rbbt-util 5.30.12 → 5.31.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/rbbt/hpc.rb

@@ -1,3 +1,6 @@
 require 'rbbt-util'
 require 'rbbt/util/cmd'
+require 'rbbt/hpc/batch'
+require 'rbbt/hpc/orchestrate'
 require 'rbbt/hpc/slurm'
+require 'rbbt/hpc/lsf'

data/lib/rbbt/hpc/batch.rb

@@ -0,0 +1,621 @@
+module HPC
+  class SBATCH < Exception; 
+    attr_accessor :directory
+    def initialize(directory)
+      @directory = directory
+    end
+  end
+
+  module TemplateGeneration
+    def exec_cmd(job, options = {})
+      env_cmd     = Misc.process_options options, :env_cmd
+      development = Misc.process_options options, :development
+
+      if options[:singularity]
+
+        group, user, user_group, scratch_group_dir, projects_group_dir = options.values_at :group, :user, :user_group, :scratch_group_dir, :projects_group_dir
+
+        singularity_img, singularity_opt_dir, singularity_ruby_inline = options.values_at :singularity_img, :singularity_opt_dir, :singularity_ruby_inline
+
+        singularity_cmd = %(singularity exec -e -B #{singularity_opt_dir}:/singularity_opt/ -B /apps/) 
+
+        if contain = options[:contain]
+          contain = File.expand_path(contain)
+          singularity_cmd << %( -C -H "#{contain}" \
+-B "#{options[:batch_dir]}" \
+-B /scratch/tmp \
+#{ group != user_group ? "-B /gpfs/projects/#{user_group}" : "" } \
+-B #{scratch_group_dir} \
+-B #{projects_group_dir} \
+-B "#{singularity_ruby_inline}":"#{contain}/.ruby_inline":rw  \
+-B ~/git:"#{contain}/git":ro \
+#{Open.exists?('~/.rbbt/software/opt/')? '-B ~/.rbbt/software/opt/:"/opt/":ro' : '' } \
+-B ~/.rbbt:"#{contain}/home/":ro)
+          singularity_cmd << " #{singularity_img} "
+        end
+        env_cmd ||= ""
+        env_cmd << " TMPDIR='#{contain}/.rbbt/tmp' "
+      end
+
+      if env_cmd
+        exec_cmd = %(env #{env_cmd} rbbt)
+      else
+        exec_cmd = %(rbbt)
+      end
+
+      exec_cmd << "--dev '#{development}'" if development
+
+      exec_cmd = singularity_cmd  + exec_cmd if singularity_cmd
+
+      exec_cmd
+    end
+
+    def rbbt_job_exec_cmd(job, options)
+
+      jobname  = job.clean_name
+      workflow = job.workflow
+      task     = job.task_name
+
+      Misc.add_defaults options, :jobname => jobname
+
+      task = Symbol === job.overriden ? job.overriden : job.task_name
+
+      if job.overriden
+        override_deps = job.rec_dependencies.
+          select{|dep| Symbol === dep.overriden }.
+          collect do |dep| 
+
+          name = [dep.workflow.to_s, dep.task_name] * "#"
+          [name, dep.path] * "="  
+        end * ","
+
+        options[:override_deps] = override_deps
+      end
+
+      # Save inputs into inputs_dir
+      inputs_dir = Misc.process_options options, :inputs_dir
+      saved = Step.save_job_inputs(job, inputs_dir) if inputs_dir
+      options[:load_inputs] = inputs_dir if saved && saved.any?
+
+      saved.each do |input|
+        options.delete input
+      end if saved
+
+      cmds = CMD.process_cmd_options options.merge(:add_option_dashes => true)
+
+      <<-EOF.strip
+workflow task #{workflow} #{task} #{cmds}
+EOF
+    end
+
+    def header(options)
+      header =<<-EOF
+#!/bin/bash
+      EOF
+
+      header
+    end
+
+    def batch_options(job, options)
+      IndiferentHash.setup(options)
+
+      batch_options = IndiferentHash.setup({})
+
+      keys = [
+        :batch_dir,
+        :batch_modules,
+        :batch_name,
+        :contain,
+        :contain_and_sync,
+        :copy_image,
+        :drbbt,
+        :env_cmd,
+        :exclusive,
+        :highmem,
+        :manifest,
+        :nodes,
+        :queue,
+        :singularity,
+        :sync,
+        :task_cpus,
+        :time,
+        :user_group,
+        :wipe_container,
+        :workdir,
+      ]
+
+      keys.each do |key|
+        next if options[key].nil?
+        batch_options[key] = Misc.process_options options, key
+      end
+
+      batch_dir = batch_options[:batch_dir]
+
+      batch_name = File.basename(batch_dir)
+      inputs_dir = File.join(batch_dir, 'inputs_dir')
+
+      keys_from_config = [
+        :queue,
+        :highmem,
+        :exclusive,
+        :env_cmd,
+        :user_group,
+        :singularity_img,
+        :singularity_opt_dir,
+        :singularity_ruby_inline,
+        :singularity
+      ]
+
+      keys_from_config.each do |key|
+        next unless batch_options.include? key
+        default_value = Rbbt::Config.get(key, "batch_#{key}", "batch")
+        next if default_value.nil? 
+        Misc.add_defaults batch_options, default_value
+      end
+
+      user = batch_options[:user] ||= ENV['USER'] || `whoami`.strip
+      group = batch_options[:group] ||= File.basename(File.dirname(ENV['HOME']))
+      batch_options[:scratch_group_dir] = File.join('/gpfs/scratch/', group)
+      batch_options[:projects_group_dir] = File.join('/gpfs/projects/', group)
+
+      if batch_options[:contain_and_sync]
+        if batch_options[:contain].nil?
+          contain_base = Rbbt::Config.get(:contain_base_dir, :batch_contain, :batch, :default => "/scratch/tmp/rbbt-[USER]")
+          contain_base = contain_base.sub('[USER]', user)
+          random_file = TmpFile.random_name
+          batch_options[:contain] = File.join(contain_base, random_file)
+        end
+
+        batch_options[:sync] ||= "~/.rbbt/var/jobs" 
+        batch_options[:wipe_container] ||= 'post'
+      end
+
+      if batch_options[:contain] && ! batch_options[:singularity]
+        options[:workdir_all] = batch_options[:contain]
+      end
+
+      Misc.add_defaults batch_options, 
+        :batch_name => batch_name,
+        :inputs_dir => inputs_dir, 
+        :queue => 'debug',
+        :nodes => 1, 
+        :step_path => job.path,
+        :task_cpus => 1,
+        :time => '2min', 
+        :env_cmd => '_JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m"',
+        :singularity_img => ENV["SINGULARITY_IMG"] || "~/rbbt.singularity.img",
+        :singularity_ruby_inline => ENV["SINGULARITY_RUBY_INLINE"] || "~/.singularity_ruby_inline",
+        :singularity_opt_dir => ENV["SINGULARITY_OPT_DIR"] || "~/singularity_opt",
+        :workdir => Dir.pwd 
+
+      exec_cmd = exec_cmd(job, batch_options)
+      rbbt_cmd = rbbt_job_exec_cmd(job, options)
+
+      Misc.add_defaults batch_options, 
+        :exec_cmd => exec_cmd,
+        :rbbt_cmd => rbbt_cmd
+
+      batch_dir = batch_options[:batch_dir]
+
+      Misc.add_defaults batch_options,
+        :fout   => File.join(batch_dir, 'std.out'),
+        :ferr   => File.join(batch_dir, 'std.err'),
+        :fjob   => File.join(batch_dir, 'job.id'),
+        :fdep   => File.join(batch_dir, 'dependencies.list'),
+        :fcfdep => File.join(batch_dir, 'canfail_dependencies.list'),
+        :fexit  => File.join(batch_dir, 'exit.status'),
+        :fsync  => File.join(batch_dir, 'sync.log'),
+        :fsexit  => File.join(batch_dir, 'sync.status'),
+        :fcmd   => File.join(batch_dir, 'command.batch')
+
+      batch_options
+    end
+
+    def meta_data(options)
+      meta =<<-EOF
+#MANIFEST: #{(options[:manifest] || []) * ", "}
+#DEPENDENCIES: #{(options[:dependencies] || []) * ", "}
+#EXEC_CMD: #{options[:exec_cmd]}
+#CMD: #{options[:rbbt_cmd]}
+#STEP_PATH: #{options[:step_path]}
+      EOF
+
+      meta = meta.split("\n").reject{|line| line =~ /: $/} * "\n"
+      meta
+    end
+
+    def load_modules(modules = [])
+      modules = modules.split(/,\s*/) if String === modules
+
+      str = ""
+      modules.each do |mod|
+        str << "module load #{ mod }" << "\n"
+      end if modules
+
+      str
+    end
+
+    def batch_system_variables
+      <<-EOF
+let MAX_MEMORY="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / 1024"
+      EOF
+    end
+
+    def prepare_environment(options = {})
+      modules = options[:batch_modules]
+
+      prepare_environment = ""
+
+      functions = ""
+
+      if contain = options[:contain]
+        contain = File.expand_path(contain)
+        functions +=<<-EOF
+function batch_erase_contain_dir(){
+    rm -Rfv '#{contain}' 2>1 >> '#{options[:fsync]}'
+}
+        EOF
+
+        prepare_environment +=<<-EOF
+if ls -A '#{contain}' &> /dev/null ; then
+  empty_contain_dir="false"
+else
+  empty_contain_dir="true"
+fi
+        EOF
+
+        prepare_environment +=<<-EOF if options[:wipe_container] == 'force'
+batch_erase_contain_dir()
+        EOF
+      end
+
+      if sync = options[:sync]
+        source = if options[:singularity]
+                   File.join(options[:contain], '.rbbt/var/jobs')
+                 elsif options[:contain]
+                   File.join(options[:contain], 'var/jobs')
+                 else
+                   '~/.rbbt/var/jobs/'
+                 end
+
+        source = File.expand_path(source)
+        sync = File.expand_path(sync)
+        functions +=<<-EOF
+function batch_sync_contain_dir(){
+  mkdir -p "$(dirname '#{sync}')"
+  rsync -avztAXHP --copy-unsafe-links "#{source}/" "#{sync}/" 2>1 >> '#{options[:fsync]}'
+  sync_es="$?" 
+  echo $sync_es > '#{options[:fsexit]}'
+  find '#{sync}' -type l -ls | awk '$13 ~ /^#{sync.gsub('/','\/')}/ { sub("#{source}", "#{sync}", $13); print $11, $13 }' | while read A B; do rm $A; ln -s $B $A; done
+}
+        EOF
+      end
+
+      if options[:singularity]
+
+        group, user, user_group, scratch_group_dir, projects_group_dir = options.values_at :group, :user, :user_group, :scratch_group_dir, :projects_group_dir
+
+        singularity_img, singularity_opt_dir, singularity_ruby_inline = options.values_at :singularity_img, :singularity_opt_dir, :singularity_ruby_inline
+
+        prepare_environment +=<<-EOF
+# Load singularity modules
+module load intel/2018.1
+module load singularity
+mkdir -p "#{singularity_opt_dir}"
+        EOF
+
+        if contain
+
+          prepare_environment +=<<-EOF
+# Prepare container for singularity
+mkdir -p "#{contain}/.rbbt/etc/"
+
+for dir in .ruby_inline git home; do
+    mkdir -p "#{contain}/$dir"
+done
+
+for tmpd in persist_locks  produce_locks  R_sockets  sensiblewrite  sensiblewrite_locks  step_info_locks  tsv_open_locks; do
+    mkdir -p "#{contain}/.rbbt/tmp/$tmpd"
+done
+
+# Copy environment 
+cp ~/.rbbt/etc/environment #{contain}/.rbbt/etc/
+
+# Set search_paths
+echo "singularity: /singularity_opt/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" > #{contain}/.rbbt/etc/search_paths
+echo "rbbt_user: /home/rbbt/.rbbt/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
+echo "outside_home: #{contain}/home/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
+echo "group_projects: #{projects_group_dir}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
+echo "group_scratch: #{scratch_group_dir}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
+echo "user_projects: #{projects_group_dir}/#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
+echo "user_scratch: #{scratch_group_dir}/#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
+          EOF
+        end
+      end
+
+      batch_system_variables + load_modules(modules) + "\n" + functions + "\n" + prepare_environment
+    end
+
+    def execute(options)
+      exec_cmd, job_cmd = options.values_at :exec_cmd, :rbbt_cmd
+
+      <<-EOF
+step_path=$( 
+      #{exec_cmd} #{job_cmd} --printpath
+)
+exit_status=$?
+
+[[ -z $BATCH_JOB_ID ]] || #{exec_cmd} workflow write_info --recursive --force=false --check_pid "$step_path" batch_job $BATCH_JOB_ID
+[[ -z $BATCH_SYSTEM ]] || #{exec_cmd} workflow write_info --recursive --force=false --check_pid "$step_path" batch_system $BATCH_SYSTEM
+      EOF
+    end
+
+    def sync_environment(options = {})
+      sync_environment = ""
+
+      if options[:sync]
+        sync_environment +=<<-EOF
+if [ $exit_status == '0' ]; then 
+  batch_sync_contain_dir
+else
+  sync_es=$exit_status
+fi
+        EOF
+      end
+
+      sync_environment
+    end
+
+    def cleanup_environment(options = {})
+      cleanup_environment = ""
+      if options[:sync]
+        if options[:wipe_container] == 'force'
+          cleanup_environment +=<<-EOF
+batch_erase_contain_dir
+          EOF
+        elsif options[:wipe_container] == 'post' || options[:wipe_container] == 'both'
+          cleanup_environment +=<<-EOF
+if [ $sync_es == '0' -a $empty_contain_dir == 'true' ]; then 
+  batch_erase_contain_dir
+fi
+          EOF
+        end
+      end
+      cleanup_environment
+    end
+
+    def coda(options)
+      coda =<<-EOF
+echo $exit_status > '#{options[:fexit]}'
+      EOF
+
+      if options[:sync]
+        coda +=<<-EOF
+if [ $sync_es == '0' ]; then
+  exit $exit_status
+else
+  exit $sync_es
+fi
+        EOF
+      else
+        coda +=<<-EOF
+exit $exit_status
+        EOF
+      end
+
+      coda
+    end
+
+    def job_template(job, options = {})
+      batch_options = batch_options job, options
+
+      header              = self.header(batch_options)
+
+      meta_data           = self.meta_data(batch_options)
+
+      prepare_environment = self.prepare_environment(batch_options)
+
+      execute             = self.execute(batch_options)
+
+      sync_environment    = self.sync_environment(batch_options)
+
+      cleanup_environment = self.cleanup_environment(batch_options)
+
+      coda                = self.coda(batch_options)
+
+      <<-EOF
+#{header}
+
+# #{Log.color :green, "0. Meta-data"}
+#{meta_data}
+
+# #{Log.color :green, "1. Prepare environment"}
+#{prepare_environment}
+
+# #{Log.color :green, "2. Execute"}
+#{execute} 
+
+# #{Log.color :green, "3. Sync and cleanup environment"}
+#{sync_environment}
+#{cleanup_environment}
+
+# #{Log.color :green, "4. Exit"}
+#{coda}
+      EOF
+    end
+
+    def prepare_submision(template, batch_dir, clean_batch_job = false, batch_dependencies = [])
+      Open.mkdir batch_dir
+      fcmd   = File.join(batch_dir, 'command.batch')
+      fdep   = File.join(batch_dir, 'dependencies.list')
+      fcfdep = File.join(batch_dir, 'canfail_dependencies.list')
+
+      Open.write(fcmd, template)
+
+      %w(std.out std.err job.id job.status dependencies.list canfail_dependencies.list exit.status sync.log inputs_dir).each do |filename|
+        path = File.join(batch_dir, filename)
+        Open.rm_rf path if File.exists? path
+      end if clean_batch_job
+
+      batch_dependencies = [] if batch_dependencies.nil?
+
+      canfail_dependencies = batch_dependencies.select{|dep| dep =~ /^canfail:(\d+)/ }.collect{|dep| dep.partition(":").last}
+      dependencies = batch_dependencies.reject{|dep| dep =~ /^canfail:(\d+)/ }
+
+      Open.write(fdep, dependencies * "\n") if dependencies.any?
+      Open.write(fcfdep, canfail_dependencies * "\n") if canfail_dependencies.any?
+
+      fcmd
+    end
+
+
+    def run_job(job, options = {})
+      system = self.to_s.split("::").last
+
+      batch_base_dir, clean_batch_job, remove_batch_dir, procpath, tail, batch_dependencies, dry_run = Misc.process_options options, 
+        :batch_base_dir, :clean_batch_job, :remove_batch_dir, :batch_procpath, :tail, :batch_dependencies, :dry_run,
+        :batch_base_dir => File.expand_path(File.join('~/rbbt-batch')) 
+
+      workflow = job.workflow
+      task_name = job.task_name
+
+      TmpFile.with_file(nil, remove_batch_dir, :tmpdir => batch_base_dir, :prefix => "#{system}_rbbt_job-#{workflow.to_s}-#{task_name}-") do |batch_dir|
+        Misc.add_defaults options, 
+          :batch_dir => batch_dir, 
+          :inputs_dir => File.join(batch_dir, "inputs_dir")
+
+        options[:procpath_performance] ||= File.join(batch_dir, "procpath##{procpath.gsub(',', '#')}") if procpath
+
+        template = self.job_template(job, options.dup)
+
+        fcmd = prepare_submision(template, options[:batch_dir], clean_batch_job, batch_dependencies)
+
+        batch_job = run_template(batch_dir, dry_run)
+
+        return batch_job unless tail
+
+        t_monitor = Thread.new do
+          self.follow_job(batch_dir, :STDERR)
+        end
+        self.wait_for_job(batch_dir)
+        t_monitor.raise Aborted
+        return unless Open.read(File.join(batch_dir, 'exit.status')).strip == '0'
+        path = Open.read(File.join(batch_dir, 'std.out')).strip
+        if Open.exists?(path) && job.path != path
+          Log.info "Path of BATCH 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
+        batch_job
+ 
+      end
+    end
+
+    def follow_job(batch_dir, tail = true)
+      fjob = File.join(batch_dir, 'job.id')
+      fout = File.join(batch_dir, 'std.out')
+      ferr = File.join(batch_dir, 'std.err')
+      fexit = File.join(batch_dir, 'exit.status')
+      fstatus = File.join(batch_dir, 'job.status')
+
+      job = Open.read(fjob).strip if Open.exists?(fjob)
+
+      if job && ! File.exists?(fexit)
+        begin
+          status_txt = job_status(job)
+          STDERR.puts Log.color(:magenta, "Status [#{job.to_i}]:")
+          STDERR.puts status_txt
+          lines = status_txt.split("\n").length
+        rescue
+          if ! File.exists?(fexit)
+            STDERR.puts Log.color(:magenta, "Job #{job.to_i} not done and not running. STDERR:")
+            STDERR.puts Open.read(ferr)
+          end
+          return
+        end
+      end
+
+      if File.exists?(fexit)
+        exit_status = Open.read(fexit)
+        if exit_status.to_i == 0
+          STDERR.puts Log.color(:magenta, "Job #{job} done with exit_status 0. STDOUT:")
+          STDERR.puts Open.read(fout)
+        else
+          STDERR.puts Log.color(:magenta, "Job #{job.to_i} done with exit_status #{exit_status}. STDERR:")
+          STDERR.puts Open.read(ferr)
+        end
+        return
+      end
+
+      if tail
+        Log.severity = 10
+        while ! File.exists? fout
+          if job
+            STDERR.puts
+            Log.clear_line(STDERR)
+            STDERR.write Log.color(:magenta, "Waiting for Output")
+            3.times do
+              STDERR.write Log.color(:magenta, ".")
+              sleep 1
+            end
+            status_txt = job_status(job)
+            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
+          end
+        end
+        STDERR.puts
+        Log.clear_line(STDERR)
+        STDERR.puts Log.color(:magenta, "Output:")
+        begin
+          status_txt = job_status(job)
+          Open.write(fstatus, status_txt) unless status_txt.nil? || status_txt.empty?
+          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)
+
+          terr = Misc.consume_stream(err, true, STDERR) if err
+          tout = Misc.consume_stream(out, true, STDOUT) if out
+
+          sleep 3 while job_status(job).include? job.to_s
+        rescue Aborted
+        ensure
+          begin
+            terr.exit if terr
+            tout.exit if tout
+            err.close if err
+            err.join if err
+          rescue Exception
+          end
+
+          begin
+            out.close if out
+            out.join if out
+          rescue Exception
+          end
+        end
+      end
+    end
+
+    def wait_for_job(batch_dir, time = 1)
+      fexit = File.join(batch_dir, 'exit.status')
+      fjob = File.join(batch_dir, 'job.id')
+      job = Open.read(fjob) if Open.exists?(fjob)
+
+      while ! Open.exists?(fexit)
+        sleep time
+      end
+    end
+
+  end
+
+  module BATCH
+    extend HPC::TemplateGeneration
+  end
+
+end
+