rbbt-util 5.32.6 → 5.32.12
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- checksums.yaml +4 -4
- data/bin/rbbt +1 -0
- data/lib/rbbt/hpc/batch.rb +23 -7
- data/lib/rbbt/hpc/slurm.rb +29 -10
- data/lib/rbbt/persist/tsv/adapter.rb +1 -5
- data/lib/rbbt/resource.rb +26 -10
- data/lib/rbbt/tsv/csv.rb +2 -2
- data/lib/rbbt/util/cmd.rb +48 -17
- data/lib/rbbt/util/log/progress/report.rb +20 -17
- data/lib/rbbt/util/migrate.rb +118 -0
- data/lib/rbbt/util/simpleDSL.rb +4 -4
- data/lib/rbbt/workflow.rb +20 -2
- data/lib/rbbt/workflow/step.rb +37 -6
- data/lib/rbbt/workflow/step/accessor.rb +2 -2
- data/lib/rbbt/workflow/util/archive.rb +31 -102
- data/lib/rbbt/workflow/util/trace.rb +2 -1
- data/share/rbbt_commands/hpc/list +11 -7
- data/share/rbbt_commands/hpc/orchestrate +6 -1
- data/share/rbbt_commands/hpc/task +6 -1
- data/share/rbbt_commands/lsf/clean +212 -0
- data/share/rbbt_commands/lsf/list +315 -0
- data/share/rbbt_commands/lsf/orchestrate +61 -0
- data/share/rbbt_commands/lsf/tail +55 -0
- data/share/rbbt_commands/lsf/task +60 -0
- data/share/rbbt_commands/migrate +3 -76
- data/share/rbbt_commands/slurm/clean +212 -0
- data/share/rbbt_commands/slurm/list +315 -0
- data/share/rbbt_commands/slurm/orchestrate +61 -0
- data/share/rbbt_commands/slurm/tail +55 -0
- data/share/rbbt_commands/slurm/task +60 -0
- data/share/rbbt_commands/workflow/forget_deps +5 -4
- data/test/rbbt/util/test_migrate.rb +36 -0
- data/test/rbbt/util/test_simpleDSL.rb +3 -3
- data/test/rbbt/workflow/util/test_archive.rb +31 -0
- metadata +96 -82
@@ -0,0 +1,61 @@
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#!/usr/bin/env ruby
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2
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3
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require 'rbbt/util/simpleopt'
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4
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require 'rbbt/workflow'
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5
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require 'rbbt/workflow/usage'
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6
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require 'rbbt/hpc'
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7
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require 'rbbt/hpc/orchestrate'
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8
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require 'time'
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9
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10
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$slurm_options = SOPT.get <<EOF
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11
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+
-dr--dry_run Print only the template
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12
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+
-cj--clean_job Clean job
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13
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+
--drbbt* Use development version of rbbt
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14
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+
-sing--singularity Use Singularity
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15
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+
-si--singularity_img* Singularity image to use
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16
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+
-ug--user_group* Use alternative user group for group project directory
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17
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+
-c--contain* Contain in directory (using Singularity)
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18
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+
-s--sync* Contain in directory and sync jobs
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19
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+
-e--exclusive Make exclusive use of the node
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20
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-hm--highmem Make use of highmem cores
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21
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+
-wc--wipe_container* Wipe the jobs from the contain directory
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22
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+
-pd--purge_deps Purge job dependencies
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23
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-CS--contain_and_sync Contain and sync to default locations
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24
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+
-ci--copy_image When using a container directory, copy image there
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25
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-t--tail Tail the logs
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26
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+
-BPP--batch_procpath* Save Procpath performance for batch job; specify only options
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27
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-q--queue* Queue
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28
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+
-t--task_cpus* Tasks
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29
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+
-tm--time* Time
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30
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+
-m--mem* SLURM minimum memory
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31
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+
-mcpu--mem_per_cpu* SLURM minimum memory per CPU
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32
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+
-lin--licenses* SLURM licenses
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33
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-cons--constraint* SLURM constraint
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34
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-W--workflows* Additional workflows
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35
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-OR--orchestration_rules* Orchestration rules
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36
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-rmb--remove_batch_basedir Remove the SLURM working directory (command, STDIN, exit status, ...)
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37
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EOF
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38
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39
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batch_system = $slurm_options.delete :batch_system
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40
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batch_system ||= 'auto'
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41
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HPC::BATCH_MODULE = HPC.batch_system batch_system
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raise ParameterException.new("Could not detect batch_system: #{Misc.fingerprint batch_system}") if HPC::BATCH_MODULE.nil?
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45
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class Step
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def run(*args)
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if done?
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self.load
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else
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51
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begin
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52
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Log.debug "Issuing SLURM job for #{self.path}"
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53
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HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options))
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54
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rescue HPC::SBATCH
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55
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end
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end
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57
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end
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58
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end
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59
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60
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ARGV.concat ["-W", $slurm_options[:workflows], '--detach'] if $slurm_options[:workflows]
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61
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load Rbbt.share.rbbt_commands.workflow.task.find
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@@ -0,0 +1,55 @@
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1
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#!/usr/bin/env ruby
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2
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3
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require 'rbbt-util'
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4
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require 'rbbt/util/simpleopt'
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5
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require 'rbbt/hpc'
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6
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7
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#$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
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8
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9
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options = SOPT.setup <<EOF
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10
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11
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Queue a job in Marenostrum
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12
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13
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$ rbbt slurm tail <directory> [options]
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14
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15
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-h--help Print this help
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16
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-d--done Done jobs only
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17
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-e--error Error jobs only
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18
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-a--aborted SLURM aboted jobs
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19
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-r--running Running jobs only
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20
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-q--queued Queued jobs only
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21
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-j--job* Job ids
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22
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-s--search* Regular expression
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23
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-t--tail* Show the last lines of the STDERR
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24
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-p--progress Report progress of job and the dependencies
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25
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-SBP--sbatch_parameters show sbatch parameters
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26
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-PERF--procpath_performance show Procpath performance summary
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27
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-sacct--sacct_peformance show sacct performance summary
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28
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-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
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29
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EOF
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30
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+
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31
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if options[:help]
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32
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if defined? rbbt_usage
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33
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rbbt_usage
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34
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else
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35
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puts SOPT.doc
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36
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end
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37
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exit 0
|
38
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end
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39
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+
|
40
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batch_system = options.delete :batch_system
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41
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batch_system ||= 'auto'
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42
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+
|
43
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HPC::BATCH_MODULE = HPC.batch_system batch_system
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44
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+
|
45
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raise ParameterException.new("Could not detect batch_system: #{Misc.fingerprint batch_system}") if HPC::BATCH_MODULE.nil?
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46
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+
|
47
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+
directory = ARGV.shift
|
48
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+
|
49
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raise ParameterException if directory.nil?
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50
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|
51
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directory = File.dirname(directory) unless File.directory?(directory)
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52
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+
|
53
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require 'rbbt/hpc/slurm'
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54
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55
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HPC::BATCH_MODULE.follow_job directory, true
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@@ -0,0 +1,60 @@
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1
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#!/usr/bin/env ruby
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2
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3
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require 'rbbt/util/simpleopt'
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4
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require 'rbbt/workflow'
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5
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require 'rbbt/workflow/usage'
|
6
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require 'rbbt/hpc'
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7
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require 'time'
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8
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+
|
9
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+
$slurm_options = SOPT.get <<EOF
|
10
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+
-dr--dry_run Print only the template
|
11
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+
-cj--clean_job Clean job
|
12
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+
--drbbt* Use development version of rbbt
|
13
|
+
-sing--singularity Use Singularity
|
14
|
+
-si--singularity_img* Singularity image to use
|
15
|
+
-ug--user_group* Use alternative user group for group project directory
|
16
|
+
-c--contain* Contain in directory (using Singularity)
|
17
|
+
-s--sync* Contain in directory and sync jobs
|
18
|
+
-e--exclusive Make exclusive use of the node
|
19
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+
-hm--highmem Make use of highmem cores
|
20
|
+
-wc--wipe_container* Wipe the jobs from the contain directory
|
21
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+
-pd--purge_deps Purge job dependencies
|
22
|
+
-CS--contain_and_sync Contain and sync to default locations
|
23
|
+
-ci--copy_image When using a container directory, copy image there
|
24
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+
-t--tail Tail the logs
|
25
|
+
-BPP--batch_procpath* Save Procpath performance for batch job; specify only options
|
26
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+
-q--queue* Queue
|
27
|
+
-t--task_cpus* Tasks
|
28
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+
-tm--time* Time
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29
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+
-m--mem* SLURM minimum memory
|
30
|
+
-mcpu--mem_per_cpu* SLURM minimum memory per CPU
|
31
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+
-lin--licenses* SLURM licenses
|
32
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+
-cons--constraint* SLURM constraint
|
33
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+
-W--workflows* Additional workflows
|
34
|
+
-rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
|
35
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+
-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
|
36
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+
EOF
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37
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+
|
38
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+
batch_system = $slurm_options.delete :batch_system
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39
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batch_system ||= 'auto'
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40
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+
|
41
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HPC::BATCH_MODULE = HPC.batch_system batch_system
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42
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+
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43
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raise ParameterException.new("Could not detect batch_system: #{Misc.fingerprint batch_system}") if HPC::BATCH_MODULE.nil?
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44
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+
|
45
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class Step
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46
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def run(*args)
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47
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if done?
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48
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self.load
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49
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+
else
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50
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begin
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51
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Log.debug "Issuing SLURM job for #{self.path}"
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52
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HPC::BATCH_MODULE.run_job(self, SOPT::GOT_OPTIONS.merge($slurm_options))
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53
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rescue HPC::SBATCH
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54
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+
end
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55
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end
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56
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end
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57
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+
end
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58
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+
|
59
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ARGV.concat ["-W", $slurm_options[:workflows]] if $slurm_options[:workflows]
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60
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+
load Rbbt.share.rbbt_commands.workflow.task.find
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@@ -38,11 +38,11 @@ step.copy_files_dir
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38
38
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dependencies = step.dependencies
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39
39
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40
40
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if remove && remove.any?
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41
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-
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42
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-
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43
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-
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41
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remove_paths = dependencies.select do |dep|
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42
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remove.include?(dep.task_name) || remove.include?([dep.workflow.to_s, dep.task_name] * "#")
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43
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end.collect{|dep| dep.path }
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44
44
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else
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45
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-
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45
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remove_paths = dependencies.collect{|dep| dep.path }
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46
46
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end
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47
47
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48
48
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step.set_info :dependencies, step.info[:dependencies].reject{|info| remove_paths.include? info.last}
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@@ -50,6 +50,7 @@ step.set_info :dependencies, step.info[:dependencies].reject{|info| remove_paths
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50
50
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if options[:purge] || options[:recursive_purge]
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51
51
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dependencies.each do |dependency|
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52
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next unless remove_paths.include? dependency.path
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53
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+
next unless Open.exists?(dependency.info_file)
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53
54
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Step.purge(dependency.path, options[:recursive_purge])
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54
55
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end
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55
56
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end
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@@ -0,0 +1,36 @@
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require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
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require 'rbbt-util'
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3
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require 'rbbt/util/migrate'
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4
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5
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class TestMigrate < Test::Unit::TestCase
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6
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def _test_source_locate
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7
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assert_equal 'var/jobs/', Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user)).last
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8
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assert Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user))[1].include?(File.join(ENV["HOME"], '.rbbt/var/jobs/'))
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9
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end
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10
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+
|
11
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def test_migrate
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12
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Open.rm_rf Rbbt.tmp.test.migration_test.find(:user)
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13
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test_file = Rbbt.tmp.test.migration_test.migration_test_file.find(:user)
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14
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Open.write(test_file, "TEST")
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15
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TmpFile.with_file do |tmpdir|
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16
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Misc.in_dir tmpdir do
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17
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Log.with_severity 0 do
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18
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Rbbt.migrate('tmp/test/migration_test/migration_test_file', :current)
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19
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+
end
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20
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end
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21
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assert_equal "TEST", Open.read(File.join(tmpdir, 'tmp/test/migration_test/migration_test_file'))
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22
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end
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23
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end
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24
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+
|
25
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def __test_migrate_turbo
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26
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Log.with_severity 0 do
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27
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TmpFile.with_file do |tmpdir|
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28
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Misc.in_dir tmpdir do
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29
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+
Rbbt.migrate('etc/config', :current, :source => 'mn1')
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30
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+
end
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31
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assert_equal "TEST", Open.read(File.join(tmpdir, 'etc/config'))
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32
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+
end
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33
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end
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34
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end
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35
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end
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36
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+
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@@ -35,12 +35,12 @@ class TestDSL < Test::Unit::TestCase
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|
35
35
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36
36
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def test_config
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37
37
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config = <<-EOC
|
38
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-
action1
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39
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-
action2
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38
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+
action1 "Hello"
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39
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+
action2 "Good bye"
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40
40
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EOC
|
41
41
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|
42
42
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begin
|
43
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-
|
43
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+
assert_equal config.split("\n").collect{|l| l.strip}, @parser.config(:action).split("\n").collect{|l| l.strip}
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44
44
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rescue SimpleDSL::NoRuby2Ruby
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45
45
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end
|
46
46
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end
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@@ -0,0 +1,31 @@
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1
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require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
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2
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require 'rbbt-util'
|
3
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require 'rbbt/workflow'
|
4
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require 'rbbt/workflow/util/archive'
|
5
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+
|
6
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module ArchiveTestWF
|
7
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extend Workflow
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8
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task :test_archive => :string do
|
9
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Open.write(file(:file1), "Test file")
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10
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"TEST"
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11
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+
end
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12
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end
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13
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+
|
14
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class TestClass < Test::Unit::TestCase
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15
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def test_migrate
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16
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job = ArchiveTestWF.job(:test_archive)
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17
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job.run
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18
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+
|
19
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Log.with_severity 0 do
|
20
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+
TmpFile.with_file do |tmpdir|
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21
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+
Misc.in_dir tmpdir do
|
22
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+
Step.migrate(job.path, :current, :delete => false, :print => false)
|
23
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+
end
|
24
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+
assert_equal "TEST", Open.read(File.join(tmpdir, 'var/jobs/ArchiveTestWF/test_archive/Default'))
|
25
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+
end
|
26
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+
end
|
27
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+
|
28
|
+
|
29
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+
end
|
30
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+
end
|
31
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+
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.32.
|
4
|
+
version: 5.32.12
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
|
-
autorequire:
|
8
|
+
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2021-
|
11
|
+
date: 2021-05-25 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|
@@ -165,7 +165,7 @@ dependencies:
|
|
165
165
|
- !ruby/object:Gem::Version
|
166
166
|
version: '0'
|
167
167
|
description: Utilities for handling tsv files, caches, etc
|
168
|
-
email: miguel.vazquez@
|
168
|
+
email: miguel.vazquez.g@bsc.es
|
169
169
|
executables:
|
170
170
|
- rbbt_query.rb
|
171
171
|
- rbbt_exec.rb
|
@@ -282,6 +282,7 @@ files:
|
|
282
282
|
- lib/rbbt/util/log/progress.rb
|
283
283
|
- lib/rbbt/util/log/progress/report.rb
|
284
284
|
- lib/rbbt/util/log/progress/util.rb
|
285
|
+
- lib/rbbt/util/migrate.rb
|
285
286
|
- lib/rbbt/util/misc.rb
|
286
287
|
- lib/rbbt/util/misc/annotated_module.rb
|
287
288
|
- lib/rbbt/util/misc/bgzf.rb
|
@@ -377,6 +378,11 @@ files:
|
|
377
378
|
- share/rbbt_commands/hpc/tail
|
378
379
|
- share/rbbt_commands/hpc/task
|
379
380
|
- share/rbbt_commands/log
|
381
|
+
- share/rbbt_commands/lsf/clean
|
382
|
+
- share/rbbt_commands/lsf/list
|
383
|
+
- share/rbbt_commands/lsf/orchestrate
|
384
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metadata: {}
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summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
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