ruby-mpi 0.3.2 → 0.4.0

data/ruby-mpi.gemspec

@@ -2,20 +2,20 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: ruby-mpi 0.3.2 ruby lib
+# stub: ruby-mpi 0.4.0 ruby lib
 # stub: ext/mpi/extconf.rb
 
 Gem::Specification.new do |s|
-  s.name = "ruby-mpi"
-  s.version = "0.3.2"
+  s.name = "ruby-mpi".freeze
+  s.version = "0.4.0"
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.require_paths = ["lib"]
-  s.authors = ["Seiya Nishizawa"]
-  s.date = "2016-02-15"
-  s.description = "A ruby binding of Message Passing Interface (MPI), which is an API specification that allows processes to communicate with one another by sending and receiving messages."
-  s.email = "seiya@gfd-dennou.org"
-  s.extensions = ["ext/mpi/extconf.rb"]
+  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib".freeze]
+  s.authors = ["Seiya Nishizawa".freeze]
+  s.date = "2024-11-22"
+  s.description = "A ruby binding of Message Passing Interface (MPI), which is an API specification that allows processes to communicate with one another by sending and receiving messages.".freeze
+  s.email = "seiya@gfd-dennou.org".freeze
+  s.extensions = ["ext/mpi/extconf.rb".freeze]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -35,42 +35,37 @@ Gem::Specification.new do |s|
     "lib/mpi/utils.rb",
     "ruby-mpi.gemspec",
     "samples/hello.rb",
+    "samples/kmeans.rb",
     "samples/narray.rb",
     "samples/narray_offset.rb",
+    "samples/pi.rb",
     "spec/ruby-mpi_spec.rb",
     "spec/spec_helper.rb",
     "test/test_utils.rb"
   ]
-  s.homepage = "http://github.com/seiya/ruby-mpi"
-  s.licenses = ["MIT"]
-  s.rubygems_version = "2.4.8"
-  s.summary = "A ruby binding of MPI"
+  s.homepage = "http://github.com/gfd-dennou-club/ruby-mpi".freeze
+  s.licenses = ["MIT".freeze]
+  s.rubygems_version = "3.2.5".freeze
+  s.summary = "A ruby binding of MPI".freeze
 
   if s.respond_to? :specification_version then
     s.specification_version = 4
+  end
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<numru-narray>, ["~> 1.0"])
-      s.add_development_dependency(%q<rspec>, [">= 2.3.0"])
-      s.add_development_dependency(%q<bundler>, [">= 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, [">= 1.5.2"])
-      s.add_development_dependency(%q<simplecov>, [">= 0"])
-      s.add_development_dependency(%q<rake-compiler>, [">= 0"])
-    else
-      s.add_dependency(%q<numru-narray>, ["~> 1.0"])
-      s.add_dependency(%q<rspec>, [">= 2.3.0"])
-      s.add_dependency(%q<bundler>, [">= 1.0.0"])
-      s.add_dependency(%q<jeweler>, [">= 1.5.2"])
-      s.add_dependency(%q<simplecov>, [">= 0"])
-      s.add_dependency(%q<rake-compiler>, [">= 0"])
-    end
+  if s.respond_to? :add_runtime_dependency then
+    s.add_runtime_dependency(%q<numru-narray>.freeze, ["~> 1.0"])
+    s.add_development_dependency(%q<rspec>.freeze, [">= 2.3.0"])
+    s.add_development_dependency(%q<bundler>.freeze, [">= 1.0.0"])
+    s.add_development_dependency(%q<jeweler>.freeze, [">= 1.5.2"])
+    s.add_development_dependency(%q<simplecov>.freeze, [">= 0"])
+    s.add_development_dependency(%q<rake-compiler>.freeze, [">= 0"])
   else
-    s.add_dependency(%q<numru-narray>, ["~> 1.0"])
-    s.add_dependency(%q<rspec>, [">= 2.3.0"])
-    s.add_dependency(%q<bundler>, [">= 1.0.0"])
-    s.add_dependency(%q<jeweler>, [">= 1.5.2"])
-    s.add_dependency(%q<simplecov>, [">= 0"])
-    s.add_dependency(%q<rake-compiler>, [">= 0"])
+    s.add_dependency(%q<numru-narray>.freeze, ["~> 1.0"])
+    s.add_dependency(%q<rspec>.freeze, [">= 2.3.0"])
+    s.add_dependency(%q<bundler>.freeze, [">= 1.0.0"])
+    s.add_dependency(%q<jeweler>.freeze, [">= 1.5.2"])
+    s.add_dependency(%q<simplecov>.freeze, [">= 0"])
+    s.add_dependency(%q<rake-compiler>.freeze, [">= 0"])
   end
 end
 

data/samples/kmeans.rb

@@ -0,0 +1,137 @@
+# Run this program using
+#
+# mpirun -np numprocs ruby kmeans.rb numpoints numclusters
+#
+# where numprocs, numpoints and numclusters are integers
+# and numprocs <= numpoints and numclusters <= numpoints
+#
+# Parallelization assumes that numclusters << numpoints
+# and that numprocs << numpoints
+#
+# The program is based on the description at
+# https://en.wikipedia.org/wiki/K-means_clustering
+
+require "mpi"
+if defined?(NumRu::NArray)
+  include NumRu
+end
+
+def generate_points count
+  x = NArray.float(count).random
+  y = NArray.float(count).random
+  return x , y 
+end
+
+MPI.Init
+
+world = MPI::Comm::WORLD
+
+size = world.size
+rank = world.rank
+
+def usage(rank)
+ if rank==0
+   print <<EOF
+Usage: mpirun -np numproc ruby #$0 numpoints numclusters
+
+       numpoints and numclusters must be integers > 0
+       numclusters <= numpoints and numproc <= numpoints
+EOF
+ end
+  MPI.Finalize
+  exit -1
+end
+
+usage(rank) if ARGV.length != 2
+usage(rank) if ( ( /^\d+$/ =~ ARGV[0] ) != 0)
+usage(rank) if ( ( /^\d+$/ =~ ARGV[1] ) != 0)
+n_points = ARGV[0].to_i
+n_clusters = ARGV[1].to_i
+usage(rank) unless n_points > size
+usage(rank) unless n_clusters > 0
+usage(rank) unless n_points >= n_clusters
+
+my_points = n_points.div(size) 
+if ( n_points % size > rank  ) 
+  my_points +=  1
+end
+
+cluster_x = NArray.float(n_clusters)
+cluster_y = NArray.float(n_clusters)
+my_cluster = NArray.int(my_points)
+min_distance = NArray.float(my_points)
+distance = NArray.float(n_clusters)
+cluster_member_count = NArray.int(n_clusters)
+total_cluster_x_sum = NArray.float(n_clusters)
+total_cluster_y_sum = NArray.float(n_clusters)
+total_cluster_member_count = NArray.int(n_clusters)
+my_cluster_x = NArray.float(n_clusters)
+my_cluster_y = NArray.float(n_clusters)
+my_cluster_member_count = NArray.int(n_clusters)
+my_energy = NArray.float(1)
+total_energy = NArray.float(1)
+random_x = NArray.float(n_clusters)
+random_y = NArray.float(n_clusters)
+
+my_x, my_y = generate_points my_points
+if rank == 0
+  cluster_x, cluster_y = generate_points n_clusters
+end
+world.Bcast(cluster_x,0)
+world.Bcast(cluster_y,0)
+
+iter = 0
+# Do 10 iterations for testing purposes
+# in practice would use some convergence 
+# criteria
+while iter < 10 do
+  # Find cluster and calculate energy
+  i = 0 
+  my_energy[0] = 0
+  while i < my_points do
+    distance = ( cluster_x - my_x[i] )**2 + ( cluster_y - my_y[i] )**2
+    min_distance = distance.min
+    my_energy[0] += min_distance
+    # If multiple minimum values, take the first one
+    my_cluster[i] = distance.eq(min_distance).where[0]
+    i +=1
+  end
+  world.Allreduce(my_energy,total_energy,MPI::Op::SUM)
+  if rank == 0
+    p total_energy[0]
+  end
+  # Find new cluster centroids
+  j = 0
+  while j < n_clusters do
+    mask = my_cluster.eq(j)
+    my_cluster_member_count[j] = mask.count_true
+    if mask.any?
+      my_cluster_x[j] = (my_x[mask]).sum
+      my_cluster_y[j] = (my_y[mask]).sum
+    end
+    j +=1
+  end
+  world.Allreduce(my_cluster_member_count,total_cluster_member_count,MPI::Op::SUM)
+  world.Allreduce(my_cluster_x,total_cluster_x_sum,MPI::Op::SUM)
+  world.Allreduce(my_cluster_y,total_cluster_y_sum,MPI::Op::SUM)
+  # If a cluster is empty, choose a random point to try
+  no_members = total_cluster_member_count.eq(0)
+  if no_members.any?
+    if rank == 0
+      random_x, random_y = generate_points no_members.count_true
+      total_cluster_member_count[no_members]= 1
+      total_cluster_x_sum[no_members] = random_x
+      total_cluster_y_sum[no_members] = random_y
+      cluster_x = total_cluster_x_sum / total_cluster_member_count
+      cluster_y = total_cluster_y_sum / total_cluster_member_count
+    end
+    world.Bcast(cluster_x,0)
+    world.Bcast(cluster_y,0)
+  else
+    cluster_x = total_cluster_x_sum / total_cluster_member_count
+    cluster_y = total_cluster_y_sum / total_cluster_member_count
+  end
+iter += 1
+end
+
+MPI.Finalize

data/samples/pi.rb

@@ -0,0 +1,59 @@
+# Run this program using
+#
+# mpirun -np 2 ruby pi.rb numpoints
+#
+# where numpoints is an integer
+# 
+# The program is based on an example from
+# https://carpentries-incubator.github.io/hpc-intro/16-parallel/index.html
+
+require "mpi"
+if defined?(NumRu::NArray)
+  include NumRu
+end
+
+def inside_circle my_count
+  x = NArray.float(my_count).random
+  y = NArray.float(my_count).random
+  a = ((x**2 + y**2) < 1.0)
+  return a.count_true
+end
+
+MPI.Init
+
+world = MPI::Comm::WORLD
+
+size = world.size
+rank = world.rank
+
+def usage(rank)
+ if rank==0
+   print <<EOF
+Usage: mpirun -np numproc ruby #$0 numpoints
+       numpoints must be an integer > 0
+EOF
+ end
+  MPI.Finalize
+  exit -1
+end
+usage(rank) if ARGV.length != 1
+usage(rank) if ( ( /^\d+$/ =~ ARGV[0] ) != 0)
+n_samples = ARGV[0].to_i
+usage(rank) unless n_samples > 0
+
+my_samples = n_samples.div(size) 
+if ( n_samples % size > rank  ) 
+  my_samples = my_samples + 1
+end
+
+my_count = NArray[0]
+count = NArray[0]
+
+my_count[0] = inside_circle my_samples 
+
+world.Reduce(my_count,count,MPI::Op::SUM,0)
+if ( rank == 0 )
+  p "Pi is approximately " + ((count[0]*4.0)/(1.0*n_samples)).to_s
+end
+
+MPI.Finalize