rbbt-util 5.25.55 → 5.25.56

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: b4ea2bebd14bb22bdb93c3f24269d0b52b5f644f
+  metadata.gz: 0c46454a4604e7ac3622114c04ae9667b602f751
+  data.tar.gz: f32e35b8f21e4e1b6c0affed3f4c1344afcd9615
 SHA512:
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+  metadata.gz: 526540540bec4f2771b7a6b32e806ecdb7de1b36b28ddefcc9610c8939258e8f1025b390d95276ab3cae4de26e86ac8971b58a28876ce89ffb206c9acb649f31
+  data.tar.gz: e3d04b79a7a8e951bc4b89b0f65fea70b4d3ad5921021fd05c8707a1436862e7847bba192b5cfe80d88232defef938efcfe026329c8e4808bda7b398e459aa8b

data/lib/rbbt/hpc.rb

@@ -208,8 +208,11 @@ singularity exec -e -C -H "$CONTAINER_DIR" "$SINGULARITY_IMG" rbbt system clean
 EOF
         end
 
+        source = File.join(File.expand_path(contain), '.rbbt/var/jobs')
+        target = File.expand_path(sync)
         coda +=<<-EOF
-rsync -avt "#{File.join(File.expand_path(contain), '.rbbt/var/jobs')}/" "#{File.expand_path(sync)}/" &>> #{fsync} 
+rsync -avt "#{source}/" "#{target}/" &>> #{fsync} 
+find '#{target}' -type l -ls | awk '$13 ~ /^#{target.gsub('/','\/')}/ { sub("#{source}", "#{target}", $13); print $11, $13 }' | while read A B; do rm $A; ln -s $B $A; done
 EOF
 
         if  contain && (wipe_container == "post" || wipe_container == "both")

data/share/rbbt_commands/workflow/task

@@ -187,7 +187,7 @@ the job dependencies recursively.
 -ljf--list_job_files List all the files produced in that step
 --load_inputs* Load inputs from a directory
 --info Show the job info
---provenance Report the jobs provenance
+-prov--provenance Report the jobs provenance
 -W--workflows* Load a list of workflows
 -R--requires* Require a list of files
 -rwt--remote_workflow_tasks* Load a yaml file describing remote workflow tasks

data/share/rbbt_commands/workflow/trace

@@ -25,6 +25,7 @@ $ rbbt workflow trace <job-result> <file.png>
 -h--height* Image Height
 -s--size* Image Size (Height and Width)
 -fg--fix_gap Remove execution gaps
+-pd--plot_data Print plot data
 EOF
 
 SOPT.usage if options[:help]
@@ -150,7 +151,21 @@ tasks_info.each do |task, info|
   stats[task] = [calls,avg_time, cpus, spark, shard]
 end
 
-puts stats.to_s
+start = data.column("Start.second").values.flatten.collect{|v| v.to_i}.min
+eend = data.column("End.second").values.flatten.collect{|v| v.to_i}.max
+total = eend - start
+Log.info "Total time elapsed: #{total} seconds"
+
+if options[:fix_gap]
+  total_gaps = Misc.sum(gaps.collect{|k,v| v})
+  Log.info "Total gaps: #{total_gaps} seconds"
+end
+
+if options[:plot_data]
+  puts data.to_s
+else
+  puts stats.to_s
+end
 
 if plot
   data.R <<-EOF, [:svg]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.55
+  version: 5.25.56
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-16 00:00:00.000000000 Z
+date: 2019-04-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake