miga-base 1.2.6.2 → 1.2.6.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3dd2a47d0472b27985d65865358d2555f67f18e63143d41b62d2a36b83edddc6
-  data.tar.gz: b90dc62b2bddcd3903493abe84b663486b57170b7b4fd65a5f63d0bf36e747b2
+  metadata.gz: 424c00c37c64745ef9bf6441793fa8ec030756c5f1c248b6195cb95cd057729d
+  data.tar.gz: f29892c2dfe4d28258e5dc31b93d15f8ce3026eafd8159940faa00681e820ece
 SHA512:
-  metadata.gz: f2b4507f9526471e64e17fc115918dcf880a0c4dfedebe111fcb98c24a7bede321b629809d8518f1bb93cb0d1c0f524bcb707309f891ee09569dd43ecc527f97
-  data.tar.gz: bf0f77f5d7879d27b5e1fb22b32a1ba42da8f41318ebdfefc92b35782ceb8538687de05647296afc6eb74d284729a73fba60520e288d33d049a7ece6e7d81de9
+  metadata.gz: 2792556398cd31e961e34a205ab9783d7377bab9418789323dfe2c9316eca998d7f37e82ee84442b529e3aca4dc7835cb90cf0c1e4d1822559b9666b24791741
+  data.tar.gz: a2d323f7f013d1e042f5d68a323585e646b671f68a6fa6dd980584d4352fe32138db049466b335c07c174d110225e55003c02a6564975ba0bb109465118858d4

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

@@ -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=walltime=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, 3].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: 1.2.6.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R