LibMesh

Starting to experiment with a minimal LibMesh interface that would allow for static remeshing.

 * On Mac OS X, it is necessary to set

  to prevent link failure with

 * First `pyximport` must not be performed in ipython or

  is thrown (see also http://permalink.gmane.org/gmane.comp.python.cython.user/5049). Subsequent `pyximports` are fine in ipython.
 * It doesn't seem to be possible to allocate a `node_iterator`. See CythonStackAllocation. Also reported as https://groups.google.com/d/topic/cython-users/bbqLQ9Q8lRk/discussion.

2013-02-13 11:15

Dusting off my libMesh branch. I need to patch `GmshIO.C` because it refuses to read Gmsh files newer than versions 2.4.

A fresh checkout of libMesh `master` doesn't build! Fails with:

 * Branch `v0.8.0` builds fine.
 * `git bisect` doesn't work optimally because there was a long stretch of builds that fail for a different reason. `git bisect skip` just causes it to continue wandering around testing things that fail for the wrong reason, i.e,
  {{{

CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /Users/guyer/Documents/research/libmesh/libmesh/build-aux/missing --run aclocal-1.12 -I m4 /Users/guyer/Documents/research/libmesh/libmesh/build-aux/missing: line 51: aclocal-1.12: command not found WARNING: 'aclocal-1.12' is missing on your system. You should only need it if

         you modified 'acinclude.m4' or 'configure.ac'.  You might want
         to install the Automake and Perl packages.  Grab them from
         any GNU archive site.
 cd . && /bin/sh /Users/guyer/Documents/research/libmesh/libmesh/build-aux/missing --run automake-1.12 --foreign

/Users/guyer/Documents/research/libmesh/libmesh/build-aux/missing: line 51: automake-1.12: command not found WARNING: 'automake-1.12' is missing on your system. You should only need it if

         you modified 'Makefile.am', 'acinclude.m4' or 'configure.ac'.
         You might want to install the Automake and Perl packages.
         Grab them from any GNU archive site.

CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /Users/guyer/Documents/research/libmesh/libmesh/build-aux/missing --run autoconf aclocal.m4:20: warning: this file was generated for autoconf 2.69. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically 'autoreconf'. /usr/bin/gm4:aclocal.m4:1085: cannot open `m4/libtool.m4': No such file or directory autom4te: /usr/bin/gm4 failed with exit status: 1 make: *** [configure] Error 1

  }}}
 * By using two different failure conditions, it looks like the first "bad magic number" failure is at 659d870a26 in libMesh's git master.
 * "`cannot open 'm4/libtool.m4': No such file or directory`" seems to arise at c157712b1c.
 * "bad magic number" arose '''before''' c157712b1c, at 6a41dc439e.
 * Further `git bisect`ion is moderately informative
  {{{

The first bad commit could be any of: 643180835df958ce44f3484885b5fc3bdceb1624 fd721144a8b5eb52342cf1bbed1b16cad96ba42a 6a41dc439e249ddcb039f7996cad81fb919e4fbf We cannot bisect more!

   }}}
 * FIled https://github.com/libMesh/libmesh/issues/42, which has gotten speedy assistance from the libMesh developers (still in progress).