miga-base 1.2.6.1 → 1.2.6.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b5d1f83d92d5799126ba3510cb944be141a3753e0b50a3cf78cb7e169bbb276e
-  data.tar.gz: c5134386df29f5bed01e54d67df9874bb92c500634ec8534b122ea66255c700b
+  metadata.gz: 3dd2a47d0472b27985d65865358d2555f67f18e63143d41b62d2a36b83edddc6
+  data.tar.gz: b90dc62b2bddcd3903493abe84b663486b57170b7b4fd65a5f63d0bf36e747b2
 SHA512:
-  metadata.gz: 1845675640dcd25837e23890940f11a6fcd51de8e54c6cc9bfc0aa0fde5dba353c6a0f7f23abb261c0b593719f835b10ac18f30d7554f39b7810f466e85d0390
-  data.tar.gz: f7fe96e5ca31c5d1aefecff3a1703e2594339526e1ca3f971792fd04bb8a8707c02f7ea64e507b663f3191d25b425c311c74ce1e6bf8ad4d700ce38714770c8a
+  metadata.gz: f2b4507f9526471e64e17fc115918dcf880a0c4dfedebe111fcb98c24a7bede321b629809d8518f1bb93cb0d1c0f524bcb707309f891ee09569dd43ecc527f97
+  data.tar.gz: bf0f77f5d7879d27b5e1fb22b32a1ba42da8f41318ebdfefc92b35782ceb8538687de05647296afc6eb74d284729a73fba60520e288d33d049a7ece6e7d81de9

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/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, 6, 1].freeze
+  VERSION = [1.2, 6, 2].freeze
 
   ##
   # Nickname for the current major.minor version.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.6.1
+  version: 1.2.6.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R