miga-base 1.2.5.3 → 1.2.6.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c0eca4dbad780bdf6cc4a739ee17fd38d23e2cca6502f8dc8d656755e4d40431
-  data.tar.gz: 18a6f228cb63c068483e82c9b857cd11ba3cffe7bf6168e8ba12c88541e6aa74
+  metadata.gz: 3dd2a47d0472b27985d65865358d2555f67f18e63143d41b62d2a36b83edddc6
+  data.tar.gz: b90dc62b2bddcd3903493abe84b663486b57170b7b4fd65a5f63d0bf36e747b2
 SHA512:
-  metadata.gz: a5955cd677402862aeb06b96246091fe511092cede22fe32027e235713683c4adfcaa2935e0b9221e856346e5c4dd241fffa42ab7b5c89d4c14facd3b49ca71d
-  data.tar.gz: 7116fb4803c97b790fea7b62199f24e24d120cc7c19358134e0065d18ca03943fdccb486c63cd96fbe64fe95d880f1639834b4b4e29c3900fdb575988deb0c27
+  metadata.gz: f2b4507f9526471e64e17fc115918dcf880a0c4dfedebe111fcb98c24a7bede321b629809d8518f1bb93cb0d1c0f524bcb707309f891ee09569dd43ecc527f97
+  data.tar.gz: bf0f77f5d7879d27b5e1fb22b32a1ba42da8f41318ebdfefc92b35782ceb8538687de05647296afc6eb74d284729a73fba60520e288d33d049a7ece6e7d81de9

data/lib/miga/cli/action/get_db.rb

@@ -12,6 +12,7 @@ class MiGA::Cli::Action::GetDb < MiGA::Cli::Action
       local: File.expand_path('.miga_db', ENV['MIGA_HOME']),
       host: MiGA::MiGA.known_hosts(:miga_db),
       pb: true,
+      reuse_archive: false,
       overwrite: true
     }
     cli.parse do |opt|
@@ -39,6 +40,10 @@ class MiGA::Cli::Action::GetDb < MiGA::Cli::Action
         '--list-versions',
         'List available versions of the database and exit'
       ) { |v| cli[:list_versions] = v }
+      opt.on(
+        '--reuse-archive',
+        'Reuse a previously downloaded archive if available'
+      ) { |v| cli[:reuse_archive] = v }
       opt.on(
         '--no-overwrite',
         'Exit without downloading if the target database already exists'
@@ -67,7 +72,7 @@ class MiGA::Cli::Action::GetDb < MiGA::Cli::Action
     check_target and return
 
     # Download and expand
-    file = download_file(@ftp, ver[:path])
+    file = download_file(@ftp, ver[:path], cli[:reuse_archive])
     check_digest(ver, file)
     unarchive(file)
     register_database(manif, db, ver)
@@ -89,13 +94,17 @@ class MiGA::Cli::Action::GetDb < MiGA::Cli::Action
     MiGA::MiGA.remote_connection(cli[:host])
   end
 
-  def download_file(ftp, path)
+  def download_file(ftp, path, reuse = false)
     cli.say "Downloading '#{path}'"
     file = File.expand_path(path, cli[:local])
-    MiGA::MiGA.download_file_ftp(ftp, path, file) do |n, size|
-      cli.advance("#{path}:", n, size) if cli[:pb]
+    if reuse && File.exist?(file)
+      cli.say "Reusing #{file}"
+    else
+      MiGA::MiGA.download_file_ftp(ftp, path, file) do |n, size|
+        cli.advance("#{path}:", n, size) if cli[:pb]
+      end
+      cli.print "\n" if cli[:pb]
     end
-    cli.print "\n" if cli[:pb]
     file
   end
 

data/lib/miga/cli/action/init/daemon_helper.rb

@@ -35,6 +35,7 @@ module MiGA::Cli::Action::Init::DaemonHelper
     v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '2').to_i
     v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '6').to_i
     v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
+    v[:nodelist] = nil # <- To enable non-default with default SSH
     cli.puts 'Setting up internal daemon defaults.'
     cli.puts 'If you don\'t understand this just leave default values:'
     v[:cmd] = cli.ask_user(
@@ -100,6 +101,7 @@ module MiGA::Cli::Action::Init::DaemonHelper
     v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
     v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '300').to_i
     v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
+    v[:nodelist] = nil # <- To enable non-default with default SSH
     cli.puts 'Setting up internal daemon defaults'
     cli.puts 'If you don\'t understand this just leave default values:'
     v[:cmd] = cli.ask_user(
@@ -135,18 +137,32 @@ module MiGA::Cli::Action::Init::DaemonHelper
 
   def configure_qsub_msub_daemon(v)
     queue       = cli.ask_user('What queue should I use?', nil, nil, true)
+    flavor      = v[:type] == 'msub' ? 'msub' :
+                  cli.ask_user('Select qsub flavor', 'torque', %w[torque sge])
     v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
     v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '300').to_i
     v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
+    v[:nodelist] = nil # <- To enable non-default with default SSH
     cli.puts 'Setting up internal daemon defaults.'
     cli.puts 'If you don\'t understand this just leave default values:'
-    v[:cmd] = cli.ask_user(
-      "How should I launch tasks?\n" \
-        "  {{variables}}: script, vars, cpus, log, task_name\n ",
-      "#{v[:type]} -q '#{queue}' -v '{{vars}}' -l nodes=1:ppn={{cpus}} " \
-        "{{script}} -j oe -o '{{log}}' -N '{{task_name}}' -l mem=9g " \
-        "-l walltime=12:00:00 | grep ."
-    )
+    if flavor == 'sge'
+      v[:cmd] = cli.ask_user(
+        "How should I launch tasks?\n" \
+          "  {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
+        "#{v[:type]} -q '#{queue}' -v '{{vars}}' -pe openmp {{cpus}} " \
+          "-j y -o '{{log}}' -N '{{task_name_simple}}' -l h_vmem=9g " \
+          "-l h_rt=walltime=12:00:00 '{{script}}' | grep . | " \
+          "perl -pe 's/^Your job (\S+) .*/$1/'"
+      )
+    else
+      v[:cmd] = cli.ask_user(
+        "How should I launch tasks?\n" \
+          "  {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
+        "#{v[:type]} -q '#{queue}' -v '{{vars}}' -l nodes=1:ppn={{cpus}} " \
+          "-j oe -o '{{log}}' -N '{{task_name}}' -l mem=9g " \
+          "-l walltime=12:00:00 '{{script}}' | grep ."
+      )
+    end
     v[:var] = cli.ask_user(
       "How should I pass variables?\n" \
         "  {{variables}}: key, value\n ",

data/lib/miga/daemon.rb

@@ -257,6 +257,7 @@ class MiGA::Daemon < MiGA::MiGA
       cpus: ppn(what),
       log: File.join(log_dir, "#{to_run[:ds_name]}.log"),
       task_name: to_run[:task_name],
+      task_name_simple: to_run[:task_name].gsub(/[^A-Za-z0-9_]/, '-'),
       miga: File.join(MiGA::MiGA.root_path, 'bin/miga').shellescape
     }
     runopts_for(:cmd, what).miga_variables(var_hsh)

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.2, 5, 3].freeze
+  VERSION = [1.2, 6, 2].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2022, 5, 19)
+  VERSION_DATE = Date.new(2022, 6, 24)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.5.3
+  version: 1.2.6.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-05-19 00:00:00.000000000 Z
+date: 2022-06-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons