Version 0.1
Table of Contents

1. Overview
2. Information and Resources
3. Obtaining MC
4. Frequently Asked Questions
5. Installation Instructions
6. Author Information
7. Copyright and Terms of Use
8. GNU GPL

NOTE: This documentation provides information about installation, configuration, and general usage of the MC libraries. Information about the programming interface provided by the MC software can be found in the Programmer's Guide.

Overview
MC (Manifold Code) is a small self-contained parallel adaptive multilevel finite element software package. MC is an adaptive multilevel finite element kernel designed to be used collaboratively with several related research tools such as MALOC, SG, and APBS. MC can be used as a small stand-alone adaptive multilevel finite element code, or it can be used with these other tools which extend the capabilities of MC in various ways. MC is designed to numerically approximate the solutions of covariant divergence-form second-order nonlinear elliptic systems of partial differential equations on domains with the structure of Riemannian two- and three-manifolds. To accomplish this task as accurately and efficiently as possible, MC employs simplex triangulations of the domain manifold, Petrov-Galerkin finite element methods, a posteriori error estimation, adaptive mesh refinement and un-refinement, continuation, Newton methods, multilevel methods, and a new low-communication approach in parallel adaptive finite element methods.
MC was designed primarily to simulate the large deformation nonlinear elastic behavior of complicated hyperelastic bodies, although it can also be used for problems such as the nonlinear Poisson-Boltzmann equation arising in biophysics, the drift-diffusion semiconductor equations, and the Hamiltonian and momentum constraints in the Einstein equations. Ongoing projects include extending MC to numerically evolve the Ricci flow equations in Geometry and the full Einstein equations in relativity physics. Examples of MC applied to some of these problems can be found in the MC gallery.
MC is a class library written in Clean OO C. "Clean" refers to the fact that the language is both legal C++ and legal ANSI/ISO/Standard C, and can be compiled with any standard C or C++ compiler. "OO" refers to the programming style employed -- object-oriented. An Clean OO C implementation consists of a set of "Objects" (Clean C structs) which are operated on by a collection of "methods" (Clean C subroutines) which always have a pointer to the Object as their first argument. This special argument is always written as "thee", analogous to the implicit "this" pointer in C++. (An Clean OO C implementation can be turned into a C++ implementation with a simple AWK/SED or Perl Script.) As a result of this Clean OO C implementation, MC can be used as a set of C++-like class libraries, it can be safely software engineered into other large software packages, and it can be built on just about any UNIX-like platform with either a C or a C++ compiler, including e.g. Linux, IRIX, and Win32. To use some of the graphics and parallel computing features, your platform must also have some form of standard INET sockets (WINSOCK will work). MC is easily buildable from source on any UNIX-like system, and uses a GNU autoconf build environment.
Unusual and interesting features of MC
The following design features of MC make it somewhat unusual and also quite general.

- Abstraction of the PDE: you define your elliptic system only through a nonlinear weak form over a domain manifold, along with an associated linearization form, also defined everywhere on the domain manifold.
- Abstraction of the domain: you define your domain manifold by giving a polyhedral representation of the topology, along with an abstract set of coordinate labels of your own interpretation, possibly consisting of multiple charts. MC works only with the topology of your domain (i.e., the connectivity of your polyhedral representation). The geometry of your domain manifold is provided only through your own form definitions, which contain the manifold metric information.
- Dimension-independence: exactly the same code paths are taken for both two- and three-dimensional problems (as well as for higher-dimensional problems). To achieve this dimension-independence, MC employs the simplex as its fundemental geometrical object.

Geometry representation and manipulation in MC
The RInged VERtex (RIVER) datastructure is at the heart of the geometry engine in MC. This datastructure maintains a mesh of simplices in 2D or 3D with near minimal storage, and yet provides fast (constant- and linear-time) access to all information necessary for refinement, un-refinement, and discretization of an operator. This datastructure also allows the 2D and 3D cases to be treated in a uniform way, with one implementation covering both cases. An interesting feature of this datastructure is that the stuctures used for vertices, simplices, and edges are all of fixed size, so that a fast array-based implementation is possible, as opposed to a less-efficient list-based approach commonly taken for unstructured meshes. For an example illustrating how the datastructure, as well as all of the adaptivity algorithms using the datastructure, can be implemented entirely in an array-based language like FORTRAN or MATLAB, have a look at MCLite, which is a MATLAB version of MC for 2-manifolds.
Computational geometry primatives (such as computing determinants of small matrices to high precision) are quite difficult to implement robustly in floating point arithmetic. To avoid these types of problems in a robust yet efficient way in MC, all low-level geometric primatives are built on top of Jonathan Shewchuk's remarkable adaptive-precision geometric predicates.
Refinement and Un-refinment in MC
MC is based on the simplex, and for adaptive refinement it employs:

- 2D bisection [longest edge (Rivara)]
- 3D bisection [longest edge (Rivara) or marked edge (Arnold-Mukherjee/Bansch/ Joe-Liu/Maubach)]

Bisection is first used to refine a subset of the simplices in the mesh (selected according to some error estimates), and then bisection is used recursively on any non-conforming simplices produced, until a conforming mesh is obtained (finite termination of this procedure can be shown for each of the above refinement procedures). The code can also perform the following refinement procedures for uniform refine ments of a given simplex mesh:

- 2D quadra-section [augmented regular (Bank)],
- 3D octa-section [augmented regular (Bey/Ong/Zhang)]

Algebraic construction of the coarse problem is supported, in both the 2D and 3D fully unstructured settings. As a result, the underlying multilevel algorithm is provably convergent in the self-adjoint-positive case. The multilevel algorithm has provably optimal convergence properties under the standard regularity assumptions, and is nearly-optimal under very weak regularity assumptions. The user must define a sequence of an algebraic prolongation operators in a standard YSMP-row-wise matrix datastructure; MC then constructs the algebraic multilevel hierarchy from the prolongation operators. An automated construction of provably stable prolongation operators for use in the multilevel algorithms and in the two-level domain decomposition algorithms used in MC is under development.
Discretization in MC
A choice of piece-wise linear or piece-wise quadratic finite element basis functions are provided. The quadratic functions are provided mainly to avoid the locking problem when simulating near-incompressible elastic materials, and for dealing with the second derivative terms appearing in the Riemann tensor in the gravitational field equations. While MC provides standard linear and quadratic elements by default, the assembly procedure and linear algebra datastructures support a wide variety of element types; in particular, different element types may be used for different components of a coupled elliptic system.
Solution of nonlinear systems in MC
When a system of nonlinear finite element equations must be solved in the code (for the case of a nonlinear elliptic system, or during the implicit time-stepping evolution of a nonlinear evolution problem), a global inexact-Newton procedure is employed, where the linearization systems are solved by linear multilevel methods. Elliptic systems are solved using either a "Gummel" de-coupling procedure, or using a coupled Newton method. Solutions with folds or bifurcations are handled with natural parameter or pseudo-arclength continuation.
The two-layer "Clean OO C" implementation of MC
MC is a set of class libraries written in pure Clean OO C, and is therefore completely portable (from PC to iMac to CRAY). This portability is achieved through the use of a very small but powerful abstraction layer, called MALOC (Minimal Abstraction Layer for Object-oriented C). The MALOC class library layer provides abstract datatypes, memory management routines, timing routines, machine epsilon, access to UNIX and INET sockets, MPI, and so on. All things that can vary from one architecture to another are abstracted out of MC and placed in the MALOC layer. To port MC to a new architecture, only the small MALOC abstraction layer needs to be ported. (Porting MALOC usually means only typing: "./configure ; make")
As a result of this pure Clean OO C implementation, MC can be used as a set of C++-like class libraries, it can be safely software engineered into other large software packages, and it can be compiled on just about any UNIX-like platform with either a C or a C++ compiler, including e.g. Linux, IRIX, and WindowsNT. To use some of the graphics and parallel computing features in MC provided by the underlying MALOC library, your platform must also have some form of standard INET sockets (WINSOCK will work).
Using MC as a set of class libraries
MC can be used as a collection of class libraries from within another application code. One creates an MC object, and then simply applies the appropriate methods to the MC object (or its sub-objects). Each object maintains its own internal state, giving the class libraries the property of re-entrancy: several MC objects can be created and manipulated to solve different PDEs on different meshes within the same application at the same time. This can be used for example to construct Gummel-like iterations for elliptic systems.
Using MC through the MCshell
While MC can be used cleanly as a collection of class libraries, it can also be used entirely through the MCshell, which is a mostly Bourne-compatible command shell. The MCshell maintains an internal environment state, and can be used to execute MCshell scripts using a high-level MC manipulation language. All important features of the MC class libraries can be manipulated by using only the MCshell, so that MC can be used either interactively, or in batch mode by executing scripts. The MCshell produces a history file of the session, which can be re-executed to recreate the previous session exactly. In addition, MCshell scripts can be executed during an interactive session by using normal Bourne shell syntax (e.g., ". filename.mcsh"). If you have ever used a command shell under UNIX, then you will be able to easily get started using MC through the MCshell. (In fact, since the MCshell is mostly Bourne-shell compatible, you could actually use it as your UNIX login shell.)
Geomview and GMV graphics through pipes and sockets in MC
MC performs all I/O through an abstracted software I/O layer in MALOC, which provides access to files, pipes, UNIX domain sockets, and INET sockets. This allows several instances of MC to work collaboratively on a problem in a distributed memory computing environment, as well as to make use of the University of Minnesota's Geomview as the primary display utility. MC can produce OFF-compatible output for use by Geomview as file input, or it can write OFF output directly to pipes, UNIX domain sockets, or INET sockets.
A socket "bridging" utility called MC-bridge is provided with MC which bridges UNIX and INET sockets, so that MC executing on a remote machine can communicate with Geomview listening to a UNIX domain socket on the local machine, using INET sockets on the local and remote machines, and then an INET-to-UNIX domain socket bridge on the local machine. MC can also produce GMV-compatible output files for use in rendering displays of solution functions with GMV from Los Alamos National Laboratory.
A minimal Geomview clone called SG can be used with MC. It mimics most of the basic features of Geomview for displaying planar polygons. It can be hung on a UNIX domain socket like Geomview. Unlike Geomview, SG can also listen directly to INET sockets, and it will run on either X11 or Win32 platforms (such as Windows NT). In the case of Windows NT, SG uses the WINSOCK API for INET socket access. The graphics in SG is done in an entirely platform-independent manner using OpenGL. The window-system specific connection to X11 or Win32 is made through "WGL" extensions to Win32 under NT, or using the SGI "GLw" widget set on any X11 platform.
Parallel computing with MC
MC implements a new approach to the use of parallel computers with adaptive finite element methods, based on the idea of local a priori and local a posteriori error estimates. The algorithm has two interesting features: (1) almost no communication is required (no boundary exchanges), and (2) only a few lines of an existing sequential adaptive code must be changed in order to implement the parallel algorithm. The new algorithm was developed jointly with Randy Bank and is described in the following paper. The communication primatives required are quite simple, and can be implemented using sockets rather than a more serious communication library such as MPI. In either case, MC accesses INET sockets and/or MPI functions through the MALOC abstraction library, and as a result MC can be used in parallel on any heterogeneous collection of UNIX and/or WINSOCK platforms.

Information and Resources
Detailed information about MC can be found in the User's Guide and Programmers's Guide.
While MC is itself a self-contained software package, it is one of several components of FETK (the Finite Element ToolKit). FETK consists of the following components written in Clean OO C:

- MALOC - Minimal Abstraction Layer for Object-oriented C programs.
- PUNC - Portable Understructure for Numerical Computing.
- GAMer - Geometry-preserving Adaptive MeshER (uses MALOC).
- SG - Socket Graphics mesh display tool (uses MALOC).
- MC - Manifold Code finite element package (uses MALOC and PUNC).
- MCX - MC eXtension libraries (uses MALOC, PUNC, and MC).

MALOC is self-contained, and requires only an ANSI-C compiler on a UNIX or Win32 platform. PUNC, GAMer, SG, and MC are also self-contained, but rely on MALOC having been previously installed on the platform. Additional features of MC are enabled if PUNC is available, but PUNC is not required to build MC. The MC eXtension libraries MCX are constructed on top of MALOC and MC, and in order install and use MCX one must first correctly configure and install both MALOC and MC. MCX is made up of a number of individual libraries developed by members of our group, or contributed by one of a number of colleagues. More information about FETK can be found on the FETK website:

- http://www.fetk.org/

Obtaining MC
MC is copyrighted, but is redistributable in source and binary form under the following license. The MC source can be downloaded from the FETK Download Page.
MC uses the low-level FETK abstraction library MALOC, as well as the low-level FETK numerical library PUNC, both of which must be installed before installing MC.
MC can also make use of FETK visualization and meshing libraries SG and GAMer, although they are not required in order to build or use MC.

Frequently Asked Questions
What is MC and what does MC stand for?
See the Overview.
How to I obtain a copy of the MC binaries and/or source code?
See the Obtaining MC section.
I managed to get a copy of "mc-VERSION.[i386|src|tar].[rpm|gz]"; how do I now install MC?
See the Installation Instructions.
You gave me a "patch.gz" file to fix a bug in MC; how do I apply the patch?
To apply patches to upgrade MC to a new version, you first obtain the patch from me or my webpage as a single file with a name like "patch.gz". You apply the patch after you have unpacked the mc.tgz file as described above. To apply the patch, cd into the directory containing the root MC directory (called "mc" after unpacking mc.tgz) and execute the "patch" program as follows (the patch program exists on most UNIX machines):

- gzip -cd patch.gz | patch -p0

Patch files are simply the output from a recursive "diff" that are used to represent all differences between two directory trees. For example, to create a patch representing the changes from version 1.0 of MC (in directory mc_1.0 for example) to version 1.1 of MC (e.g. in directory mc_1.1), I would normally type the following:

- diff -r -u -N mc_1.0 mc_1.1 > patch1
- gzip -v patch1

which would produce the gzipped patch file "patch1.gz". If you had previously installed version 1.0 of MC but would like to upgrade to version 1.1 of MC, you could just download the file "patch1.gz" and apply the changes using the program "patch" as above, rather than downloading and reinstalling the entire version 1.1 of MC.
I really don't know what I'm doing; how to I get more documentation for MC?
The User's Guide and the Programmers's Guide contain all of the MC documentation.
Why did you develop MC? There are many other finite element packages, right?
I wanted to solve some nonlinear elliptic and parabolic systems that arise in geometry and physics using adaptive finite element methods, as part of some projects I became involved in at Caltech in 1994. It quickly became clear that there were no publicly available software packages for handling some of the more difficult features of these problems (rapid nonlinearities, three spatial dimensions, systems, complex differential operators, and manifold domains requiring multiple charts).
I decided to try to build an adaptive multilevel finite element code based on the 2-simplex and the 3-simplex, for general coupled second-order nonlinear elliptic systems on 2- and 3-manifolds. The idea was to be as general, simple, and robust as possible; the only real restriction I made early on was that the principle part of the differential operator had to be in divergence form, so that piecewise linear finite elements had a chance of making sense. This has now loosened up a bit, due to the fact that the element itself has been abstracted out and placed in the domain of the user-defined code.
The design philosophy followed Randy Bank's two-dimensional finite element code PLTMG in many ways, with appropriate modifications to handle the three-dimensional case as transparently as possibly, always keeping in mind the need to handle general nonlinear systems on manifold domains.
Another reason that I wrote MC is that I find I don't really understand an algorithm until I implement it. In this sense, MC is an algorithm research tool that I have grown from scratch to allow me to experiment with adaptive multilevel finite element methods, numerical continuation methods, iterative methods for linear and nonlinear algebraic systems, and so forth. I use it in conjunction with MCLite (a 2D version of MC written entirely in the MATLAB language) for research and teaching.
What is in all of these subdirectories? Where exactly is "MC"?
MC consists of several (class) libraries from which you will call routines to handle your application. You will need to write a main driver program (and any supporting routines you need to define your problem) and then link to the libraries. Alternatively, you can use MC's builtin lexer/parser in an interactive session by starting up "mcsh", the MCshell. The MCshell looks and feels very much like bash (a superset of the bourne shell), and you can write small scripts to control almost everything in the MC class library, completely through the MCshell, without writing a line of C or C++.
As described in the file "INSTALL", you will build all of the libraries in one shot for your particular architecture, along with various test programs to verify that the various pieces are functioning correctly. The libraries end up in "mc/lib", and the header files are in subdirectories in "mc/inc".
After the build, you will be ready to work with your particular application main driver, and you just need to link to the libraries. Sample main drivers and makefiles are in the "mc/examples/*" subdirectories. Things are setup for you to work completely in one of those directories. Of course, all you really have to do is link to the MC libraries, so you can use it how you like; the makefiles and drivers in "mc/examples/*" just provide an example of how to get MC working correctly. I actually develop and use MC by working mainly from one of those subdirectories.
The following directory tree is created when you unpack the MC "mc.tgz" distribution file by following the instructions in the INSTALL document:

                                         mc
                                         |
                             ------------------------
                            /      |     |      |    \
                           config doc examples src tools

The src directory has the additional subdirectory structure for each library forming MC:

                                         src
                                          |
                            ----------------------------
                           /    |   |    |    |    |    \
                         aprx  bam base gem mcsh  nam  pde

Within each library source directory is an additional subdirectory, "mc". The "mc" subdirectory contains public headers for the library, representing the library API; these headers will be installed in the specified header install directory during the install procedure after building MC.
The following is a brief description of each subdirectory of the package.

        mc             - The entire MC package
        mc/config      - GNU Autoconf scripts and non-unix config files
        mc/doc         - MC documentation
        mc/examples    - Complex examples and data files for using MC
        mc/src         - MC source code (all source and headers)
        mc/src/aaa_inc - Header installation tools
        mc/src/aaa_lib - Library installation tools
        mc/src/*/mc    - The MC headers (API)
        mc/src/aprx    - Source for M. Holst's APRX (APRoXimation Methods)
        mc/src/base    - Source for M. Holst's BASE (MC foundation headers)
        mc/src/bam     - Source for M. Holst's BAM  (Block Algebraic Methods)
        mc/src/gem     - Source for M. Holst's GEM  (Geometry Engine Methods)
        mc/src/mcsh    - Source for M. Holst's MCSH (The MC Shell)
        mc/src/nam     - Source for M. Holst's NAM  (Nonlinear Algebraic Methods)
        mc/src/pde     - Source for M. Holst's PDE  (Partial Diff. Equation)
        mc/tools       - Some binary tools for use with MC

Okay, I seem to have installed MC correctly; how do I actually use it now?
Using MC is pretty simple; it is a very object-oriented implementation, although it is written in C. It is actually written in an object-oriented form of "Clean C", which is the overlapping subset of ANSI/Standard C and C++, so you can compile the code as a legal C++ or ANSI/Standard C code. Using the code consists of constructing objects (represented by C structs) and manipulating these objects using appropriate methods (represented by C functions which follow a certain object-oriented prototype convention).
You provide the definition of your differential operator by providing a PDE object. This object contains several pieces of information, including information about the spatial dimension, number of unknowns per spatial point, and so on. This object must also contain pointers to the functions defining the various functions in your PDE, such as the weak form of your differential operator evaluated at a point, a linearization bilinear form evalulated at a point, and a dirichlet boundary function. By looking at the example files "mypde.c" in "mc/examples/*", you will see exactly how to construct this PDE object. Some example PDE definitions also appear in "mc/examples/*".
Once you have built this PDE object as in the example file pde.c, you then construct a MCsh object, which requires your PDE object as an input parameter. At this point, you can use appropriate methods to operate on the MCsh object to accomplish the solution of your PDE. The example drivers main.c in "mc/examples/*" show how to call the more important methods to operate on the MCsh object, such as discretize your elliptic system with piecewise linear finite elements over 2- or 3-simplices, solve the discrete system, do a posteriori error estimation, mesh refinement, solve again, etc, in a way modeled after Randy Bank's two-dimensional code "PLTMG". The sample main driver main.c includes a single header file "mc/inc/mc/mcsh.h", which includes everything the MC package needs. The sample problem file mypde.c also includes this single header file, which provides the definition of the PDE object, as well as prototypes for the functions which the PDE object function pointers will point to.
Finally, you specify your manifold domain by using a particular MCsh method, giving the name of the mesh file as a parameter. The mesh file has a very simple format; there are example mesh files in the "mc/examples/*".
Rather than giving a more detailed explanation of the usage of MC here, it seems to me that the best way to see how it works is to study the example main program and supporting routines in the "mc/examples/*" subdirectories; these are well-documented, and you should be able to modify the driver to handle your application. Or, simply start up mc, the MCshell.
What is the class hierarchy? How are the various libraries related?
Detailed information on the class relationships can be found in the Programmers's Guide. The following directed graph shows the class library dependencies. (This tends to evolve as MC is developed.)

       MALOC ==> base ==> gem ==> aprx ==> nam ==> mcsh
                  ||              /\ /\
                  ======> bam ====|| ||
                          /\         ||
                          ||         ||
                          ||         ==== pde (PDE is partially user-supplied)
                          ||
                         PUNC (if installed)

Wait! I have a bunch of other questions, such as:

- What in tarnation is "Clean OO C"?
- Why is MC written in Clean OO C rather than C++ or Objective-C?
- Why is MC written on top of this other package with a weird name (MALOC)?
- I want to extend MC and/or MALOC in some way; what is the "Coding Style"?
- I wrote a cool extension; how do I get it included in MC and/or MALOC?

These and other related questions are addressed in the MALOC FAQ, which is distributed as the README file in the MALOC source distribution.

Installation Instructions
Available distribution formats
MC is distributed in both binary format (as a binary RPM file mc-VERSION.i386.rpm for i386-based versions of Linux) and in source format (as a source RPM file mc-VERSION.src.rpm and as a gzipped tar file "mc-VERSION.tar.gz").
Installation using the binary RPM file
The following rpm command will install all of the MC headers and libraries into /usr/local/include and /usr/local/lib, and will install the MC documentation into /usr/share/doc/packages/mc:

        rpm -Uvh mc-VERSION.i386.rpm

Installation and rebuilding from sources using the source RPM file
The following rpm command will unpack the source rpm file "mc-VERSON.src.rpm" into the MC gzipped tar file containing the sources called "mc-VERSION.tar.tar.gz" and into a small RPM spec file called "mc-VERSON.spec":

        rpm -Uvh mc-VERSION.src.rpm

The sources can then be unpacked and built using the directions for the gzipped tar file below. Alternatively, the following rpm command will do these steps for you:

        rpm -bp mc-VERSION.spec

Rebuilding binary and source RPM files from the gzipped tar file
The MC sources contain the RPM spec file "mc-VERSON.spec" in the root source directory; as a result, rebuilding the RPM files from sources can be done using the rpm command:

        rpm -ta mc-VERSION.tar.gz

The result will be the corresponding source and binary rpm files, named "mc-VERSON.src.rpm" and "mc-VERSION.i386.rpm". Normally, these files are written to /usr/src/redhat/SRPMS and /usr/src/redhat/RPMS respectively, but you must be logged in as root for these to work. The destination directories can be overriden using arguments to the rpm program (see the rpm manpage).
Installation and building from sources using the gzipped tar file
The following command will unpack MC into a number of subdirectories and files on any UNIX machine (and on any WinNT machine with the GNU-Win32 tools gzip and tar).

        gzip -dc mc.tgz | tar xvf -

MC is essentially a multilevel adaptive finite element "kernel". It is designed to be easily extended through the use of extension packages which are constructed on top of MC. The extension packages that I have written such such as MCgp (MC for Geometric PDEs) are also distributed as gzipped tar files (e.g. "mcgp.tgz"). The installation instructions for such extension packages are identical to the instructions below for the MC kernel (e.g., substitute "MCgp" for every occurance of "MC" below).
Building the package using the GNU "configure" shell script and "make"
The "configure" shell script in the "mc" directory (the toplevel directory created when you unpacked the MC tgz file) will build the entire package. This is a standard GNU autoconf-generated configuration script. For a list of the possible configuration options, type:

        ./configure --help

You should be able to build MC by simply typing:

        ./configure
        make
        make install

However, it is often advantageous to keep the original source directory pristine; the configure script can actually be run outside the source tree, which will keep all files created by the build outside the source tree. (This idea is related to the section below describing how to build binaries for multiple architectures at the same time using the same source tree, and requires that your version of make has the VPATH facility, such as GNU make.) For example, I build MC in a separate directory from the source tree as follows:

        gzip -dc mc.tgz | tar xvf -
        mkdir mc_build
        cd mc_build
        ../mc/configure
        make
        make install

Building binaries for multiple architectures in the same source directory
If you have a version of "make" that supports the VPATH facility (such as any recent version of GNU make), then you can build the package for multiple architectures in the same source directory (in fact, you can do the compiles at the same time without collisions). This is very useful if you have your home directory on an NFS volume that you share among multiple architectures, such as SGI, Linux, etc. To build MC for all the systems at the same time, you simply make an additional subdirectory in the main MC directory for each architecture, copy "configure" into it, "cd" into the subdirectory, and then install as above. For example, on a linux machine you would do the following:

        mkdir linux
        cp configure linux/.
        cd linux
        ./configure
        make
        make install

If you mount the same NFS home directory on for example an OpenStep box, you could at the same time do the following:

        mkdir next
        cp configure next/.
        cd next
        ./configure
        make
        make install

Again, both builds can actually be done outside the source tree rather than in a subdirectory of the source tree, as described in the previous section.
Building shared libraries rather than static libraries
(MIKE: give an overview of libtool.)
Rebuilding the configure script and the Makefile.in files
If for some reason you actually need to rebuild the configure script or the Makefile.in files using the GNU autoconf suite, you should read the block of documentation at the top of the configure.in file. The commentary I put there explains exactly how the GNU autoconf suite must be used and in what order, and exactly what files are produced at each step of the process. A script called "bootstrap" which automates this process is located in the config subdirectory of the MC source tree.
Platform-specific information
Below is some platform-specific build/usage information for MC.

- Linux (Source: M. Holst, UCSD)
  Things should work as described above.
- FreeBSD/NetBSD/OpenBSD (Source: M. Holst, UCSD)
  Things should work as described above.
- OpenStep (Source: M. Holst, UCSD)
  Things should just work, but you may have to set the CC environment variable as follows before typing ./configure:

          export CC="/bin/cc"

  or you might need to use:

          export CC="/bin/cc -ObjC"

- IRIX (Source: M. Holst, UCSD)
  If you are on a 64-bit IRIX box such as an Onyx, Octane, or Origin, set the CC environment variable as follows before typing ./configure:

          export CC="/bin/cc -64"

  If you are on a 32-bit IRIX box such as an O2 or Indy, set the CC environment variable as follows before typing ./configure:

          export CC="/bin/cc -32"

- Win32 (Source: M. Holst, UCSD)
  Unless you have the Cygwin environment, you need to use one of the included project file collections for one of the commercially available ANSI C or C++ compilers for the Win32 environment.

What you end up with
Once the build completes via the configure/make procedure above with no errors, you will want to cd into an example directory to get started, e.g. "cd examples/generic" (or "cd mc/examples/generic"). In the example directories you will find:

        mypde.c    --> Example partial differential equation definition file
        mypde.h    --> The prototypes of the functions that you must provide
        myelm.c    --> Example element definition file
        main.c     --> compiled and linked with mypde.c to become --> mcsh

The "main.c" example uses MC's builtin-lexer/parser to parse commands in an interpreted interactive session I call the "MCshell", or "mcsh". You will want to start with mcsh by typing "./mcsh", which will fire up a shell that looks and feels like bash (a bourne-compatible command shell). Type "help" at the command prompt for help.
If mcsh works like it was designed, you won't need any more information to use MC. If you want to know more about the details of the numerical methods in MC, or about the implementation details such as the socket communication layer, have a look in "mc/doc" for documentation.
Using MC on a parallel computer
MALOC provides abstractions to both INET sockets and MPI for communication support in parallel computing software. MC inherits this capability from the MALOC library. Control of the overall structure is accomplished through MCshell (enhanced MALOC-shell) scripts you write, or through calls to the MC library. (Going through the MCshell is much simpler, and you have access to all the communication possibilities through the MCshell.)
Several instances of MC can be used collaboratively in parallel through the use of either INET sockets or MPI. Control of the overall structure is accomplished through the MCshell scripts you write. You can also write your own main program and use the vmp library directly (using vmp's "Oracle" class is quite straightforward), but going through the MCshell is much simpler, and you have access to all the communication possibilities through the MCshell.
Several examples of scripts which perform parallel adaptive elliptic solves may be found in the "mc/examples/generic/mcsh" subdirectory. To run one of the scripts and actually get some parallel computation to occur requires the following (e.g. for an MPI-based computation, using the MPICH startup environment):

1. Build MC with MPI enabled; this is usually accomplished simply by giving an argument to the GNU configure script:

           ./configure --enable-mpi

   Note that if your installation of MPI is located in an unusual directory, then the configuration script may have trouble finding the MPI library (libmpi.a) or the MPI header file (mpi.h). If so, then MPI will not be enabled. The configure script prints out the state of affairs quite clearly as to whether it found the library and the header. If you have MPI and configure is not finding it, then read the section of this installation guide entitled "Getting MC to find your installation of MPI" for several different solutions.
2. Copy one of the parallel MCshell scripts from "mc/examples/generic/mcsh/" into your working directory as "rc.mcsh".
   --Alternatively--
   Copy one of the parallel MCshell scripts from "mc/examples/generic/mcsh/" into some other directory that will contain all input and output files for your run as "rc.mcsh", AND then set the environment variable MCSH_HOME to that directory. If I wanted all file i/o to occur in the temporary directory /tmp/mc, I would place the following in my ~/.bash_profile file:

           export MCSH_HOME="/tmp/mc"

   and I would place the following in my ~/.ssh/environment file:

           MCSH_HOME=/tmp/mc

   (This last is required if you use ssh for your MPI remote shell.)
3. Start up mcsh using MPICH's "mpirun" command as follows:

           mpirun -np 4 mcsh

4. Sit back and wait for the processes to finish their work.

Getting MC to find your installation of MPI
If your installation of MPI is located in an unusual directory, then the configuration script may have trouble finding the MPI library (libmpi.a) or the MPI header file (mpi.h). Again, the configure script prints out the state of affairs quite clearly as to whether it found the library and the header. If you have MPI and configure is not finding it, then here are several possible solutions, each of which usually works. They are listed in preferred order (i.e. you should try Solution 1 first, and if that doesn't work try Solution 2, and so on).

- Solution 1:
  Have your system administrator install MPI in a proper system directory so that MC (and other AUTOCONF-based codes) can find it!
- Solution 2:
  1. Find the location of libmpi.a and mpi.h on your system, either by asking your sysadmin, poking around yourself, or (if you have it) using the "locate" utility:

             locate mpi.h
             locate libmpi.a
             locate libmpich.a

     On my Redhat6.2 Linux box, the following output is produced:

             bash:~% locate mpi.h
             /usr/share/mpi/include/mpi.h
             bash:~% locate libmpi.a
             bash:~% locate libmpich.a
             /usr/share/mpi/lib/libmpich.a

     Therefore the MPI header is installed as:

             /usr/share/mpi/include/mpi.h

     and the MPI library is installed as:

             /usr/share/mpi/lib/libmpich.a

  2. Before running the configure script, preset the FETK_MPI_INCLUDE and FETK_MPI_LIBRARY environment variables to point to the directories containing mpi.h and libmpi.a (or libmpich.a). Under bash, using the results from the example above, I would do this as follows:

             export FETK_MPI_INCLUDE=/usr/share/mpi/include
             export FETK_MPI_LIBRARY=/usr/share/mpi/lib
             ./configure --enable-mpi
             make clean; make; make install

     The configure script should now report that it successfully found the library and header and thus enabled MPI, and then MC should compile without error.

Debugging using the ElectricFence malloc debug library
To allow ElectricFence to intercept all calls to malloc, free, and related dynamic memory allocation system calls, simply run the configure script as follows:

        ./configure --enable-efence
        make clean; make; make install

Author Information
MC (Manifold Code, or Michael's Code) was conceived, designed, and implemented over several years by Michael Holst, beginning with an initial implementation in 1994. Various colleagues have contributed ideas and/or code to MC (see the credits list below).

        MC (Manifold Code)
        Copyright (C) 1994--

        Michael Holst               TELE:  (858) 534-4899
        Department of Mathematics   FAX:   (858) 534-5273
        UC San Diego, AP&M 5739     EMAIL: mholst@ccom.ucsd.edu
        La Jolla, CA 92093 USA      WEB:   http://ccom.ucsd.edu/~mholst

MC was designed to be the finite element kernel on top of a platform abstraction layer MALOC, and is usually used with a socket graphics tool called SG (both MALOC and SG were also developed by Michael Holst). MC was developed almost entirely on a home-grown 90Mhz Pentium PC running various flavors of Linux and [Free|Net|Open]BSD, using primarily GNU, BSD, and other free software development tools. Most of the development occurred during the hours of 10pm to 2am on a daily basis for several years, under heavy influence of Starbuck's coffee, with helpful advice provided by Mac and Mochi (two cats knowledgable in socket programming and numerical analysis).
MC was released under the GNU GPL (GNU General Public License) beginning with the initial implementation in 1994, and continues to be released under this license. What this means is that like all GNU software, MC is freely redistributable in source code form following the rules outlined in the text of the GNU GPL. You should have received a copy of the GNU GPL with this distribution of MC; a copy can be found here. If you did not receive a copy of the GNU GPL, please write to me and also write to: The Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
Software included in the MC source code package
A complete roadmap to the source code forming the MC package can be found above. While the core MC classes were developed by Michael Holst, the following single file is currently also included with MC:

        mc/src/gem/pred.c    - J. Shewchuk's geometric "predicates.c"

Computational geometry primatives are quite difficult to implement robustly in floating point arithmetic; we use Jonathan Shewchuk's adaptive precision predicates for our low-level geometric primatives (basically for computing determinants of small matrices).
Credits
Below is a credits list for the people that have contributed to MC in one way or another. The fields below follow the credits file format used in the Linux kernel CREDITS file to allow for easy manipulation via shell scripts. The fields are as follows:

              N: name of contributor
              E: email address
              W: web address
              P: PGP key ID and fingerprint
              D: description of primary contributions
              S: snail-mail address

    N: Michael Holst
    E: mholst@ccom.ucsd.edu
    W: http://ccom.ucsd.edu/~mholst
    P: 1024/0xB5212DCD
    D: mc/*                      -- The package structure
    D: mc/acconfig.h             -- The platform abstraction information
    D: mc/configure.in           -- The GNU autoconf/automake structure
    D: mc/config/*               -- The GNU autoconf/automake shell scripts
    D: mc/doc/*                  -- The package documentation
    D: mc/examples/*             -- The package examples
    D: mc/src/aaa_inc/*          -- Library header build structure
    D: mc/src/aaa_lib/*          -- Static and shared library build structure
    D: mc/src/base/*             -- Foundation headers
    D: mc/src/aprx/*             -- M. Holst's APpRoXimation library
    D: mc/src/bam/*              -- M. Holst's Basic Algebraic Methods library
    D: mc/src/gem/*              -- M. Holst's GEometry Machine library
    D: mc/src/mcsh/*             -- M. Holst's MCSHell library
    D: mc/src/nam/*              -- M. Holst's Nonlinear Algebraic Methods library
    D: mc/src/pde/*              -- M. Holst's PDE library
    D: mc/tools/*                -- Tools built on the libraries
    S: Department of Mathematics
    S: UC San Diego, AP&M 5739
    S: La Jolla, CA 92093 USA

    N: Steve Bond
    E: bond@ccom.ucsd.edu
    D: mc/maloc.spec             -- RPM support (for building src/binary RPMs)
    D: mc/src/bam/*              -- Improved matrix library (supports MG and HB)
    S: Department of Mathematics
    S: UC San Diego
    S: La Jolla, CA 92093 USA

Contacting the Author
If you have questions or comments about MC, please feel free to contact me at mholst@ccom.ucsd.edu.

Copyright and Terms of Use Please acknowledge your use of MC and FETK by citing:

- M. Holst, Adaptive numerical treatment of elliptic systems on manifolds. Advances in Computational Mathematics, 15 (2001), pp. 139-191.

This version of MC is distributed under the following guidelines:

- MC (Manifold Code)
  Copyright (C) 1994-2010 Michael Holst
  This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
  You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.

GNU GPL
The GPL (GNU General Public License) below is copyrighted by the Free Software Foundation. However, the instance of software that it refers to, my package in this case, is copyrighted by myself as the author of the package. Any additional software that I distribute with my software is copyrighted by the authors of those pieces of software (see the individual source files for author information). ---Michael Holst

    		    GNU GENERAL PUBLIC LICENSE
    		       Version 2, June 1991

     Copyright (C) 1989, 1991 Free Software Foundation, Inc.
     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
     Everyone is permitted to copy and distribute verbatim copies
     of this license document, but changing it is not allowed.

    			    Preamble

      The licenses for most software are designed to take away your
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       TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION

      0. This License applies to any program or other work which contains
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        b) You must cause any work that you distribute or publish, that in
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      3. You may copy and distribute the Program (or a work based on it,
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      4. You may not copy, modify, sublicense, or distribute the Program
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      5. You are not required to accept this License, since you have not
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    			    NO WARRANTY

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    		     END OF TERMS AND CONDITIONS

    	    How to Apply These Terms to Your New Programs

      If you develop a new program, and you want it to be of the greatest
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        (one line to give the program's name and a brief idea of what it does.)
        Copyright (C) 19yy  < name of author >

        This program is free software; you can redistribute it and/or modify
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        (at your option) any later version.

        This program is distributed in the hope that it will be useful,
        but WITHOUT ANY WARRANTY; without even the implied warranty of
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        You should have received a copy of the GNU General Public License
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    Also add information on how to contact you by electronic and paper mail.

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