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 bin 2009-09-01 Raymond Toy Raymond Toy [3fc88b] Ignore sse2f.
 doc 2013-03-26 Akshay Srinivasan Akshay Srinivasan [ba36a2] Merge branch 'tensor' of ssh://matlisp.git.sour...
 lib-src 2014-03-20 Akshay Srinivasan Akshay Srinivasan [5b70af] Removed some garbled letters from dot.lisp.
 src 2014-05-04 Akshay Srinivasan Akshay Srinivasan [a59673] Added cs-matrix -> standard tensor copy method.
 tests 2014-04-02 Akshay Srinivasan Akshay Srinivasan [a195dc] Saving state.
 .gitignore 2011-03-04 Raymond Toy Raymond Toy [ac01ce] Ignore *~.
 AUTHORS 2013-08-23 Akshay Srinivasan Akshay Srinivasan [6fb610] Cleaned up random.
 COPYING 2011-01-25 Raymond Toy Raymond Toy [f32b09] Merge changes from automake-snapshot-2011-01-25...
 COPYRIGHT 2000-04-13 simsek simsek [9894bf] This is the Matlisp copyright.
 ChangeLog 2011-01-25 Raymond Toy Raymond Toy [f32b09] Merge changes from automake-snapshot-2011-01-25...
 HOWTO 2000-07-11 simsek simsek [e36834] *** empty log message ***
 INSTALL 2011-03-02 Raymond Toy Raymond Toy [b5b63a] Fix instructions. autoreconf before cd build.
 ISSUES 2011-04-21 Raymond Toy Raymond Toy [e30fc3] Note build issue on OSX 10.6 and m4.
 Makefile 2001-04-25 Raymond Toy Raymond Toy [b97d10] Don't remove config.status and config.log for m...
 Makefile.am 2013-03-26 Akshay Srinivasan Akshay Srinivasan [ba36a2] Merge branch 'tensor' of ssh://matlisp.git.sour...
 NEWS 2011-02-18 Raymond Toy Raymond Toy [c2b87b] Add GELSY. From Evan Monroig, with permission.
 README 2014-03-25 Akshay Srinivasan Akshay Srinivasan [6a5d74] Updated README.
 config.guess 2005-06-19 Raymond Toy Raymond Toy [70b149] I don't really remember, but I think this is an...
 config.lisp.in 2013-03-26 Akshay Srinivasan Akshay Srinivasan [ba36a2] Merge branch 'tensor' of ssh://matlisp.git.sour...
 config.sub 2005-06-19 Raymond Toy Raymond Toy [70b149] I don't really remember, but I think this is an...
 configure 2013-09-10 Akshay Srinivasan Akshay Srinivasan [f8b87a] Made changes to build on a Mac.
 configure.ac 2013-09-10 Akshay Srinivasan Akshay Srinivasan [f8b87a] Made changes to build on a Mac.
 install-sh 2000-04-13 simsek simsek [ddaad2] A script used by 'configure'
 matlisp.asd 2014-05-04 Akshay Srinivasan Akshay Srinivasan [5b7710] Added fibonacci.lisp to ASDF.
 packages.lisp 2014-04-02 Akshay Srinivasan Akshay Srinivasan [a195dc] Saving state.
 purgargs.awk 2000-07-11 simsek simsek [56fba8] o Initial revision
 save.lisp 2011-02-18 Raymond Toy Raymond Toy [2cabcf] Make save-matlisp-library work again with asdf.
 start.lisp.in 2012-07-24 Akshay Srinivasan Akshay Srinivasan [855c68] Merge branch 'master' into tensor

Read Me

# -*- Mode: org -*-
MatLisp is intended to be a base for scientific computation in Lisp.
This is the development branch of Matlisp.

MatLisp is made from a mixture of CLOS, lots of macros and a healthy disdain for
other programming languages :) The old version of Matlisp was aimed mostly towards
handling matrices: being a Lispy-interface to BLAS/LAPACK amongst other things.

The version in development is intended for more general usage. The current version can handle
general dense tensors, sparse matrices, and more!

It generates and compiles type-specialized generic methods on the fly, and uses lots of macros
to simplify writing very tight loops.

* Why MatLisp(and Lisp)?
  Lisp is a very hacker friendly language - the difference between
  source and binary is almost non-existent. With Lisp, you have at your disposable
  the complete Lisp language, with CLOS, macros, and tons of libraries.
  Using compilers such as SBCL, and macros.

** How does this compare to Matlab, SciPy, Octave, R etc?
   These packages are in a much more mature stage than Matlisp. This also implies
   that we lack a lot of the features which come from having a thriving ecosystem.
   However, Matlisp was built with the hope that expressibility and performance don't
   necessarily have to mutually exclusive; in that we're not alone: Lush, and Julia
   both have similar goals.

   The usual scientific environment is an amalgamation of a slow, interpreted, dynamically
   typed language with tons of libraries and sugary interfaces to BLAS/LAPACK.

   On the other hand, Common Lisp, is compiled + interpreted, dynamically typed + optional type
   declarations + type inferencing, and comes with an awesome development environment: SLIME.
   It, of course, suffers from the ultimate sin, not being popular.

   With all things equal(which they are not), Matlisp(+SBCL) beats or is about as
   fast as any of these packages; if you really want to squeeze every bit of
   computational power, you can in most cases optimize loops, so that they're
   as fast as C. However, there are limitations to what you can do vs C, because
   of the Lisp implementation overheads (things like SSE, blocked computation).

   For instance,
   > (defun mm (A B C)
       (einstein-sum real-tensor (j k i) (ref C i j) (* (ref A i j) (ref B j k))))
   basically generates an extremely tight naive 3-loop version of GEMM (can you figure
   out the reason for the odd loop-index ordering ?), which is only about 10 times as
   slow the optimized version of GEMM in OpenBLAS (which does blocked computation).
   The performance with SBCL for the above is within 10-15% of the corresponding C
   code.

* How to Install
  Matlisp uses CFFI for callng foreign functions. That said, the FFI
  capabilities of different lisps are quite different. So if your Lisp
  implementation supports callbacks and calling plain C functions and
  maps float simple-arrays into C-type arrays in memory, it shouldn't
  be too hard to get it working (if it doesn't work already). We've tested
  Matlisp on CCL and SBCL. The build system is cranky with all the new changes.


  Linux/Unix Installation:
  ========================

  One of the design goals of Matlisp was to ensure the consistency of
  installation.  Matlisp is currently distributed as source code and the
  user must do a compilation.  A great deal of effort was put into a
  configure script that determines machine parameters, system libraries
  and without bothering the user.

  The installation follows in a few easy steps:

  Download and install quicklisp http://www.quicklisp.org/beta/; make sure the quicklisp directory is "~/quicklisp/"
  (This step makes sure that CFFI is available, more advanced users can skip this and install
  CFFI and make it visible to ASDF).

  Download the Matlisp:
  > git clone git://git.code.sf.net/p/matlisp/git matlisp-git
  > cd matlisp-git
  > git checkout tensor

  Install all the configuration scripts the first time.
  > autoreconf --install

  Create a build directory.  (You can use any name you like).
  > mkdir build
  > cd build

  Use the following if you want to build and use the reference blas/lapack implementation.
  > ../configure --libdir=$PWD/lib --enable-static=no --enable-<lisp> --with-lisp-exec=<exec>
  (<lisp> \in {sbcl, ccl, cmucl, acl})
  You don't need to build matlisp in order to use a different lisp implementations (yes, this
  is quite redundant).

  If you already have a optimized version of BLAS/LAPACK:
  > ../configure --libdir=$PWD/lib --enable-static=no --enable-<lisp> --with-lisp-exec=<exec> --with-external-blas-lapack=<path>
  On linux, <path> is usually /usr/lib/
  On Mac OSX, you can use vecLib by setting <path> to /System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/A/

  If configure does not select the desired Fortran compiler and
  compiler flags, you can specify them like this:
  ../configure F77=f77 FFLAGS='-g -O -KPIC' ...

  Avanti!
  > make
  This should land you in a lisp shell at the end.

  To use matlisp after building just call
  CL-USER> (load "<matlisp-path>/build/start.lisp")
  CL-USER> (in-package :matlisp)

* Example usage
  More documentation will be added as things reach a nicer stage of development.

  ;;Creation
  MATLISP> (copy! (randn '(2 2)) (zeros '(2 2) 'complex-tensor))
  #<COMPLEX-TENSOR #(2 2)
  -1.5330     -1.67578E-2
  -.62578     -.63278
  >

  ;;gemv
  MATLISP> (let ((a (randn '(2 2)))
		 (b (randn 2)))
	     (gemv 1 a b nil nil))
  #<REAL-TENSOR #(2)
  1.1885     0.95746
  >

  ;;Tensor contraction
  MATLISP> (let ((H (randn '(2 2 2)))
		 (b (randn 2))
		 (c (randn 2))
		 (f (zeros 2)))
	     (einstein-sum real-tensor (i j k) (ref f i) (* (ref H i j k) (ref b j) (ref c k))))
  #<REAL-TENSOR #(2)
  0.62586     -1.1128
  >

* Progress Tracker
** What works ?
   * Generic template structure.
   * Double real, complex tensor structures in place.
   * Templates for optimized BLAS methods in Lisp.
   * Automatic switching between Lisp routines and BLAS.
   * Inplace slicing, real - imag views for complex tensors.
   * copy, scal, dot, swap, axpy, gemv, gemm, getrf/getrs (lu), geev(eig), potrf/potrs(chol), geqr
   * permutation class, sorting, conversion between action and
     cycle representations.
   * mod-loop works, can produce very quick multi-index loops.
   * einstein macro works, can produce optimized loops.

** TODO : What remains ? (Help!)
*** Functionality
   * Make everything in src/old/ compatible with new datastrutures.
   * Add negative stride support, ala Python.
   * Tensor contraction: Hard to do very quickly.
     Might have to copy stuff into a contiguous array; like Femlisp.
   * LAPACK: Add interfaces to remaining functions.
   * DFFTPACK: computing FFTs
   * QUADPACK: Move from f2cl-ed version to the Fortran one.
   * MINPACK: Move from f2cl-ed version to the Fortran one.
   * ODEPACK: Add abstraction for DLSODE, and DLSODAR may others too.

*** Syntactic sugar
   * Add array slicing macros
   * Might have to add something to make it compatible with old Matlisp.

*** Gnuplot interface
   * Make gnuplot interface more usable.

*** Python-bridge
    (C)Python has far too many things, that we cannot even begin to hope to replicate.
    Burgled-batteries has a lot of things which could be useful in talking to CPython.

    Getting standard-tensor <-> numpy tranlation should be enough. Mostly care about
    matplotlib at the moment.

*** Add infix to Matlisp
    Added Mark Kantrowicz' infix package into lib-src. Should be straight forward to use it,
    although changes are not strictly local.

*** Support linking to libraries ?
    Parse header files with cffi-grovel.

*** Documentation, tests
    * Write documentation.
      Fix the formatting for docstrings. Maybe move to TeXinfo (like femlisp).
    * Write tests
      Use cl-rt stuff to write more tests. Probably even add benchmarks.

*** Symbolics, AD, more fancy stuff {wishlist}
   * Use things like macrofy to work with Maxima
   * Provide seamless AD, Symbolic differentiation and numerical function calls, ala scmutils.
   * Symbolic stuff tends to fit in easily with the lisp-based BLAS routines.
     Port code from src/classes/symbolic-tensor.lisp

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