rbbt-util 5.31.1 → 5.31.7
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checksums.yaml
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@@ -1,7 +1,7 @@
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 34e7a247caa69fc1c5f63d78ed8dd0884f8a57bb85940f5331484482115b4169
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data.tar.gz: 0c390b5aa9c71bf06f0964bb8a5f21b1a1d500c9865c442a7365532094949e15
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 47c595b2129fcdadc2caf5c7d3ae2c0ea005b5d0969c96eb49fef69a6773430dc02fc83f2abfed47492d4fa66c09b43c5ab3f28a4667465cb612d3aaff9261c7
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data.tar.gz: 82db64ecc144b0d29169a6736bf9df736b3ccb3355117f3808a0b1c631b35f1ca5e91f36cfdd96a6e5c823767ace2b12ebb3666af068a794d859a15683917f00
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data/lib/rbbt/hpc/batch.rb
CHANGED
@@ -11,30 +11,35 @@ module HPC
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env_cmd = Misc.process_options options, :env_cmd
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development = Misc.process_options options, :development
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if contain = options[:contain]
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contain = File.expand_path(contain)
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env_cmd ||= ""
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env_cmd << " TMPDIR='#{contain}/.rbbt/tmp' "
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end
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if options[:singularity]
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group, user, user_group, scratch_group_dir, projects_group_dir = options.values_at :group, :user, :user_group, :scratch_group_dir, :projects_group_dir
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singularity_img, singularity_opt_dir, singularity_ruby_inline = options.values_at :singularity_img, :singularity_opt_dir, :singularity_ruby_inline
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singularity_cmd = %(singularity exec -e -B #{singularity_opt_dir}:/singularity_opt/ -B
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singularity_cmd = %(singularity exec -e -B #{singularity_opt_dir}:/singularity_opt/ -B "#{singularity_ruby_inline}":"/.singularity_ruby_inline":rw )
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if contain
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contain = File.expand_path(contain)
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if contain && options[:hardened]
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singularity_cmd << %( -C -H "#{contain}" \
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-B "/.singularity_ruby_inline":"#{contain}/.singularity_ruby_inline":rw
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-B "#{options[:batch_dir]}" \
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-B /scratch/tmp \
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#{ group != user_group ? "-B /gpfs/projects/#{user_group}" : "" } \
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-B #{scratch_group_dir} \
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-B #{projects_group_dir} \
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-B
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-B /apps/ \
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-B ~/git:"#{contain}/git":ro \
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#{Open.exists?('~/.rbbt/software/opt/')? '-B ~/.rbbt/software/opt/:"/opt/":ro' : '' } \
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-B ~/.rbbt:"#{contain}/home/":ro)
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singularity_cmd << " #{singularity_img} "
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end
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singularity_cmd << " #{singularity_img} "
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end
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if env_cmd
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@@ -170,7 +175,7 @@ EOF
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batch_options[:wipe_container] ||= 'post'
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end
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if batch_options[:contain] && ! batch_options[:
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if batch_options[:contain] && ! batch_options[:hardened]
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options[:workdir_all] = batch_options[:contain]
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end
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@@ -304,7 +309,7 @@ module load singularity
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mkdir -p "#{singularity_opt_dir}"
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EOF
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if contain
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if contain && options[:hardened]
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prepare_environment +=<<-EOF
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# Prepare container for singularity
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data/lib/rbbt/hpc/lsf.rb
CHANGED
@@ -7,7 +7,8 @@ module HPC
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def self.batch_system_variables
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<<-EOF
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-
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[[ -z $LSB_MAX_MEM_RUSAGE ]] || MAX_MEMORY=$LSB_MAX_MEM_RUSAGE
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[[ -z $MAX_MEMORY ]] && let MAX_MEMORY="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / 1024"
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BATCH_JOB_ID=$LSF_JOBID
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BATCH_SYSTEM=LSF
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EOF
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data/lib/rbbt/resource/util.rb
CHANGED
@@ -33,9 +33,9 @@ end
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module Resource
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def set_software_env(software_dir)
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software_dir.find_all.reverse.each do |software_dir|
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software_dir.opt.find_all.reverse.each do |software_dir|
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next unless software_dir.exists?
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software_dir = File.expand_path(software_dir)
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software_dir = File.expand_path(File.dirname(software_dir))
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opt_dir = File.join(software_dir, 'opt')
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bin_dir = File.join(opt_dir, 'bin')
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@@ -2,7 +2,7 @@ require_relative 'ansible/workflow'
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require 'rbbt/workflow/usage'
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module Ansible
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def self.play(playbook, inventory = nil)
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def self.play(playbook, inventory = nil, verbose = false)
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inventory = Rbbt.etc.ansible_inventory.find
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Log.with_severity 0 do
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TmpFile.with_file do |tmp|
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@@ -10,7 +10,11 @@ module Ansible
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Open.write(tmp, [playbook].to_yaml)
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playbook = tmp
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end
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if verbose
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CMD.cmd_log("ansible-playbook -i #{inventory} -v #{playbook}")
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else
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CMD.cmd_log("ansible-playbook -i #{inventory} #{playbook}")
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end
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end
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end
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end
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@@ -46,7 +50,7 @@ module Ansible
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def self.playbook(file, task = nil, options = {})
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task = 'default' if task.nil?
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workflow = Workflow.require_workflow
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workflow = Workflow === file ? file : Workflow.require_workflow(file)
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task = workflow.tasks.keys.last if workflow.tasks[task].nil?
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workflow2playbook workflow, task, options
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end
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@@ -99,6 +99,7 @@ class Step
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if String === value && File.exists?(value)
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Open.ln_s(value, path)
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else
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value = value.collect{|v| v = "#{v}" if Path === v; v }if Array === value
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value = "#{value}" if Path === value
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Open.write(path + '.yaml', value.to_yaml)
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end
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@@ -549,7 +550,7 @@ class Step
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def aborted?
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status = self.status
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status == :aborted || ((status != :cleaned && status != :noinfo && status != :setup && status != :noinfo) && nopid?)
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status == :aborted || ((status != :dependencies && status != :cleaned && status != :noinfo && status != :setup && status != :noinfo) && nopid?)
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end
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# {{{ INFO
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@@ -147,6 +147,8 @@ get_git(){
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git pull origin master
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git rebase master
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git stash apply
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git submodule init
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git submodule update
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fi
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else
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if [ $version == 'none' ];then
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@@ -154,6 +156,10 @@ get_git(){
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else
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git clone --recursive "$url" "$name" -b $version
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fi
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cd "$name"
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git submodule init
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git submodule update
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fi
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clean_build
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
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--- !ruby/object:Gem::Specification
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2
2
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name: rbbt-util
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3
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version: !ruby/object:Gem::Version
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4
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-
version: 5.31.
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version: 5.31.7
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2021-03-
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date: 2021-03-26 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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