rbbt-util 5.25.8 → 5.25.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 9e5188a78754f01da5c96eee01e0448bebb34a1c
+  metadata.gz: f1eb2767b3e3f8adcb67bfc0fbc05d79000130a9
+  data.tar.gz: d3314ccd8960e4780887978e9b8745a31276b9f1
 SHA512:
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-  data.tar.gz: dd4f867fa4e20a6a8eaf8e53d8cdd8a782f5181e2fb5863004c028f1a8ce8bcf82c2d67b5469e5f8d9c3a437417af4a053a05c80db85f55b0db61a44a58dbd84
+  metadata.gz: 465aefada76bce2c950aa535098ef03652a2793fe7030c1532557f72d9cd0d856479511247339152ef8e8a2084abe0436662a9e8ba6fc9ba1bf8833fa50f3e50
+  data.tar.gz: 84827530eee0ed691bfadfd1e137f801921f96c071b7ef016a9542896190e3ba6ad0f24603188fd81eba4f8e070364ebde39f7f27f2b9aa20feb5742ef97c0c3

data/lib/rbbt/hpc.rb

@@ -16,6 +16,7 @@ module Marenostrum
       copy_image       = options.delete :copy_image
       exclusive        = options.delete :exclusive
       highmem          = options.delete :highmem
+      inputs_dir       = options.delete :inputs_dir
 
       if contain_and_sync
         contain = "/scratch/tmp/rbbt" if contain.nil?
@@ -101,19 +102,35 @@ mkdir -p "$SINGULARITY_RUBY_INLINE"
 
       if contain
         env +=<<-EOF
+
+# Prepare container dir
 CONTAINER_DIR="#{contain}"
 mkdir -p $CONTAINER_DIR/.rbbt/etc/
 for tmpd in persist_locks  produce_locks  R_sockets  sensiblewrite  sensiblewrite_locks  step_info_locks  tsv_open_locks; do
     mkdir -p $CONTAINER_DIR/.rbbt/tmp/$tmpd
 done
+
+# Copy environment 
 cp ~/.rbbt/etc/environment $CONTAINER_DIR/.rbbt/etc/
+
+# Set search_paths
 echo "rbbt_user: /home/rbbt/.rbbt/{TOPLEVEL}/{SUBPATH}" > $CONTAINER_DIR/.rbbt/etc/search_paths
 echo "home: $CONTAINER_DIR/home/{TOPLEVEL}/{SUBPATH}" >> $CONTAINER_DIR/.rbbt/etc/search_paths
 echo "group_projects: $CONTAINER_DIR/projects/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> $CONTAINER_DIR/.rbbt/etc/search_paths
 echo "group_scratch: $CONTAINER_DIR/scratch/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> $CONTAINER_DIR/.rbbt/etc/search_paths
 echo "user_projects: $CONTAINER_DIR/projects/#{ENV['USER']}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> $CONTAINER_DIR/.rbbt/etc/search_paths
 echo "user_scratch: $CONTAINER_DIR/scratch/#{ENV['USER']}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> $CONTAINER_DIR/.rbbt/etc/search_paths
+echo "/scratch/tmp/rbbt/projects/rbbt/workflows/" > $CONTAINER_DIR/.rbbt/etc/workflow_dir
         EOF
+        
+        if inputs_dir
+          env +=<<-EOF
+
+# Copy inputs
+cp -R '#{inputs_dir}' $CONTAINER_DIR/inputs
+          EOF
+          rbbt_cmd = rbbt_cmd.sub(inputs_dir, "#{contain}/inputs")
+        end
 
         if copy_image
           env +=<<EOF
@@ -162,7 +179,7 @@ EOF
 #{cmd}
 
 # Save exit status
-echo $? > #{fexit}
+exit_status=$?
 
 # Clean job.id, since we are done
 rm #{fjob}
@@ -195,6 +212,12 @@ unset sync_es
 EOF
         end
       end
+      coda +=<<-EOF
+
+# Write exit status to file
+echo $exit_status > #{fexit}
+unset exit_status
+EOF
 
       template = [header, env, run, coda] * "\n"
 
@@ -281,7 +304,7 @@ EOF
         STDERR.puts Log.color(:magenta, "Output:")
         begin
           CMD.cmd("squeue --job #{job} > #{fstatus}")
-          out = CMD.cmd("tail -f '#{fout}'", :pipe => true) if File.exists? fout
+          out = CMD.cmd("tail -f '#{fout}'", :pipe => true) if File.exists?(fout) and not tail == :STDERR
           err = CMD.cmd("tail -f '#{ferr}'", :pipe => true) if File.exists? ferr
 
           Misc.consume_stream(err, true, STDERR) if err
@@ -309,27 +332,8 @@ EOF
       fjob = File.join(workdir, 'job.id')
       job = Open.read(fjob) if Open.exists?(fjob)
 
-      status_txt = CMD.cmd("squeue --job #{job}").read
-      STDERR.puts Log.color(:magenta, "Status [#{job.to_i}]:")
-      STDERR.puts status_txt
-      lines = status_txt.split("\n").length
 
       while ! Open.exists?(fexit)
-        STDERR.puts
-        Log.clear_line(STDERR)
-        STDERR.write Log.color(:magenta, "Waiting for end")
-        3.times do
-          STDERR.write Log.color(:magenta, ".")
-          sleep 1
-        end
-        status_txt = CMD.cmd("squeue --job #{job}").read
-        lines.times do
-          Log.clear_line(STDERR)
-        end
-        Log.clear_line(STDERR)
-        STDERR.puts Log.color(:magenta, "Status [#{job.to_i}]:")
-        STDERR.puts status_txt
-        lines = status_txt.split("\n").length
         sleep time
       end
     end
@@ -338,18 +342,33 @@ EOF
       workflow = job.workflow
       task = job.task_name
       name = job.clean_name
-      TmpFile.with_file(nil, false) do |tmp_directory|
+      keep_workdir = options.delete :keep_SLURM_workdir 
+      TmpFile.with_file(nil, !keep_workdir) do |tmp_directory|
         workdir = options[:workdir] ||= File.join(tmp_directory, 'workdir')
         inputs_dir = File.join(tmp_directory, 'inputs_dir')
         Step.save_job_inputs(job, inputs_dir)
+        options[:inputs_dir] = inputs_dir
         cmd = ['workflow', 'task', workflow.to_s, task.to_s, '-pf', '-jn', name, '--load_inputs', inputs_dir, '--log', (options[:log] || Log.severity).to_s]
+
+        %w(workflows requires remote_workflow_tasks override_deps).each do |key|
+          next unless options[key]
+          cmd += ["--#{key.to_s}", options[key]]
+        end
+
         template = self.template(cmd, options)
         self.issue_template(template, options)
+        t_monitor = Thread.new do
+          self.follow_job(workdir, :STDERR)
+        end
         self.wait_for_job(workdir)
-        path = Open.read(File.join(workdir, 'std.out'))
-        if job.path != path
-          Log.medium "Path of SLURM job #{path} is different from original job #{job.path}. Stablishing link."
+        t_monitor.raise Aborted
+        return unless Open.read(File.join(workdir, 'exit.status')).strip == '0'
+        path = Open.read(File.join(workdir, 'std.out')).strip
+        if Open.exists?(path) && job.path != path
+          Log.info "Path of SLURM job #{path} is different from original job #{job.path}. Stablishing link."
           Open.ln path, job.path
+          Open.ln path + '.info', job.path + '.info'  if Open.exists?(path + '.info')
+          Open.ln path + '.files', job.path + '.files' if Open.exists?(path + '.files')
         end
       end
     end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.8
+  version: 5.25.9
 platform: ruby
 authors:
 - Miguel Vazquez