rbbt-util 5.26.89 → 5.26.91
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/workflow/util/archive.rb +3 -2
- data/share/rbbt_commands/workflow/slurm +38 -0
- metadata +3 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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3
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metadata.gz: cf3015ae621537a668dd0dfc4d88629013baaa64f566e0c1367d9456f223d90d
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4
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data.tar.gz: 94f1605ffde34b1781b3b46bd7dd3fa6fb361a5345aae5a7f37da6f1626d3f6c
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: f020fe934da94e1f454e087cfd4baf002f5d7f6260fbc3f803a2f48e5b3d5ae21816c68ce1ac3dc4431b8ceb7e4f97557e0220b9dc57690f3591ee82adcb27f8
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7
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data.tar.gz: 648f2530c6e4fa265adf7092c5abdc7d3c7b508751a0969575f2731a4d364937279d7cd7cfc3b1718f7fce6981a67398e7c63b312cca92db01a43f239901c532
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@@ -1,3 +1,4 @@
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require 'rbbt/workflow/remote/ssh/driver'
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class Step
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def self.link_job(path, target_dir, task = nil, workflow = nil)
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Path.setup(target_dir)
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@@ -124,7 +125,7 @@ class Step
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relocate = options[:relocate]
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paths = if options[:source]
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-
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SSHDriver.run(options[:source], <<-EOF).split("\n")
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require 'rbbt-util'
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require 'rbbt/workflow'
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@@ -155,7 +156,7 @@ puts files * "\n"
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end
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target = if options[:target]
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-
target =
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target = SSHDriver.run(options[:target], <<-EOF).split("\n").first
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require 'rbbt-util'
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path = "var/jobs"
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resource = #{resource.to_s}
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@@ -0,0 +1,38 @@
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#!/usr/bin/env ruby
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require 'rbbt/util/simpleopt'
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require 'rbbt/workflow'
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require 'rbbt/workflow/usage'
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require 'rbbt/hpc'
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require 'time'
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$slurm_options = SOPT.get <<EOF
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-dr--dry_run Print only the template
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-cj--clean_job Clean job
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--drbbt Use development version of rbbt
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-sing--singularity Use Singularity
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-c--contain* Contain in directory (using Singularity)
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-s--sync* Contain in directory and sync jobs
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-e--exclusive Make exclusive use of the node
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-hm--highmem Make use of highmem cores
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-wc--wipe_container* Wipe the jobs from the contain directory
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-CS--contain_and_sync Contain and sync to default locations
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-ci--copy_image When using a container directory, copy image there
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-t--tail Tail the logs
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-q--queue* Queue
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-t--task_cpus* Tasks
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-tm--time* Time
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-S--server* SLURM login node
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EOF
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class Step
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def run(*args)
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if done?
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self.load
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else
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Marenostrum::SLURM.run_job(self, SOPT::GOT_OPTIONS.merge($slurm_options))
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end
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end
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end
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load Rbbt.share.rbbt_commands.workflow.task.find
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: rbbt-util
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version: !ruby/object:Gem::Version
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version: 5.26.
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version: 5.26.91
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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: 2019-11-
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date: 2019-11-28 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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@@ -426,6 +426,7 @@ files:
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- share/rbbt_commands/workflow/remote/list
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- share/rbbt_commands/workflow/remote/remove
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- share/rbbt_commands/workflow/server
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- share/rbbt_commands/workflow/slurm
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- share/rbbt_commands/workflow/task
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- share/rbbt_commands/workflow/trace
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- share/unicorn.rb
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