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Compiling LAMMPS (3Apr13, But Likely Others) In Ubuntu 10.04 Part 1. Using MPICH2 And FFTW2 (And Ubuntu Notes On Installing Intel Fortran And C++ Composers XE for Linux)

Saturday, April 6th, 2013

I’ll qualify this post by saying that (1) I have given up on Ubuntu 11.x and 12.x because they are consistently unstable on my hardware (so, if you have issues running this installation on those versions, I may not be of much help (although I suspect things should work)), (2) I am starting this install from a fresh 32-bit Desktop Ubuntu 10.04 install (so do not know if there are any issues with other software one might have installed on a Linux box if a problem comes up), and (3) the procedure comes out of the current lack of an Ubuntu binary currently listed as available (as of 6 April 2013) from the LAMMPS website (lammps.sandia.gov/download.html#ubuntu). If (3) changes and is available in an MPI form, what’s below will hopefully be unnecessary.

Building Trouble And Solutions

My initial “just unzip, untar, and make linux” attempt on a fresh 10.04 install produced the following error (which I’m reproducing in the expectation that you found this page by typing one of the errors below into a search engine, so you’ll find the error and the solutions). NOTE: I build all my programs in /opt for organizational purposes (so replace accordingly):

user@machine:/opt/lammps-3Apr13/src$ sudo make linux

make[1]: Entering directory `/opt/lammps-3Apr13/src/Obj_linux'
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_restart.cpp > write_restart.d
/bin/sh: icc: not found
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_data.cpp > write_data.d
/bin/sh: icc: not found
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../verlet.cpp > verlet.d
/bin/sh: icc: not found
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../velocity.cpp > velocity.d
/bin/sh: icc: not found
...
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../angle_charmm.cpp > angle_charmm.d
/bin/sh: icc: not found
icc -O  -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -c ../angle_charmm.cpp
make[1]: icc: Command not found
make[1]: *** [angle_charmm.o] Error 127
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'
make: *** [linux] Error 2

Obviously, problem Number 1 is the lack of the Intel C Compiler (icc). My solution to this was to download the non-commercial version of the Intel C++ Composer XE for Linux (then I grabbed the Intel Fortran Composer XE for Linux because, well, why not?) currently available from software.intel.com/en-us/non-commercial-software-development (which means this link may be subject to change, so search for “intel c++ noncommercial” in the event).

Unzipping, untaring, and running ./install.sh will, on a fresh Ubuntu install, give you errors that g++ and a proper Java runtime environment are not available on the computer (as part of the pre-requisite search). This is easily solved before the Intel installs by the following (one of which is needed for LAMMPS anyway). I specifically chose the openJDK, but Java 6 or 7 should also do.

sudo apt-get install build-essential openjdk-6-*

After these installs, both Intel Composers should install just fine. If you’re installing LAMMPS into a directory that you, the user, has access to, then adding /opt/intel/bin to your PATH will provide you no compiler errors (related to location). If you attempt to install LAMMPS in a directory you, the user, do not have access to, you have to run the install with sudo, which then doesn’t likely have the /opt/intel/bin directory in the root PATH, in which case the solution is simply to add a symbolic link for icc into /user/local/bin.

sudo ln -s /opt/intel/bin/icc /usr/local/bin

With icc accessible, running another sudo make linux produces the following errors:

sudo make clean-all
sudo make linux

make[1]: Entering directory `/opt/lammps-3Apr13/src/Obj_linux'
icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_restart.cpp > write_restart.d
../write_restart.cpp(15): catastrophic error: cannot open source file "mpi.h"
  #include "mpi.h"
                  ^

icc -O -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_data.cpp > write_data.d
../write_data.cpp(15): catastrophic error: cannot open source file "mpi.h"
  #include "mpi.h"
                  ^
...

icc -O  -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -c ../angle_charmm.cpp
../pointers.h(25): catastrophic error: cannot open source file "mpi.h"
  #include "mpi.h"
                  ^

compilation aborted for ../angle_charmm.cpp (code 4)
make[1]: *** [angle_charmm.o] Error 4
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'
make: *** [linux] Error 2

The new problem is now an MPI problem, requiring the installation of (as recommended from the LAMMPS linux Makefile) MPICH. Reading the Makefile (you mean you didn’t check this first?) also indicates the need for FFTW2. We can install all of the needed files in one shot with apt-get (and I include build-essential here for completeness, as you either did or didn’t install it while trying to solve the icc problem above).

sudo apt-get install build-essential mpich-bin libmpich1.0-dev mpi-doc fftw2 fftw-dev libxaw7-dev libmpich2-dev

This still does not solve the mpi.h issue above, which is a problem with the settings in Makefile.linux (which, apparently, are not Ubuntu-compatible). The solution is, and this is why this is Part 1, to change Makefile.linux to make it compatible with the mpicc compiler in Ubuntu (I will attempt to get it working with icc next). The tweak to my Makefile.linux is provided below (an amalgam of some other Makefile settings. Comment out or delete what’s there and add the sections without the “#” to the file):

#######################################################################
## My modified settings are below:

CC = mpicxx
CCFLAGS = -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK
DEPFLAGS =	-M

LINK = $(CC)
LINKFLAGS = -O
SIZE = size

USRLIB = -lfftw

ARCHIVE =	ar
ARFLAGS =	-rc

#######################################################################
## Comment the following out or delete them:

# CC =		icc
# CCFLAGS =	-O
# SHFLAGS =	-fPIC
# DEPFLAGS =	-M

# LINK =		icc
# LINKFLAGS =	-O
# LIB =           -lstdc++
# SIZE =		size

# ARCHIVE =	ar
# ARFLAGS =	-rc
# SHLIBFLAGS =	-shared

I will say that, in some of my searches, I found reference to the use of USRLIB -lmpi. If this is included in the Makefile.linux, you will get the following error upon mpicc (MPICH2) compilation:

/usr/bin/ld: cannot find -lmpl
collect2: ld returned 1 exit status
make[1]: *** [../lmp_linux] Error 1
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'
make: *** [linux] Error 2

So, don’t include -lmpi.

With the above Makefile modifications, building of LAMMPS seems to go quite well until the following error is produced:

mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK  -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -c ../dump_dcd.cpp
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK  -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -c ../dump_image.cpp
../dump_image.cpp:32:21: error: jpeglib.h: No such file or directory
../dump_image.cpp: In member function ‘virtual int LAMMPS_NS::DumpImage::modify_param(int, char**)':
../dump_image.cpp:904: warning: suggest parentheses around assignment used as truth value
../dump_image.cpp:911: warning: suggest parentheses around assignment used as truth value
../dump_image.cpp:964: warning: suggest parentheses around assignment used as truth value
../dump_image.cpp:971: warning: suggest parentheses around assignment used as truth value
../dump_image.cpp: In member function ‘void LAMMPS_NS::DumpImage::create_image()':
../dump_image.cpp:611: warning: ‘diameter' may be used uninitialized in this function
../dump_image.cpp:612: warning: ‘color' may be used uninitialized in this function
../dump_image.cpp:612: warning: ‘color1' may be used uninitialized in this function
../dump_image.cpp:612: warning: ‘color2' may be used uninitialized in this function
make[1]: *** [dump_image.o] Error 1
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'
make: *** [linux] Error 2

The jpeglib.h error can likely be solved by installing only one of the libraries below, but I didn’t bother to identify which one, instead indiscriminately installing a whole set based on the recommendation of dev.xonotic.org/projects/xonotic/wiki/Repository_Access (having found this link at forums.xonotic.org/showthread.php?tid=1252 – but I removed some of the install that I’m sure was not needed):

sudo apt-get install libxxf86dga-dev libxcb-xf86dri0-dev libxpm-dev libxxf86vm-dev libsdl1.2-dev libsdl-image1.2-dev libclalsadrv-dev libasound2-dev libxext-dev

Finally, a successful build!

make[1]: Entering directory `/opt/lammps-3Apr13/src/Obj_linux'
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_restart.cpp > write_restart.d
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../write_data.cpp > write_data.d
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../verlet.cpp > verlet.d
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../velocity.cpp > velocity.d
mpicxx -O -DFFT_FFTW -DLAMMPS_GZIP -DMPICH_IGNORE_CXX_SEEK -DLAMMPS_GZIP -DLAMMPS_JPEG  -DMPICH_SKIP_MPICXX  -DFFT_FFTW   -M ../variable.cpp > variable.d
…
write_data.o write_restart.o  -lmpich -lpthread -lfftw -ljpeg   -o ../lmp_linux
size ../lmp_linux
   text	   data	    bss	    dec	    hex	filename
3654398	   6928	    264	3661590	 37df16	../lmp_linux
make[1]: Leaving directory `/opt/lammps-3Apr13/src/Obj_linux'

At this point, you can move the lmp_linux executable anywhere (or, as I find myself doing, just keep it in the lammps-DATE/src folder for when you perform subsequent builds).

Running An MPI Calculations

If you’ve never run through an MPI calculation, you’ll get the following errors when you first try to run lmp_linux:

cannot connect to local mpd (/tmp/mpd2.console_user); possible causes:
  1. no mpd is running on this host
  2. an mpd is running but was started without a "console" (-n option)
In case 1, you can start an mpd on this host with:
    mpd &
and you will be able to run jobs just on this host.
For more details on starting mpds on a set of hosts, see
the MPICH2 Installation Guide.

**********

user@machine:/opt/lammps-3Apr13/src$ mpd &

configuration file /home/damianallis/.mpd.conf not found
A file named .mpd.conf file must be present in the user's home
directory (/etc/mpd.conf if root) with read and write access
only for the user, and must contain at least a line with:
MPD_SECRETWORD=
One way to safely create this file is to do the following:
  cd $HOME
  touch .mpd.conf
  chmod 600 .mpd.conf
and then use an editor to insert a line like
  MPD_SECRETWORD=mr45-j9z
into the file.  (Of course use some other secret word than mr45-j9z.)

[1]+  Exit 255                mpd

Simply follow the instructions to put a .mdp.conf in your ~/ folder, start mpd with “mpd &,” and run LAMMPS with the following command below (which uses 2 cores (-np 2)).

NOTE: My LAMMPS test (being brand new to it) was to run the first test available from icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_Help. Following the instructions therein (DOWNLOAD: Al99.eam.alloy (780 KB) and calc_fcc.in (1 KB)):

sudo mpirun -np 2 ./lmp_linux < calc_fcc.in

Which should produce the following output:

LAMMPS (3 Apr 2013)
Lattice spacing in x,y,z = 4 4 4
Created orthogonal box = (0 0 0) to (4 4 4)
  1 by 1 by 2 MPI processor grid
Lattice spacing in x,y,z = 4 4 4
Created 4 atoms
Replicating atoms ...
  orthogonal box = (0 0 0) to (4 4 4)
  1 by 1 by 2 MPI processor grid
  4 atoms
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
Setting up minimization ...
Memory usage per processor = 2.40372 Mbytes
Step PotEng Lx Ly Lz Press Pxx Pyy Pzz eatoms 
       0   -13.417787            4            4            4     29590.11     29590.11     29590.11     29590.11   -13.417787 
      10   -13.439104         4.04         4.04         4.04    5853.9553    5853.9553    5853.9553    5853.9553   -13.439104 
      14       -13.44         4.05         4.05         4.05     2.726913     2.726913     2.726913     2.726913       -13.44 
Loop time of 0.0287241 on 2 procs for 14 steps with 4 atoms

Minimization stats:
  Stopping criterion = linesearch alpha is zero
  Energy initial, next-to-last, final = 
        -13.4177872966     -13.4399999525     -13.4399999525
  Force two-norm initial, final = 3.54599 0.000335006
  Force max component initial, final = 3.54599 0.000335006
  Final line search alpha, max atom move = 0.0625 2.09379e-05
  Iterations, force evaluations = 14 19

Pair  time (%) = 0.00206506 (7.18931)
Neigh time (%) = 0 (0)
Comm  time (%) = 0.00481999 (16.7803)
Outpt time (%) = 0.000162005 (0.564006)
Other time (%) = 0.021677 (75.4664)

Nlocal:    2 ave 2 max 2 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost:    603 ave 603 max 603 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Neighs:    140 ave 162 max 118 min
Histogram: 1 0 0 0 0 0 0 0 0 1

Total # of neighbors = 280
Ave neighs/atom = 70
Neighbor list builds = 0
Dangerous builds = 0
Total energy (eV) = -13.439999952539944061;
Number of atoms = 4;
Lattice constant (Angstoms) = 4.049999999999998046;
Cohesive energy (eV) = -3.3599999881349860154;
All done!

ChemMedChem Cover For April 2013 – Treating Type II Diabetes Through B12 Conjugation

Saturday, March 23rd, 2013

The back cover picture shows two views at 150 degree rotation of vitamin B12 conjugated to the potent anti- hyperglycemia peptide glucagon-like peptide-1 (GLP-1). The conjugate displays similar receptor binding and agonism to unconjugated GLP-1, including insulin potentiation from human transplant pancreatic islet cells, which bodes well for oral delivery of GLP-1 through the B12 dietary pathway. For more details, see the Communication by Robert P. Doyle et al. on p. 582 ff.

From the free press department… The cover for the April, 2013 issue of ChemMEDChem (just the cover art this time, no theoretical content in the associated article. All the theory’s figured out!). I’m still awaiting the journal’s posting of the article content but wanted to get something up in March. For related content, see the discussion on the “MedChemComm September 2012 Front Cover Image For The ‘Examining The Effects Of Vitamin B12 Conjugation…’ Paper” post or any of the B12-related posts on this site (www.somewhereville.com/index.php?s=b12). This work is similar in scope to the B12-insulin bioconjugate work in the previous studies, but now includes a different peptide (glucagon-like peptide-1) with similar properties.

NAMOT Pre-Release 2.2.0-pre4 In OSX 10.8 (Maybe Older Versions)

Sunday, January 13th, 2013

A recent visit to the College of Nanoscale Science and Engineering (CNSE) at SUNY Albany inspired a few new DNA ideas that I decided would be greatly simplified by having NAMOT available again for design. Having failed at the base install of the NAMOT 2 version and, unfortunately, not having NAMOT available in Fink for a simple installation, the solution became to build the pre-release from scratch. Ignoring the many errors one encounters while walking through an OSX/Xcode/Fink/X11 bootstrap, the final procedure worked well and without major problem. As usual, the error messages at varied steps are provided below because, I assume, those messages are what you’re searching for when you find your way here.

0. Required Installations

You’ll need the following installed for this particular build. I believe XCode is the only thing that you’ll have to pay for (if you don’t already have it. I seem to remember paying $5 through the App Store).

1. XCode

The OSX Developer Suite – developer.apple.com/xcode

2. XQuartz

An OSX (X.Org) X Window System – xquartz.macosforge.org/landing/

3. Fink

An OSX port program for a host of Unix codes and libraries – www.finkproject.org

3a. GSL

The GNU Scientific (C and C++) Libraries – www.gnu.org/software/gsl. This will be installed with Fink.

3b. LessTif

An OSF/Motif clone (made available for OSX through Fink) – lesstif.sourceforge.net. This will be installed with Fink.

4. NAMOT2.2.0-pre4

The -pre4 is currently available (from 2003) from sourceforge.net/projects/namot/files/. I did not try -pre3 and had no luck with the official 2 release.

And, with that…

1. XCode

Blindly follow the install procedure. Several steps below deal with working around the default install locations (specifically, /sw).

2. XQuartz

If you don’t have XQuartz installed, you’re configure step…

cd Downloads
cd namot-2.2.0-pre4
./configure 

will produce the following error…

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
creating libtool
checking for X... no
checking for main in -lX11... no
NAMOT requires Xwindows

Blindly follow the XQuartz install process. After the installations, you’ll receive the same error as above. The –x-libraries= and –x-includes= additions to configure below direct the script to the proper libraries and includes.

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

Hopefully, you’ll find yourself past the first install problem and onto the second problem.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
creating libtool
checking for X... libraries /usr/X11/lib/, headers /usrX11/include/
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... no
NAMOT requires GNU Scientific Library

3. Fink

The next two codes that need to be installed are the GNU Scientific Libraries and LessTif, both of which are much easier to install using Fink. It is generally useful for many other codes as well, so a good program for any computational chemist to have on hand. The install should be non-problematic despite having to build it from source in 10.6 – 10.8 (as of January 2013). If you build with all the default settings, you’ll have no trouble after.

cd Downloads
cd fink-0.34.4
./bootstrap 

I chose the default settings throughout.

Fink must be installed and run with superuser (root) privileges. Fink can automatically try to become root when it's run from a user account. Since you're currently running this script as a normal user, the method you choose will also be used immediately for this script. Available methods:

(1)	Use sudo
(2)	Use su
(3)	None, fink must be run as root

Choose a method: [1] 

...

You should now have a working Fink installation in '/sw'. You still need package descriptions if you want to compile packages yourself. You can get them by running either of the commands: 'fink selfupdate-rsync', to update via rsync (generally preferred); or 'fink selfupdate-cvs', to update via CVS (more likely to work through a firewall).

Run '. /sw/bin/init.sh' to set up this terminal session environment to use Fink. To make the software installed by Fink available in all of your future terminal shells, add '. /sw/bin/init.sh' to the init script '.profile' or '.bash_profile' in your home directory. The program /sw/bin/pathsetup.sh can help with this. Enjoy.

Then you run the final step in Fink below:

/sw/bin/pathsetup.sh

Which will produce the following two pop-ups notifying you of shell modifications.

3a. GSL

With the install of Fink, you need to install GSL and LessTif. If you try to install either immediately after installation…

fink install gsl

…you’ll receive the following error:

Password:
Scanning package description files..........
Information about 305 packages read in 0 seconds.
no package found for "gsl"
Failed: no package found for specification 'gsl'!

Required after the installation is a fink selfupdate.

fink selfupdate

As usual, follow the default settings…

fink needs you to choose a SelfUpdateMethod.

(1)	cvs
(2)	Stick to point releases
(3)	rsync

Choose an update method [3] 
/usr/bin/find /sw/fink -name CVS -type d -print0 | xargs -0 /bin/rm -rf
fink is setting your default update method to rsync
...
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-i386
New package: dists/stable/main/binary-darwin-i386/base/base-files_1.9.13-1_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/base/fink-mirrors_0.34.4.1-1_darwin-i386.deb

Which then leads to a successful GSL install.

fink install gsl

Producing the following output…

Information about 12051 packages read in 1 seconds.
The package 'gsl' will be built and installed.
Reading build dependency for gsl-1.15-1...
Reading dependency for gsl-1.15-1...
Reading runtime dependency for gsl-1.15-1...
Reading dependency for gsl-shlibs-1.15-1...
...
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-i386
New package: dists/stable/main/binary-darwin-i386/sci/gsl-shlibs_1.15-1_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/sci/gsl_1.15-1_darwin-i386.deb

Attempting a fresh build after the GSL step…

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

…then still produces the following error:

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... no
NAMOT requires GNU Scientific Library

As mentioned above, there are a few redirects that need to be made after the XCode / Fink install to put libraries and includes where, in this case, NAMOT expects them. To perform this task, we’ll be using symbolic links.

sudo ln -s /sw/include/gsl /usr/include/
sudo ln -s /sw/lib/libgsl* /usr/lib

Now attempting a build…

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include

Gets you past the GSL issue.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
…
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... yes
checking for main in -lgsl... yes
checking for XShmCreateImage in -lXext... yes
checking for main in -lXt... yes
checking for main in -lXm... no
NAMOT requires Motif...try LessTif(http://www.lesstif.org)

3b. LessTif

The LessTif symbolic links work the same as the GSL symbolic links. This fink install may take a while.

fink install lesstif

Output below…

Information about 12051 packages read in 1 seconds.
The package 'lesstif' will be built and installed.
Reading build dependency for lesstif-0.95.2-4...
Reading dependency for lesstif-0.95.2-4...
Reading runtime dependency for lesstif-0.95.2-4...
...
Setting up lesstif (0.95.2-4) ...
Clearing dependency_libs of .la files being installed

Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-i386
New package: dists/stable/main/binary-darwin-i386/x11/app-defaults_20010814-12_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/x11/lesstif-bin_0.95.2-4_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/x11/lesstif-shlibs_0.95.2-4_darwin-i386.deb
New package: dists/stable/main/binary-darwin-i386/x11/lesstif_0.95.2-4_darwin-i386.deb
./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

But, unfortunately, the LessTif libraries are not in the expected locations.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
checking for IceConnectionNumber in -lICE... yes
checking for main in -lX11... yes
checking for main in -lgslcblas... yes
checking for main in -lgsl... yes
checking for XShmCreateImage in -lXext... yes
checking for main in -lXt... yes
checking for main in -lXm... no
NAMOT requires Motif...try LessTif(http://www.lesstif.org)

So we add the symbolic links…

sudo ln -s /sw/lib/libXm.* /usr/lib
sudo ln -s /sw/include/Xm /usr/include

Which, finally, runs configure…

./configure --x-libraries=/usr/X11/lib/ --x-includes=/usrX11/include/

…with no errors.

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
...
config.status: creating docs/demos/curve/Makefile
config.status: creating docs/demos/dit/Makefile
config.status: creating docs/demos/Makefile
config.status: creating config.h
config.status: executing depfiles commands

NOTE: The make step with Python 2.6 produces the following error below. I did not diagnose this beyond the failure to build under 10.6. OSX 10.8 comes with Python 2.7, which did not produce this problem (I’m assuming this is the origin of the problem).

make

…will produce the following error at the pngwriter.c step.

/bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I..    -DLIB_HOME="\"/usr/local/share/namot\"" -DHELP_FILE_DIR="\"/usr/local/share/namot\"" -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -I/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/config -g -O2 -c -o _pynamot_la-pngwriter.lo `test -f 'pngwriter.c' || echo './'`pngwriter.c
gcc -DHAVE_CONFIG_H -I. -I. -I.. -DLIB_HOME=\"/usr/local/share/namot\" -DHELP_FILE_DIR=\"/usr/local/share/namot\" -I/System/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -I/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/config -g -O2 -c pngwriter.c -MT _pynamot_la-pngwriter.lo -MD -MP -MF .deps/_pynamot_la-pngwriter.TPlo  -fno-common -DPIC -o _pynamot_la-pngwriter.lo
pngwriter.c: In function 'dump_PNG':
pngwriter.c:28: error: 'png_structp' undeclared (first use in this function)
pngwriter.c:28: error: (Each undeclared identifier is reported only once
pngwriter.c:28: error: for each function it appears in.)
pngwriter.c:28: error: expected ';' before 'png_ptr'
pngwriter.c:29: error: 'png_infop' undeclared (first use in this function)
pngwriter.c:29: error: expected ';' before 'info_ptr'
pngwriter.c:30: error: 'png_byte' undeclared (first use in this function)
pngwriter.c:30: error: 'row_pointers' undeclared (first use in this function)
pngwriter.c:30: error: expected expression before ')' token
pngwriter.c:31: error: 'png_text' undeclared (first use in this function)
pngwriter.c:31: error: expected ';' before 'text_ptr'
pngwriter.c:39: warning: incompatible implicit declaration of built-in function 'memset'
pngwriter.c:39: error: 'text_ptr' undeclared (first use in this function)
pngwriter.c:47: error: 'png_ptr' undeclared (first use in this function)
pngwriter.c:47: error: 'PNG_LIBPNG_VER_STRING' undeclared (first use in this function)
pngwriter.c:48: error: 'png_voidp' undeclared (first use in this function)
pngwriter.c:57: error: 'info_ptr' undeclared (first use in this function)
pngwriter.c:60: error: 'png_infopp' undeclared (first use in this function)
pngwriter.c:82: error: 'PNG_COLOR_TYPE_RGB' undeclared (first use in this function)
pngwriter.c:82: error: 'PNG_INTERLACE_ADAM7' undeclared (first use in this function)
pngwriter.c:83: error: 'PNG_COMPRESSION_TYPE_DEFAULT' undeclared (first use in this function)
pngwriter.c:83: error: 'PNG_FILTER_TYPE_DEFAULT' undeclared (first use in this function)
pngwriter.c:85: error: 'PNG_sRGB_INTENT_ABSOLUTE' undeclared (first use in this function)
pngwriter.c:90: error: 'PNG_TEXT_COMPRESSION_NONE' undeclared (first use in this function)
pngwriter.c:93: error: 'PNG_TEXT_COMPRESSION_zTXt' undeclared (first use in this function)
pngwriter.c:104: error: expected expression before ')' token
make[2]: *** [_pynamot_la-pngwriter.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

The build on 10.8 continues as below, with a few warnings about the symbolic link usage that do not seem to affect the program usability (or continued build).

make

Results below…

make  all-recursive
Making all in src
source='namot_wrap.c' object='_pynamot_la-namot_wrap.lo' libtool=yes \
	depfile='.deps/_pynamot_la-namot_wrap.Plo' tmpdepfile='.deps/_pynamot_la-namot_wrap.TPlo' \
	depmode=gcc3 /bin/sh ../depcomp \
	/bin/sh ../libtool --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I..    -DLIB_HOME="\"/usr/local/share/namot\"" -DHELP_FILE_DIR="\"/usr/local/share/namot\"" -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -I/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/config -g -O2 -c -o _pynamot_la-namot_wrap.lo `test -f 'namot_wrap.c' || echo './'`namot_wrap.c

...

*** Warning: linker path does not have real file for library -lXm.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libXm and none of the candidates passed a file format test
*** using a file magic. Last file checked: /sw/lib/libXm.la

*** Warning: linker path does not have real file for library -lgsl.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libgsl and none of the candidates passed a file format test
*** using a file magic. Last file checked: /sw/lib/libgsl.la

*** Warning: linker path does not have real file for library -lgslcblas.
*** I have the capability to make that library automatically link in when
*** you link to this library.  But I can only do this if you have a
*** shared version of the library, which you do not appear to have
*** because I did check the linker path looking for a file starting
*** with libgslcblas and none of the candidates passed a file format test
*** using a file magic. Last file checked: /sw/lib/libgslcblas.la

*** Warning: libtool could not satisfy all declared inter-library
*** dependencies of module _pynamot.  Therefore, libtool will create
*** a static module, that should work as long as the dlopening
*** application is linked with the -dlopen flag.

...

Making all in libs
make[2]: Nothing to be done for `all'.
Making all in docs
Making all in helpfiles
make[3]: Nothing to be done for `all'.
Making all in demos
Making all in 6way
make[4]: Nothing to be done for `all'.
Making all in bending
make[4]: Nothing to be done for `all'.
Making all in cube
make[4]: Nothing to be done for `all'.
Making all in curve
make[4]: Nothing to be done for `all'.
Making all in dit
make[4]: Nothing to be done for `all'.
make[4]: Nothing to be done for `all-am'.
make[3]: Nothing to be done for `all-am'.
Making all in etc
make[2]: Nothing to be done for `all'.

Finally, the install…

make install

Which produces the following:

Making install in src
/bin/sh ../mkinstalldirs /usr/local/lib
 /bin/sh ../libtool --mode=install /usr/bin/install -c  _pynamot.la /usr/local/lib/_pynamot.la
/usr/bin/install -c .libs/_pynamot.lai /usr/local/lib/_pynamot.la
/usr/bin/install -c .libs/_pynamot.a /usr/local/lib/_pynamot.a
ranlib /usr/local/lib/_pynamot.a
chmod 644 /usr/local/lib/_pynamot.a
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `DYLD_LIBRARY_PATH' environment variable
     during execution

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
...
/bin/sh ../mkinstalldirs /usr/local/share/namot
 /usr/bin/install -c -m 644 Namot2.512 /usr/local/share/namot/Namot2.512
 /usr/bin/install -c -m 644 Namot2.600 /usr/local/share/namot/Namot2.600
 /usr/bin/install -c -m 644 Namot2.700 /usr/local/share/namot/Namot2.700
 /usr/bin/install -c -m 644 icon1.xv /usr/local/share/namot/icon1.xv
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.

With luck, your launching of NAMOT will open XQuartz and produce a fully operational NAMOT session.

namot

And, for more assistance with producing DNA files for GROMACS, consider the Modifications To The ffG53a6.rtp And ffG53a5.rtp Residue Topology Files Required For Using GROMOS96-NAMOT-GROMACS v1, sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To GROMOS96 Format For GROMACS Topology Generation v1, and sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To ffAMBER Format For GROMACS Topology Generation v1 pages on this blog.

A Most Unlikely Obvious Molecule: DNA And Its Consequences – Slides From The CNY Skeptics Talk

Friday, November 9th, 2012

I’ve been fortunate twice this year to have the Central New York (CNY) Skeptics force me to commit to a presentation topics I thought were worth presenting. As a complement to the audio that will appear at some point on the CNY Skeptics site, I’ve posted the non-animated slides as a PDF below. And the press photo’s from a way-back Excelsior Cornet Band gig where I had too long a wait between playing and marching.


Download: DGAllis_CNY_Skeptics_DNA_Lecture_7_Nov_2012.pdf, 8.3 MB

CNY Skeptics Presents Damian Allis, Ph.D., on “A Most Unlikely Obvious Molecule: DNA And Its Consequences”

Wednesday, November 7, 2012, 7:00 pm
DeWitt Community Library at Shoppingtown Mall
Buckland Community Room

DNA is Nature’s medium of digital information storage and access from which cellular machinery produces life itself. The 60 years of advances in our understanding of DNA have run in parallel with advances in computer technology and information science, and we are now entering an age of whole-genome maps, customized diagnoses, medicines, and dosages from genetic testing, and genetic modification that may eradicate some disorders completely. From super crops to super humans, the genetic information age offers humanity many different possible outcomes. This lecture will cover some of the history, machinery, possibilities, and consequences of DNA life.

Dr. Damian Allis is a research professor in the Department of Chemistry at Syracuse University, research fellow with the Forensic and National Security Sciences Institute, and bioinformaticist for Aptamatrix, Inc. He contains approximately 20 billion miles of DNA.

GROMACS 4.5.5, OpenMPI 1.6, And FFTW 3.3.2 Compilation Under Mountain Lion (OSX 10.8) With XCode (And A Little Help From Homebrew)

Tuesday, August 28th, 2012

Minus a few glitches easily fixed with the right software, this build wasn’t bad at all (and thanks to Adam Lindsay for the title catch).

Now sitting in front of a new Core i7 MacBook Pro, one of the first compilations I wanted to have finished for new projects was GROMACS 4.5.5. As my procedure for compiling GROMACS 3.3.3 had been a highly-traveled page, I wanted to provide a brief summary of my successful 4.5.5 compilation.

A Few Piece Of Info

1. XCode

This used to be disc-download and install, now it’s available as a free download from the App Store (1.57 GB download, so plan to do something else while you wait for the download).

2. Homebrew

Having Homebrew installed in Mountain Lion made the installation of FFTW easy and OpenMPI trivial once gfortran was equally trivially installed. Therefore, to make your life easier, I can’t recommend a Homebrew installation enough. For additional install tweaks, I followed the following page: gist.github.com/1860902

Installation Procedure

1. Download gromacs 4.5.5

…and place it in your home folder (will go to Downloads most likely, drag it to your home folder for ease of building).

2. Extract into your home holder

…with a double-click, making ~/gromacs-4.5.5.

3. brew install fftw

With the install of Homebrew, you’ll simply run the following from a terminal window and produce the following output:

brew install fftw

==> Downloading http://www.fftw.org/fftw-3.3.2.tar.gz
######################################################################## 100.0%
==> ./configure --enable-single --enable-sse --enable-shared --disable-debug 
--prefix=/usr/local/Cellar/fftw/3.3.2 --enable-threads --disable-fortran
==> make install
==> make clean
==> ./configure --enable-sse2 --enable-shared --disable-debug 
--prefix=/usr/local/Cellar/fftw/3.3.2 --enable-threads --disable-fortran
==> make install
==> make clean
==> ./configure --enable-long-double --enable-shared --disable-debug 
--prefix=/usr/local/Cellar/fftw/3.3.2 --enable-threads --disable-fortran
==> make install
/usr/local/Cellar/fftw/3.3.2: 34 files, 13M, built in 2.7 minutes

4. brew install gfortran

If you don’t install gfortran FIRST and try to install OpenMPI, you’ll get the following error in Homebrew:

==> Downloading http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.tar.bz2
######################################################################## 100.0%
Error: This formula requires a fortran compiler, but we could not find one by
looking at the FC environment variable or searching your PATH for `gfortran`.
Please take one of the following actions:

  - Decide to use the build of gfortran 4.2.x provided by Homebrew using
        `brew install gfortran`

  - Choose another Fortran compiler by setting the FC environment variable:
        export FC=/path/to/some/fortran/compiler
    Using an alternative compiler may produce more efficient code, but we will
    not be able to provide support for build errors.

So don’t. Installing gfortran will produce the following:

brew install gfortran

==> Downloading http://r.research.att.com/tools/gcc-42-5666.3-darwin11.pkg
######################################################################## 100.0%
==> Installing gfortran 4.2.4 for XCode 4.2 (build 5666) or higher
==> Caveats
Brews that require a Fortran compiler should not use:
  depends_on 'gfortran'

The preferred method of declaring Fortran support is to use:
  def install
    ...
    ENV.fortran
    ...
  end

==> Summary
/usr/local/Cellar/gfortran/4.2.4-5666.3: 86 files, 72M, built in 39 seconds

5. brew install openmpi

This is what allows you to use all cores on your machine and is not in the default XCode install.

brew install openmpi

==> Downloading http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.tar.bz2
Already downloaded: /Library/Caches/Homebrew/open-mpi-1.6.tar.bz2
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.

==> ./configure --prefix=/usr/local/Cellar/open-mpi/1.6 --enable-ipv6
==> make all
==> make install
/usr/local/Cellar/open-mpi/1.6: 674 files, 21M, built in 5.9 minutes

6. cd gromacs-4.5.5

7. ./configure –enable-float –enable-mpi

You’ll produce output such as found in: 2012august29_gromacs455_configure.txt

You’ll also get two odd errors at the end of the ./configure run that do not affect the rest of the procedure:

./configure --enable-float --enable-mpi

...
./configure: line 29242: sort: No such file or directory
./configure: line 29239: sed: No such file or directory

So ignore them.

NOTE: If you’ve been going by my 3.3.3 procedure and used…

./configure --enable-mpi --enable-double

You’ll get the following error when you try to run make:

Making all in include
Making all in .
make[2]: Nothing to be done for `all-am'.
Making all in types
make[2]: Nothing to be done for `all'.

...

/bin/sh ../../libtool --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\"   -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT genborn_sse2_double.lo -MD -MP -MF .deps/genborn_sse2_double.Tpo -c -o genborn_sse2_double.lo genborn_sse2_double.c
 mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT genborn_sse2_double.lo -MD -MP -MF .deps/genborn_sse2_double.Tpo -c genborn_sse2_double.c  -fno-common -DPIC -o .libs/genborn_sse2_double.o
genborn_sse2_double.c:931: internal compiler error: Segmentation fault: 11
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
make[3]: *** [genborn_sse2_double.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

So don’t do that, either. The proper flag is the enable-float.

8. make

This will produce the output available for download at: 2012august29_gromacs455_make.txt

9. make install

This will produce the output available for download at: 2012august29_gromacs455_make_install.txt

10. make links

This will produce the short piece of output reproduced below.

cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \
	for i in $programs; do \
	   (test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
	done

And with that, you should be able to run all programs from a terminal window.

Obligatory

  • CNYO

  • Sol. Sys. Amb.

  • Salt City Miners

  • Ubuntu 4 Nano

  • NMT Review

  • N-Fact. Collab.

  • T R P Nanosys

  • Nano Gallery

  • nano gallery
  • Aerial Photos

    More @ flickr.com

    Syracuse Scenes

    More @ flickr.com