miga-base 1.2.6.2 → 1.2.6.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3dd2a47d0472b27985d65865358d2555f67f18e63143d41b62d2a36b83edddc6
-  data.tar.gz: b90dc62b2bddcd3903493abe84b663486b57170b7b4fd65a5f63d0bf36e747b2
+  metadata.gz: 13f2f36c50de313a8f5f29fc4901d4ce44b37437b3609a730ba5ebeee3053874
+  data.tar.gz: 743e19d52c2b581f2fc4114ded20ec5d3e3a9db19a0647d78b75d97b191b3b08
 SHA512:
-  metadata.gz: f2b4507f9526471e64e17fc115918dcf880a0c4dfedebe111fcb98c24a7bede321b629809d8518f1bb93cb0d1c0f524bcb707309f891ee09569dd43ecc527f97
-  data.tar.gz: bf0f77f5d7879d27b5e1fb22b32a1ba42da8f41318ebdfefc92b35782ceb8538687de05647296afc6eb74d284729a73fba60520e288d33d049a7ece6e7d81de9
+  metadata.gz: ee5c3434107c935b1bb9466127c8c87cac77e58039c787f5049be571d680063e610541da2396630cb9aea7e84083c97eb8d7950fe1a9feec0d58d6dbda61781a
+  data.tar.gz: e46c90206a22308e8a9e3c2ed55eff1cebc9948e98d9b6f7ac9b392edcd461b119a994a0d8170180c03a479903e388c842353b6aafbc079a3176b48019f924df

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

@@ -136,9 +136,9 @@ module MiGA::Cli::Action::Init::DaemonHelper
   end
 
   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])
+    queue       = cli.ask_user('What queue should I use?', nil, nil, true)
     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
@@ -151,8 +151,8 @@ module MiGA::Cli::Action::Init::DaemonHelper
           "  {{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/'"
+          "-l h_rt=12:00:00 '{{script}}' | grep . " \
+          "| perl -pe 's/^Your job (\\S+) .*/$1/'"
       )
     else
       v[:cmd] = cli.ask_user(
@@ -172,13 +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/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, 2].freeze
+  VERSION = [1.2, 6, 5].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: 1.2.6.2
+  version: 1.2.6.5
 platform: ruby
 authors:
 - Luis M. Rodriguez-R