rbbt-util 5.33.7 → 5.33.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: f4272048a5c86e74b051600f0db895ea42f4ad51509a0de9ce88452d27133746
-  data.tar.gz: f10d19e028de390beb5e2649c7d2f1e0a7754d3235abe3eeba2790946b347f64
+  metadata.gz: aaa014ffdad4e098212cc3f7cefc4d04ac62a7f7fcbf17bbbab9415c6253d9ef
+  data.tar.gz: b8a2a233686ec2f229ed79bb19d87d8eb79ad945142305f7b61dcdb11f5f7912
 SHA512:
-  metadata.gz: 0667eb9d5783d7722c33f72a66a1c406d330d086a37660aa7682006d10fe15860a9e4cbfcb461f17ed15b146fa294a6f6d8158d937884f14dc7952908f63c357
-  data.tar.gz: f3ba25b347bc4a7f7b56ecdbd1a0bef932b646ac030b3d98fe6ddb76f36a6863073f4692747ceef32c42e4344538a7ee19b531a25b16cc2fa208b201887b441e
+  metadata.gz: 564242bef1dd92c2f53a5fe6c967624de26d7ae7eeb4da1ef2a1f682db9cf6d4b0bf0f8e76b3a600afe6af7bb443df28a8fe50e570c3c56265319eb607d6c1fc
+  data.tar.gz: ac7c01fa7e8fccdff8dfc861b82f28889a68f77886c198ff55b09558b36857ec9c29a8bae979bc7d088f311ad81515676bc7a4cc30097fd6c4b7586e6838c0e3

data/lib/rbbt/hpc/orchestrate.rb

@@ -13,7 +13,11 @@ module HPC
       all_deps = rec_dependencies + [job]
 
       all_deps.each do |dep|
-        Step.prepare_for_execution(dep)
+        begin
+          Step.prepare_for_execution(dep)
+        rescue RbbtException
+          next
+        end
       end
 
     end
@@ -40,8 +44,8 @@ module HPC
 
       IndiferentHash.setup(rules)
 
-      Log.high "Compute batches"
       batches = HPC::Orchestration.job_batches(rules, job)
+      Log.high "Compute #{batches.length} batches"
 
       batch_ids = {}
       while batches.any?
@@ -79,7 +83,7 @@ module HPC
           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(: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)
+          puts Log.color(:yellow, "Options: ") + job_options.inspect
           batch_ids[top] = top[:top_level].task_signature
         else
           id = run_job(top[:top_level], job_options)

data/lib/rbbt/resource/path.rb

@@ -167,8 +167,7 @@ module Path
 
     @path ||= {}
     rsearch_paths = (resource and resource.respond_to?(:search_paths)) ? resource.search_paths : nil 
-    key_elems = [where, caller_lib, rsearch_paths, paths]
-    key = Misc.obj2digest(key_elems.inspect)
+    key = [where, caller_lib, rsearch_paths, paths].inspect
     self.sub!('~/', Etc.getpwuid.dir + '/') if self.include? "~"
 
     return @path[key] if @path[key]

data/lib/rbbt/resource/util.rb

@@ -1,13 +1,26 @@
 module Path
 
   def self.caller_lib_dir(file = nil, relative_to = ['lib', 'bin'])
-    file = caller.reject{|l| 
-      l =~ /rbbt\/(?:resource\.rb|workflow\.rb)/ or
-      l =~ /rbbt\/resource\/path\.rb/ or
-      l =~ /rbbt\/persist.rb/ or
-      l =~ /rbbt\/util\/misc\.rb/ or
-      l =~ /progress-monitor\.rb/ 
-    }.first.sub(/\.rb[^\w].*/,'.rb') if file.nil?
+    #file = caller.reject{|l| 
+    #  l =~ /rbbt\/(?:resource\.rb|workflow\.rb)/ or
+    #  l =~ /rbbt\/resource\/path\.rb/ or
+    #  l =~ /rbbt\/persist.rb/ or
+    #  l =~ /rbbt\/util\/misc\.rb/ or
+    #  l =~ /progress-monitor\.rb/ 
+    #}.first.sub(/\.rb[^\w].*/,'.rb') if file.nil?
+    
+    
+    if file.nil?
+      caller_dup = caller.dup
+      while file = caller_dup.shift
+        break unless file =~ /rbbt\/(?:resource\.rb|workflow\.rb)/ or
+          file =~ /rbbt\/resource\/path\.rb/ or
+          file =~ /rbbt\/persist.rb/ or
+          file =~ /rbbt\/util\/misc\.rb/ or
+          file =~ /progress-monitor\.rb/ 
+      end
+      file = file.sub(/\.rb[^\w].*/,'.rb')
+    end
 
     relative_to = [relative_to] unless Array === relative_to
     file = File.expand_path(file)

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

@@ -80,7 +80,7 @@ module Misc
       end
     when (defined? TSV and TSV)
       obj.with_unnamed do
-        "TSV:{"<< fingerprint(obj.all_fields|| []).inspect << ";" << fingerprint(obj.keys).inspect << "}"
+        "TSV:{"<< fingerprint(obj.all_fields|| []) << ";" << fingerprint(obj.keys) << "}"
       end
     when Hash
       if obj.length > 10
@@ -297,14 +297,14 @@ module Misc
     str = case obj
           when nil
             'nil'
+          when Symbol 
+            obj.to_s
           when TrueClass
             'true'
           when FalseClass
             'false'
           when Hash
             "{"<< obj.collect{|k,v| obj2str(k) + '=>' << obj2str(v)}*"," << "}"
-          when Symbol 
-            obj.to_s
           when (defined?(Path) and Path)
             if defined?(Step) && Open.exists?(Step.info_file(obj))
               obj2str(Workflow.load_step(obj))
@@ -324,9 +324,10 @@ module Misc
             end
           when String
             good_filename = Misc.is_filename?(obj, false) && ! %w(. ..).include?(obj) && %w(. /).include?(obj[0])
-            is_path = Path === obj
-            if good_filename && ! is_path
-              obj2str Path.setup(obj.dup)
+            if good_filename 
+              obj = obj.dup
+              obj.extend Path
+              obj2str obj
             else
               obj = obj.chomp if String === obj
               if obj.length > HASH2MD5_MAX_STRING_LENGTH
@@ -339,7 +340,7 @@ module Misc
             if obj.length > HASH2MD5_MAX_ARRAY_LENGTH
               "[" << sample_large_obj(obj, HASH2MD5_MAX_ARRAY_LENGTH).collect{|v| obj2str(v)} * "," << "]"
             else
-              "[" << obj.collect{|v| obj2str(v)} * "," << "]"
+              "[" << obj.collect{|v| obj2str(v) } * "," << "]"
             end
           when TSV::Parser
             remove_long_items(obj)

data/share/install/software/lib/install_helpers

@@ -185,6 +185,10 @@ compile(){
     local name=$1; shift
     local extra="$@"
 
+    if [ -f bootstrap ]; then
+      ./bootstrap
+    fi
+
     if [ -f Makefile -o -f makefile ]; then
         make -j 4 || exit -1
         make install || echo "No install"

data/share/rbbt_commands/hpc/list

@@ -22,6 +22,7 @@ $ rbbt slurm list [options]
 -s--search* Regular expression
 -t--tail* Show the last lines of the STDERR
 -l--long Show more entries
+-c--compressed Show compressed information about entries
 -p--progress Report progress of job and the dependencies
 -BP--batch_parameters show batch parameters
 -BPP--batch_procpath show Procpath performance summary
@@ -185,6 +186,40 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
  end
 
 
+ count += 1
+
+ if options[:compressed] 
+   status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) :  Log.color(:green, id)  
+   if different_system
+     status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  Log.color(:green, id)  
+   else
+     status = 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 
+   prog_rep = []
+   if options[:progress] 
+     step_line = Open.read(fcmd).split("\n").select{|line| line =~ /^#STEP_PATH:/}.first
+     if step_line
+       require 'rbbt/workflow'
+       step_path = step_line.split(": ").last.strip
+       step = Step.new step_path
+       step.load_dependencies_from_info
+       has_bar = false
+       (step.rec_dependencies + [step]).reverse.each do |j|
+         next if j.done? 
+         if j.file(:progress).exists?
+           bar = Log::ProgressBar.new 
+           bar.load(j.file(:progress).yaml)
+           prog_rep << bar.report_msg.split("·")[0..1]
+         end
+       end
+     end
+   end
+   workflow, task, name = step_path.split("/")[-3..-1]
+   job_str = [Log.color(:yellow, workflow), Log.color(:magenta, task), name] * "/"
+   puts [job_str, status, prog_rep ].flatten * " "
+   next
+ end
+
  puts Log.color :blue, dir
  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
@@ -232,22 +267,22 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    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
+     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])
+     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
@@ -309,8 +344,6 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    end
  end
 
- count += 1
-
 end
 
 puts 

data/share/rbbt_commands/lsf/list

@@ -22,6 +22,7 @@ $ rbbt slurm list [options]
 -s--search* Regular expression
 -t--tail* Show the last lines of the STDERR
 -l--long Show more entries
+-c--compressed Show compressed information about entries
 -p--progress Report progress of job and the dependencies
 -BP--batch_parameters show batch parameters
 -BPP--batch_procpath show Procpath performance summary
@@ -185,6 +186,40 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
  end
 
 
+ count += 1
+
+ if options[:compressed] 
+   status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) :  Log.color(:green, id)  
+   if different_system
+     status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  Log.color(:green, id)  
+   else
+     status = 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 
+   prog_rep = []
+   if options[:progress] 
+     step_line = Open.read(fcmd).split("\n").select{|line| line =~ /^#STEP_PATH:/}.first
+     if step_line
+       require 'rbbt/workflow'
+       step_path = step_line.split(": ").last.strip
+       step = Step.new step_path
+       step.load_dependencies_from_info
+       has_bar = false
+       (step.rec_dependencies + [step]).reverse.each do |j|
+         next if j.done? 
+         if j.file(:progress).exists?
+           bar = Log::ProgressBar.new 
+           bar.load(j.file(:progress).yaml)
+           prog_rep << bar.report_msg.split("·")[0..1]
+         end
+       end
+     end
+   end
+   workflow, task, name = step_path.split("/")[-3..-1]
+   job_str = [Log.color(:yellow, workflow), Log.color(:magenta, task), name] * "/"
+   puts [job_str, status, prog_rep ].flatten * " "
+   next
+ end
+
  puts Log.color :blue, dir
  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
@@ -232,22 +267,22 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    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
+     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])
+     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
@@ -309,8 +344,6 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    end
  end
 
- count += 1
-
 end
 
 puts 

data/share/rbbt_commands/slurm/list

@@ -22,6 +22,7 @@ $ rbbt slurm list [options]
 -s--search* Regular expression
 -t--tail* Show the last lines of the STDERR
 -l--long Show more entries
+-c--compressed Show compressed information about entries
 -p--progress Report progress of job and the dependencies
 -BP--batch_parameters show batch parameters
 -BPP--batch_procpath show Procpath performance summary
@@ -185,6 +186,40 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
  end
 
 
+ count += 1
+
+ if options[:compressed] 
+   status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) :  Log.color(:green, id)  
+   if different_system
+     status = exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" :  Log.color(:green, id)  
+   else
+     status = 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 
+   prog_rep = []
+   if options[:progress] 
+     step_line = Open.read(fcmd).split("\n").select{|line| line =~ /^#STEP_PATH:/}.first
+     if step_line
+       require 'rbbt/workflow'
+       step_path = step_line.split(": ").last.strip
+       step = Step.new step_path
+       step.load_dependencies_from_info
+       has_bar = false
+       (step.rec_dependencies + [step]).reverse.each do |j|
+         next if j.done? 
+         if j.file(:progress).exists?
+           bar = Log::ProgressBar.new 
+           bar.load(j.file(:progress).yaml)
+           prog_rep << bar.report_msg.split("·")[0..1]
+         end
+       end
+     end
+   end
+   workflow, task, name = step_path.split("/")[-3..-1]
+   job_str = [Log.color(:yellow, workflow), Log.color(:magenta, task), name] * "/"
+   puts [job_str, status, prog_rep ].flatten * " "
+   next
+ end
+
  puts Log.color :blue, dir
  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
@@ -232,22 +267,22 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    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
+     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])
+     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
@@ -309,8 +344,6 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    end
  end
 
- count += 1
-
 end
 
 puts 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.33.7
+  version: 5.33.8
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-03-10 00:00:00.000000000 Z
+date: 2022-03-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake