Add scientific computing libraries (#3390)

Add the following:
  arpack_ng.rb
  hdf5.rb
  openmpi.rb
  superlu.rb

Rename liblapack.rb to lapack.rb and update

Update armadillo from 8.400.0 to 9.600.5

Add pre-built binaries

packages/armadillo.rb

@@ -3,35 +3,40 @@ require 'package'
 class Armadillo < Package
   description 'Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use'
   homepage 'http://arma.sourceforge.net/'
-  version '8.400.0'
-  source_url 'https://downloads.sourceforge.net/project/arma/armadillo-8.400.0.tar.xz'
-  source_sha256 '5cb6bc2f457a9d6a0758cfb15c418d48289909daccd79d0e428452029285dd9b'
+  version '9.600.5'
+  source_url 'https://downloads.sourceforge.net/project/arma/armadillo-9.600.5.tar.xz'
+  source_sha256 'dd9cd664282f2c3483af194ceedc2fba8559e0d20f8782c640fd6f3ac7cac2bf'
 
   binary_url ({
-    aarch64: 'https://dl.bintray.com/chromebrew/chromebrew/armadillo-8.400.0-chromeos-armv7l.tar.xz',
-     armv7l: 'https://dl.bintray.com/chromebrew/chromebrew/armadillo-8.400.0-chromeos-armv7l.tar.xz',
-       i686: 'https://dl.bintray.com/chromebrew/chromebrew/armadillo-8.400.0-chromeos-i686.tar.xz',
-     x86_64: 'https://dl.bintray.com/chromebrew/chromebrew/armadillo-8.400.0-chromeos-x86_64.tar.xz',
+    aarch64: 'https://dl.bintray.com/chromebrew/chromebrew/armadillo-9.600.5-chromeos-armv7l.tar.xz',
+     armv7l: 'https://dl.bintray.com/chromebrew/chromebrew/armadillo-9.600.5-chromeos-armv7l.tar.xz',
+       i686: 'https://dl.bintray.com/chromebrew/chromebrew/armadillo-9.600.5-chromeos-i686.tar.xz',
+     x86_64: 'https://dl.bintray.com/chromebrew/chromebrew/armadillo-9.600.5-chromeos-x86_64.tar.xz',
   })
   binary_sha256 ({
-    aarch64: '97a7f23c22e8dcd9b92806918bd2a5f7a72230f8b16033ca3dfc6ebebc8fc2f5',
-     armv7l: '97a7f23c22e8dcd9b92806918bd2a5f7a72230f8b16033ca3dfc6ebebc8fc2f5',
-       i686: 'bbefa4f2c66db16180c367d4e6bb568cbcf9abd5d26b19266f9d744e93ebda9c',
-     x86_64: 'd2dc68a222aa585676e5ea325970ded3015ad817027aca890199bc7f5c090799',
+    aarch64: 'cabc00c9184da1185c0fcbe834c1447e0e31a9ff34b9c2ede39f7419b95768cc',
+     armv7l: 'cabc00c9184da1185c0fcbe834c1447e0e31a9ff34b9c2ede39f7419b95768cc',
+       i686: 'cead7ef29533291a9070b8b1cddf6d909c224463e0e984a4d5bf49a208f17590',
+     x86_64: '313502ef0f2c9c701c4e5c59d456a6105c8aba4c63bc0a77a829649ffa2e9e78',
   })
 
-  depends_on 'openblas'
+  depends_on 'arpack_ng'
+  depends_on 'hdf5'
+  depends_on 'superlu'
 
   def self.build
-    system "./configure",
+    suffix = ''
+    suffix = '64' if ARCH == 'x86_64'
+    system 'cmake',
+           '-DCMAKE_BUILD_TYPE=Release',
            "-DCMAKE_INSTALL_PREFIX=#{CREW_PREFIX}",
-           "-DCMAKE_INSTALL_LIBDIR=#{CREW_LIB_PREFIX}"
-    system "make"
+           "-DCMAKE_INSTALL_LIBDIR=#{ARCH_LIB}",
+           "-DARPACK_LIBRARY=#{CREW_LIB_PREFIX}/libarpack#{suffix}.so",
+           '.'
+    system 'make'
   end
 
   def self.install
-    system "make",
-           "DESTDIR=#{CREW_DEST_DIR}",
-           "install"
+    system 'make', "DESTDIR=#{CREW_DEST_DIR}", 'install'
   end
 end

packages/arpack_ng.rb

+require 'package'
+
+class Arpack_ng < Package
+  description 'Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.'
+  homepage 'https://github.com/opencollab/arpack-ng'
+  version '3.7.0'
+  source_url 'https://github.com/opencollab/arpack-ng/archive/3.7.0.tar.gz'
+  source_sha256 '972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6'
+
+  binary_url ({
+    aarch64: 'https://dl.bintray.com/chromebrew/chromebrew/arpack_ng-3.7.0-chromeos-armv7l.tar.xz',
+     armv7l: 'https://dl.bintray.com/chromebrew/chromebrew/arpack_ng-3.7.0-chromeos-armv7l.tar.xz',
+       i686: 'https://dl.bintray.com/chromebrew/chromebrew/arpack_ng-3.7.0-chromeos-i686.tar.xz',
+     x86_64: 'https://dl.bintray.com/chromebrew/chromebrew/arpack_ng-3.7.0-chromeos-x86_64.tar.xz',
+  })
+  binary_sha256 ({
+    aarch64: '8ac867cd31ef8c507039105de1e6467807c30a75f1752ab43650d82348b558d0',
+     armv7l: '8ac867cd31ef8c507039105de1e6467807c30a75f1752ab43650d82348b558d0',
+       i686: '8c2096851e7868c456220480b315d8ba84b5c188d8bf193cf8ce8abea6b20eb4',
+     x86_64: '83b1d11cbc66d977dc2287f8273a39527bd33c302b81baaa84172c110b6aeed1',
+  })
+
+  depends_on 'lapack'
+  depends_on 'openblas'
+  depends_on 'openmpi'
+  depends_on 'ld_default' => :build
+
+  def self.patch
+    # Fix Unknown CMake command "check_symbol_exists".
+    # See https://techoverflow.net/2019/06/20/how-to-fix-unknown-cmake-command-check_symbol_exists/.
+    system "sed -i '1iinclude(CheckSymbolExists)' CMakeLists.txt"
+  end
+
+  def self.build
+    Dir.mkdir 'build'
+    Dir.chdir 'build' do
+      suffix = ''
+      interface = 'OFF'
+      if ARCH == 'x86_64'
+        suffix = '64'
+        interface = 'ON'
+      end
+      # Use the gold linker. 
+      old_ld = `ld_default g`.chomp
+      system 'cmake',
+             '-DCMAKE_BUILD_TYPE=Release',
+             "-DCMAKE_INSTALL_PREFIX=#{CREW_PREFIX}",
+             "-DBLAS_LIBRARIES=#{CREW_LIB_PREFIX}/libopenblas.so",
+             "-DINTERFACE64=#{interface}",
+             "-DLIBSUFFIX=#{suffix}",
+             '-DBUILD_SHARED_LIBS=ON',
+             '-DEXAMPLES=ON',
+             '-DICB=ON',
+             '-DMPI=ON',
+             '..'
+      system 'make'
+      system 'ld_default', "#{old_ld}"
+    end
+  end
+
+  def self.install
+    Dir.chdir 'build' do
+      system 'make', "DESTDIR=#{CREW_DEST_DIR}", 'install'
+    end
+  end
+end

packages/hdf5.rb

+require 'package'
+
+class Hdf5 < Package
+  description 'HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.'
+  homepage 'https://www.hdfgroup.org/'
+  version '1.10.5'
+  source_url 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5.tar.bz2'
+  source_sha256 '68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44'
+
+  binary_url ({
+    aarch64: 'https://dl.bintray.com/chromebrew/chromebrew/hdf5-1.10.5-chromeos-armv7l.tar.xz',
+     armv7l: 'https://dl.bintray.com/chromebrew/chromebrew/hdf5-1.10.5-chromeos-armv7l.tar.xz',
+       i686: 'https://dl.bintray.com/chromebrew/chromebrew/hdf5-1.10.5-chromeos-i686.tar.xz',
+     x86_64: 'https://dl.bintray.com/chromebrew/chromebrew/hdf5-1.10.5-chromeos-x86_64.tar.xz',
+  })
+  binary_sha256 ({
+    aarch64: 'e1f92f38039d13d530ef8dee9f0c2bf3ddb9be9be3a60adee6bb82dc87a62a3a',
+     armv7l: 'e1f92f38039d13d530ef8dee9f0c2bf3ddb9be9be3a60adee6bb82dc87a62a3a',
+       i686: 'd56fe7f4f5e7234fad92a98cd081a812d07f4906c190ba3d615c1a14ca188957',
+     x86_64: '258e724a97f0943a940f1b8663a591efeff11ffc507ca51ecd0ffe38b3997fdb',
+  })
+
+  def self.build
+    system './configure',
+           "--prefix=#{CREW_PREFIX}",
+           "--libdir=#{CREW_LIB_PREFIX}",
+           '--disable-maintainer-mode',
+           '--disable-static'
+    system 'make'
+  end
+
+  def self.install
+    system "make", "DESTDIR=#{CREW_DEST_DIR}", "install"
+  end
+end

packages/lapack.rb

+require 'package'
+
+class Lapack < Package
+  description 'Lapack is a linear algebra package.'
+  homepage 'https://www.netlib.org/lapack/'
+  version '3.8.0-1'
+  source_url 'https://www.netlib.org/lapack/lapack-3.8.0.tar.gz'
+  source_sha256 'deb22cc4a6120bff72621155a9917f485f96ef8319ac074a7afbc68aab88bcf6'
+
+  binary_url ({
+    aarch64: 'https://dl.bintray.com/chromebrew/chromebrew/lapack-3.8.0-1-chromeos-armv7l.tar.xz',
+     armv7l: 'https://dl.bintray.com/chromebrew/chromebrew/lapack-3.8.0-1-chromeos-armv7l.tar.xz',
+       i686: 'https://dl.bintray.com/chromebrew/chromebrew/lapack-3.8.0-1-chromeos-i686.tar.xz',
+     x86_64: 'https://dl.bintray.com/chromebrew/chromebrew/lapack-3.8.0-1-chromeos-x86_64.tar.xz',
+  })
+  binary_sha256 ({
+    aarch64: 'f93b9afdd088faa48b11735b7467a2056f13efc98d0edc158166364f1edd795d',
+     armv7l: 'f93b9afdd088faa48b11735b7467a2056f13efc98d0edc158166364f1edd795d',
+       i686: '3f3d266856c00034b1f3a1efad00a4a8d838ecbc3682cc7a3788fbb209ff0da7',
+     x86_64: '45aec7ef9a9c37e098be7fd80b88c580bef29181b398e6e4c8d15cee9ddf7456',
+  })
+
+  depends_on 'python27'
+
+  def self.build
+    Dir.mkdir 'build'
+    Dir.chdir 'build' do
+      system 'cmake',
+             '-DCMAKE_BUILD_TYPE=Release',
+             "-DCMAKE_INSTALL_PREFIX=#{CREW_PREFIX}",
+             "-DCMAKE_INSTALL_LIBDIR=#{CREW_LIB_PREFIX}",
+             '-DBUILD_SHARED_LIBS=ON',
+             '..'
+      system 'make'
+    end
+  end
+
+  def self.install
+    Dir.chdir 'build' do
+      system 'make', "DESTDIR=#{CREW_DEST_DIR}", 'install'
+    end
+  end
+end

packages/liblapack.rb

-require 'package'
-
-class Liblapack < Package                 # The first character of the class name must be upper case
-  description 'Lapack is a linear algebra package.'
-  homepage 'http://www.netlib.org/lapack/#_lapack_version_3_8_0'
-  version '3.8.0'
-  source_url 'http://www.netlib.org/lapack/lapack-3.8.0.tar.gz'
-  source_sha256 'deb22cc4a6120bff72621155a9917f485f96ef8319ac074a7afbc68aab88bcf6'   # Use the command "sha256sum"
-
-  binary_url ({
-    aarch64: 'https://dl.bintray.com/chromebrew/chromebrew/liblapack-3.8.0-chromeos-armv7l.tar.xz',
-     armv7l: 'https://dl.bintray.com/chromebrew/chromebrew/liblapack-3.8.0-chromeos-armv7l.tar.xz',
-       i686: 'https://dl.bintray.com/chromebrew/chromebrew/liblapack-3.8.0-chromeos-i686.tar.xz',
-     x86_64: 'https://dl.bintray.com/chromebrew/chromebrew/liblapack-3.8.0-chromeos-x86_64.tar.xz',
-  })
-  binary_sha256 ({
-    aarch64: 'b0a873d5eae0a920c67c7fd7101b1c4d8f2486f46a553632b5bc1e3792618c6d',
-     armv7l: 'b0a873d5eae0a920c67c7fd7101b1c4d8f2486f46a553632b5bc1e3792618c6d',
-       i686: 'df07a794c858335da05f4ca3ad547d8aa86e4a5472035c32e83524288315ef6c',
-     x86_64: '049da8a6932acae411f33f603ce0a4a2b1544cfda49627033068947f323cf36e',
-  })
-
-  depends_on 'cmake' => :build
-
-  def self.build
-    Dir.mkdir 'build'
-    Dir.chdir 'build' do
-    system "cmake .. -DCMAKE_INSTALL_PREFIX=#{CREW_PREFIX} -DCMAKE_INSTALL_LIBDIR=#{CREW_DEST_LIB_PREFIX}"
-    system "make"
-    end
-  end
-
-  def self.install
-    Dir.chdir 'build' do
-    system "make", "DESTDIR=#{CREW_DEST_DIR}", "install"
-    end
-  end  
-end

packages/openmpi.rb

+require 'package'
+
+class Openmpi < Package
+  description 'The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners.'
+  homepage 'https://www.open-mpi.org/'
+  version '4.0.1'
+  source_url 'https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.1.tar.bz2'
+  source_sha256 'cce7b6d20522849301727f81282201d609553103ac0b09162cf28d102efb9709'
+
+  binary_url ({
+    aarch64: 'https://dl.bintray.com/chromebrew/chromebrew/openmpi-4.0.1-chromeos-armv7l.tar.xz',
+     armv7l: 'https://dl.bintray.com/chromebrew/chromebrew/openmpi-4.0.1-chromeos-armv7l.tar.xz',
+       i686: 'https://dl.bintray.com/chromebrew/chromebrew/openmpi-4.0.1-chromeos-i686.tar.xz',
+     x86_64: 'https://dl.bintray.com/chromebrew/chromebrew/openmpi-4.0.1-chromeos-x86_64.tar.xz',
+  })
+  binary_sha256 ({
+    aarch64: '6ebfd586e6e8efcbdda5ec1c69356bf29adc2c15844405fc9fd6b595330cebff',
+     armv7l: '6ebfd586e6e8efcbdda5ec1c69356bf29adc2c15844405fc9fd6b595330cebff',
+       i686: '7b95e3be4d88619c4abdbe3df69534b023955699ec7633f310cb77bf320514d0',
+     x86_64: '3985ef364b793db8053ae6a3640549a635bdda668134100e3017b17634e82eed',
+  })
+
+  def self.build
+    system './configure',
+           "--prefix=#{CREW_PREFIX}",
+           "--libdir=#{CREW_LIB_PREFIX}",
+           '--disable-maintainer-mode'
+    system 'make'
+  end
+
+  def self.install
+    system "make", "DESTDIR=#{CREW_DEST_DIR}", "install"
+  end
+end

packages/superlu.rb

+require 'package'
+
+class Superlu < Package
+  description 'SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations.'
+  homepage 'https://portal.nersc.gov/project/sparse/superlu/'
+  version '5.2.1'
+  source_url 'https://github.com/xiaoyeli/superlu/archive/v5.2.1.tar.gz'
+  source_sha256 '77582501dedef295eb74e4dc9433e2816d2d8be211eae307379c13d93c65bc71'
+
+  binary_url ({
+    aarch64: 'https://dl.bintray.com/chromebrew/chromebrew/superlu-5.2.1-chromeos-armv7l.tar.xz',
+     armv7l: 'https://dl.bintray.com/chromebrew/chromebrew/superlu-5.2.1-chromeos-armv7l.tar.xz',
+       i686: 'https://dl.bintray.com/chromebrew/chromebrew/superlu-5.2.1-chromeos-i686.tar.xz',
+     x86_64: 'https://dl.bintray.com/chromebrew/chromebrew/superlu-5.2.1-chromeos-x86_64.tar.xz',
+  })
+  binary_sha256 ({
+    aarch64: 'ba7c045b4aefe809e33de9fe35476cca3ed62af1e38ec162c5e199d36d8181e1',
+     armv7l: 'ba7c045b4aefe809e33de9fe35476cca3ed62af1e38ec162c5e199d36d8181e1',
+       i686: '5f72a5326b985427af744b7de4d379141bb71acf3a0611726ff14fc8832019b5',
+     x86_64: '349e683c9d47ecd626543ed10fd2a76561eeb122ecfff7e45d67798db53c5d2c',
+  })
+
+  def self.build
+    Dir.mkdir 'build'
+    Dir.chdir 'build' do
+      system 'cmake',
+             "-DCMAKE_INSTALL_PREFIX=#{CREW_PREFIX}",
+             "-DCMAKE_INSTALL_LIBDIR=#{ARCH_LIB}",
+             '-DCMAKE_BUILD_TYPE=Release',
+             '-DBUILD_SHARED_LIBS=ON',
+             '..'
+      system 'make'
+    end
+  end
+
+  def self.check
+    Dir.chdir 'build' do
+      system 'make', 'test'
+    end
+  end
+
+  def self.install
+    Dir.chdir 'build' do
+      system 'make', "DESTDIR=#{CREW_DEST_DIR}", 'install'
+    end
+  end
+end