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.
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