rbbt-util 5.33.4 → 5.33.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1e780efeaa15611ce5835bb314b9ad378719f9f744228a2c9a8a765c202e10e1
-  data.tar.gz: 7338f595861b6f93ea0043ffabe9e78762c1acc478669f989ea23dc84820a213
+  metadata.gz: f4272048a5c86e74b051600f0db895ea42f4ad51509a0de9ce88452d27133746
+  data.tar.gz: f10d19e028de390beb5e2649c7d2f1e0a7754d3235abe3eeba2790946b347f64
 SHA512:
-  metadata.gz: 6650b5f00f6e2b8a9ccb3b2d389357ee0b9f551166d185aa2c5ec2c635150e2274c75af35fa6dc66cb09abeaa3c9e445a344015bee616ef78607933337c67e6f
-  data.tar.gz: 4847e30f91c1fc388cb83bb842966fdf73cf150d4ed528b89e755d8ae5ed732e6886b7939031664fa0671b386c34e3daaf4ce0873f0991c4711b70bce03ed5c2
+  metadata.gz: 0667eb9d5783d7722c33f72a66a1c406d330d086a37660aa7682006d10fe15860a9e4cbfcb461f17ed15b146fa294a6f6d8158d937884f14dc7952908f63c357
+  data.tar.gz: f3ba25b347bc4a7f7b56ecdbd1a0bef932b646ac030b3d98fe6ddb76f36a6863073f4692747ceef32c42e4344538a7ee19b531a25b16cc2fa208b201887b441e

data/lib/rbbt/hpc/batch.rb

@@ -544,7 +544,7 @@ env > #{batch_options[:fenv]}
         Misc.add_defaults options, 
           :batch_dir => batch_dir, 
           :inputs_dir => File.join(batch_dir, "inputs_dir"),
-          :workflows => workflows_to_load * ","
+          :workflows => workflows_to_load.uniq * ","
 
         options[:procpath_performance] ||= File.join(batch_dir, "procpath##{procpath.gsub(',', '#')}") if procpath
 

data/lib/rbbt/hpc/orchestrate/chains.rb

@@ -1,6 +1,7 @@
 module HPC
   module Orchestration
     def self.check_chains(chains, job)
+      return [] if Symbol === job.overriden
       matches = []
       chains.each do |name, chain|
         next unless chain[:tasks].include?(job.workflow.to_s)
@@ -36,95 +37,6 @@ module HPC
       (job.dependencies + job.input_dependencies).uniq.select{|d| ! d.done? || d.dirty? }
     end
 
-    #def self.job_workload(job)
-    #  workload = []
-    #  heap = []
-    #  heap << job
-    #  while job = heap.pop
-    #    next if job.done?
-    #    workload << job
-    #    heap.concat job_dependencies(job)
-    #    heap.uniq!
-    #  end
-    #  workload.uniq
-    #end
-
-    #def self.top_level_job(jobs)
-    #  top = jobs.select do |job|
-    #    (jobs - job_workload(job)).empty? &&
-    #      (job_workload(job) - jobs).select{|j| (job_workload(j) & jobs).any? }.empty?
-    #  end
-    #  return nil if top.length != 1
-    #  top.first
-    #end
-
-    #def self.job_chains(rules, job)
-    #  workload = job_workload(job)
-    #  chains = parse_chains(rules)
-
-    #  chain_jobs = {}
-    #  workload.each do |job|
-    #    check_chains(chains, job).each do |match|
-    #      chain_jobs[match] ||= []
-    #      chain_jobs[match] << job
-    #    end
-    #  end
-
-    #  job_chains = []
-
-    #  seen = []
-    #  chain_jobs.sort_by{|name,jobs| jobs.length }.reverse.each do |name,jobs|
-    #    remain = jobs - seen
-    #    next unless remain.length > 1
-    #    top_level_job = top_level_job(jobs)
-    #    next if top_level_job.nil?
-    #    job_chains << {:jobs => remain, :rules => chains[name][:rules], :top_level_job => top_level_job}
-    #    seen.concat remain
-    #  end
-
-    #  job_chains
-    #end
-
-    #def self._job_chains(rules, job)
-    #  workload = job_workload(job)
-    #  chains = parse_chains(rules)
-
-    #  matches = check_chains(chains, job)
-
-    #  job_chains = {}
-    #  job.dependencies.each do |dep|
-    #    dep_chains = _job_chains(rules, dep)
-    #    matches.each do |match|
-    #      if dep_chains[match] && dep_chains[match].include?(dep)
-    #        dep_chains[match].prepend job
-    #      end
-    #    end
-    #    job_chains.merge!(dep_chains)
-    #  end
-
-    #  matches.each do |match|
-    #    job_chains[match] ||= [job]
-    #  end
-
-    #  job_chains
-    #end
-
-    #def self.job_chains(rules, job)
-    #  job_chains = self._job_chains(rules, job)
-    #  iif job_chains
-    #  chains = parse_chains(rules)
-
-    #  seen = []
-    #  job_chains.collect do |name,jobs|
-    #    remain = jobs - seen
-    #    next unless remain.length > 1
-    #    top_level_job = top_level_job(jobs)
-    #    next if top_level_job.nil?
-    #    seen.concat remain
-    #    {:jobs => remain, :rules => chains[name][:rules], :top_level_job => top_level_job}
-    #  end.compact
-    #end
-
     def self.job_chains(rules, job)
       chains = self.parse_chains(rules)
 

data/lib/rbbt/hpc/orchestrate.rb

@@ -5,6 +5,19 @@ require 'rbbt/hpc/orchestrate/batches'
 module HPC
   module Orchestration
 
+    def prepare_for_execution(job)
+      rec_dependencies = job.rec_dependencies(true)
+
+      return if rec_dependencies.empty?
+
+      all_deps = rec_dependencies + [job]
+
+      all_deps.each do |dep|
+        Step.prepare_for_execution(dep)
+      end
+
+    end
+
     def orchestrate_job(job, options)
       options.delete "recursive_clean"
       options.delete "clean_task"
@@ -14,6 +27,9 @@ module HPC
       options.delete "detach"
       options.delete "jobname"
 
+      Log.high "Prepare for exec"
+      prepare_for_execution(job)
+
       if options[:orchestration_rules]
         rules = YAML.load(Open.read(options[:orchestration_rules]))
       elsif Rbbt.etc.slurm["default.yaml"].exists?
@@ -24,6 +40,7 @@ module HPC
 
       IndiferentHash.setup(rules)
 
+      Log.high "Compute batches"
       batches = HPC::Orchestration.job_batches(rules, job)
 
       batch_ids = {}
@@ -31,7 +48,8 @@ module HPC
         top = batches.select{|b| b[:deps].nil? || (b[:deps] - batch_ids.keys).empty? }.first
         raise "No batch without unmet dependencies" if top.nil?
         batches.delete top
-        job_options = options.merge(top[:rules])
+
+        job_options = HPC::Orchestration.merge_rules(options, top[:rules])
 
         if top[:deps].nil?
           batch_dependencies = [] 
@@ -59,7 +77,9 @@ module HPC
 
         if options[:dry_run]
           puts Log.color(:magenta, "Manifest: ") + Log.color(:blue, job_options[:manifest] * ", ") + " - tasks: #{job_options[:task_cpus] || 1} - time: #{job_options[:time]} - config: #{job_options[:config_keys]}"
-          puts Log.color(:yellow, "Deps: ") + Log.color(:blue, job_options[:batch_dependencies]*", ")
+          puts Log.color(:magenta, "Deps: ") + Log.color(:blue, job_options[:batch_dependencies]*", ")
+          puts Log.color(:yellow, "Path: ") + top[:top_level].path
+          puts Log.color(:yellow, "Options: ") + Misc.fingerprint(job_options)
           batch_ids[top] = top[:top_level].task_signature
         else
           id = run_job(top[:top_level], job_options)

data/lib/rbbt/hpc/slurm.rb

@@ -32,6 +32,8 @@ export BATCH_SYSTEM=SLURM
       constraint     = Misc.process_options options, :constraint
       gres           = Misc.process_options options, :gres
 
+      constraint     = [constraint, "highmem"].compact * "&" if highmem
+
       mem            = Misc.process_options options, :mem
       mem_per_cpu    = Misc.process_options options, :mem_per_cpu
 
@@ -50,14 +52,15 @@ export BATCH_SYSTEM=SLURM
                        "cpus-per-task" => task_cpus,
                        "nodes" => nodes,
                        "time" => time,
+                       "constraint" => constraint,
                        "exclusive" => exclusive,
-                       "highmem" => highmem,
                        "licenses" => licenses,
                        "gres" => gres,
                        "mem" => mem,
                        "mem-per-cpu" => mem_per_cpu,
       }
 
+
       header =<<-EOF
 #!/bin/bash
       EOF

data/lib/rbbt/util/migrate.rb

@@ -1,4 +1,6 @@
 module Rbbt 
+
+  prepare_for_execution(job)
   def self.migrate_source_paths(path, resource = Rbbt, source = nil)
     if source
       lpath, *paths = Misc.ssh_run(source, <<-EOF).split("\n")
@@ -44,6 +46,8 @@ puts resource[path].find(search_path)
     excludes += (options[:exclude] || "").split(/,\s*/)
     excludes_str = excludes.collect{|s| "--exclude '#{s}'" } * " "
 
+    hard_link = options[:hard_link]
+
     other = options[:other] || []
 
     test_str = options[:test] ? '-nv' : ''
@@ -82,6 +86,8 @@ puts resource[path].find(search_path)
         # rsync_args = "-avztAXHP --copy-unsafe-links"
         rsync_args = "-avztAHP --copy-unsafe-links"
 
+        rsync_args << " --link-dest '#{source_path}'" if hard_link && ! options[:source]
+
         cmd = "rsync #{rsync_args} #{test_str} #{files_from_str} #{excludes_str} '#{source_path}' #{target_path} #{other * " "}"
 
         cmd << " && rm -Rf #{source_path}" if options[:delete] && ! options[:files]

data/lib/rbbt/workflow/definition.rb

@@ -93,22 +93,22 @@ module Workflow
         Open.rm_rf self.files_dir if Open.exist? self.files_dir
         FileUtils.cp_r dep.files_dir, self.files_dir if Open.exist?(dep.files_dir)
 
-        if dep.overriden
+        if dep.overriden || ! Workflow.job_path?(dep.path)
           Open.link dep.path, self.tmp_path
         else
           Open.ln_h dep.path, self.tmp_path
-        end
 
-        case remove.to_s
-        when 'true'
-          dep.clean
-        when 'recursive'
-          (dep.dependencies + dep.rec_dependencies).uniq.each do |d|
-            next if d.overriden
-            d.clean unless config(:remove_dep, d.task_signature, d.task_name, d.workflow.to_s, :default => true).to_s == 'false'
-          end
-          dep.clean unless config(:remove_dep, dep.task_signature, dep.task_name, dep.workflow.to_s, :default => true).to_s == 'false'
-        end unless dep.overriden
+          case remove.to_s
+          when 'true'
+            dep.clean
+          when 'recursive'
+            (dep.dependencies + dep.rec_dependencies).uniq.each do |d|
+              next if d.overriden
+              d.clean unless config(:remove_dep, d.task_signature, d.task_name, d.workflow.to_s, :default => true).to_s == 'false'
+            end
+            dep.clean unless config(:remove_dep, dep.task_signature, dep.task_name, dep.workflow.to_s, :default => true).to_s == 'false'
+          end 
+        end
       else
         if Open.exists?(dep.files_dir)
           Open.rm_rf self.files_dir 

data/lib/rbbt/workflow/step/run.rb

@@ -181,8 +181,8 @@ class Step
     #  end
     #end
 
-    Log.high "Some newer files found: #{Misc.fingerprint outdated_time}" if outdated_time.any?
-    Log.high "Some outdated files found: #{Misc.fingerprint outdated_dep}" if outdated_dep.any?
+    Log.medium "Some newer files found: #{Misc.fingerprint outdated_time}" if outdated_time.any?
+    Log.medium "Some outdated files found: #{Misc.fingerprint outdated_dep}" if outdated_dep.any?
 
     outdated_time + outdated_dep
   end

data/lib/rbbt/workflow/util/orchestrator.rb

@@ -5,10 +5,10 @@ module Workflow
 
     def self.job_workload(job)
       workload = {job => []}
-      return workload if job.done?
+      return workload if job.done? && ! job.dirty?
 
       job.dependencies.each do |dep|
-        next if dep.done?
+        next if dep.done? && ! job.dirty?
         workload.merge!(job_workload(dep))
         workload[job] += workload[dep]
         workload[job] << dep
@@ -16,7 +16,7 @@ module Workflow
       end
 
       job.input_dependencies.each do |dep|
-        next if dep.done?
+        next if dep.done? && ! job.dirty?
         workload.merge!(job_workload(dep))
         workload[job] += workload[dep]
         workload[job] << dep

data/share/Rlib/plot.R

@@ -38,3 +38,4 @@ geom_entity <- function (real.geom = NULL, mapping = NULL, data = NULL, stat = "
     rg
 }
 
+rbbt.ggplot2.rotate_x_labels <- function(){ theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust=1)) }

data/share/rbbt_commands/hpc/list

@@ -21,6 +21,7 @@ $ rbbt slurm list [options]
 -j--job* Job ids
 -s--search* Regular expression
 -t--tail* Show the last lines of the STDERR
+-l--long Show more entries
 -p--progress Report progress of job and the dependencies
 -BP--batch_parameters show batch parameters
 -BPP--batch_procpath show Procpath performance summary
@@ -40,6 +41,8 @@ end
 batch_system = options.delete :batch_system
 batch_system ||= 'auto'
 
+long = options.delete :long
+
 HPC::BATCH_MODULE = HPC.batch_system batch_system
 
 raise ParameterException.new("Could not detect batch_system: #{Misc.fingerprint batch_system}") if HPC::BATCH_MODULE.nil?
@@ -183,24 +186,24 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
 
 
  puts Log.color :blue, dir
- puts Log.color(:magenta, "Creation: ") << File.mtime(File.join(dir, 'command.batch')).to_s
- puts Log.color(:magenta, "Started: ") << File.ctime(File.join(dir, 'std.err')).to_s if File.exist?(File.join(dir, 'std.err'))
- puts Log.color(:magenta, "Manifest: ") << Log.color(:yellow, manifest) 
+ puts Log.color(:magenta, "Creation: ") << File.mtime(File.join(dir, 'command.batch')).to_s if long
+ puts Log.color(:magenta, "Started: ") << File.ctime(File.join(dir, 'std.err')).to_s if File.exist?(File.join(dir, 'std.err')) && long
+ puts Log.color(:magenta, "Manifest: ") << Log.color(:yellow, manifest) if long
  puts Log.color(:magenta, "Step path: ") << Log.color(:yellow, step_path)
  puts Log.color(:magenta, "Done: ") << File.mtime(File.join(dir, 'exit.status')).to_s if File.exist?(File.join(dir, 'exit.status'))
- puts Log.color(:magenta, "Exec: ") << (exe || "Missing")
- puts Log.color(:magenta, "CMD: ") << (Log.color(:yellow, cmd) || "Missing")
- puts Log.color(:magenta, "HOME: ") << Log.color(:yellow, container_home) if container_home
+ puts Log.color(:magenta, "Exec: ") << (exe || "Missing") if long
+ puts Log.color(:magenta, "CMD: ") << (Log.color(:yellow, cmd) || "Missing") if long
+ puts Log.color(:magenta, "HOME: ") << Log.color(:yellow, container_home) if container_home && long
  if different_system
    puts Log.color(:magenta, "Job ID (#{Log.color(:red, job_batch_system)}): ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  Log.color(:green, id)  )
  else
    puts Log.color(:magenta, "Job ID: ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  (running_jobs.include?(id) || $norunningjobs ? Log.color(:green, id) : Log.color(:red, id) ))
- end
+ end 
  puts Log.color(:magenta, "Dependencies: ") << deps * ", " if deps
  puts Log.color(:magenta, "Dependencies (can fail): ") << cadeps * ", " if cadeps
- puts Log.color(:magenta, "Nodes: ") << nodes * ", "
+ puts Log.color(:magenta, "Nodes: ") << nodes * ", " if long
  puts Log.color(:magenta, "Time elapsed: ") << Misc.format_seconds(time_elapsed) if time_elapsed
- puts Log.color(:magenta, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? || File.exists?(File.join(dir, 'exit.status')) ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)")
+ puts Log.color(:magenta, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? || File.exists?(File.join(dir, 'exit.status')) ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)") if long
 
  if options[:batch_parameters]
    puts Log.color(:magenta, "BATCH parameters: ")
@@ -281,7 +284,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
      puts CMD.cmd("grep -i -w 'Completed step' #{File.join(dir, 'std.err')} | grep -v 'Retrying dep.' | tail -n #{tail.to_i}", :no_fail => true).read
    else
      puts Log.color(:magenta, "Log tail: ")
-     puts CMD.cmd(" cat #{File.join(dir, 'std.err')} | grep -v '^[^\\s:]*\\[3.m'  | tail -n #{tail.to_i} ").read
+     puts CMD.cmd(" cat #{File.join(dir, 'std.err')} | grep -v '^[^\\s:]*\\[3.m'  | grep -v -e '^[[:space:]]*$' | grep -v  \"\\(STDOUT\\|STDERR\\):[[:space:]]*$\" | tail -n #{tail.to_i} ").read
    end
  end
 

data/share/rbbt_commands/hpc/tail

@@ -10,7 +10,7 @@ options = SOPT.setup <<EOF
 
 Queue a job in Marenostrum
 
-$ rbbt slurm tail <directory> [options] 
+$ rbbt slurm tail <directory|jobid> [options] 
 
 -h--help Print this help
 EOF
@@ -35,8 +35,28 @@ directory = ARGV.shift
 
 raise ParameterException if directory.nil?
 
-directory = File.dirname(directory) unless File.directory?(directory)
+if directory =~ /^[0-9]*$/
+  workdir = File.expand_path('~/rbbt-batch')
+  Path.setup(workdir)
+
+  workdir.glob("**/job.id").each do |file|
+    next unless directory == Open.read(file).strip
+    directory = File.dirname(file)
+    break
+  end
+end
+
+raise ParameterException, "Could not identify job #{directory}" unless File.exists?(directory)
 
 require 'rbbt/hpc/slurm'
 
+command_txt = Open.read(File.join(directory, 'command.batch'))
+if m = command_txt.match(/#STEP_PATH: (.*)/)
+  step_path = m[1]
+else
+  step_path = nil
+end
+
+puts Log.color(:magenta, "Step path: ") + step_path if step_path
+
 HPC::BATCH_MODULE.follow_job directory, true

data/share/rbbt_commands/lsf/list

@@ -21,6 +21,7 @@ $ rbbt slurm list [options]
 -j--job* Job ids
 -s--search* Regular expression
 -t--tail* Show the last lines of the STDERR
+-l--long Show more entries
 -p--progress Report progress of job and the dependencies
 -BP--batch_parameters show batch parameters
 -BPP--batch_procpath show Procpath performance summary
@@ -40,6 +41,8 @@ end
 batch_system = options.delete :batch_system
 batch_system ||= 'auto'
 
+long = options.delete :long
+
 HPC::BATCH_MODULE = HPC.batch_system batch_system
 
 raise ParameterException.new("Could not detect batch_system: #{Misc.fingerprint batch_system}") if HPC::BATCH_MODULE.nil?
@@ -183,24 +186,24 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
 
 
  puts Log.color :blue, dir
- puts Log.color(:magenta, "Creation: ") << File.mtime(File.join(dir, 'command.batch')).to_s
- puts Log.color(:magenta, "Started: ") << File.ctime(File.join(dir, 'std.err')).to_s if File.exist?(File.join(dir, 'std.err'))
- puts Log.color(:magenta, "Manifest: ") << Log.color(:yellow, manifest) 
+ puts Log.color(:magenta, "Creation: ") << File.mtime(File.join(dir, 'command.batch')).to_s if long
+ puts Log.color(:magenta, "Started: ") << File.ctime(File.join(dir, 'std.err')).to_s if File.exist?(File.join(dir, 'std.err')) && long
+ puts Log.color(:magenta, "Manifest: ") << Log.color(:yellow, manifest) if long
  puts Log.color(:magenta, "Step path: ") << Log.color(:yellow, step_path)
  puts Log.color(:magenta, "Done: ") << File.mtime(File.join(dir, 'exit.status')).to_s if File.exist?(File.join(dir, 'exit.status'))
- puts Log.color(:magenta, "Exec: ") << (exe || "Missing")
- puts Log.color(:magenta, "CMD: ") << (Log.color(:yellow, cmd) || "Missing")
- puts Log.color(:magenta, "HOME: ") << Log.color(:yellow, container_home) if container_home
+ puts Log.color(:magenta, "Exec: ") << (exe || "Missing") if long
+ puts Log.color(:magenta, "CMD: ") << (Log.color(:yellow, cmd) || "Missing") if long
+ puts Log.color(:magenta, "HOME: ") << Log.color(:yellow, container_home) if container_home && long
  if different_system
    puts Log.color(:magenta, "Job ID (#{Log.color(:red, job_batch_system)}): ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  Log.color(:green, id)  )
  else
    puts Log.color(:magenta, "Job ID: ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  (running_jobs.include?(id) || $norunningjobs ? Log.color(:green, id) : Log.color(:red, id) ))
- end
+ end 
  puts Log.color(:magenta, "Dependencies: ") << deps * ", " if deps
  puts Log.color(:magenta, "Dependencies (can fail): ") << cadeps * ", " if cadeps
- puts Log.color(:magenta, "Nodes: ") << nodes * ", "
+ puts Log.color(:magenta, "Nodes: ") << nodes * ", " if long
  puts Log.color(:magenta, "Time elapsed: ") << Misc.format_seconds(time_elapsed) if time_elapsed
- puts Log.color(:magenta, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? || File.exists?(File.join(dir, 'exit.status')) ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)")
+ puts Log.color(:magenta, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? || File.exists?(File.join(dir, 'exit.status')) ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)") if long
 
  if options[:batch_parameters]
    puts Log.color(:magenta, "BATCH parameters: ")
@@ -281,7 +284,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
      puts CMD.cmd("grep -i -w 'Completed step' #{File.join(dir, 'std.err')} | grep -v 'Retrying dep.' | tail -n #{tail.to_i}", :no_fail => true).read
    else
      puts Log.color(:magenta, "Log tail: ")
-     puts CMD.cmd(" cat #{File.join(dir, 'std.err')} | grep -v '^[^\\s:]*\\[3.m'  | tail -n #{tail.to_i} ").read
+     puts CMD.cmd(" cat #{File.join(dir, 'std.err')} | grep -v '^[^\\s:]*\\[3.m'  | grep -v -e '^[[:space:]]*$' | grep -v  \"\\(STDOUT\\|STDERR\\):[[:space:]]*$\" | tail -n #{tail.to_i} ").read
    end
  end
 

data/share/rbbt_commands/lsf/tail

@@ -10,7 +10,7 @@ options = SOPT.setup <<EOF
 
 Queue a job in Marenostrum
 
-$ rbbt slurm tail <directory> [options] 
+$ rbbt slurm tail <directory|jobid> [options] 
 
 -h--help Print this help
 EOF
@@ -35,8 +35,28 @@ directory = ARGV.shift
 
 raise ParameterException if directory.nil?
 
-directory = File.dirname(directory) unless File.directory?(directory)
+if directory =~ /^[0-9]*$/
+  workdir = File.expand_path('~/rbbt-batch')
+  Path.setup(workdir)
+
+  workdir.glob("**/job.id").each do |file|
+    next unless directory == Open.read(file).strip
+    directory = File.dirname(file)
+    break
+  end
+end
+
+raise ParameterException, "Could not identify job #{directory}" unless File.exists?(directory)
 
 require 'rbbt/hpc/slurm'
 
+command_txt = Open.read(File.join(directory, 'command.batch'))
+if m = command_txt.match(/#STEP_PATH: (.*)/)
+  step_path = m[1]
+else
+  step_path = nil
+end
+
+puts Log.color(:magenta, "Step path: ") + step_path if step_path
+
 HPC::BATCH_MODULE.follow_job directory, true

data/share/rbbt_commands/slurm/list

@@ -21,6 +21,7 @@ $ rbbt slurm list [options]
 -j--job* Job ids
 -s--search* Regular expression
 -t--tail* Show the last lines of the STDERR
+-l--long Show more entries
 -p--progress Report progress of job and the dependencies
 -BP--batch_parameters show batch parameters
 -BPP--batch_procpath show Procpath performance summary
@@ -40,6 +41,8 @@ end
 batch_system = options.delete :batch_system
 batch_system ||= 'auto'
 
+long = options.delete :long
+
 HPC::BATCH_MODULE = HPC.batch_system batch_system
 
 raise ParameterException.new("Could not detect batch_system: #{Misc.fingerprint batch_system}") if HPC::BATCH_MODULE.nil?
@@ -183,24 +186,24 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
 
 
  puts Log.color :blue, dir
- puts Log.color(:magenta, "Creation: ") << File.mtime(File.join(dir, 'command.batch')).to_s
- puts Log.color(:magenta, "Started: ") << File.ctime(File.join(dir, 'std.err')).to_s if File.exist?(File.join(dir, 'std.err'))
- puts Log.color(:magenta, "Manifest: ") << Log.color(:yellow, manifest) 
+ puts Log.color(:magenta, "Creation: ") << File.mtime(File.join(dir, 'command.batch')).to_s if long
+ puts Log.color(:magenta, "Started: ") << File.ctime(File.join(dir, 'std.err')).to_s if File.exist?(File.join(dir, 'std.err')) && long
+ puts Log.color(:magenta, "Manifest: ") << Log.color(:yellow, manifest) if long
  puts Log.color(:magenta, "Step path: ") << Log.color(:yellow, step_path)
  puts Log.color(:magenta, "Done: ") << File.mtime(File.join(dir, 'exit.status')).to_s if File.exist?(File.join(dir, 'exit.status'))
- puts Log.color(:magenta, "Exec: ") << (exe || "Missing")
- puts Log.color(:magenta, "CMD: ") << (Log.color(:yellow, cmd) || "Missing")
- puts Log.color(:magenta, "HOME: ") << Log.color(:yellow, container_home) if container_home
+ puts Log.color(:magenta, "Exec: ") << (exe || "Missing") if long
+ puts Log.color(:magenta, "CMD: ") << (Log.color(:yellow, cmd) || "Missing") if long
+ puts Log.color(:magenta, "HOME: ") << Log.color(:yellow, container_home) if container_home && long
  if different_system
    puts Log.color(:magenta, "Job ID (#{Log.color(:red, job_batch_system)}): ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  Log.color(:green, id)  )
  else
    puts Log.color(:magenta, "Job ID: ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  (running_jobs.include?(id) || $norunningjobs ? Log.color(:green, id) : Log.color(:red, id) ))
- end
+ end 
  puts Log.color(:magenta, "Dependencies: ") << deps * ", " if deps
  puts Log.color(:magenta, "Dependencies (can fail): ") << cadeps * ", " if cadeps
- puts Log.color(:magenta, "Nodes: ") << nodes * ", "
+ puts Log.color(:magenta, "Nodes: ") << nodes * ", " if long
  puts Log.color(:magenta, "Time elapsed: ") << Misc.format_seconds(time_elapsed) if time_elapsed
- puts Log.color(:magenta, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? || File.exists?(File.join(dir, 'exit.status')) ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)")
+ puts Log.color(:magenta, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? || File.exists?(File.join(dir, 'exit.status')) ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)") if long
 
  if options[:batch_parameters]
    puts Log.color(:magenta, "BATCH parameters: ")
@@ -281,7 +284,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
      puts CMD.cmd("grep -i -w 'Completed step' #{File.join(dir, 'std.err')} | grep -v 'Retrying dep.' | tail -n #{tail.to_i}", :no_fail => true).read
    else
      puts Log.color(:magenta, "Log tail: ")
-     puts CMD.cmd(" cat #{File.join(dir, 'std.err')} | grep -v '^[^\\s:]*\\[3.m'  | tail -n #{tail.to_i} ").read
+     puts CMD.cmd(" cat #{File.join(dir, 'std.err')} | grep -v '^[^\\s:]*\\[3.m'  | grep -v -e '^[[:space:]]*$' | grep -v  \"\\(STDOUT\\|STDERR\\):[[:space:]]*$\" | tail -n #{tail.to_i} ").read
    end
  end
 

data/share/rbbt_commands/slurm/tail

@@ -10,7 +10,7 @@ options = SOPT.setup <<EOF
 
 Queue a job in Marenostrum
 
-$ rbbt slurm tail <directory> [options] 
+$ rbbt slurm tail <directory|jobid> [options] 
 
 -h--help Print this help
 EOF
@@ -35,8 +35,28 @@ directory = ARGV.shift
 
 raise ParameterException if directory.nil?
 
-directory = File.dirname(directory) unless File.directory?(directory)
+if directory =~ /^[0-9]*$/
+  workdir = File.expand_path('~/rbbt-batch')
+  Path.setup(workdir)
+
+  workdir.glob("**/job.id").each do |file|
+    next unless directory == Open.read(file).strip
+    directory = File.dirname(file)
+    break
+  end
+end
+
+raise ParameterException, "Could not identify job #{directory}" unless File.exists?(directory)
 
 require 'rbbt/hpc/slurm'
 
+command_txt = Open.read(File.join(directory, 'command.batch'))
+if m = command_txt.match(/#STEP_PATH: (.*)/)
+  step_path = m[1]
+else
+  step_path = nil
+end
+
+puts Log.color(:magenta, "Step path: ") + step_path if step_path
+
 HPC::BATCH_MODULE.follow_job directory, true

data/share/rbbt_commands/workflow/prov

@@ -37,7 +37,7 @@ file = ARGV.shift
 $seen = []
 def get_step(file)
   file = File.expand_path(file)
-  file = file.sub(/\.(info|files)/,'')
+  file = file.sub(/\.(info|files)$/,'')
   $seen << file
   Workflow.load_step file
 end

data/share/rbbt_commands/workflow/task

@@ -219,8 +219,8 @@ help = !!options.delete(:help)
 do_fork = !!options.delete(:fork)
 detach = !!options.delete(:detach)
 do_exec = !!options.delete(:exec)
-clean = !!options.delete(:clean)
 clean_task = options.delete(:clean_task)
+clean = !!options.delete(:clean) || clean_task
 override_deps = options.delete(:override_deps)
 recursive_clean = !!options.delete(:recursive_clean)
 out = options.include?(:output) ? File.open(options[:output], 'wb') : STDOUT

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.33.4
+  version: 5.33.7
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-03-03 00:00:00.000000000 Z
+date: 2022-03-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake