| FETK | |
| The Finite Element ToolKit | |
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Developed by the MCP Research Group at the UCSD Center for Computational Mathematics |
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MC User's Guide
Version 0.1 Table of Contents
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.
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:
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 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: 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):
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:
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
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------------------------
/ | | | \
config doc examples src tools
The src directory has the additional subdirectory structure for each library forming MC:
src
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----------------------------
/ | | | | | \
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:
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.
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):
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).
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) 1994-2010
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:
This version of MC is distributed under the following guidelines:
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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software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
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When we speak of free software, we are referring to freedom, not
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To protect your rights, we need to make restrictions that forbid
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We protect your rights with two steps: (1) copyright the software, and
(2) offer you this license which gives you legal permission to copy,
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The precise terms and conditions for copying, distribution and
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GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
under the terms of this General Public License. The "Program", below,
refers to any such program or work, and a "work based on the Program"
means either the Program or any derivative work under copyright law:
that is to say, a work containing the Program or a portion of it,
either verbatim or with modifications and/or translated into another
language. (Hereinafter, translation is included without limitation in
the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
running the Program is not restricted, and the output from the Program
is covered only if its contents constitute a work based on the
Program (independent of having been made by running the Program).
Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's
source code as you receive it, in any medium, provided that you
conspicuously and appropriately publish on each copy an appropriate
copyright notice and disclaimer of warranty; keep intact all the
notices that refer to this License and to the absence of any warranty;
and give any other recipients of the Program a copy of this License
along with the Program.
You may charge a fee for the physical act of transferring a copy, and
you may at your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Program or any portion
of it, thus forming a work based on the Program, and copy and
distribute such modifications or work under the terms of Section 1
above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices
stating that you changed the files and the date of any change.
b) You must cause any work that you distribute or publish, that in
whole or in part contains or is derived from the Program or any
part thereof, to be licensed as a whole at no charge to all third
parties under the terms of this License.
c) If the modified program normally reads commands interactively
when run, you must cause it, when started running for such
interactive use in the most ordinary way, to print or display an
announcement including an appropriate copyright notice and a
notice that there is no warranty (or else, saying that you provide
a warranty) and that users may redistribute the program under
these conditions, and telling the user how to view a copy of this
License. (Exception: if the Program itself is interactive but
does not normally print such an announcement, your work based on
the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Program,
and can be reasonably considered independent and separate works in
themselves, then this License, and its terms, do not apply to those
sections when you distribute them as separate works. But when you
distribute the same sections as part of a whole which is a work based
on the Program, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the
entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
exercise the right to control the distribution of derivative or
collective works based on the Program.
In addition, mere aggregation of another work not based on the Program
with the Program (or with a work based on the Program) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.
3. You may copy and distribute the Program (or a work based on it,
under Section 2) in object code or executable form under the terms of
Sections 1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable
source code, which must be distributed under the terms of Sections
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c) Accompany it with the information you received as to the offer
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except as expressly provided under this License. Any attempt
otherwise to copy, modify, sublicense or distribute the Program is
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However, parties who have received copies, or rights, from you under
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license would not permit royalty-free redistribution of the Program by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Program.
If any portion of this section is held invalid or unenforceable under
any particular circumstance, the balance of the section is intended to
apply and the section as a whole is intended to apply in other
circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system, which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.
8. If the distribution and/or use of the Program is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Program under this License
may add an explicit geographical distribution limitation excluding
those countries, so that distribution is permitted only in or among
countries not thus excluded. In such case, this License incorporates
the limitation as if written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time. Such new versions will
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address new problems or concerns.
Each version is given a distinguishing version number. If the Program
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either of that version or of any later version published by the Free
Software Foundation. If the Program does not specify a version number of
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Foundation.
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NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
REPAIR OR CORRECTION.
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WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
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
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
(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
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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) 19yy name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
< signature of Ty Coon >, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Library General
Public License instead of this License.
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