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<h1 align="center">MALOC User's Guide</h1>
<p>
<h3 align="center">0.1</h3>  <center>
<b><em>A comment can go here.</b></em></center>

<h2>Table of Contents</h2>
<ol>
<li> <a href="#overview">Overview</a>
<li> <a href="#resources">Information and Resources</a>
<li> <a href="#download">Obtaining MALOC</a>
<li> <a href="#faq">Frequently Asked Questions</a>
<li> <a href="#install">Installation Instructions</a>
<li> <a href="#author">Author Information</a>
<li> <a href="#license">Copyright and Terms of Use</a>
<li> <a href="#gpl">GNU GPL</a>
</ol>

<i>
NOTE:
</i>
This documentation provides information about installation, configuration,
and general usage of the MALOC libraries. 
Information about the programming interface provided by the MALOC software
can be found in the <a href="api/html/index.html">Programmer's Guide</a>.

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<hr>

<h2><a name="overview">Overview</a></h2>

<p>
MALOC (Minimal Abstraction Layer for Object-oriented C) is a small,
portable, abstract C environment library for object-oriented
C programming.
MALOC is used as the foundation layer for a number of scientific
applications, including MC, SG, and APBS.
MALOC can be used as a small stand-alone abstraction environment for
writing portable C programs which need access to resources which
are typically architecture-dependent, such as INET sockets, timing routines,
and so on.
MALOC 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 an application code and placed in MALOC.
To port the application code to a new architecture, only the small MALOC 
library needs to be ported (usually just "./configure ; make").
MALOC takes the pain of varying UNIX (and Win32) platforms with
differing library and header layous completely out of the 
software development picture.

<p>
MALOC is a class library written in 
<a href="#cooc">Clean OO C</a>.
"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, MALOC 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).
MALOC is easily buildable from source on any UNIX-like system, and uses a
GNU autoconf build environment.

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<hr>

<h2><a name="resources">Information and Resources</a></h2>

<p>
Detailed information about MALOC can be found in the
<a href="index.html">User's Guide</a>
and
<a href="api/html/index.html">Programmers's Guide</a>.

<p>
While MALOC 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:
<ul>
<li> MALOC - Minimal Abstraction Layer for Object-oriented C programs.
<li> PUNC  - Portable Understructure for Numerical Computing.
<li> SG    - Socket Graphics mesh display tool (uses MALOC).
<li> MC    - Manifold Code finite element package (uses MALOC and PUNC).
<li> MCX   - MC eXtension libraries (uses MALOC, PUNC, and MC). 
</ul>

<p>
MALOC is self-contained, and requires only an ANSI-C compiler on a UNIX
or Win32 platform.  PUNC, 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:
<ul>
<li> <a href="http://www.fetk.org/">http://www.fetk.org/</a>
</ul>

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<hr>

<h2><a name="download">Obtaining MALOC</a></h2>

<p>
MALOC is copyrighted, but is redistributable in source and binary form
under the following <a href="#license">license</a>.
The MALOC source and binary code
can be downloaded from the following locations:
<ul>
<li> <a href="http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.tar.gz">
     http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.tar.gz
     </a>
<li> <a href="http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.i386.rpm">
     http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.i386.rpm
     </a>
<li> <a href="http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.i686.rpm">
     http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.i686.rpm
     </a>
<li> <a href="http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.ia64.rpm">
     http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.ia64.rpm
     </a>
<li> <a href="http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.ppc64pseries.rpm">
     http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.ppc64pseries.rpm
     </a>
<li> <a href="http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.x86_64.rpm">
     http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-2.x86_64.rpm
     </a>
</ul>

<p>
<ul>
<li> <a href="http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-5.tar.gz">
     BETA: http://cam.ucsd.edu/~mholst/codes/maloc/maloc-0.1-5.tar.gz
     </a>
</ul>

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<hr>

<h2><a name="faq">Frequently Asked Questions</a></h2>

<p>
<b>
What is MALOC and what does MALOC stand for?
</b>

<p>
See the <a href="#overview">Overview</a>.

<p>
<b>
How to I obtain a copy of the MALOC binaries and/or source code?
</b>

<p>
See the <a href="#download">Obtaining MALOC</a> section.

<p>
<b>
I managed to get a copy of "maloc-VERSION.[i386|src|tar].[rpm|gz]";
how do I now install MALOC?
</b>

<p>
See the <a href="#install">Installation Instructions</a>.

<p>
<b>
You gave me a "patch.gz" file to fix a bug in MALOC; how do I apply the patch?
</b>

<p>
To apply patches to upgrade MALOC 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 maloc-VERSION.tar.gz file as
described in the installation instructions.
To apply the patch, cd into the directory containing the root MALOC directory
(called "maloc" after unpacking maloc-VERSION.tar.gz) and execute the "patch"
program as follows (the patch program exists on most UNIX machines):
<ul>
<li>gzip -cd patch.gz | patch -p0
</ul>

<p>
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 MALOC (in directory
maloc_1.0 for example) to version 1.1 of MALOC (e.g. in directory maloc_1.1),
I would normally type the following:
<ul>
<li> diff -r -u -N maloc_1.0 maloc_1.1 > patch1
<li> gzip -v patch1
</ul>
which would produce the gzipped patch file "patch1.gz".  If you had previously
installed version 1.0 of MALOC but would like to upgrade to version 1.1 of
MALOC, 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 MALOC.

<p>
<b>
I really don't know what I'm doing; how to I get more documentation for MALOC?
</b>

<p>
The 
<a href="index.html">User's Guide</a>
and the
<a href="api/html/index.html">Programmers's Guide</a>
contain all of the MALOC documentation.

<p>
<b>
Why did you develop MALOC?  Can't you just use ANSI-C?
</b>

<p>
Anyone who has ported C codes that use sockets and signals to various UNIX
machines quickly realizes that there has to be a better way to do things.
GNU Autoconf solves this problem, but also then writing a small C library
which holds all of the autoconf-generated machine-dependent details
internally simplifies software development a great deal.  MALOC plays this
role in MC as well as in the entire FEtk project.

<p>
<b>
What is in all of these subdirectories?  Where exactly is "MALOC"?
</b>

<p>
MALOC consists of several (class) libraries from which you will call routines
to handle your application.  You simply link your application to the MALOC
static or shared library.  The MC package automatically looks for the MALOC
libraries as part of its Autoconf configuration process.
<pre style="font-family: Courier New">
                                   maloc
                                     |
                         ------------------------
                        /      |     |      |    \ 
                       config doc examples src tools
</pre>
The src directory has the additional subdirectory structure:
<pre style="font-family: Courier New">
                                   src
                                    |
                         -------------------------
                        /     |      |    |   |   \
                    aaa_inc aaa_lib base psh vsh vsys
</pre>
Within each library source directory is an additional subdirectory,
"maloc".  The "maloc" 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 MALOC.  

<p>
The following is a brief description of each subdirectory of the package.
<pre style="font-family: Courier New">
    maloc             - The entire MALOC package
    maloc/config      - GNU Autoconf scripts and non-unix config files
    maloc/doc         - MALOC documentation
    maloc/examples    - Complex examples and data files for using MALOC
    maloc/src         - MALOC source code (all source and headers)
    maloc/src/aaa_inc - Header installation tools
    maloc/src/aaa_lib - Library installation tools
    maloc/src/*/maloc - The MALOC headers (API)
    maloc/src/base    - Source for M. Holst's BASE  (MALOC foundation headers)
    maloc/src/vsys    - Source for M. Holst's VSYS  (Virtual SYStem layer)
    maloc/src/vsh     - Source for M. Holst's VSH   (Virtual command SHell)
    maloc/src/psh     - Source for M. Holst's PSH   (Parallel vSH extension)
    maloc/tools       - Some binary tools for use with MALOC
</pre>

<p>
<b>
Okay, I seem to have installed MALOC correctly; how do I actually use it now?
</b>

<p>
Using MALOC is pretty simple; it is a very object-oriented implementation,
although it is written in C.  It is actually written in an object-oriented
way using a subset of ANSI/Standard C, sometimes referred to as
<a href="#cooc">Clean OO C</a>.
Clean C refers to 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).

<p>
<b>
What is the class hierarchy?  How are the various libraries related?
</b>

<p>
Detailed information on the class relationships can be found
in the 
<a href="api/html/index.html">Programmers's Guide</a>.
The following directed graph shows the class library dependencies.
(This tends to evolve as MALOC is developed.)
<pre style="font-family: Courier New">
   ANSI-C ===> base ==> vsys ==> vsh ==> psh
                         /\       /\      /\
                         ||       ||      ||
               UNIX/INET sockets  ||     MPI
                                  ||
                               signals
</pre>

<p>
<b>
<a name="cooc">
What is <i>Clean C</i>?
</a>
</b>

<p>
Clean C is simply a subset of ISO C which is compatible with
(the current draft) standard C++; i.e., Clean C is the intersection of
the standard accepted definitions of C and C++.
ISO C is currently the internationally accepted version of C; ISO C was
previously called ANSI C, and the term Standard C (as opposed to Tradiational
or K&R C) is also now used for ISO C.
Clean C programs are ISO C programs that use only the
new C++-style function prototypes, and avoid using names 
that are reserved words in C++ (such as class, public, etc).
There are a few other differences between ISO C and C++ that one has to
be careful of (such as struct/union scopes, typedef syntax, storage classes,
const and cast usage, initializers, "sizeof" differences), 
but the prototypes and reserved words are the main restrictions.
Clean C programs can then be compiled with any ISO C compiler
or any standard C++ compiler on any architecture.
In other words, Clean C programs are actually C++ programs, but they only use
C++ features that can be handled with an ISO C compiler.
Clean C is a very small, simple, fast, powerful, yet extremely portable
language.
The name "Clean C" for this C dialect seems to have been first coined in
the book of Harbison and Steele, "C: A Reference Manual"; this excellent
C reference has a thorough discussion of the various dialects of C.

<p>
<b>
What is <i>Clean OO C</i>?
</b>

<p>
The "OO" in "Clean OO C"
refers to the programming style
employed -- Object Oriented (it does not refer to syntax as did the
word "Clean" above).
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.)
Much like C++, a careful Clean OO C implementation 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 Win32.

<p>
<b>
Why <i>would</i> someone program in Clean OO C?
</b>

<p>
Clean OO C seems to be a good language compromise:
a very small language, but powerful enough to provide a great deal of
abstraction.
In addition, one can continue to use various integrated C++ development
environments under Win32 (such as the Watcom and Microsoft products),
making use of the symbolic debuggers and so on,
since Clean OO C programs are still legal C++ programs.
The book of A. Holub, "C+C++: Programming with Objects in C and C++" was
a very useful guide for doing an object-oriented implementation in (ISO) C.

<p>
Avoiding use of the <tt>inline</tt> function in C++
is a difficult sacrifice to make 
in moving to Clean OO C (note that GCC actually provides the
inline function, although most ISO C compilers do not).
Inlining in Clean OO C can be emulated using macros.
This can be made reasonably
safe by implementing two versions of all macro'd routines --
a normal Clean OO C routine, and a macro version.
Switching between the two can be as simple as setting or unsetting a 
macro in a makefile; this way if things start to go wrong, the macros can be 
turned into real functions with prototypes, and the code can be stepped 
through with a debugger.
Another useful feature of C++, from a practical large-package software 
engineering point of view,
is the "public/protected/private" keywords in class definitions.
This functionality can be recovered to a small
degree by careful use of header files and the "static" keyword
in a Clean OO C implementation.

<p>
<b>
Why is MALOC written in <i>Clean OO C</i> rather than C++ or Objective-C?
</b>

<p>
A brief explanation can be found <a href="#cooc">here</a>.

<p>
<b>
I want to write software to extend MALOC; besides the <i>Clean OO C</i>
framework, what is the "Coding Style"?
</b>

<p>
A fairly complete description of the coding style guidelines used in
writing MALOC (and all of FEtk) can be found in the
<a href="api/html/index.html">Programmers's Guide</a>.

<p>
<b>
I wrote a cool MALOC extension; how do I get it included in the MALOC package?
</b>

<p>
To keep the core FEtk libraries as small, efficient, stable, and
bullet-proof as possible, I distribute extensions to any of MALOC,
PUNC, MC, and/or SG in a package called MCX (MC eXtension Library).
MCX is developed collaboratively by a number of collaborators.
In addition, several application-specific software
packages have been written such as GPDE (Geometric PDE) which use
FEtk to solve a number of different application problems.
If you wish to contribute to MCX, and are willing to release you
contributions under the GNU GPL, then I would be delighted to include
it in MCX.

<p>
If you need special modifications to FEtk to support your particular
contribution or your particular FEtk-based application, let me know.
If you provide me with a clear description of an interface to FEtk that you
need, then I will almost always consider making the modifications to FEtk
for you.  In any event, the general guideline for such proposed changes is
that they be fairly minimal to avoid breaking too many other things that
rely on the existing structure of FEtk, and general enough to be useful
for other extensions (and in particular, not application-specific).

<!--------------------------------------------------------------------------->
<hr>

<h2><a name="install">Installation Instructions</a></h2>

<p>
<b>
Available distribution formats
</b>

<p>
MALOC is distributed in both binary format (as a binary RPM file
maloc-VERSION.i386.rpm for i386-based versions of Linux) and in source
format (as a source RPM file maloc-VERSION.src.rpm and as a gzipped tar
file "maloc-VERSION.tar.gz").

<p>
<b>
Installation using the binary RPM file
</b>

<p>
The following rpm command will install all of the MALOC headers and libraries
into /usr/local/include and /usr/local/lib, and will install the MALOC
documentation into /usr/share/doc/packages/maloc:
<pre style="font-family: Courier New">
    rpm -Uvh maloc-VERSION.i386.rpm
</pre>

<p>
<b>
Installation and rebuilding from sources using the source RPM file
</b>

<p>
The following rpm command will unpack the source rpm file
"maloc-VERSON.src.rpm" into the MALOC gzipped tar file containing
the sources called "maloc-VERSION.tar.tar.gz" and into a small RPM
spec file called "maloc-VERSON.spec":
<pre style="font-family: Courier New">
    rpm -Uvh maloc-VERSION.src.rpm
</pre>
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:
<pre style="font-family: Courier New">
    rpm -bp maloc-VERSION.spec
</pre>

<p>
<b>
Rebuilding binary and source RPM files from the gzipped tar file
</b>

<p>
The MALOC sources contain the RPM spec file "maloc-VERSON.spec" in the
root source directory; as a result, rebuilding the RPM files from sources
can be done using the rpm command:
<pre style="font-family: Courier New">
    rpm -ta maloc-VERSION.tar.gz
</pre>
The result will be the corresponding source and binary rpm files,
named "maloc-VERSON.src.rpm" and "maloc-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).

<p>
<b>
Installation and building from sources using the gzipped tar file
</b>

<p>
The following command will unpack 
MALOC into a number of subdirectories and files on any UNIX machine
(and on any WinNT machine with the GNU-Win32 tools gzip and tar).
<pre style="font-family: Courier New">
    gzip -dc maloc-VERSION.tar.gz | tar xvf -
</pre>

<p>
<b>
Building the package using the GNU "configure" shell script and "make"
</b>

<p>
The "configure" shell script in the "maloc" directory (the toplevel
directory created when you unpacked the MALOC tar.gz file) will build the entire
package.  This is a standard GNU autoconf-generated configuration script.
For a list of the possible configuration options, type:
<pre style="font-family: Courier New">
    ./configure --help
</pre>
You should be able to build MALOC by simply typing:
<pre style="font-family: Courier New">
    ./configure
    make
    make install
</pre>
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 MALOC in a separate directory from the
source tree as follows:
<pre style="font-family: Courier New">
    gzip -dc maloc-VERSION.tar.gz | tar xvf -
    mkdir maloc_build
    cd maloc_build
    ../maloc/configure
    make
    make install
</pre>

<p>
<b>
Building binaries for multiple architectures in the same source directory
</b>

<p>
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 MALOC for all the systems at the same time,
you simply make an additional subdirectory in the main MALOC 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:
<pre style="font-family: Courier New">
    mkdir linux
    cp configure linux/.
    cd linux
    ./configure
    make
    make install
</pre>
If you mount the same NFS home directory on for example an OpenStep box,
you could at the same time do the following:
<pre style="font-family: Courier New">
    mkdir next
    cp configure next/.
    cd next
    ./configure
    make
    make install
</pre>
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.

<p>
<b>
Building shared libraries rather than static libraries
</b>

<p>
(MIKE: give an overview of libtool.)

<p>
<b>
Rebuilding the configure script and the Makefile.in files
</b>

<p>
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 MALOC source tree.

<p>
<b>
Platform-specific information
</b>

<p>
Below is some platform-specific build/usage information for MALOC.
<ul>
<li>Linux   (Source:  M. Holst, UCSD)
<p>
    Things should work as described above.
<p>
<li>FreeBSD/NetBSD/OpenBSD   (Source:  M. Holst, UCSD)
<p>
    Things should work as described above.
<p>
<li>OpenStep   (Source:  M. Holst, UCSD)
<p>
    Things should just work, but you may have to set the CC environment
    variable as follows before typing ./configure:
<pre style="font-family: Courier New">
    export CC="/bin/cc"
</pre>
    or you might need to use:
<pre style="font-family: Courier New">
    export CC="/bin/cc -ObjC"
</pre>
<p>
<li>IRIX   (Source:  M. Holst, UCSD)
<p>
    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: 
<pre style="font-family: Courier New">
    export CC="/bin/cc -64"
</pre>
    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: 
<pre style="font-family: Courier New">
    export CC="/bin/cc -32"
</pre>
<p>

<li>Win32   (Source:  M. Holst, UCSD)
<p>
    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.
</ul>

<p>
<b>
What you end up with
</b>

<p>
Once the build completes via the "configure;make;make install" procedure above
with no errors, the MALOC library (libmaloc.a and/or libmaloc.so) is installed
into the specified installation directory.  You can also build some useful
tools that employ the MALOC library by cd-ing into the "tools" subdirectory and
repeating the "configure;make;make install" procedure.

<p>
<b>
Using MALOC on a parallel computer
</b>

<p>
MALOC provides abstractions to both INET sockets and MPI for communication
support in parallel computing software.  Control of the overall structure is
accomplished through MALOC-shell scripts you write, or through calls to the
MALOC library.  (Going through the MALOC-shell is much simpler, and you have
access to all the communication possibilities through the MALOC-shell.)
The use of the parallel features of MALOC is explained in more detail in
the documentation that is included in the MC library.

<p>
<b>
Getting MALOC to find your installation of MPI
</b>

<p>
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).
<ul>
<li>Solution 1:  
<p>
    Have your system administrator install MPI in a proper system
    directory so that MALOC (and other AUTOCONF-based codes) can find it!
<p>
<li>Solution 2:  
<ol>
<li>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:
<pre style="font-family: Courier New">
    locate mpi.h
    locate libmpi.a
    locate libmpich.a
</pre>
    On my Redhat6.2 Linux box, the following output is produced:
<pre style="font-family: Courier New">
    bash:~% locate mpi.h
    /usr/share/mpi/include/mpi.h
    bash:~% locate libmpi.a
    bash:~% locate libmpich.a
    /usr/share/mpi/lib/libmpich.a
</pre>
    Therefore the MPI header is installed as:
<pre style="font-family: Courier New">
    /usr/share/mpi/include/mpi.h
</pre>
    and the MPI library is installed as:
<pre style="font-family: Courier New">
    /usr/share/mpi/lib/libmpich.a
</pre>

<li>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:
<pre style="font-family: Courier New">
    export FETK_MPI_INCLUDE=/usr/share/mpi/include
    export FETK_MPI_LIBRARY=/usr/share/mpi/lib
    ./configure --enable-mpi
    make clean; make; make install
</pre>
    The configure script should now report that it successfully
    found the library and header and thus enabled MPI, and then
    MALOC should compile without error.
</ol>
</ul>

<!--------------------------------------------------------------------------->
<hr>

<h2><a name="author">Author Information</a></h2>

<p>
MALOC (Minimal Abstraction Layer for Object-oriented C) 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 MALOC
(see the credits list below).
<pre style="font-family: Courier New">
    MALOC (Minimal Abstraction Layer for Object-oriented C)
    Copyright (C) 1994-2006

    Michael Holst               TELE:  (858) 534-4899
    Department of Mathematics   FAX:   (858) 534-5273
    UC San Diego, AP&M 5739     EMAIL: mholst@math.ucsd.edu
    La Jolla, CA 92093 USA      WEB:   http://cam.ucsd.edu/~mholst
</pre>
MALOC was designed to be a portable abstraction layer for use in the
development of MC (Manifold Code), an adaptive multilevel finite element
package also developed by Michael Holst.
MALOC 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).

<p>
MALOC 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 softare, MALOC 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 MALOC; a copy can be found
<a href="#gpl">here</a>.
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.

<p>
<b>
Credits
</b>

<p>
Below is a credits list for the people that have
contributed to MALOC 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:
<pre style="font-family: Courier New">
          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
</pre>
<pre style="font-family: Courier New">
N: Michael Holst
E: mholst@math.ucsd.edu
W: http://cam.ucsd.edu/~mholst
P: 1024/0xB5212DCD
D: maloc/*                      -- The package structure
D: maloc/acconfig.h             -- The platform abstraction information
D: maloc/configure.in           -- The GNU autoconf/automake structure
D: maloc/config/*               -- The GNU autoconf/automake shell scripts
D: maloc/doc/*                  -- The package documentation
D: maloc/examples/*             -- The package examples
D: maloc/src/aaa_inc/*          -- Library header build structure
D: maloc/src/aaa_lib/*          -- Static and shared library build structure
D: maloc/src/base/*             -- M. Holst's MALOC Foundation headers
D: maloc/src/vsys/*             -- M. Holst's Virtual System abstraction layer
D: maloc/src/vsh/*              -- M. Holst's Virtual Shell abstraction layer
D: maloc/src/psh/*              -- M. Holst's Parallel virtual Shell
D: maloc/tools/*                -- Tools built on the libraries
S: Department of Mathematics
S: UC San Diego, AP&M 5739
S: La Jolla, CA 92093 USA

N: Nathan Baker
E: nbaker@wasabi.ucsd.edu
D: maloc/src/psh/vcom.c         -- Vcom Class (MPI abstraction)
S: Department of Chemistry
S: UC San Diego
S: La Jolla, CA 92093 USA

N: Steve Bond
E: bond@math.ucsd.edu
D: maloc/maloc.spec             -- RPM support (for building src/binary RPMs)
S: Department of Mathematics
S: UC San Diego
S: La Jolla, CA 92093 USA
</pre> 

<p>
<b>
Contacting the Author
</b>

<p>
If you have questions or comments about MALOC, please feel free to contact
me at <a HREF="mailto:mholst@math.ucsd.edu">mholst@math.ucsd.edu</a>.

<!--------------------------------------------------------------------------->
<hr>

<h2><a name="license">Copyright and Terms of Use</a></h2>

<i>Please acknowledge your use of MALOC and FEtk</i> by citing:
<ul>
<li> M. Holst, Adaptive numerical treatment of elliptic systems on manifolds.
     <i>Advances in Computational Mathematics</i>,
     <b>15</b> (2001), pp. 139-191.
</ul>

<p>
This version of MALOC is distributed under the following guidelines:

<ul>
<li>
   MALOC (Minimal Abstraction Layer for Object-oriented C)
<br>
   Copyright (C) 1994-2006  Michael Holst
   
<p>
   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.
   
<p>
   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.
   
<p>
   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.
</ul>

<!--------------------------------------------------------------------------->
<hr>

<h2><a name="gpl">GNU GPL</a></h2>

<p>
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

<!--------------------------------------------------------------------------->

<pre style="font-family: Courier New">
		    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
freedom to share and change it.  By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
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
the GNU Library General Public License instead.)  You can apply it to
your programs, too.

  When we speak of free software, we are referring to freedom, not
price.  Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
this service if you wish), that you receive source code or can get it
if you want it, that you can change the software or use pieces of it
in new free programs; and that you know you can do these things.

  To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
distribute copies of the software, or if you modify it.

  For example, if you distribute copies of such a program, whether
gratis or for a fee, you must give the recipients all the rights that
you have.  You must make sure that they, too, receive or can get the
source code.  And you must show them these terms so they know their
rights.

  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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  Also, for each author's protection and ours, we want to make certain
that everyone understands that there is no warranty for this free
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  Finally, any free program is threatened constantly by software
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  The precise terms and conditions for copying, distribution and
modification follow.

		    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
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the term "modification".)  Each licensee is addressed as "you".

Activities other than copying, distribution and modification are not
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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
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    part thereof, to be licensed as a whole at no charge to all third
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    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
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    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
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  3. You may copy and distribute the Program (or a work based on it,
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If distribution of executable or object code is made by offering
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distribution of the source code, even though third parties are not
compelled to copy the source along with the object code.

  4. You may not copy, modify, sublicense, or distribute the Program
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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  5. You are not required to accept this License, since you have not
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the only way you could satisfy both it and this License would be to
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If any portion of this section is held invalid or unenforceable under
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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
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This section is intended to make thoroughly clear what is believed to
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  8. If the distribution and/or use of the Program is restricted in
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may add an explicit geographical distribution limitation excluding
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  9. The Free Software Foundation may publish revised and/or new versions
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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
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.
</pre>

</TD>
</TABLE>
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