miga-base 1.2.6.2 → 1.2.6.3

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  SHA256:
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@@ -151,8 +151,8 @@ module MiGA::Cli::Action::Init::DaemonHelper
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  " {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
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  "#{v[:type]} -q '#{queue}' -v '{{vars}}' -pe openmp {{cpus}} " \
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  "-j y -o '{{log}}' -N '{{task_name_simple}}' -l h_vmem=9g " \
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- "-l h_rt=walltime=12:00:00 '{{script}}' | grep . | " \
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- "perl -pe 's/^Your job (\S+) .*/$1/'"
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+ "-l h_rt=walltime=12:00:00 '{{script}}' | grep . " \
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+ "| perl -pe 's/^Your job (\S+) .*/$1/'"
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  )
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  else
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  v[:cmd] = cli.ask_user(
@@ -172,13 +172,23 @@ module MiGA::Cli::Action::Init::DaemonHelper
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  'What should I use to separate variables?', ','
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  )
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  if v[:type] == 'qsub'
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- v[:alive] = cli.ask_user(
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- "How can I know that a process is still alive?\n" \
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- " Output should be 1 for running and 0 for non-running\n" \
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- " {{variables}}: pid\n ",
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- "qstat -f '{{pid}}' | grep ' job_state =' | perl -pe 's/.*= //' " \
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- "| grep '[^C]' | tail -n 1 | wc -l | awk '{print $1}'"
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- )
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+ if flavor == 'sge'
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+ v[:alive] = cli.ask_user(
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+ "How can I know that a process is still alive?\n" \
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+ " Output should be 1 for running and 0 for non-running\n" \
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+ " {{variables}}: pid\n ",
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+ "qstat -j '{{pid}}' -s pr 2>/dev/null | head -n 1 | wc -l " \
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+ "| awk '{print $1}'"
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+ )
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+ else
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+ v[:alive] = cli.ask_user(
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+ "How can I know that a process is still alive?\n" \
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+ " Output should be 1 for running and 0 for non-running\n" \
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+ " {{variables}}: pid\n ",
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+ "qstat -f '{{pid}}' | grep ' job_state =' | perl -pe 's/.*= //' " \
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+ "| grep '[^C]' | tail -n 1 | wc -l | awk '{print $1}'"
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+ )
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+ end
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  v[:kill] = cli.ask_user(
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  "How should I terminate tasks?\n" \
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  " {{variables}}: pid\n ",
data/lib/miga/version.rb CHANGED
@@ -12,7 +12,7 @@ module MiGA
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  # - String indicating release status:
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  # - rc* release candidate, not released as gem
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  # - [0-9]+ stable release, released as gem
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- VERSION = [1.2, 6, 2].freeze
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+ VERSION = [1.2, 6, 3].freeze
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  ##
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  # Nickname for the current major.minor version.
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: miga-base
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  version: !ruby/object:Gem::Version
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- version: 1.2.6.2
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+ version: 1.2.6.3
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  platform: ruby
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  authors:
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  - Luis M. Rodriguez-R