miga-base 1.2.6.0 → 1.2.6.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: d9309d82f51e9bfce7cc18c8b32de6ab1491cf1fc3fd9b5af660298490bac2b8
+  metadata.gz: 424c00c37c64745ef9bf6441793fa8ec030756c5f1c248b6195cb95cd057729d
+  data.tar.gz: f29892c2dfe4d28258e5dc31b93d15f8ce3026eafd8159940faa00681e820ece
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+  data.tar.gz: a2d323f7f013d1e042f5d68a323585e646b671f68a6fa6dd980584d4352fe32138db049466b335c07c174d110225e55003c02a6564975ba0bb109465118858d4

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 ",
@@ -156,13 +172,23 @@ module MiGA::Cli::Action::Init::DaemonHelper
       'What should I use to separate variables?', ','
     )
     if v[:type] == 'qsub'
-      v[:alive] = cli.ask_user(
-        "How can I know that a process is still alive?\n" \
-          "  Output should be 1 for running and 0 for non-running\n" \
-          "  {{variables}}: pid\n ",
-        "qstat -f '{{pid}}' | grep ' job_state =' | perl -pe 's/.*= //' " \
-          "| grep '[^C]' | tail -n 1 | wc -l | awk '{print $1}'"
-      )
+      if flavor == 'sge'
+        v[:alive] = cli.ask_user(
+          "How can I know that a process is still alive?\n" \
+            "  Output should be 1 for running and 0 for non-running\n" \
+            "  {{variables}}: pid\n ",
+          "qstat -j '{{pid}}' -s pr 2>/dev/null | head -n 1 | wc -l " \
+            "| awk '{print $1}'"
+        )
+      else
+        v[:alive] = cli.ask_user(
+          "How can I know that a process is still alive?\n" \
+            "  Output should be 1 for running and 0 for non-running\n" \
+            "  {{variables}}: pid\n ",
+          "qstat -f '{{pid}}' | grep ' job_state =' | perl -pe 's/.*= //' " \
+            "| grep '[^C]' | tail -n 1 | wc -l | awk '{print $1}'"
+        )
+      end
       v[:kill] = cli.ask_user(
         "How should I terminate tasks?\n" \
           "  {{variables}}: pid\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, 6, 0].freeze
+  VERSION = [1.2, 6, 3].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, 23)
+  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: 1.2.6.0
+  version: 1.2.6.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-05-23 00:00:00.000000000 Z
+date: 2022-06-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons