorted issues with root permissions and variable definitions as per the standard procedure for Amber10 installation.

I'll begin with the short procedure and bare minimum notes, then will address a multitude of specific problems that may (did) arise during all of the build procedures.  The purpose for listing everything, it is hoped, is to make these errors appear in google during searches so that, when you come/came across the errors, your search will have provided some amount of useful feedback (and, for a few of the problems I had with previous builds of other programs, this blog is the ONLY thing that comes up in google).

Some of the content below is an extension of the single-processor build of Amber10 I posted previously.  In the interest of keeping the reading to a minimum, the short procedure below is light on explanations that are provided in the long procedure that follows.  If you're running on a multi-core computer (and who isn't anymore), you likely want to take advantage of the MPI capability, so I would advise simply following the procedure below and IGNORING the previous post (as I also state at the top of the previous page).

Enough blabbering.


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)

Amber10, OpenMPI 1.3, Ubuntu 8.10: The Easy, Teenage New York Version

0a. I assume you're working from a fresh installation of Ubuntu 8.10.  Some of what is below is Ubuntu-specific because of the way that Ubuntu decides to deal with the Root/Administrator/User relationship.  That said, much is the same and I'll try to remark accordingly.

0b. As with the previous post, I am writing this with an expected audience of a non-technical Linux user, which means more detail of the steps and not just "cd $HOME and ./config -> make -> make install."  If the steps are too obvious to you, find someone who thinks a Terminal window is one that won't close and let them do it.  Speaking of…

0c. Everything below is done from a Terminal window.  The last icon you will use is the Terminal icon you click on.  If you've never had the pleasure in Ubuntu Desktop, go to Applications -> Accessories -> Terminal.  You can save yourself some time dragging around menus by hovering over the Terminal icon, right-clicking, and "Add this launcher to panel."

0d. One more thing for the absolute newbies.  I am assuming that you've used Firefox to download OpenMPI 1.3, the AmberTools 1.2 and Amber10 bz2 files, and the bugfix.all files for AmberTools 1.2 and Amber10 (more on that in 0e).  That's all you'll need for the installation below.  Note that I'm not dealing with X11 (library specifications and other testing to do first), MKL (the Intel Math Kernel Library), or the GOTO BLAS libraries.  The default download folder for Firefox in a fresh installation of Ubuntu is the Desktop.  I will assume your files are on the Desktop, which will then be moved around in the installation procedure below.

0e. bugfix.all (Amber10) and bugfix.all (AmberTools 1.2) – Yes, the Amber people provide both of these files for the two different programs using the same name.  As I assume you're using Firefox to download these files from their respective pages, I recommend that you RENAME the bugfix.all file for AmberTools 1.2 to bugfix_at.all, which is the naming convention I use in the patching step of the installation process (just to keep the confusion down).  In case you've not had the pleasure yet, instead of clicking on the bugfix.all link on each page and saving the file that loads, simply right-click and "Save Link As…", then save the AmberTools 1.2 bugfix.all file as bugfix_at.all.

0f. This OpenMPI 1.3 build and series of Amber10 tests assumes SMP (symmetric multi-processing) only, meaning you run only with the CPUs on your motherboard.  The setup of OpenMPI for cluster-based computing is a little more complicated and is not presented below (but is in process for write-up).

0g. And, further, I am not using the OpenMPI you can install by simply sudo apt-get install libopenmpi1 linopenmpi-dev openmpi-bin openmpi-doc for two reasons.  First, that installs OpenMPI 1.2.8 (I believe), which mangles one of the tests in such a way that I feared for subsequent stability in Amber10 work I might find myself doing.  Second, I want to eventually be able to build OpenMPI around other Fortran compilers (specifically g95 or the Intel Fortran Compiler) or INSERT OPTION X and, therefore, prefer to build from source.

So, from a Terminal window, the mostly comment-free/comment-minimal and almost flawless procedure is as follows.  Blindly assume that everything I am doing, especially in regards to WHERE this build is occurring and WHAT happens in the last few steps, is for a good reason (explained in detail later)…

0. cd $HOME (if you're not in your $HOME directory already or don't know where it is)

1. sudo apt-get update (requires administrative password)

2. sudo apt-get install ssh g++ g++-multilib g++-4.3-multilib gcc-4.3-doc libstdc++6-4.3-dbg libstdc++6-4.3-doc flex bison fort77 netcdf-bin gfortran gfortran-multilib gfortran-doc gfortran-4.3-multilib gfortran-4.3-doc libgfortran3-dbg autoconf autoconf2.13 autobook autoconf-archive gnu-standards autoconf-doc libtool gettext patch libblas3gf liblapack3gf libgfortran2 markdown csh (this is my ever-growing list of necessary programs and libraries that are not installed as part of a fresh Ubuntu installation)

3. pico .bashrc

Add the following lines to the bottom of this file.  This will make more sense shortly…


export MPI_HOME

Crtl-X and the Enter Key twice to Exit

4. source .bashrc

5. pico. profile

Add the following line to the bottom of this file.


Crtl-X and the Enter Key twice to Exit

6. source .profile

7. mv $HOME/Desktop/Amber* $HOME/Documents/ (this assumes the downloaded files are on the desktop)

8. mv $HOME/Desktop/openmpi-1.3 $HOME/Documents/ (this assumes the downloaded files are on the desktop)

9. cd $HOME/Documents/

10. gunzip openmpi-1.3.tar.gz

11. tar xvf openmpi-1.3.tar

12. cd openmpi-1.3

13. ./configure –prefix=/ (installs the MPI binaries and libraries into /. Avoids library errors I ran across despite MPI_HOME, but may be fixable. Copious output to follow.  For my results, click HERE)

14. sudo make all install (this installs binaries and libraries into "/". Copious output to follow.  For my results, click HERE)

15. cd $HOME/Documents/

16. tar xvjf Amber10.tar.bz2

17. tar xvjf AmberTools-1.2.tar.bz2

18. mv $HOME/Desktop/bugfix* $HOME/Documents/$AMBERHOME (moves bugfix files to the Amber directory)


20. patch -p0 -N -r patch-rejects < bugfix_at.all (patches AmberTools)

21. patch -p0 -N -r patch-rejects < bugfix.all (patches Amber10)

22. cd src/

23. ./configure_at -noX11

24. make -f Makefile_at (copious output to follow.  For my results, click HERE)

25. cd ../bin/

26. pico

At the top of the file, change sh to bash

Crtl-X and the Enter Key twice to Exit

27. cd ../test/

28. make -f Makefile_at test (copious output to follow.  For my results, click HERE)

29. cd ../src/

30. ./configure_amber -openmpi gfortran

31. make parallel (copious output to follow.  For my results, click HERE)

32. cd $HOME/.ssh/ (at this step, we allow auto-login in ssh so that the multiple mpirun tests do not require that you supply your password constantly)

33. ssh-keygen -t dsa

34. cat >> authorized_keys2

35. chmod 644 authorized_keys2

36. cd $AMBERHOME/test/

37. csh

38. setenv DO_PARALLEL 'mpirun -np N' (here, N is the number of processors you wish to use on your mobo)

39. make test.parallel.MM (copious output to follow.  For my results, click HERE)

40. exit (exits the csh shell)

41. sudo cp -r $HOME/Documents/amber10 /opt/amber10

42. cd $HOME

43. rm -r $HOME/Documents/amber10 (this deletes the build directory.  Delete or keep as you like)

44. pico .bashrc

Make the following change to the bottom of this file.


Crtl-X and the Enter Key twice to Exit

45. source .bashrc

46. pico .profile

Make the following change to the bottom of this file.


Crtl-X and the Enter Key twice to Exit

47. source .profile

That is it!  In theory, you should now have a complete and tested Amber10 and AmberTools 1.2 build sitting in /opt/amber10.

Amber10, OpenMPI 1.3, Ubuntu 8.10: The Notes

What follows is the complete list of problems, questions, errors, issues, and general craziness from much trial and error for the installation procedure above.  As you can guess from my constant mentioning of Ubuntu in my statements-with-qualifications, some of these problems likely will not occur in other distros.  My primary reason for the extended discussion below is so that the errors and issues make their way into google so that people searching for fixes to these problems (if they come across them) will see actual content (if they choose to read it) and maybe find a reasonable fix.

I'll be expanding in sections by grouping numbers above.

0a – 0g Installation Preparations

I've not much to add here except that OpenMPI is likely not the only way to install MPI Amber10 in Ubuntu, but I think it is easier than MPICH2 to set up cross-cluster calculations on a switch'ed network.  My stronger preference for OpenMPI stems from both past positive experience with OpenMPI and GROMACS (specifically on my Macbook Pro) and eventual success with OpenMPI 1.2.X and Abinit 5.6.5.  I had hoped to use the same version of OpenMPI for GROMACS, Amber10, and Abinit, but ran into a yet-to-be-resolved issue with OpenMPI 1.3.x in the building of Abinit (the problem is, apparently, resolved in the upcoming 1.4.1 build, but I'm not much for using release candidates.  I'll be discussing this in an upcoming Abinit installation post based on my previous Abinit installation post).

1 – 2 apt-get

My listed apt-get installation set contains many, many programs and libraries that are not necessarily needed in the OpenMPI and Amber10 build but are required for other programs.  The apt-get approach is still much cleaner than installing the entire OpenSuse or Fedora DVD, but you do find yourself scrambling the first time you try to install anything to determine what programs are missing.  You don't know you need csh installed until the test scripts fail.  You forget about ssh until you run mpirun for the first time.  I do not yet know if MKL, GOTO, or any of the X11-based AmberTools programs require additional libraries to be installed, so the above apt-get list may grow.  Check the comments section at bottom for updates.

The list below shows essential programs and libraries AND their suggested additional installs. As long as you're online and apt-get'ing anyway, might as well not risk missing something for your next compiling adventure.

g++ g++-multilib  g++-4.3-multilib  gcc-4.3-doc  libstdc++6-4.3-dbg  libstdc++6-4.3-doc

gfortran gfortran-multilib gfortran-doc gfortran-4.3-multilib gfortran-4.3-doc libgfortran3-dbg

autoconf autoconf2.13 autobook autoconf-archive gnu-standards autoconf-doc libtool gettext

flex bison

ssh csh patch markdown fort77 netcdf-bin libblas3gf liblapack3gf libgfortran2

3 – 9 .bashrc and .profile Modifications, Building In Your Own Directory

For a number of programs, the procedure from source is ./configure, make, and make install, make install often only responsible for moving folders into the correct directories (specifically, directories only root has access to, such as /usr/local/bin, /lib, and /opt).  In many distributions, this final step is actually sudo make install.  This division of make and make install is not preserved in Amber, which complicates the Ubuntu build slightly.  The building in $HOME/Documents (as I've described the procedure above) saves you from having to constantly sudo the extraction and building process in directories you, the typical user, do not have access to write into.

Working in $HOME\Documents (or any of your $HOME folders) allows for the complete build and testing of AmberTools and Amber10.

The other benefit from doing as much in $HOME as possible is the lack of a need to define variables as the root user (specifically, AMBERHOME, MPI_HOME, and DO_PARALLEL) by setting variables in the root .bashrc and .profile files, adding lines to the Makefiles for AmberTools and Amber10, or setting variables at prompts.  This variable specification issue arises because when you run a program with sudo, you invoke the root privileges and the root variable definitions, so any specifications you make for your PATH or these Amber-specific variables are lost.

Once the build is complete in the $HOME/Documents folder, we move the entire directory into /opt, my default location for all programs I build from source (but $HOME/Documents is just fine as well once the PATH is set).

10 – 14 OpenMPI 1.3

So, why not then use OpenMPI 1.2.x?  The build of Amber10 works just fine with OpenMPI 1.2.x in Ubuntu with all of the installation specifications described in Step 2 of the short procedure (the extensive apt-get).  The problem with 1.2.x occurs for a single test after the Amber10 build that I've not yet figured out a workaround for, but the error is sinister enough that I decided to not risk similar errors in my own Amber work and, instead, use OpenMPI 1.3.x, which does not suffer the same error.  The only (ONLY) test to fail with OpenMPI 1.2.x is the cnstph (constant pH simulation) test, which runs perfectly well but fails at the close of the calculation (you can test this yourself by changing the nstlim value in the mdin file to any arbitrarily large number).  The failure message, which kills the test series, is below.  This job also fails if you simply try to run it independently of the pre-defined test set (not the make test.parallel.MM, but cd'ing into the cnstph directory, setting variables, and running the script).

cd cnstph && ./Run.cnstph
[ubuntu-desktop:18263] *** Process received signal ***
[ubuntu-desktop:18263] Signal: Segmentation fault (11)
[ubuntu-desktop:18263] Signal code: Address not mapped (1)
[ubuntu-desktop:18263] Failing at address: 0x9069d2cb0
[ubuntu-desktop:18264] *** Process received signal ***
[ubuntu-desktop:18265] *** Process received signal ***
[ubuntu-desktop:18265] Signal: Segmentation fault (11)
[ubuntu-desktop:18265] Signal code: Address not mapped (1)
[ubuntu-desktop:18265] Failing at address: 0x907031c70
[ubuntu-desktop:18264] Signal: Segmentation fault (11)
[ubuntu-desktop:18264] Signal code: Address not mapped (1)
[ubuntu-desktop:18264] Failing at address: 0x906dbdc00
[ubuntu-desktop:18263] [ 0] /lib/ [0x2b17b5bef0f0]
[ubuntu-desktop:18263] [ 1] /usr/local/lib/ [0x2b17b4c10937]
[ubuntu-desktop:18263] [ 2] /usr/local/lib/ [0x2b17b4c122bb]
[ubuntu-desktop:18263] [ 3] /home/userid/Documents/amber10/exe/sander.MPI(sander_+0x73ce) [0x4c6ec2]
[ubuntu-desktop:18264] [ 0] /lib/ [0x2abd8f5810f0]
[ubuntu-desktop:18264] [ 1] /usr/local/lib/ [0x2abd8e5a2937]
[ubuntu-desktop:18264] [ 2] /usr/local/lib/ [0x2abd8e5a42bb]
[ubuntu-desktop:18264] [ 3] /home/userid/Documents/amber10/exe/sander.MPI(sander_+0x73ce) [0x4c6ec2]
[ubuntu-desktop:18264] [ 4] /home/userid/Documents/amber10/exe/sander.MPI(MAIN__+0xf0a) [0x4bfa66]
[ubuntu-desktop:18264] [ 5] /home/userid/Documents/amber10/exe/sander.MPI(main+0x2c) [0x88309c]
[ubuntu-desktop:18264] [ 6] /lib/ [0x2abd8f7ad466]
[ubuntu-desktop:18264] [ 7] /home/userid/Documents/amber10/exe/sander.MPI [0x43a649]
[ubuntu-desktop:18264] *** End of error message ***
[ubuntu-desktop:18263] [ 4] /home/userid/Documents/amber10/exe/sander.MPI(MAIN__+0xf0a) [0x4bfa66]
[ubuntu-desktop:18263] [ 5] /home/userid/Documents/amber10/exe/sander.MPI(main+0x2c) [0x88309c]
[ubuntu-desktop:18263] [ 6] /lib/ [0x2b17b5e1b466]
[ubuntu-desktop:18263] [ 7] /home/userid/Documents/amber10/exe/sander.MPI [0x43a649]
[ubuntu-desktop:18263] *** End of error message ***
[ubuntu-desktop:18265] [ 0] /lib/ [0x2ba0032600f0]
[ubuntu-desktop:18265] [ 1] /usr/local/lib/ [0x2ba002281937]
[ubuntu-desktop:18265] [ 2] /usr/local/lib/ [0x2ba0022832bb]
[ubuntu-desktop:18265] [ 3] /home/userid/Documents/amber10/exe/sander.MPI(sander_+0x73ce) [0x4c6ec2]
[ubuntu-desktop:18265] [ 4] /home/userid/Documents/amber10/exe/sander.MPI(MAIN__+0xf0a) [0x4bfa66]
[ubuntu-desktop:18265] [ 5] /home/userid/Documents/amber10/exe/sander.MPI(main+0x2c) [0x88309c]
[ubuntu-desktop:18265] [ 6] /lib/ [0x2ba00348c466]
[ubuntu-desktop:18265] [ 7] /home/userid/Documents/amber10/exe/sander.MPI [0x43a649]
[ubuntu-desktop:18265] *** End of error message ***
mpirun noticed that job rank 0 with PID 18262 on node ubuntu-desktop exited on signal 11 (Segmentation fault).
3 additional processes aborted (not shown)
./Run.cnstph:  Program error
make[1]: *** [test.sander.GB] Error 1
make[1]: Leaving directory `/home/userid/Documents/amber10/test'
make: *** [test.sander.GB.MPI] Error 2

Errors like this one scare me to no end, especially when the error seems to be in the proper termination of a process (such as writing final positions or data files) and you risk such errors occurring after 2 week simulations with no way to get your data back.  If you decide (if it's already installed, for instance) to use OpenMPI 1.2.x with Amber10 but still want to test the build, I'd suggest simply commenting out (#) the line

# cd cnstph && ./Run.cnstph

from the Makefile in the ../test directory.  I can't imagine this happens in all other distributions, but I also don't know what the problem could be given that all of the other tests work just fine.  That said, there's a failed test for the OpenMPI 1.3.x build as well when you forget to run the tests from csh, but that has nothing to do with OpenMPI (see below).

16 – 19 Building Amber10 and AmberTools At $HOME

As described in the 3 – 9 section above, the problem with not building in your $HOME directory is the passing of variables in the build processes.  For instance, if you set MPI_HOME in your $HOME .bashrc file and then sudo make parallel, the error you'll see is

Starting installation of Amber10 (parallel) at Mon Mar  9 22:30:36 EDT 2009.
cd sander; make parallel
make[1]: Entering directory `/opt/amber10/src/sander'
cpp -traditional -I/usr/local/include -P -xassembler-with-cpp -Dsecond=ambsecond -DBINTRAJ -DMPI  constants.f > _constants.f
/usr/local/bin/mpif90 -c -O3 -fno-range-check -fno-second-underscore -ffree-form  -o constants.o _constants.f
Cannot open configuration file /usr/share/openmpi/mpif90-wrapper-data.txt
Error parsing data file mpif90: Not found
make[1]: *** [constants.o] Error 243
make[1]: Leaving directory `/opt/amber10/src/sander'
make: *** [parallel] Error 2

because the MPI_HOME variable is not specified for root.  Performing the compilation in $HOME/Documents avoids this issue.

If you want to build Amber and AmberTools in /opt as root for some reason and do not want to deal with modifying the .bashrc and .profile files in /root, you can modify the appropriate Amber files to define the variables needed for both building and testing. For AmberTools testing, you need to define AMBERHOME, which you do at the top of Makefile_at.

cd ../test/

sudo pico Makefile_at

include ../src/config.h


test: is_amberhome_defined \

sudo make -f Makefile_at test

For the Amber10 build process, you would need to modify configure_amber at the top of the file to specify the MPI_HOME variable.

sudo pico configure_amber

#set -xv

export MPI_HOME

command="$0 $*"

For the Amber10 testing process, you would need to assign both AMBERHOME (so the tests know where to look for the executables) and DO_PARALLEL (so the tests know to use OpenMPI) at the top of the file.

cd ../test/

sudo pico Makefile

include ../src/config_amber.h


DO_PARALLEL=mpirun -np 4


It otherwise makes no difference at all how you choose to do things so long as the program gets built.  Much of the Ubuntu literature I've stumbled across attempts to make people avoid doing anything to change the root account settings, which was the approach I chose to use in the "Easy" procedure above.

20 – 21 Patching Amber10 and AmberTools 1.2

No surprises and not necessary for building.  Do it anyway.  And patch is included as one of the apt-get'ed programs.  Simply be cognizant of the naming of the bugfix files (the directories are the same for both Amber10 and AmberTools and the patch is simply applied to the files it finds).

22 – 24 Building AmberTools

Your choices for the AmberTools build are fairly limited.  Via configure_at –help,

Usage: ./configure_at [flags] compiler

where compiler is one of:

gcc, icc, solaris_cc, irix_cc, osf1_cc

If not specified then gcc is used.

Option flags:

-mpi        use MPI for parallelization
-scalapack  use ScaLAPACK for linear algebra (utilizes MPI)
-openmp     Use OpenMP pragmas for parallelization (icc, solaris_cc,gcc(>4.2))
-opteron    options for solaris/opteron
-ultra2     options for solaris/ultra2
-ultra3     options for solaris/ultra3
-ultra4     options for solaris/ultra4
-bit64      64-bit compilation for solaris
-perflib    Use solaris performance library in lieu of LAPACK and BLAS
-cygwin     modifications for cygwin/windows
-p4         use optimizations specific for the Intel Pentium4 processor
-altix      use optimizations specific for the SGI Altix with icc
-static     create statically linked executables
-noX11      Do not build programs that require X11 libraries, e.g. xleap.
-nobintraj  Delete support for binary (netCDF) trajectory files
-nosleap    Do not build sleap, which requires unantiquated compilers.

Environment variables:
MKL_HOME    If present, will link in Intel's MKL libraries (icc,gcc)
GOTO        If present, and MKL_HOME is not set, will use this location
for the Goto BLAS routines

We're building gcc (default) with the above installs.  Running ./configure -noX11 with the apt-get-installed programs above should produce the following output.

Setting AMBERHOME to /home/userid/Documents/amber10

Testing the C compiler:
mpicc  -m64 -o testp testp.c

Obtaining the C++ compiler version:
g++ -v
The version is ../src/configure
[: 520: 3: unexpected operator

Testing the g77 compiler:
g77 -O2 -fno-automatic -finit-local-zero -o testp testp.f
./configure_at: 538: g77: not found
./configure_at: 539: ./testp: not found
Unable to compile a Fortran program using g77 -O2 -fno-automatic -finit-local-zero

Testing the gfortran compiler:
gfortran -O1 -fno-automatic -o testp testp.f

Testing flex:

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'

25 – 28 Testing AmberTools

As a quick head's up, if you don't have csh installed, your test will fail at the following step with the following error:

cd ptraj_rmsa && ./Run.rms
/bin/sh: ./Run.rms: not found
make: *** [test.ptraj] Error 127

Otherwise, you can see the output from my test set HERE.  Installing csh is much easier than modifying multiple Run scripts.

That said, the one fix I do perform is to modify the file only slightly in accordance with the post by Mark Williamson on the Vanderbilt University Amber Listserve (the first stumbling block a ran into during testing).

29 – 31 Building Parallel Amber10

Running ./configure_amber -openmpi gfortran should output the following:

Setting AMBERHOME to /home/userid/Documents/amber10

Setting up Amber configuration file for architecture: gfortran
Using parallel communications library: openmpi
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

Testing the Fortran compiler:
gfortran -O0 -fno-range-check -fno-second-underscore -o testp testp.f

——   Configuring the netCDF libraries:   ——–

Configuring netcdf; (may be time-consuming)
NETCDF configure succeeded.
MPI_HOME is set to /

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

32 – 35 Automatic ssh Login

These step saves you from constantly having to input your password for the mpirun testing phase.  This strictness to password provision is because of ssh (and, because I have machines both online and accessible, I prefer to deal with setting up the ssh side right instead of not having that layer of security).  The first time you run mpirun, ssh will throw back at you the following:

The authenticity of host ‘userid-desktop (' can't be established.
RSA key fingerprint is eb:86:24:66:67:0a:7a:7b:44:95:a6:83:d2:a8:68:01.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added ‘terahertz-desktop' (RSA) to the list of known hosts.

Generating the automatic login file for ssh will look like the following:

Generating public/private dsa key pair.
Enter file in which to save the key (/home/userid/.ssh/id_dsa):
Created directory '/home/userid/.ssh'.
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/userid/.ssh/id_dsa.
Your public key has been saved in /home/userid/.ssh/
The key fingerprint is:
54:84:68:79:3b:ec:17:41:c9:96:98:10:df:4f:cc:42 userid@userid-desktop
The key's randomart image is:
+–[ DSA 1024]—-+

36 – 40 Testing Amber10

If you're not in csh, either this test fails…

cd rdc && ./Run.dip
if: Badly formed number.
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/home/userid/Documents/amber10/test'
make: *** [test.sander.BASIC.MPI] Error 2

or this one…

cd pheMTI && ./Run.lambda0
This test must be run in parallel
make: *** [test.sander.TI] Error 1

Again, re-writing scripts is far less fun than sudo apt-get install csh and forgetting about it.

41 – 47 Moving The Built Amber10 and AmberTools

The final sequence of steps moves the $HOME/Documents-built amber10 into /opt (if you choose to), removes the build from your $HOME directory, and resets your PATH and AMBERHOME variables in .bashrc and .profile, thereby completing the build process.

And Finally…

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.

Building Abinit 5.6.5 (And Other Versions) And OpenMPI 1.3 (And Others) From Sources In Ubuntu 8.10 (Intrepid Ibex)

NOTE 25 March 2009: The problem with Open-MPI and Abinit is related to the version of Open-MPI.  1.3.x is used below, while 1.2.x allows you to use the .files for running batch-based Abinit calculations.  See for additional notes.

The purpose of the HPLIP fix reported in a previous post was to install Abinit in Ubuntu via apt-get in order to employ the procedure used by Hooper et al in Chemical Physics Letters to calculate infrared intensities in the low-frequency region for solid-state terahertz (THz) assignments (phew!).  The problem is that the apt-get install of Abinit is an older and serial (non-parallel) version.  Further compounding the problem, the OpenMPI version one can install via apt-get (sudo apt-get install openmpi-bin) does not have F90 (Fortran 90) support, so one cannot simply install OpenMPI, install one of the pre-compiled versions of Abinit, and start using those other processors either on the board or plugged into a gigabit switch.

As long as you're building one from source anyway, you might as well build them both.  As has been the case in several of my previous posts involving code compilation, the procedure below assumes as little as possible from you (the code builder).  The scientific audience that potentially serves to gain the most from the procedure is, in my past experience, in need of as much detail as possible to explain what is happening and to spell it out in enough detail that ANYONE could do it.  While I'm a great fan of Open Source Software, I think the best way to make an academic software novice go to a catalog and buy GUI-based computational chemistry software is to tell them only to ./configure, make, and make install.


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 (taken from HERE)

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

Step 1. Install Ubuntu 8.10 Desktop or Server (borrowed from HERE)

Default installation, simply walk through the entire installation process. For DHCP people, this should be no problem once the machine reboots.  I've been having an odd issue with the fixed IP address machine I'm working on that I provide the workaround for below (which, hopefully, you do not need, but it reminds me to diagnose it properly later).  Specifically, IP information was not being saved for edited connections.  I don't know if this is GUI-related (not saving changes) or permission-related (not being allowed to make persistent changes).  As a quick ifconfig fix described in more detail HERE (eth0 being your ethernet card (likely eth0 if you've only one card), 128.230.XXX.XXX is half my local IP address + half none of your business, and gw is the gateway for your subnet (probably XXX.XXX.XXX.1)):

sudo ifconfig eth0 down
sudo ifconfig eth0 128.230.XXX.XXX netmask up
sudo route add default gw 128.230.XXX.XXX

Step 2. Terminal (stolen from HERE)

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 (evolved from HERE)

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 Abinit, 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 g++ gfortran autoconf patch csh netcdf-bin [continued on next line]
ssh libblas3gf liblapack3gf libgfortran2 

This installs seven base programs and many additional programs and libraries (for the record, I did not need to install libblas3gf, liblapack3gf, or libgfortran2 to successfully compile both OpenMPI and Abinit on my first attempt, but the Abinit version available by apt-get lists these libraries at dependencies and they did not appear to be installed on the original Ubuntu installation but are clearly there upon compilation (which I assume means they are provided and compiled as needed by Abinit), so this is just an extra "what if?" safety on my part). For those that do not know, you discover which of these programs are required by running an installation, reading the output when the build fails, installing the necessary programs, then cycling through the install-fail step until you get to the end.

Why gfortran?  or, why not fort77?  In the compilation of Amber10, I had some issue with running the tests using gfortran that required script modification I was not inclined to attempt.  In trying to build OpenMPI, I received the following error that, you guessed it, went away using gfortran (yes, only the bottom line is of any relevance, but using the whole section does fill the page out a bit).

*** Fortran 77 compiler
checking for gfortran… no
checking for g77… no
checking for f77… f77
checking whether we are using the GNU Fortran 77 compiler… yes
checking whether f77 accepts -g… yes
checking if Fortran 77 compiler works… yes
checking f77 external symbol convention… double underscore
checking if C and Fortran 77 are link compatible… yes
checking to see if F77 compiler likes the C++ exception flags… skipped (no C++ exceptions flags)
checking if Fortran 77 compiler supports LOGICAL… yes
checking size of Fortran 77 LOGICAL… 4
checking for C type corresponding to LOGICAL… int
checking alignment of Fortran LOGICAL… 4
checking if Fortran 77 compiler supports LOGICAL*1… yes
checking size of Fortran 77 LOGICAL*1… 1
checking for C type corresponding to LOGICAL*1… char
checking alignment of Fortran LOGICAL*1… 1
checking if Fortran 77 compiler supports LOGICAL*2… yes
checking size of Fortran 77 LOGICAL*2… 2
checking for C type corresponding to LOGICAL*2… short
checking alignment of Fortran LOGICAL*2… 2
checking if Fortran 77 compiler supports LOGICAL*4… yes
checking size of Fortran 77 LOGICAL*4… 4
checking for C type corresponding to LOGICAL*4… int
checking alignment of Fortran LOGICAL*4… 4
checking if Fortran 77 compiler supports LOGICAL*8… no
checking if Fortran 77 compiler supports INTEGER… yes
checking size of Fortran 77 INTEGER… 4
checking for C type corresponding to INTEGER… int
checking alignment of Fortran INTEGER… 4
checking if Fortran 77 compiler supports INTEGER*1… yes
checking size of Fortran 77 INTEGER*1… 1
checking for C type corresponding to INTEGER*1… char
checking alignment of Fortran INTEGER*1… 1
checking if Fortran 77 compiler supports INTEGER*2… yes
checking size of Fortran 77 INTEGER*2… 2
checking for C type corresponding to INTEGER*2… short
checking alignment of Fortran INTEGER*2… 2
checking if Fortran 77 compiler supports INTEGER*4… yes
checking size of Fortran 77 INTEGER*4… 4
checking for C type corresponding to INTEGER*4… int
checking alignment of Fortran INTEGER*4… 4
checking if Fortran 77 compiler supports INTEGER*8… yes
checking size of Fortran 77 INTEGER*8… configure: error: Could not determine size of INTEGER*8

Admittedly, switching compilers is not much of a proper fix when either should work, but, since this install revolves around apt-get anyway, I decided to not dig any further into script modification than I needed to (so you don't have to, either).

autoconf and netcdf-bin are required for the Abinit build (well, autoconf for the makemake step).

You don't realize you need ssh until you try to run a parallel instance of OpenMPI and get the error below (I reproduce the error in total below because someone will invariably search based on some part of the error message.  Hope this explains it!  You can compile OpenMPI without ssh, but ssh is more generally useful than you might initially realize, so might as well have it installed from the get-go):

ssh: connect to host [machine] port 22: Connection refused
A daemon (pid 27364) died unexpectedly with status 255 while attempting
to launch so we are aborting.

There may be more information reported by the environment (see above).

This may be because the daemon was unable to find all the needed shared
libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
location of the shared libraries on the remote nodes and this will
automatically be forwarded to the remote nodes.
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
mpirun: clean termination accomplished

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

Step 4: .profile Modifications

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.  You will note that the new directory that Abinit creates after building is (with the building in /opt) /opt/etsf/abinit/5.6/, which is fine with me (that's what the PATH specification below is for and, as long as it stays in /opt, I'm not bothered with the location).


(or cd $HOME, but the default operation for cd is to return you to your home directory)

pico .profile

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


Again, this changes if you want the Abinit executables somewhere else.  As for the library specification, I'll cover that below.

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

To make these changes to your account, make sure you're in your home directory…

source .profile

Step 5. Installing g95 (lifted from HERE)

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 Abinit (and you can simply install the other flavor over the old one).

At, 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.

Step 6. Installing OpenMPI 1.3

It is hoped that this step is also the missing piece for the Amber10 parallel build which may or may not be appearing shortly on this website (if it works).  OpenMPI is the MPI (message passing interface) program used as the conduit through which a number of comp. chem. programs distribute calculations over multiple processors (both on the same board (SMP) and between machines on a network).  I suspect MPICH and MPICH2 are just as well, but OSX uses OpenMPI and the pre-compiled Abinit binaries work through OpenMPI (which I expect will continue to be the case for future versions of the program).  Once THIS version of OpenMPI is compiled (with F90 support via g95), I suspect you should be all set for future Abinit versions.

With gfortran and g95 properly installed, the build of OpenMPI 1.3 is trivial.  Simply download the OpenMPI source (which, with Firefox, will likely place it on the Desktop) and move the source to /opt to begin the build.

sudo cp ~/Desktop/openmpi-1.3.tar.gz /opt/
cd /opt
sudo tar xvjf openmpi-1.3.tar.gz

will make a folder openmpi-1.3 in opt/

cd openmpi-1.3


A considerable amount of output follows.  To see what an otherwise flawless installation looks like, you can view my output HERE.

sudo make all install

A considerable amount of output follows.  To see what an otherwise flawless installation looks like, you can view my output HERE.

There is one more step for the Abinit build that I would have expected to be handled by the specification of  LD_LIBRARY_PATH in .profile but are not.  There are several MPI libraries that Abinit needs for its parallel compilation that are placed in /usr/local/lib without links to those libraries placed anywhere else.  Abinit seems to force itself to look in /lib.  The fix is either to place the files below into /lib or to make links (ln -s).  I opted to simply copy them into /lib.  And you learn this list of files the hard way (four build attempts of Abinit with errors for each of the file sets below).

sudo cp /usr/local/lib/libopen-pal.* /lib
sudo cp /usr/local/lib/libmpi* /lib
sudo cp /usr/local/lib/libopen-rte.* /lib

Step 7. Installing Abinit 5.6.5

The relative ease with which this install occurs (after the work above) from sources is a credit to the Abinit developer community.  To begin, download the Abinit source

sudo cp ~/Desktop/abinit-5.6.5.tar.gz /opt/

cd /opt

sudo tar xvjf abinit-5.6.5.tar.gz 

will make a folder abinit-5.6.5 in opt/.  To install, we'll be going nearly by the book…

The instructions are contained in the
doc/install_notes directory .

You can find instructions in

In short, if you have bazaar installed, and got one version from
the archive, the steps are :
(1) ./config/scripts/makemake    (or */*/makemake)
(2) ./configure  (or first create a tmp directory, then cd tmp, then ../configure)
(3) ./make       (or ./make multi  for using 4 proc of an SMP machine)
Then you might also need
(4) ./make install

… with the usual sudo modifications.  the makemake step requires autoconf be installed (which we did in our apt-get install list).

cd abinit-5.6.5

sudo ./config/scripts/makemake

will generate the output provided HERE.  For the compilation of Abinit, we want mpi support, so we run ./configure as follows:

sudo ./configure --enable-mpi="yes"

With all of the compilers and libraries properly places as described above, this configure process provides the flawless output provided HERE.  To build, it is simply:

sudo make multi

will generate the output provided HERE.

Random Aside: For some reason, I tried the sudo make multi_alt build option first and received the BigDFT_API error.  Listed purely for academic reasons, but if you see this error and you used multi_alt, don't use multi_alt (because bigdft_api.mod, the associated file, shows up nowhere in google).

cd src/defs ; make
make[1]: Entering directory `/opt/abinit-5.6.5/src/defs'
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_basis.o defs_basis.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_aimfields.o defs_aimfields.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_aimprom.o defs_aimprom.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_datatypes.o defs_datatypes.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_berry.o defs_berry.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_dyson.o defs_dyson.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_elphon.o defs_elphon.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_fftdata.o defs_fftdata.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_interfaces.o defs_interfaces.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_parameters.o defs_parameters.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_scalapack.o defs_scalapack.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_suscep.o defs_suscep.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_time.o defs_time.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_wannier90.o defs_wannier90.F90
/usr/local/bin/mpif90 -DHAVE_CONFIG_H -I. -I -I -I  -I/opt/abinit-5.6.5/plugins/bigdft   -g -O2  -c -o defs_wvltypes.o defs_wvltypes.F90

use BigDFT_API
Fatal Error: Can't open module file 'bigdft_api.mod' for reading at (1): No such file or directory
make[1]: *** [defs_wvltypes.o] Error 1
make[1]: Leaving directory `/opt/abinit-5.6.5/src/defs'
make: *** [multi_alt] Error 2

sudo make install

will generate the output provided HERE.  The result is a set of executables installed in /opt/etsf/abinit/5.6/bin, which is specified in our PATH statement in .profile.

Step 8. Running Calculations With mpirun

The above was almost pleasant.  If you are running the serial version of Abinit (abinis), which is also built with the parallel installation, you simply need to type the following at a Terminal prompt.

abinis < inputfile.script >& outputfile.output

because our PATH is already specified in .profile.

MPI calculations require a bit more out of your fingers.  For the specific build I have performed here, there is also one very odd issue with the parallel run that I am still trying to work out the solution to (but it is by no means mission-critical to the proper compilation AND the workaround is dumb to put it mildly, so it hasn't stopped me from this Ubuntu/OpenMPI/Abinit post).

To run parallel Abinit on a multi-processor box (that is, SMP.  The actual multi-node cluster setup is in progress), the command is SUPPOSED to be follows:

mpirun -np N /opt/etsf/abinit/5.6/bin/abinip < input.file >& output

Where N is the number of processors.  For mpirun, you need to specify the full path to the executable (which, for the build above, is as Abinit installs abinip when thebuild occurs in the /opt directory).  The input.file specification is as per the Abinit users manual so I won't go into it here. You will also be asked to supply your password because I've done nothing to the setup of ssh (you are, in effect, logging into your machine to run the MPI calculation).

Now, when the above is run, this is the error that I get:

abinit : nproc,me=           4           0

Give name for formatted input file:
At line 127 of file iofn1.F90 (unit = 5, file = 'stdin')
Fortran runtime error: End of file
abinit : nproc,me=           4           1
abinit : nproc,me=           4           2
abinit : nproc,me=           4           3
mpirun has exited due to process rank 0 with PID 7131 on
node terahertz-desktop exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

What is supposed to happen is that the input.file file lists the files that Abinit requires to perform the run and provides these files by name one-at-a-time as Abinit requests them upon start-up.  For some reason, the input.file file is not being read properly or is not being read at all before the job crashes.  Oddities noted in the above order of the output include

(1) the abinit : nproc,me= values are not grouped above the "Give name for formatted input file:" <- Abinit does not appear to be trying to read the text from the nproc,me lines as actual input data, as you have to provide all of the files before Abinit will crash with a wrong file name.

(2) At line 127 of file iofn1.F90 <- this is an Abinit file that is repsonsible for reading the contents of input.files.  So, is the problem with this fine in Abinit? Well…

(3) The serial build of Abinit (abinis) runs just fine with input.file <- which leads me to conclude that the problem is mpirun-related.  I hope to resolve this (I'm sure it will be trivial) and post my error accordingly.

What's the work-around?  Simple.  Copy the contents of the input.file file (literally Crtl+C with the text selected) and paste it after running this command:

mpirun -np N /opt/etsf/abinit/5.6/bin/abinip

Abinit will ask for the files in order AND your Crtl+C includes the carraige returns at the end of each line, so you are effectively feeding Abinit the same content it would read from the input.file file if, in fact, it was capable of reading the input.file file.

Final Thoughts (ripped from HERE)

There will be a bit more to follow, perhaps significantly more if the Intel Fortran Compiler yields a considerable speed-up in calculation times as reported by Torsten Hoefler in his Abinit-specific survey of compilers and parallelization codes.  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.…