rbbt-util 5.29.4 → 5.30.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3ec6302ccfe3f38a074f7f0d10511090c8f4db4186228ad93adb2888e0edbf5e
-  data.tar.gz: fcaa50b654461f128b9539fc47ed00b008d3f713e89b8bbe963c2b898c3c168b
+  metadata.gz: d45adac7949e3fea0d710418d93837cf0aa715bcedb2212c6e68f8dd749382ae
+  data.tar.gz: 9a9857c6b1565b9ed55f18f50fb1b242a1477dd6868111e10252ecc0c286ca44
 SHA512:
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-  data.tar.gz: d79cc4afa294d63cebd79f73b759bc46c3c4e0285db7be7406a594aa49e5b572b0c4f91b98c73b5f64c31c908d58d8dee43853ec18b1ead9e814b4370de0d60d
+  metadata.gz: 9dac4b1211fd40894f00b1a84f4f10abad83f2169579ec327a8da86f05b4274cc11e2192902638eb78b9de8f39351993f17a3b08dd5390a0f2c04ef385a0e1a2
+  data.tar.gz: 01b9d69b003088e78f2665b57e9ed8acc8104143bc826aabe49059e77fd0e20279d9393245f7bb20efcab807180273f31d2285a62113947cf151571a96f2d949

data/lib/rbbt/hpc/orchestrate.rb

@@ -83,7 +83,7 @@ module HPC
 
         deps = seen[dep.path] ||= self.orchestrate_job(dep, options, skip_dep, seen)
         if job.canfail_paths.include? dep.path
-          [deps].flatten.collect{|id| ['canfail', id] * ":"}
+          [deps].flatten.compact.collect{|id| ['canfail', id] * ":"}
         else
           deps
         end

data/lib/rbbt/hpc/slurm.rb

@@ -33,7 +33,8 @@ module HPC
       group = File.basename(File.dirname(ENV['HOME']))
 
       if contain_and_sync
-        contain = "/scratch/tmp/rbbt-#{user}" if contain.nil?
+        random_file = TmpFile.random_name
+        contain = "/scratch/tmp/rbbt-#{user}/#{random_file}" if contain.nil?
         sync = "~/.rbbt/var/jobs" if sync.nil?
         wipe_container = "post" if wipe_container.nil?
       end
@@ -243,7 +244,7 @@ EOF
         end
 
         if contain
-          rbbt_cmd << " " << %(--workdir_all='#{contain.gsub("'", '\'')}/.rbbt/var/jobs')
+          rbbt_cmd << " " << %(--workdir_all='#{contain.gsub("'", '\'')}/workdir')
         end
       end
 
@@ -251,6 +252,10 @@ EOF
       cmd =<<-EOF
 #{exec_cmd} \\
 #{rbbt_cmd}
+EOF
+      annotate_cmd =<<-EOF
+#{exec_cmd} \\
+workflow write_info --recursive --force=false --check_pid "$step_path" slurm_job $SLURM_JOB_ID 
 EOF
 
       header +=<<-EOF
@@ -260,11 +265,14 @@ EOF
       run +=<<-EOF
 
 # Run command
-#{cmd}
+step_path=$(#{cmd})
 
 # Save exit status
 exit_status=$?
 
+# Annotate info with SLURM job_info
+#{annotate_cmd}
+
 EOF
 
       # CODA
@@ -286,7 +294,7 @@ EOF
           sync = sync.strip
           source = File.join(File.expand_path(contain), source)
         else
-          source = File.join(File.expand_path(contain), '.rbbt/var/jobs')
+          source = File.join(File.expand_path(contain), 'workdir/var/jobs')
         end
 
         target = File.expand_path(sync)
@@ -516,7 +524,11 @@ EOF
       dry_run          = options.delete :dry_run
       tail             = options.delete :tail
       dependencies     = options.delete :slurm_dependencies
+      procpath         = options.delete :SLURM_procpath
+
       options[:jobname] = job.clean_name
+      log_level         = options.delete :log
+      log_level       ||= Log.severity
 
       workflow = job.workflow
 
@@ -541,15 +553,14 @@ EOF
         inputs_dir = File.join(tmp_directory, 'inputs_dir')
         saved = Step.save_job_inputs(job, inputs_dir)
 
-        if saved && saved.any?
-          options[:inputs_dir] = inputs_dir
-          cmd = ['workflow', 'task', workflow.to_s, task.to_s, '-pf', '--load_inputs', inputs_dir, '--log', (options[:log] || Log.severity).to_s]
-        else
-          cmd = ['workflow', 'task', workflow.to_s, task.to_s, '-pf', '--log', (options[:log] || Log.severity).to_s]
-        end
+        cmd = ['workflow', 'task', workflow.to_s, task.to_s, '--printpath', '--log', log_level.to_s]
+
+        cmd << "--procpath_performance='#{tmp_directory}/procpath##{procpath.gsub(',', '#')}'" if procpath
 
         cmd << "--override_deps='#{override_deps.gsub("'", '\'')}'" if override_deps and not override_deps.empty?
 
+        cmd << "--load_inputs='#{inputs_dir}'" if saved && saved.any?
+
         template = self.template(cmd, options)
         jobid = self.issue_template(template, options.merge(:slurm_basedir => slurm_basedir, :dry_run => dry_run, :slurm_dependencies => dependencies))
 

data/lib/rbbt/persist/tsv/adapter.rb

@@ -104,9 +104,6 @@ module Persist
         write(true) if closed? || ! write?
         res = begin
                 yield
-              rescue Exception
-                Log.exception $!
-                raise $!
               ensure
                 close
               end
@@ -115,7 +112,6 @@ module Persist
     end
 
     def read_and_close
-      #return yield if @locked
       if read? || write?
         begin
           return yield
@@ -134,6 +130,41 @@ module Persist
       end
     end
 
+    def read_lock
+      read if closed?
+      if read?
+        return yield
+      end
+
+      lock do
+        close
+        read true
+        begin
+          yield
+        end
+      end
+    end
+
+    def write_lock
+      write if closed?
+      if write?
+        begin
+          return yield
+        ensure
+          close
+        end
+      end
+
+      lock do
+        close
+        write true
+        begin
+          yield
+        end
+      end
+    end
+
+
     def merge!(hash)
       hash.each do |key,values|
         self[key] = values
@@ -141,38 +172,38 @@ module Persist
     end
 
     def range(*args)
-      self.read_and_close do
+      self.read_lock do
         super(*args)
       end
     end
 
     def include?(*args)
-      self.read_and_close do
+      self.read_lock do
         super(*args) #- TSV::ENTRY_KEYS.to_a
       end
     end
 
     def [](*args)
-      self.read_and_close do
+      self.read_lock do
         super(*args) #- TSV::ENTRY_KEYS.to_a
       end
     end
 
     def []=(*args)
-      self.write_and_close do
+      self.write_lock do
         super(*args) #- TSV::ENTRY_KEYS.to_a
       end
     end
 
     def keys(*args)
-      self.read_and_close do
+      self.read_lock do
         super(*args)
       end
     end
 
 
     def prefix(key)
-      self.read_and_close do
+      self.read_lock do
         range(key, 1, key + MAX_CHAR, 1)
       end
     end
@@ -184,13 +215,13 @@ module Persist
 
 
     def size(*args)
-      self.read_and_close do
+      self.read_lock do
         super(*args)
       end
     end
 
     def each(*args, &block)
-      self.read_and_close do
+      self.read_lock do
         super(*args, &block)
       end
     end
@@ -208,7 +239,7 @@ module Persist
     end
 
     def values_at(*keys)
-      self.read_and_close do
+      self.read_lock do
         keys.collect do |k|
           self[k]
         end

data/lib/rbbt/tsv.rb

@@ -113,11 +113,12 @@ module TSV
 
     data.entity_options = entity_options
 
-    if Path === source and data.identifiers
-      data.identifiers = Path.setup(data.identifiers, source.pkgdir, source.resource)
+    if Path === source && data.identifiers
+      Path.setup(data.identifiers, source.pkgdir, source.resource)
     end
 
     if data.respond_to? :persistence_path
+      data.read
       data
     else
       h = data.dup

data/lib/rbbt/util/cmd.rb

@@ -217,7 +217,7 @@ module CMD
     end
   end
 
-  def self.cmd_log(*args)
+  def self.cmd_pid(*args)
     all_args = *args
 
     all_args << {} unless Hash === all_args.last
@@ -248,4 +248,9 @@ module CMD
     nil
   end
 
+  def self.cmd_log(*args)
+    cmd_pid(*args)
+    nil
+  end
+
 end

data/lib/rbbt/util/misc/options.rb

@@ -242,48 +242,6 @@ module Misc
 
     return options
 
-    options = {}
-    string.split(/#/).each do |str|
-      if str.match(/(.*)=(.*)/)
-        option, value = $1, $2
-      else
-        option, value = str, true
-      end
-
-      option = option.sub(":",'').to_sym if option.chars.first == ':'
-      value  = value.sub(":",'').to_sym if String === value and value.chars.first == ':'
-
-      if value == true
-        options[option] = option.to_s.chars.first != '!' 
-      else
-        options[option] = Thread.start do
-          $SAFE = 0;
-          case 
-          when value =~ /^(?:true|T)$/i
-            true
-          when value =~ /^(?:false|F)$/i
-            false
-          when Symbol === value
-            value
-          when (String === value and value =~ /^\/(.*)\/$/)
-            Regexp.new /#{$1}/
-          else
-            begin
-              Kernel.const_get value
-            rescue
-              begin  
-                raise if value =~ /[a-z]/ and defined? value
-                eval(value) 
-              rescue Exception
-                value 
-              end
-            end
-          end
-        end.value
-      end
-    end
-
-    options
   end
 
 end

data/lib/rbbt/util/procpath.rb

@@ -0,0 +1,49 @@
+require 'rbbt/util/cmd'
+module ProcPath
+  CMD.tool :procpath do
+    'pip install procpath'
+  end
+
+  def self.record(pid, path, options = {})
+    IndiferentHash.setup(options)
+    options = Misc.add_defaults options, "interval" => 30
+
+    cmd_options = %w(interval recnum reevalnum).inject({}){|acc,k| acc[k] = options[k]; acc}
+
+    Log.debug "ProcPath recording #{pid} in #{path} (#{Misc.fingerprint options})"
+    procpath_thread = Thread.new do 
+      begin
+        procpath_pid = CMD.cmd_pid(:procpath, "record --database-file '#{path}' '$..children[?(@.stat.pid == #{pid})]'", cmd_options.merge(:nofail => true, :add_option_dashes => true))
+      rescue Exception
+        Log.exceptions $!
+        Process.kill "INT", procpath_pid
+      end
+    end
+
+    procpath_thread.report_on_exception = false
+
+    Process.wait pid.to_i
+    procpath_thread.raise Interrupt
+  end
+
+  def self.plot(path, output, options = {})
+    IndiferentHash.setup(options)
+    options = Misc.add_defaults options, "query-name" => 'rss', 'epsilon' => 0.5, "moving-average-window" => 10
+
+    cmd_options = %w(query-name epsilon monitor-average-window title logarithmic after before custom-query-file custom-value-expr).inject({}){|acc,k| acc[k] = options[k]; acc}
+    CMD.cmd_log(:procpath, "plot --database-file '#{path}' --plot-file '#{output}' ", cmd_options.merge(:nofail => true, :add_option_dashes => true))
+  end
+
+  def self.monitor(pid, path)
+    database, options_str = path.split("#")
+    options = options_str.nil? ? {} : Misc.string2hash(options_str)
+
+    database = File.expand_path database
+    Log.low "ProcPath monitor #{pid} in #{database} (#{Misc.fingerprint options})"
+
+    ProcPath.record(pid, database + '.sqlite3', options)
+    ProcPath.plot(database + '.sqlite3', database + '.cpu.svg', options.merge("query-name" => 'cpu'))
+    ProcPath.plot(database + '.sqlite3', database + '.rss.svg', options.merge("query-name" => 'rss'))
+  end
+end
+

data/lib/rbbt/workflow.rb

@@ -190,7 +190,7 @@ module Workflow
       return Misc.string2const Misc.camel_case(wf_name)
     end
 
-    Log.info{"Loading workflow #{wf_name}"}
+    Log.high{"Loading workflow #{wf_name}"}
     require_local_workflow(wf_name) or 
     (Workflow.autoinstall and `rbbt workflow install #{Misc.snake_case(wf_name)} || rbbt workflow install #{wf_name}` and require_local_workflow(wf_name)) or raise("Workflow not found or could not be loaded: #{ wf_name }")
     begin

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

@@ -505,8 +505,8 @@ class Step
 
   def running? 
     return false if ! (started? || status == :ending)
-    pid = info[:pid]
-    return nil if pid.nil?
+    return nil unless Open.exist?(self.pid_file)
+    pid = Open.read(self.pid_file).to_i
 
     return false if done? or error? or aborted? 
 
@@ -530,8 +530,7 @@ class Step
   end
 
   def nopid?
-    pid = info[:pid] || Open.exists?(pid_file)
-    ! pid && ! (status.nil? || status == :aborted || status == :done || status == :error || status == :cleaned)
+    ! Open.exists?(pid_file) && ! (status.nil? || status == :aborted || status == :done || status == :error || status == :cleaned)
   end
 
   def aborted?

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

@@ -373,7 +373,6 @@ class Step
                 Log.exception $!
               ensure
                 Step.purge_stream_cache
-                set_info :pid, nil
                 Open.rm pid_file if Open.exist?(pid_file)
               end
             end
@@ -388,7 +387,6 @@ class Step
                 _clean_finished
               rescue
                 stop_dependencies
-                set_info :pid, nil
                 Open.rm pid_file if Open.exist?(pid_file)
               end
             end
@@ -449,7 +447,7 @@ class Step
     ensure 
       no_load = false unless IO === result
       Open.rm pid_file if Open.exist?(pid_file) unless no_load
-      set_info :pid, nil unless no_load
+      #set_info :pid, nil unless no_load
     end
   end
 
@@ -559,7 +557,7 @@ class Step
           RbbtSemaphore.post_semaphore(semaphore) if semaphore
           Kernel.exit! -1
         end
-        set_info :pid, nil
+        #set_info :pid, nil
       ensure
         RbbtSemaphore.post_semaphore(semaphore) if semaphore
       end

data/lib/rbbt/workflow/usage.rb

@@ -57,7 +57,7 @@ module Task
       puts Log.color(:magenta, "Input select options")
       puts
       selects.collect{|p| p}.uniq.each do |input,options|
-        puts Log.color(:blue, input.to_s + ": ") << Misc.format_paragraph(options.collect{|o| o.to_s} * ", ") << "\n"
+        puts Log.color(:blue, input.to_s + ": ") << Misc.format_paragraph(options.collect{|o| Array === o ? o.first.to_s : o.to_s} * ", ") << "\n"
         puts unless Log.compact
       end
       puts

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

@@ -232,7 +232,7 @@ puts resource[path].find(search_path)
           ppp Open.read(tmp_include_file)
           puts cmd 
         else
-          CMD.cmd_log(cmd)
+          CMD.cmd_log(cmd, :log => Log::INFO)
         end
       end
     end

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

@@ -78,6 +78,7 @@ class Step
     name = info[:name] || File.basename(path)
     status = :unsync if status == :done and not Open.exist?(path)
     status = :notfound if status == :noinfo and not Open.exist?(path)
+
     str = " " * offset
     str << prov_report_msg(status, name, path, info)
     step.dependencies.reverse.each do |dep|
@@ -90,7 +91,7 @@ class Step
         if expand_repeats
           str << Log.color(:green, Log.uncolor(prov_report(dep, offset+1, task)))
         else
-          str << Log.color(:green, " " * (offset + 1) + Log.uncolor(prov_report_msg(status, name, path, info)))
+          str << Log.color(:green, " " * (offset + 1) + Log.uncolor(prov_report_msg(dep.status, dep.info[:name], dep.path, dep.info)))
         end
       end
     end if step.dependencies

data/share/rbbt_commands/migrate

@@ -107,6 +107,6 @@ real_paths.each do |source|
     puts cmd 
     exit 0
   else
-    CMD.cmd_log(cmd)
+    CMD.cmd_log(cmd, :log => Log::INFO)
   end
 end

data/share/rbbt_commands/slurm/list

@@ -21,6 +21,8 @@ $ rbbt mnl [options]
 -s--search* Regular expression
 -t--tail* Show the last lines of the STDERR
 -SBP--sbatch_parameters show sbatch parameters
+-PERF--procpath_performance show Procpath performance summary
+-sacct--sacct_peformance show sacct performance summary
 EOF
 
 if options[:help]
@@ -69,7 +71,7 @@ workdir.glob("**/command.slurm").sort_by{|f| File.mtime(f)}.each do |fcmd|
  end
 
  if m = Open.read(fcmd).match(/# Run command\n(.*?)\n/im)
-  exe = m[1]
+  exe = m[1].sub('step_path=$(','')
  else
   exe = nil
  end
@@ -96,15 +98,24 @@ workdir.glob("**/command.slurm").sort_by{|f| File.mtime(f)}.each do |fcmd|
  if File.exists?(fstatus = File.join(dir, 'job.status'))
   nodes = Open.read(fstatus).split("\n").last.split(/\s+/).last.split(",")
  elsif job_nodes[id]
-  nodes = job_nodes[id]
+  nodes = job_nodes[id].reject{|n| n.include? "("}
  else
   nodes = []
  end
 
+ if File.exists?(File.join(dir, 'exit.status'))
+   now = File.ctime(File.join(dir, 'exit.status'))
+ else
+   now = Time.now
+ end
+
  if File.exists?(File.join(dir, 'std.out'))
+  cerrt = File.ctime File.join(dir, 'std.err')
+  coutt = File.ctime File.join(dir, 'std.out')
   outt = File.mtime File.join(dir, 'std.out')
   errt = File.mtime File.join(dir, 'std.err')
-  time_diff = Time.now - [outt, errt].max
+  time_diff = now - [outt, errt].max
+  time_elapsed = now - [cerrt, coutt].min
  end
 
  fdep = File.join(dir, 'dependencies.list')
@@ -113,14 +124,19 @@ workdir.glob("**/command.slurm").sort_by{|f| File.mtime(f)}.each do |fcmd|
  fcadep = File.join(dir, 'canfail_dependencies.list')
  cadeps = Open.read(fcadep).split("\n") if File.exists?(fcadep)
 
- if done || error || aborted || running || queued || jobid || search
+ if done || error || aborted || running || queued || jobid 
    select = false
    select = true if done && exit_status == 0
    select = true if error && exit_status && exit_status != 0 
    select = true if aborted && (exit_status.nil? && ! running_jobs.include?(id))
-   select = true if queued && deps && (running_jobs & deps).any?
-   select = true if running && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
+   is_running =  exit_status.nil? && running_jobs.include?(id) && (!deps || (running_jobs & deps).empty?)
+   select = true if queued && deps && (running_jobs & deps).any? || queued && is_running && nodes.empty?
+   select = true if running && nodes.any? && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
    select = true if jobid && jobid.split(",").include?(id)
+   select &= search && cmd.match(/#{search}/) if search
+   next unless select 
+ elsif search
+   select = false
    select = true if search && cmd.match(/#{search}/)
    next unless select 
  end
@@ -128,6 +144,7 @@ workdir.glob("**/command.slurm").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.slurm')).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, "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")
@@ -136,13 +153,70 @@ workdir.glob("**/command.slurm").sort_by{|f| File.mtime(f)}.each do |fcmd|
  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, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)")
+ 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)")
 
  if options[:sbatch_parameters]
    puts Log.color(:magenta, "SBATCH parameters: ")
-   puts Log.color :blue, CMD.cmd('grep "^#SBATCH" |tail -n +6', :in => Open.read(fcmd)).read.strip
+   text = CMD.cmd('grep "^#SBATCH" |tail -n +6', :in => Open.read(fcmd)).read.strip
+   lines = text.split("\n").collect{|line| header, _sep, value = line.partition(/\s+/); Log.color(:yellow, header + ": ") + value}
+   puts Log.color :yellow, lines * "\n"
  end
 
+ fprocpath = File.join(dir, 'procpath.sqlite3')
+ if options[:procpath_performance]  && Open.exists?(fprocpath)
+   puts Log.color(:magenta, "Procpath summary: ")
+   require 'rbbt/tsv/csv'
+   meta = TSV.csv(CMD.cmd("sqlite3 -header -csv #{fprocpath} 'select * from meta;' "))
+   perf = TSV.csv(CMD.cmd("sqlite3 -header -csv #{fprocpath} 'select * from record;' "))
+
+   page_size = meta["page_size"].first.to_f
+   clock_ticks = meta["clock_ticks"].first.to_f
+
+   cpu_average = {}
+   rss_average = {}
+   perf.through :key, ["ts", 'stat_pid', "stat_utime", "stat_stime", "stat_cutime", "stat_cstime", "stat_rss"] do |k, values|
+    time, stat_pid, ucpu, scpu, ccpu, cscpu, rss = values
+    time = time.to_f
+
+    cpu = Misc.sum([ucpu, scpu].collect{|v| v.to_f})
+    cpu_average[stat_pid] ||= {}
+    cpu_average[stat_pid][time] ||= []
+    cpu_average[stat_pid][time] << cpu.to_f
+    rss_average[time] ||= []
+    rss_average[time] << rss.to_f * page_size
+   end
+
+   ticks = 0
+   cpu_average.each do |stat_pid, cpu_average_pid|
+    start = cpu_average_pid.keys.sort.first
+    eend = cpu_average_pid.keys.sort.last
+    ticks += Misc.sum(cpu_average_pid[eend]) - Misc.sum(cpu_average_pid[start])
+   end
+   start = rss_average.keys.sort.first
+   eend = rss_average.keys.sort.last
+   time_elapsed = eend - start
+   ticks = 1 if ticks == 0
+   time_elapsed = 1 if time_elapsed == 0
+   puts Log.color(:yellow, "CPU average: ") + "%.2f" % ( ticks / clock_ticks / time_elapsed * 100).to_s
+   puts Log.color(:yellow, "RSS average: ") + "%.2f GB" % Misc.mean(rss_average.collect{|t,l| Misc.sum(l) / (1024 * 1024 * 1024)}).to_s 
+   puts Log.color(:yellow, "Time: ") + Misc.format_seconds((eend - start))
+
+ end
+
+ if options[:sacct_peformance]
+   begin
+    tsv = TSV.open(CMD.cmd("sacct -j #{id} -o 'jobid,AveRSS,MaxRSS,MaxDiskRead,MaxDiskWrite' -P|grep 'JobID\\|\.batch'"), :header_hash => '', :sep => "|", :type => :list)
+    values = tsv[tsv.keys.first]
+    if values.compact.any?
+     puts Log.color(:magenta, "SACCT performance: ")
+     puts values.zip(values.fields).collect{|v,t| Log.color(:yellow, t + ": ")  + v.to_s } * "\n"
+    end
+   rescue
+   end
+ end
+
+
  if tail && File.exists?(File.join(dir, 'std.err'))
    if exit_status && exit_status != 0
      puts Log.color(:magenta, "First error or exception found: ")

data/share/rbbt_commands/slurm/orchestrate

@@ -21,6 +21,7 @@ $slurm_options = SOPT.get <<EOF
 -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
+-SPERF--SLURM_procpath* Save Procpath performance for SLURM job; specify only options
 -q--queue* Queue
 -t--task_cpus* Tasks
 -W--workflows* Additional workflows

data/share/rbbt_commands/slurm/task

@@ -20,6 +20,7 @@ $slurm_options = SOPT.get <<EOF
 -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
+-SPERF--SLURM_procpath* Save Procpath performance for SLURM job; specify only options
 -q--queue* Queue
 -t--task_cpus* Tasks
 -W--workflows* Additional workflows

data/share/rbbt_commands/tsv/slice

@@ -35,7 +35,7 @@ file = case file
 fields = options[:fields]
 raise ParameterException, "Please specify the fields to slice" if fields.nil?
 
-options[:header_hash] = options["header_hash"]
+options[:header_hash] ||= options["header_hash"]
 
 case
 when options[:tokyocabinet]
@@ -45,8 +45,8 @@ when options[:tokyocabinet_bd]
   tsv = Persist.open_tokyocabinet(file, false, nil, TokyoCabinet::BDB)
   puts tsv.summary
 else
-  stream = TSV.traverse file, options.merge(:into => :stream, :type => :list, :keys => fields, :unnamed => true) do |*p|
-    p * "\t"
+  stream = TSV.traverse file, options.merge(:into => :stream, :type => :list, :fields => fields.split(","), :unnamed => true) do |k,fields,names|
+    [k,fields].flatten * "\t"
   end
   puts stream.read
   exit 0

data/share/rbbt_commands/workflow/info

@@ -86,7 +86,7 @@ messages = info[:messages]
 backtrace = info[:backtrace]
 pid = info[:pid]
 exception = info[:exception]
-rest = info.keys - [:inputs, :dependencies, :status, :time_elapsed, :messages, :backtrace, :exception, :pid, :archived_info]
+rest = info.keys - [:inputs, :dependencies, :status, :time_elapsed, :messages, :backtrace, :exception, :archived_info]
 
 
 puts Log.color(:magenta, "File") << ": " << step.path

data/share/rbbt_commands/workflow/task

@@ -203,6 +203,7 @@ The `recursive_clean` cleans all the job dependency steps recursively.
 -prec--prepare_cpus* Number of dependencies prepared in parallel
 -rwt--remote_workflow_tasks* Load a yaml file describing remote workflow tasks
 -od--override_deps* Override deps using 'Workflow#task=<path>' array_separated
+-PERF--procpath_performance* Measure performance using procpath
 EOF
 
 workflow = ARGV.shift
@@ -407,6 +408,23 @@ begin
     exit 0
   end
 
+  if options[:procpath_performance]
+    require 'rbbt/util/procpath'
+    current_pid = job.info[:pid]
+    job.fork
+    job.soft_grace
+    sleep 2 if job.info[:pid] == current_pid
+    if job.info[:pid] != current_pid
+      pid = job.info[:pid]
+      begin
+        ProcPath.monitor(pid, options[:procpath_performance])
+      rescue Errno::ECHILD
+        Log.warn "Procpath didn't find process #{pid} to monitor. Maybe it finished already"
+      rescue
+        Log.warn "Procpath failed: #{$!.message}"
+      end
+    end
+  end
 
   if do_fork
     ENV["RBBT_NO_PROGRESS"] = "true"
@@ -423,7 +441,6 @@ begin
     res = job
   end
 
-
   if options.delete(:printpath)
     job.join
     raise job.messages.last if (job.error? || job.aborted?) && job.messages

data/share/rbbt_commands/workflow/write_info

@@ -0,0 +1,52 @@
+#!/usr/bin/env ruby
+
+require 'rbbt/workflow'
+
+require 'rbbt-util'
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+Examine the info of a job result
+
+$ rbbt workflow info <job-result> <key> <value>
+
+-h--help Help
+-f--force Write info even if key is already present
+-r--recursive Write info for all dependencies as well
+-p--check_pid Check that recursive jobs where created by the same process
+EOF
+
+SOPT.usage if options[:help]
+
+file, key, value = ARGV
+
+force, recursive, check_pid = options.values_at :force, :recursive, :check_pid
+
+def get_step(file)
+  file = file.sub(/\.(info|files)/,'')
+  step = Workflow.load_step file
+  step
+end
+
+raise ParameterException if key.nil? || value.nil?
+
+if %w(DELETE nil).include? value
+  value = nil
+  force = true
+end
+
+step = get_step file
+
+step.set_info key, value if force || ! step.info.include?(key)
+
+pid = step.info[:pid]
+host = step.info[:pid_hostname]
+
+step.rec_dependencies.each do |dep|
+  dep.set_info key, value if (force || ! dep.info.include?(key)) && (!check_pid || dep.info[:pid].to_s == pid and dep.info[:pid_hostname] == host)
+rescue
+  Log.warn "Could no set info #{key} for #{dep.path}: #{$!.message}"
+end if recursive

data/test/rbbt/util/test_procpath.rb

@@ -0,0 +1,23 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/util/procpath'
+
+class TestProcPath < Test::Unit::TestCase
+  def test_record_and_plot
+    Log.with_severity 0 do
+      pid = Process.fork do
+        a = ""
+        (0..1000).each do 
+          a << (0..rand(10000).to_i).to_a.collect{|i| "TEST #{i}" } * " "
+          sleep 0.1
+        end
+      end
+
+      TmpFile.with_file(nil, false) do |db|
+
+        ProcPath.record(pid, db, :interval => '1', "recnum" => 100)
+        ProcPath.plot(db, db + '.svg', "moving-average-window" => 1 )
+      end
+    end
+  end
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.29.4
+  version: 5.30.4
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-01-28 00:00:00.000000000 Z
+date: 2021-02-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -300,6 +300,7 @@ files:
 - lib/rbbt/util/misc/system.rb
 - lib/rbbt/util/named_array.rb
 - lib/rbbt/util/open.rb
+- lib/rbbt/util/procpath.rb
 - lib/rbbt/util/python.rb
 - lib/rbbt/util/semaphore.rb
 - lib/rbbt/util/simpleDSL.rb
@@ -438,6 +439,7 @@ files:
 - share/rbbt_commands/workflow/server
 - share/rbbt_commands/workflow/task
 - share/rbbt_commands/workflow/trace
+- share/rbbt_commands/workflow/write_info
 - share/unicorn.rb
 - share/workflow_config.ru
 - test/rbbt/annotations/test_util.rb
@@ -516,6 +518,7 @@ files:
 - test/rbbt/util/test_log.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_procpath.rb
 - test/rbbt/util/test_python.rb
 - test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_simpleDSL.rb
@@ -563,6 +566,7 @@ test_files:
 - test/rbbt/workflow/test_task.rb
 - test/rbbt/resource/test_path.rb
 - test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_procpath.rb
 - test/rbbt/util/misc/test_omics.rb
 - test/rbbt/util/misc/test_pipes.rb
 - test/rbbt/util/misc/test_format.rb