rbbt-util 5.26.89 → 5.26.91

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 94f1605ffde34b1781b3b46bd7dd3fa6fb361a5345aae5a7f37da6f1626d3f6c
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data/lib/rbbt/workflow/util/archive.rb

@@ -1,3 +1,4 @@
+require 'rbbt/workflow/remote/ssh/driver'
 class Step
   def self.link_job(path, target_dir, task = nil, workflow = nil)
     Path.setup(target_dir)
@@ -124,7 +125,7 @@ class Step
     relocate = options[:relocate]
 
     paths = if options[:source]
-              SSHClient.run(options[:source], <<-EOF).split("\n")
+              SSHDriver.run(options[:source], <<-EOF).split("\n")
 require 'rbbt-util'
 require 'rbbt/workflow'
 
@@ -155,7 +156,7 @@ puts files * "\n"
             end
 
     target = if options[:target] 
-               target = SSHClient.run(options[:target], <<-EOF).split("\n").first
+               target = SSHDriver.run(options[:target], <<-EOF).split("\n").first
 require 'rbbt-util'
 path = "var/jobs"
 resource = #{resource.to_s}

data/share/rbbt_commands/workflow/slurm

@@ -0,0 +1,38 @@
+#!/usr/bin/env ruby
+
+require 'rbbt/util/simpleopt'
+require 'rbbt/workflow'
+require 'rbbt/workflow/usage'
+require 'rbbt/hpc'
+require 'time'
+
+$slurm_options = SOPT.get <<EOF
+-dr--dry_run Print only the template
+-cj--clean_job Clean job
+--drbbt Use development version of rbbt 
+-sing--singularity Use Singularity
+-c--contain* Contain in directory (using Singularity)
+-s--sync* Contain in directory and sync jobs
+-e--exclusive Make exclusive use of the node
+-hm--highmem Make use of highmem cores
+-wc--wipe_container* Wipe the jobs from the contain directory
+-CS--contain_and_sync Contain and sync to default locations
+-ci--copy_image When using a container directory, copy image there
+-t--tail Tail the logs
+-q--queue* Queue
+-t--task_cpus* Tasks
+-tm--time* Time
+-S--server* SLURM login node
+EOF
+
+class Step
+    def run(*args)
+        if done?
+            self.load
+        else
+            Marenostrum::SLURM.run_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        end
+    end
+end
+
+load Rbbt.share.rbbt_commands.workflow.task.find

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.89
+  version: 5.26.91
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-11-25 00:00:00.000000000 Z
+date: 2019-11-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -426,6 +426,7 @@ files:
 - share/rbbt_commands/workflow/remote/list
 - share/rbbt_commands/workflow/remote/remove
 - share/rbbt_commands/workflow/server
+- share/rbbt_commands/workflow/slurm
 - share/rbbt_commands/workflow/task
 - share/rbbt_commands/workflow/trace
 - share/unicorn.rb