scbi_mapreduce 0.0.40 → 0.0.45

data/skeleton/simple/launch_only_workers.rb

@@ -0,0 +1,29 @@
+#!/usr/bin/env ruby
+
+$: << File.dirname(__FILE__)
+
+require "logger"
+
+$: << '/Users/dariogf/progs/ruby/gems/scbi_mapreduce/lib'
+
+require 'scbi_mapreduce'
+require 'my_worker_manager'
+
+
+$LOG = Logger.new(STDOUT)
+$LOG.datetime_format = "%Y-%m-%d %H:%M:%S"
+
+ip='10.247.255.5'
+port = 50000
+workers = 8
+
+custom_worker_file = File.join(File.dirname(__FILE__),'my_worker.rb')
+
+$LOG.info 'Starting server'
+
+
+worker_launcher = ScbiMapreduce::WorkerLauncher.new(ip,port, workers, custom_worker_file, STDOUT)
+worker_launcher.launch_workers_and_wait
+
+# launch processor server
+$LOG.info 'Closing workers'

metadata

@@ -1,96 +1,71 @@
 --- !ruby/object:Gem::Specification
 name: scbi_mapreduce
 version: !ruby/object:Gem::Version
-  version: 0.0.40
-  prerelease: 
+  version: 0.0.45
 platform: ruby
 authors:
-- Dario Guerrero
+- dariogf
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-09-16 00:00:00.000000000 Z
+date: 2016-03-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: eventmachine
+  name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.12.0
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 0.12.0
-- !ruby/object:Gem::Dependency
-  name: json
-  requirement: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
+        version: '1.7'
+  type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '1.7'
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: rake
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '10.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.0'
+        version: '10.0'
 - !ruby/object:Gem::Dependency
-  name: newgem
+  name: eventmachine
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.5.3
-  type: :development
+        version: 0.12.0
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.5.3
+        version: 0.12.0
 - !ruby/object:Gem::Dependency
-  name: hoe
+  name: json
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '3.6'
-  type: :development
+        version: '0'
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '3.6'
+        version: '0'
 description: scbi_mapreduce brings parallel and distributed computing capabilities
   to your code, with a very easy to use framework that allows you to exploit your
   clustered or cloud computational resources.
@@ -99,90 +74,107 @@ email:
 executables:
 - scbi_mapreduce
 extensions: []
-extra_rdoc_files:
-- History.txt
-- Manifest.txt
-- PostInstall.txt
-- README.rdoc
-- skeleton/simple/README.txt
-- skeleton/remove_mids/README.txt
-- skeleton/dummy_calcs/README.txt
+extra_rdoc_files: []
 files:
-- History.txt
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/scbi_mapreduce
+- lib/scbi_mapreduce.rb
 - lib/scbi_mapreduce/error_handler.rb
+- lib/scbi_mapreduce/launcher.sh
 - lib/scbi_mapreduce/main_worker.rb
 - lib/scbi_mapreduce/manager.rb
+- lib/scbi_mapreduce/version.rb
 - lib/scbi_mapreduce/work_manager.rb
 - lib/scbi_mapreduce/worker.rb
-- lib/scbi_mapreduce/launcher.sh
-- lib/scbi_mapreduce/zlib_serializer.rb
 - lib/scbi_mapreduce/worker_launcher.rb
-- lib/scbi_mapreduce.rb
-- Manifest.txt
-- PostInstall.txt
-- Rakefile
-- README.rdoc
-- script/console
-- script/destroy
-- script/generate
-- test/drb_test/main.rb
-- test/drb_test/my_worker.rb
-- test/drb_test/my_worker_manager.rb
-- test/drb_test/scbi_drb_checkpoint
-- test/drb_test/scbi_mapreduce_checkpoint
-- test/test_helper.rb
-- test/test_scbi_drb.rb
-- bin/scbi_mapreduce
-- skeleton/simple/main.rb
-- skeleton/simple/my_worker.rb
-- skeleton/simple/my_worker_manager.rb
-- skeleton/simple/README.txt
+- lib/scbi_mapreduce/zlib_serializer.rb
+- scbi_mapreduce.gemspec
+- skeleton/.DS_Store
+- skeleton/dummy_calcs/.DS_Store
+- skeleton/dummy_calcs/README.txt
+- skeleton/dummy_calcs/lib/calculations.rb
+- skeleton/dummy_calcs/lib/thread_pool.rb
+- skeleton/dummy_calcs/linear_implementation.rb
+- skeleton/dummy_calcs/main.rb
+- skeleton/dummy_calcs/my_worker.rb
+- skeleton/dummy_calcs/my_worker_manager.rb
+- skeleton/dummy_calcs/threads_implementation.rb
+- skeleton/old/dummy_calculations/README.txt
+- skeleton/old/dummy_calculations/lib/calculations.rb
+- skeleton/old/dummy_calculations/lib/thread_pool.rb
+- skeleton/old/dummy_calculations/main.rb
+- skeleton/old/dummy_calculations/my_worker.rb
+- skeleton/old/dummy_calculations/my_worker_manager.rb
+- skeleton/old/dummy_calculations/threads_implementation.rb
+- skeleton/old/sequences_blast/README.txt
+- skeleton/old/sequences_blast/launch_only_workers.rb
+- skeleton/old/sequences_blast/lib/db/mids.fasta
+- skeleton/old/sequences_blast/lib/db/mids.fasta.nhr
+- skeleton/old/sequences_blast/lib/db/mids.fasta.nin
+- skeleton/old/sequences_blast/lib/db/mids.fasta.nog
+- skeleton/old/sequences_blast/lib/db/mids.fasta.nsd
+- skeleton/old/sequences_blast/lib/db/mids.fasta.nsi
+- skeleton/old/sequences_blast/lib/db/mids.fasta.nsq
+- skeleton/old/sequences_blast/lib/find_mids.rb
+- skeleton/old/sequences_blast/lib/thread_pool.rb
+- skeleton/old/sequences_blast/linear_implementation.rb
+- skeleton/old/sequences_blast/logs/worker0_osiris-2.local_log.txt
+- skeleton/old/sequences_blast/logs/worker1_osiris-2.local_log.txt
+- skeleton/old/sequences_blast/main.rb
+- skeleton/old/sequences_blast/my_worker.rb
+- skeleton/old/sequences_blast/my_worker_manager.rb
+- skeleton/old/sequences_blast/results.fastq
+- skeleton/old/sequences_blast/test_threads.rb
+- skeleton/old/sequences_blast/threads_implementation.rb
+- skeleton/remove_mids/README.txt
 - skeleton/remove_mids/launch_only_workers.rb
 - skeleton/remove_mids/lib/db/mids.fasta
+- skeleton/remove_mids/lib/db/mids.fasta.nhr
+- skeleton/remove_mids/lib/db/mids.fasta.nin
+- skeleton/remove_mids/lib/db/mids.fasta.nog
+- skeleton/remove_mids/lib/db/mids.fasta.nsd
+- skeleton/remove_mids/lib/db/mids.fasta.nsi
+- skeleton/remove_mids/lib/db/mids.fasta.nsq
 - skeleton/remove_mids/lib/find_mids.rb
 - skeleton/remove_mids/lib/global_match.rb
 - skeleton/remove_mids/linear_implementation.rb
 - skeleton/remove_mids/main.rb
 - skeleton/remove_mids/my_worker.rb
 - skeleton/remove_mids/my_worker_manager.rb
-- skeleton/remove_mids/README.txt
-- skeleton/dummy_calcs/lib/calculations.rb
-- skeleton/dummy_calcs/lib/thread_pool.rb
-- skeleton/dummy_calcs/linear_implementation.rb
-- skeleton/dummy_calcs/main.rb
-- skeleton/dummy_calcs/my_worker.rb
-- skeleton/dummy_calcs/my_worker_manager.rb
-- skeleton/dummy_calcs/README.txt
-- skeleton/dummy_calcs/threads_implementation.rb
-- .gemtest
-homepage: http://www.scbi.uma.es/downloads
-licenses: []
-post_install_message: PostInstall.txt
-rdoc_options:
-- --main
-- README.rdoc
+- skeleton/remove_mids/results.fastq558292
+- skeleton/remove_mids/results.fastq662870
+- skeleton/simple/README.txt
+- skeleton/simple/launch_only_workers.rb
+- skeleton/simple/main.rb
+- skeleton/simple/my_worker.rb
+- skeleton/simple/my_worker_manager.rb
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: scbi_mapreduce
-rubygems_version: 1.8.24
+rubyforge_project: 
+rubygems_version: 2.4.4
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: scbi_mapreduce brings parallel and distributed computing capabilities to
-  your code, with a very easy to use framework that allows you to exploit your clustered
-  or cloud computational resources.
-test_files:
-- test/test_helper.rb
-- test/test_scbi_drb.rb
+  your code.
+test_files: []

data/History.txt

@@ -1,93 +0,0 @@
-=== 0.0.40 2013-09-05
-
-Generation of additional statistics, write, read and working times
-
-=== 0.0.39 2012-10-01
-
-Sleep on SIGCONT to solve wake up issue with PBS
-
-=== 0.0.38 2012-04-13
-
-Automatic checkpointing improvements
-
-=== 0.0.37 2011-10-20
-
-Memory management improvement
-
-=== 0.0.36 2011-10-14
-
-Automatically search for a valid network if a preffered one is not provided
-
-=== 0.0.35 2011-07-07
-
-Change method to retrieve a list of available ips
-
-=== 0.0.34 2011-07-07
-
-Close ssh after worker creation with nohup
-
-=== 0.0.33 2011-06-23
-
-Changed worker launching method to avoid process count overkill
-
-=== 0.0.32 2011-06-20
-
-Removed ruby 1.9.2 requisite
-
-=== 0.0.31 2011-06-17
-
-Total connected workers stats
-
-=== 0.0.30 2011-06-17
-
-Report local workers
-
-=== 0.0.29 2011-06-13
-
-First rubygems release
-
-=== 0.0.21 2011-05-19
-
-added zlib serialization
-
-=== 0.0.20 2011-05-18
-
-Own serializer
-
-=== 0.0.19 2011-05-11
-
-Added dummy_calculations skeleton
-
-=== 0.0.18 2011-05-11
-
-Added fibo skeleton
-
-=== 0.0.17 2011-05-09
-
-New sequence Skeleton
-
-=== 0.0.16 2011-05-05
-
-Automatically create log directory
-
-=== 0.0.4 2010-08-26
-
-* 1 minor fix:
-  * add initial config interchange between server and workers
-
-
-=== 0.0.3 2010-08-24
-
-* 1 minor fix:
-  * changed start_worker from post_init
-
-
-=== 0.0.2 2010-08-06
-
-* 1 minor fix:
-  * changed logs names
-
-=== 0.0.1 2010-06-11
-
-* 1 major enhancement:
-  * Initial release

data/Manifest.txt

@@ -1,47 +0,0 @@
-History.txt
-lib/scbi_mapreduce/error_handler.rb
-lib/scbi_mapreduce/main_worker.rb
-lib/scbi_mapreduce/manager.rb
-lib/scbi_mapreduce/work_manager.rb
-lib/scbi_mapreduce/worker.rb
-lib/scbi_mapreduce/launcher.sh
-lib/scbi_mapreduce/zlib_serializer.rb
-lib/scbi_mapreduce/worker_launcher.rb
-lib/scbi_mapreduce.rb
-Manifest.txt
-PostInstall.txt
-Rakefile
-README.rdoc
-script/console
-script/destroy
-script/generate
-test/drb_test/logs
-test/drb_test/main.rb
-test/drb_test/my_worker.rb
-test/drb_test/my_worker_manager.rb
-test/drb_test/scbi_drb_checkpoint
-test/drb_test/scbi_mapreduce_checkpoint
-test/test_helper.rb
-test/test_scbi_drb.rb
-bin/scbi_mapreduce
-skeleton/simple/main.rb
-skeleton/simple/my_worker.rb
-skeleton/simple/my_worker_manager.rb
-skeleton/simple/README.txt
-skeleton/remove_mids/launch_only_workers.rb
-skeleton/remove_mids/lib/db/mids.fasta
-skeleton/remove_mids/lib/find_mids.rb
-skeleton/remove_mids/lib/global_match.rb
-skeleton/remove_mids/linear_implementation.rb
-skeleton/remove_mids/main.rb
-skeleton/remove_mids/my_worker.rb
-skeleton/remove_mids/my_worker_manager.rb
-skeleton/remove_mids/README.txt
-skeleton/dummy_calcs/lib/calculations.rb
-skeleton/dummy_calcs/lib/thread_pool.rb
-skeleton/dummy_calcs/linear_implementation.rb
-skeleton/dummy_calcs/main.rb
-skeleton/dummy_calcs/my_worker.rb
-skeleton/dummy_calcs/my_worker_manager.rb
-skeleton/dummy_calcs/README.txt
-skeleton/dummy_calcs/threads_implementation.rb