nmatrix-gemv 0.0.3
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- checksums.yaml +7 -0
- data/.gitignore +29 -0
- data/.rspec +2 -0
- data/.travis.yml +14 -0
- data/Gemfile +7 -0
- data/README.md +29 -0
- data/Rakefile +225 -0
- data/ext/nmatrix_gemv/binary_format.txt +53 -0
- data/ext/nmatrix_gemv/data/complex.h +399 -0
- data/ext/nmatrix_gemv/data/data.cpp +298 -0
- data/ext/nmatrix_gemv/data/data.h +771 -0
- data/ext/nmatrix_gemv/data/meta.h +70 -0
- data/ext/nmatrix_gemv/data/rational.h +436 -0
- data/ext/nmatrix_gemv/data/ruby_object.h +471 -0
- data/ext/nmatrix_gemv/extconf.rb +254 -0
- data/ext/nmatrix_gemv/math.cpp +1639 -0
- data/ext/nmatrix_gemv/math/asum.h +143 -0
- data/ext/nmatrix_gemv/math/geev.h +82 -0
- data/ext/nmatrix_gemv/math/gemm.h +271 -0
- data/ext/nmatrix_gemv/math/gemv.h +212 -0
- data/ext/nmatrix_gemv/math/ger.h +96 -0
- data/ext/nmatrix_gemv/math/gesdd.h +80 -0
- data/ext/nmatrix_gemv/math/gesvd.h +78 -0
- data/ext/nmatrix_gemv/math/getf2.h +86 -0
- data/ext/nmatrix_gemv/math/getrf.h +240 -0
- data/ext/nmatrix_gemv/math/getri.h +108 -0
- data/ext/nmatrix_gemv/math/getrs.h +129 -0
- data/ext/nmatrix_gemv/math/idamax.h +86 -0
- data/ext/nmatrix_gemv/math/inc.h +47 -0
- data/ext/nmatrix_gemv/math/laswp.h +165 -0
- data/ext/nmatrix_gemv/math/long_dtype.h +52 -0
- data/ext/nmatrix_gemv/math/math.h +1069 -0
- data/ext/nmatrix_gemv/math/nrm2.h +181 -0
- data/ext/nmatrix_gemv/math/potrs.h +129 -0
- data/ext/nmatrix_gemv/math/rot.h +141 -0
- data/ext/nmatrix_gemv/math/rotg.h +115 -0
- data/ext/nmatrix_gemv/math/scal.h +73 -0
- data/ext/nmatrix_gemv/math/swap.h +73 -0
- data/ext/nmatrix_gemv/math/trsm.h +387 -0
- data/ext/nmatrix_gemv/nm_memory.h +60 -0
- data/ext/nmatrix_gemv/nmatrix_gemv.cpp +90 -0
- data/ext/nmatrix_gemv/nmatrix_gemv.h +374 -0
- data/ext/nmatrix_gemv/ruby_constants.cpp +153 -0
- data/ext/nmatrix_gemv/ruby_constants.h +107 -0
- data/ext/nmatrix_gemv/ruby_nmatrix.c +84 -0
- data/ext/nmatrix_gemv/ttable_helper.rb +122 -0
- data/ext/nmatrix_gemv/types.h +54 -0
- data/ext/nmatrix_gemv/util/util.h +78 -0
- data/lib/nmatrix-gemv.rb +43 -0
- data/lib/nmatrix_gemv/blas.rb +85 -0
- data/lib/nmatrix_gemv/nmatrix_gemv.rb +35 -0
- data/lib/nmatrix_gemv/rspec.rb +75 -0
- data/nmatrix-gemv.gemspec +31 -0
- data/spec/blas_spec.rb +154 -0
- data/spec/spec_helper.rb +128 -0
- metadata +186 -0
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/////////////////////////////////////////////////////////////////////
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// = NMatrix
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//
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// A linear algebra library for scientific computation in Ruby.
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// NMatrix is part of SciRuby.
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//
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// NMatrix was originally inspired by and derived from NArray, by
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// Masahiro Tanaka: http://narray.rubyforge.org
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//
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// == Copyright Information
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//
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// SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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// NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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//
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// Please see LICENSE.txt for additional copyright notices.
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//
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// == Contributing
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//
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// By contributing source code to SciRuby, you agree to be bound by
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// our Contributor Agreement:
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//
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// * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
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//
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// == nm_memory.h
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//
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// Macros for memory allocation and freeing
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/**
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* We define these macros, which just call the ruby ones, as this makes
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* debugging memory issues (particularly those involving interaction with
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* the ruby GC) easier, as it's posssible to add debugging code temporarily.
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*/
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#ifndef __NM_MEMORY_H__
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#define __NM_MEMORY_H__
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#include <ruby.h>
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#define NM_ALLOC(type) (ALLOC(type))
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#define NM_ALLOC_N(type, n) (ALLOC_N(type, n))
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#define NM_REALLOC_N(var, type, n) (REALLOC_N(var, type, n))
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#define NM_ALLOCA_N(type, n) (ALLOCA_N(type, n))
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#define NM_FREE(var) (xfree(var))
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#define NM_ALLOC_NONRUBY(type) ((type*) malloc(sizeof(type)))
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//Defines whether to do conservative gc registrations, i.e. those
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//registrations that we're not that sure are necessary.
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//#define NM_GC_CONSERVATIVE
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#ifdef NM_GC_CONSERVATIVE
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#define NM_CONSERVATIVE(statement) (statement)
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#else
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#define NM_CONSERVATIVE(statement)
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#endif //NM_GC_CONSERVATIVE
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#endif
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/////////////////////////////////////////////////////////////////////
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// = NMatrix
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//
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// A linear algebra library for scientific computation in Ruby.
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// NMatrix is part of SciRuby.
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//
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// NMatrix was originally inspired by and derived from NArray, by
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// Masahiro Tanaka: http://narray.rubyforge.org
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//
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// == Copyright Information
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//
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// SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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// NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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//
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// Please see LICENSE.txt for additional copyright notices.
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//
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// == Contributing
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//
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// By contributing source code to SciRuby, you agree to be bound by
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// our Contributor Agreement:
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//
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// * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
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//
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// == nmatrix.cpp
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//
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// Main C++ source file for NMatrix. Contains Init_nmatrix and most Ruby
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// instance and class methods for NMatrix. Also responsible for calling Init
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// methods on related modules.
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/*
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* Standard Includes
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*/
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extern "C" {
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#if defined HAVE_CBLAS_H
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#include <cblas.h>
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#elif defined HAVE_ATLAS_CBLAS_H
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#include <atlas/cblas.h>
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#endif
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#if defined HAVE_CLAPACK_H
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#include <clapack.h>
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#elif defined HAVE_ATLAS_CLAPACK_H
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#include <atlas/clapack.h>
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#endif
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}
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#include <ruby.h>
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#include <algorithm> // std::min
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#include <fstream>
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/*
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* Project Includes
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*/
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#include "nmatrix_gemv_config.h"
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#include "types.h"
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#include "data/data.h"
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#include "math/math.h"
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//#include "util/io.h"
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//#include "storage/storage.h"
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//#include "storage/list/list.h"
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//#include "storage/yale/yale.h"
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#include "nmatrix_gemv.h"
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#include "ruby_constants.h"
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/*
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* Ruby internals
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*/
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/*
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* Macros
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*/
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/*
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* Global Variables
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*/
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namespace nm {
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} // end of namespace nm
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extern "C" {
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#include "ruby_nmatrix.c"
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} // end of extern "C"
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/////////////////////////////////////////////////////////////////////
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// = NMatrix
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//
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// A linear algebra library for scientific computation in Ruby.
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5
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// NMatrix is part of SciRuby.
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//
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// NMatrix was originally inspired by and derived from NArray, by
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// Masahiro Tanaka: http://narray.rubyforge.org
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//
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// == Copyright Information
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//
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// SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
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// NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
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//
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// Please see LICENSE.txt for additional copyright notices.
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//
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// == Contributing
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//
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// By contributing source code to SciRuby, you agree to be bound by
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// our Contributor Agreement:
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//
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// * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
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//
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// == nmatrix.h
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//
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// C and C++ API for NMatrix, and main header file.
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#ifndef NMATRIX_H
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#define NMATRIX_H
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/*
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* Standard Includes
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*/
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#include <ruby.h>
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#ifdef __cplusplus
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#include <cmath>
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#include <cstring>
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#else
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#include <math.h>
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#include <string.h>
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#endif
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#ifdef BENCHMARK
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// SOURCE: http://stackoverflow.com/questions/2349776/how-can-i-benchmark-a-c-program-easily
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#ifdef __cplusplus
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#include <sys/ctime>
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#include <sys/cresource>
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#else
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#include <sys/time.h>
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#include <sys/resource.h>
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#endif
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#endif
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#include "nm_memory.h"
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/*
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* Macros
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*/
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#define RUBY_ZERO INT2FIX(0)
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#ifndef SIZEOF_INT
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#error SIZEOF_INT undefined
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#else
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#if SIZEOF_INT == 8
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#define DEFAULT_DTYPE INT64
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#define SIZE_T INT64
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#else
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#if SIZEOF_INT == 4
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#define DEFAULT_DTYPE INT32
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#define SIZE_T INT32
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#else
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#if SIZEOF_INT == 2
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#define DEFAULT_DTYPE INT16
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#define SIZE_T INT16
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#else
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#error Unhandled SIZEOF_INT -- please #define SIZE_T and DEFAULT_DTYPE manually.
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#endif
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#endif
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#endif
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#endif
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/*
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* == Macros for Concurrent C and C++ Header Maintenance
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*
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* These macros look complicated, but they're really not so bad. They're also important: they ensure that whether our
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* header file (nmatrix.h) is read by a C++ or a C compiler, all the same data structures and enumerators exist, albeit
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* with slightly different names.
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*
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* "But wait," you say, "You use structs. Structs exist in C and C++. Why use a macro to set them up?"
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*
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* Well, in C, you have to be explicit about what a struct is. You can actually get around that requirement by using a
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* typedef:
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*
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* typedef struct STORAGE { ... } STORAGE;
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*
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* Also, we use C++ inheritance, which is obviously not allowed in C. So we have to ensure that the base class's members
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* are exposed properly to our child classes.
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*
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* The macros also allow us to put all of our C++ types into namespaces. For C, we prefix everything with either nm_ or
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* NM_ to distinguish our declarations from those in other libraries.
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*/
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#ifdef __cplusplus /* These are the C++ versions of the macros. */
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/*
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* If no block is given, return an enumerator. This copied straight out of ruby's include/ruby/intern.h.
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*
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* rb_enumeratorize is located in enumerator.c.
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*
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* VALUE rb_enumeratorize(VALUE obj, VALUE meth, int argc, VALUE *argv) {
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* return enumerator_init(enumerator_allocate(rb_cEnumerator), obj, meth, argc, argv);
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* }
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*/
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//opening portion -- this allows unregistering any objects in use before returning
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#define RETURN_SIZED_ENUMERATOR_PRE do { \
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if (!rb_block_given_p()) {
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//remaining portion
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#ifdef RUBY_2
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#ifndef RETURN_SIZED_ENUMERATOR
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#undef RETURN_SIZED_ENUMERATOR
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// Ruby 2.0 and higher has rb_enumeratorize_with_size instead of rb_enumeratorize.
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// We want to support both in the simplest way possible.
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#define RETURN_SIZED_ENUMERATOR(obj, argc, argv, size_fn) \
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return rb_enumeratorize_with_size((obj), ID2SYM(rb_frame_this_func()), (argc), (argv), (size_fn)); \
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} \
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} while (0)
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#endif
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#else
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#undef RETURN_SIZED_ENUMERATOR
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#define RETURN_SIZED_ENUMERATOR(obj, argc, argv, size_fn) \
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return rb_enumeratorize((obj), ID2SYM(rb_frame_this_func()), (argc), (argv)); \
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} \
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} while (0)
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#endif
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#define NM_DECL_ENUM(enum_type, name) nm::enum_type name
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#define NM_DECL_STRUCT(type, name) type name;
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#define NM_DEF_STORAGE_ELEMENTS \
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NM_DECL_ENUM(dtype_t, dtype); \
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size_t dim; \
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size_t* shape; \
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size_t* offset; \
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int count; \
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STORAGE* src;
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#define NM_DEF_STORAGE_CHILD_STRUCT_PRE(name) struct name : STORAGE {
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#define NM_DEF_STORAGE_STRUCT_POST(name) };
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#define NM_DEF_STORAGE_STRUCT \
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struct STORAGE { \
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NM_DEF_STORAGE_ELEMENTS; \
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};
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#define NM_DEF_STRUCT_PRE(name) struct name {
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#define NM_DEF_STRUCT_POST(name) };
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#define NM_DEF_ENUM(name, ...) \
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namespace nm { \
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enum name { \
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__VA_ARGS__ \
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}; \
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} // end of namespace nm
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#else /* These are the C versions of the macros. */
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#define NM_DECL_ENUM(enum_type, name) nm_ ## enum_type name
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#define NM_DECL_STRUCT(type, name) struct NM_ ## type name;
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#define NM_DEF_STORAGE_ELEMENTS \
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NM_DECL_ENUM(dtype_t, dtype); \
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size_t dim; \
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size_t* shape; \
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size_t* offset; \
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int count; \
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STORAGE* src;
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#define NM_DEF_STORAGE_CHILD_STRUCT_PRE(name) typedef struct NM_ ## name { \
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NM_DEF_STORAGE_ELEMENTS;
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+
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#define NM_DEF_STORAGE_STRUCT_POST(name) } NM_ ## name;
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+
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#define NM_DEF_STORAGE_STRUCT \
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typedef struct NM_STORAGE { \
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NM_DEF_STORAGE_ELEMENTS; \
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} NM_STORAGE;
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+
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193
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+
#define NM_DEF_STRUCT_PRE(name) typedef struct NM_ ## name {
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194
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+
#define NM_DEF_STRUCT_POST(name) } NM_ ## name;
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+
|
196
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+
#define NM_DEF_ENUM(name, ...) \
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typedef enum nm_ ## name { \
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__VA_ARGS__ \
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} nm_ ## name;
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+
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201
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+
#endif /* End of C/C++ Parallel Header Macro Definitions */
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202
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+
|
203
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+
|
204
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+
/*
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* Types
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*/
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+
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208
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#define NM_NUM_DTYPES 13 // data/data.h
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#define NM_NUM_STYPES 3 // storage/storage.h
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210
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+
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+
//#ifdef __cplusplus
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//namespace nm {
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//#endif
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+
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215
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/* Storage Type -- Dense or Sparse */
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NM_DEF_ENUM(stype_t, DENSE_STORE = 0,
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LIST_STORE = 1,
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YALE_STORE = 2);
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219
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+
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/* Data Type */
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NM_DEF_ENUM(dtype_t, BYTE = 0, // unsigned char
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INT8 = 1, // char
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+
INT16 = 2, // short
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224
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+
INT32 = 3, // int
|
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+
INT64 = 4, // long
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FLOAT32 = 5, // float
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+
FLOAT64 = 6, // double
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|
+
COMPLEX64 = 7, // Complex64 class
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229
|
+
COMPLEX128 = 8, // Complex128 class
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230
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+
RATIONAL32 = 9, // Rational32 class
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+
RATIONAL64 = 10, // Rational64 class
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+
RATIONAL128 = 11, // Rational128 class
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233
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+
RUBYOBJ = 12); // Ruby VALUE type
|
234
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+
|
235
|
+
NM_DEF_ENUM(symm_t, NONSYMM = 0,
|
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|
+
SYMM = 1,
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237
|
+
SKEW = 2,
|
238
|
+
HERM = 3,
|
239
|
+
UPPER = 4,
|
240
|
+
LOWER = 5);
|
241
|
+
|
242
|
+
//#ifdef __cplusplus
|
243
|
+
//}; // end of namespace nm
|
244
|
+
//#endif
|
245
|
+
|
246
|
+
/* struct STORAGE */
|
247
|
+
NM_DEF_STORAGE_STRUCT;
|
248
|
+
|
249
|
+
/* Dense Storage */
|
250
|
+
NM_DEF_STORAGE_CHILD_STRUCT_PRE(DENSE_STORAGE); // struct DENSE_STORAGE : STORAGE {
|
251
|
+
size_t* stride;
|
252
|
+
void* elements;
|
253
|
+
NM_DEF_STORAGE_STRUCT_POST(DENSE_STORAGE); // };
|
254
|
+
|
255
|
+
/* Yale Storage */
|
256
|
+
NM_DEF_STORAGE_CHILD_STRUCT_PRE(YALE_STORAGE);
|
257
|
+
void* a; // should go first
|
258
|
+
size_t ndnz; // Strictly non-diagonal non-zero count!
|
259
|
+
size_t capacity;
|
260
|
+
size_t* ija;
|
261
|
+
NM_DEF_STORAGE_STRUCT_POST(YALE_STORAGE);
|
262
|
+
|
263
|
+
// FIXME: NODE and LIST should be put in some kind of namespace or something, at least in C++.
|
264
|
+
NM_DEF_STRUCT_PRE(NODE); // struct NODE {
|
265
|
+
size_t key;
|
266
|
+
void* val;
|
267
|
+
NM_DECL_STRUCT(NODE*, next); // NODE* next;
|
268
|
+
NM_DEF_STRUCT_POST(NODE); // };
|
269
|
+
|
270
|
+
NM_DEF_STRUCT_PRE(LIST); // struct LIST {
|
271
|
+
NM_DECL_STRUCT(NODE*, first); // NODE* first;
|
272
|
+
NM_DEF_STRUCT_POST(LIST); // };
|
273
|
+
|
274
|
+
/* List-of-Lists Storage */
|
275
|
+
NM_DEF_STORAGE_CHILD_STRUCT_PRE(LIST_STORAGE); // struct LIST_STORAGE : STORAGE {
|
276
|
+
// List storage specific elements.
|
277
|
+
void* default_val;
|
278
|
+
NM_DECL_STRUCT(LIST*, rows); // LIST* rows;
|
279
|
+
NM_DEF_STORAGE_STRUCT_POST(LIST_STORAGE); // };
|
280
|
+
|
281
|
+
|
282
|
+
|
283
|
+
/* NMATRIX Object */
|
284
|
+
NM_DEF_STRUCT_PRE(NMATRIX); // struct NMATRIX {
|
285
|
+
NM_DECL_ENUM(stype_t, stype); // stype_t stype; // Method of storage (csc, dense, etc).
|
286
|
+
NM_DECL_STRUCT(STORAGE*, storage); // STORAGE* storage; // Pointer to storage struct.
|
287
|
+
NM_DEF_STRUCT_POST(NMATRIX); // };
|
288
|
+
|
289
|
+
/* Structs for dealing with VALUEs in use so that they don't get GC'd */
|
290
|
+
|
291
|
+
typedef struct __NM_GC_LL_NODE {
|
292
|
+
VALUE* val;
|
293
|
+
size_t n;
|
294
|
+
__NM_GC_LL_NODE* next;
|
295
|
+
} nm_gc_ll_node;
|
296
|
+
|
297
|
+
typedef struct __NM_GC_HOLDER {
|
298
|
+
__NM_GC_LL_NODE* start;
|
299
|
+
} nm_gc_holder;
|
300
|
+
|
301
|
+
#define NM_MAX_RANK 15
|
302
|
+
|
303
|
+
#define UnwrapNMatrix(obj,var) Data_Get_Struct(obj, NMATRIX, var)
|
304
|
+
|
305
|
+
#define NM_STORAGE(val) (NM_STRUCT(val)->storage)
|
306
|
+
#ifdef __cplusplus
|
307
|
+
#define NM_STRUCT(val) ((NMATRIX*)(DATA_PTR(val)))
|
308
|
+
#define NM_STORAGE_LIST(val) ((LIST_STORAGE*)(NM_STORAGE(val)))
|
309
|
+
#define NM_STORAGE_YALE(val) ((YALE_STORAGE*)(NM_STORAGE(val)))
|
310
|
+
#define NM_STORAGE_DENSE(val) ((DENSE_STORAGE*)(NM_STORAGE(val)))
|
311
|
+
#else
|
312
|
+
#define NM_STRUCT(val) ((struct NM_NMATRIX*)(DATA_PTR(val)))
|
313
|
+
#define NM_STORAGE_LIST(val) ((struct NM_LIST_STORAGE*)(NM_STORAGE(val)))
|
314
|
+
#define NM_STORAGE_YALE(val) ((struct NM_YALE_STORAGE*)(NM_STORAGE(val)))
|
315
|
+
#define NM_STORAGE_DENSE(val) ((struct NM_DENSE_STORAGE*)(NM_STORAGE(val)))
|
316
|
+
#endif
|
317
|
+
|
318
|
+
#define NM_SRC(val) (NM_STORAGE(val)->src)
|
319
|
+
#define NM_DIM(val) (NM_STORAGE(val)->dim)
|
320
|
+
#define NM_DTYPE(val) (NM_STORAGE(val)->dtype)
|
321
|
+
#define NM_STYPE(val) (NM_STRUCT(val)->stype)
|
322
|
+
#define NM_SHAPE(val,i) (NM_STORAGE(val)->shape[(i)])
|
323
|
+
#define NM_SHAPE0(val) (NM_STORAGE(val)->shape[0])
|
324
|
+
#define NM_SHAPE1(val) (NM_STORAGE(val)->shape[1])
|
325
|
+
#define NM_DEFAULT_VAL(val) (NM_STORAGE_LIST(val)->default_val)
|
326
|
+
|
327
|
+
#define NM_DENSE_COUNT(val) (nm_storage_count_max_elements(NM_STORAGE_DENSE(val)))
|
328
|
+
#define NM_DENSE_ELEMENTS(val) (NM_STORAGE_DENSE(val)->elements)
|
329
|
+
#define NM_SIZEOF_DTYPE(val) (DTYPE_SIZES[NM_DTYPE(val)])
|
330
|
+
#define NM_REF(val,slice) (RefFuncs[NM_STYPE(val)]( NM_STORAGE(val), slice, NM_SIZEOF_DTYPE(val) ))
|
331
|
+
|
332
|
+
#define NM_MAX(a,b) (((a)>(b))?(a):(b))
|
333
|
+
#define NM_MIN(a,b) (((a)>(b))?(b):(a))
|
334
|
+
#define NM_SWAP(a,b,tmp) {(tmp)=(a);(a)=(b);(b)=(tmp);}
|
335
|
+
|
336
|
+
#define NM_CHECK_ALLOC(x) if (!x) rb_raise(rb_eNoMemError, "insufficient memory");
|
337
|
+
|
338
|
+
#define RB_FILE_EXISTS(fn) (rb_funcall(rb_const_get(rb_cObject, rb_intern("File")), rb_intern("exists?"), 1, (fn)) == Qtrue)
|
339
|
+
|
340
|
+
#define CheckNMatrixType(v) if (TYPE(v) != T_DATA || (RDATA(v)->dfree != (RUBY_DATA_FUNC)nm_delete && RDATA(v)->dfree != (RUBY_DATA_FUNC)nm_delete_ref)) rb_raise(rb_eTypeError, "expected NMatrix on left-hand side of operation");
|
341
|
+
|
342
|
+
#define NM_IsNMatrix(obj) \
|
343
|
+
(rb_obj_is_kind_of(obj, cNMatrix) == Qtrue)
|
344
|
+
|
345
|
+
#define NM_IsNVector(obj) \
|
346
|
+
(rb_obj_is_kind_of(obj, cNVector) == Qtrue)
|
347
|
+
|
348
|
+
#define RB_P(OBJ) \
|
349
|
+
rb_funcall(rb_stderr, rb_intern("print"), 1, rb_funcall(OBJ, rb_intern("object_id"), 0)); \
|
350
|
+
rb_funcall(rb_stderr, rb_intern("puts"), 1, rb_funcall(OBJ, rb_intern("inspect"), 0));
|
351
|
+
|
352
|
+
|
353
|
+
#ifdef __cplusplus
|
354
|
+
typedef VALUE (*METHOD)(...);
|
355
|
+
|
356
|
+
//}; // end of namespace nm
|
357
|
+
#endif
|
358
|
+
|
359
|
+
/*
|
360
|
+
* Functions
|
361
|
+
*/
|
362
|
+
|
363
|
+
#ifdef __cplusplus
|
364
|
+
|
365
|
+
extern "C" {
|
366
|
+
#endif
|
367
|
+
|
368
|
+
void Init_nmatrix_gemv();
|
369
|
+
|
370
|
+
#ifdef __cplusplus
|
371
|
+
}
|
372
|
+
#endif
|
373
|
+
|
374
|
+
#endif // NMATRIX_H
|