X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ff2e2d7b53edfec33a77ad1ff2b5a83f02a5be80..b25d2ec2950f6e2ffa9943a15c87441ebd6672b2:/services/api/script/crunch-dispatch.rb

diff --git a/services/api/script/crunch-dispatch.rb b/services/api/script/crunch-dispatch.rb
index bb7ce7e12d..a2bb65f0d7 100755
--- a/services/api/script/crunch-dispatch.rb
+++ b/services/api/script/crunch-dispatch.rb
@@ -61,63 +61,68 @@ class Dispatcher
     end
   end
 
-  def sinfo
+  def each_slurm_line(cmd, outfmt, max_fields=nil)
+    max_fields ||= outfmt.split(":").size
+    max_fields += 1  # To accommodate the node field we add
     @@slurm_version ||= Gem::Version.new(`sinfo --version`.match(/\b[\d\.]+\b/)[0])
     if Gem::Version.new('2.3') <= @@slurm_version
-      `sinfo --noheader -o '%n:%t'`.strip
+      `#{cmd} --noheader -o '%n:#{outfmt}'`.each_line do |line|
+        yield line.chomp.split(":", max_fields)
+      end
     else
       # Expand rows with hostname ranges (like "foo[1-3,5,9-12]:idle")
       # into multiple rows with one hostname each.
-      `sinfo --noheader -o '%N:%t'`.split("\n").collect do |line|
-        tokens = line.split ":"
+      `#{cmd} --noheader -o '%N:#{outfmt}'`.each_line do |line|
+        tokens = line.chomp.split(":", max_fields)
         if (re = tokens[0].match /^(.*?)\[([-,\d]+)\]$/)
-          re[2].split(",").collect do |range|
+          tokens.shift
+          re[2].split(",").each do |range|
             range = range.split("-").collect(&:to_i)
-            (range[0]..range[-1]).collect do |n|
-              [re[1] + n.to_s, tokens[1..-1]].join ":"
+            (range[0]..range[-1]).each do |n|
+              yield [re[1] + n.to_s] + tokens
             end
           end
         else
-          tokens.join ":"
+          yield tokens
         end
-      end.flatten.join "\n"
+      end
     end
   end
 
+  def slurm_status
+    slurm_nodes = {}
+    each_slurm_line("sinfo", "%t") do |hostname, state|
+      state.sub!(/\W+$/, "")
+      state = "down" unless %w(idle alloc down).include?(state)
+      slurm_nodes[hostname] = {state: state, job: nil}
+    end
+    each_slurm_line("squeue", "%j") do |hostname, job_uuid|
+      slurm_nodes[hostname][:job] = job_uuid if slurm_nodes[hostname]
+    end
+    slurm_nodes
+  end
+
   def update_node_status
-    if Server::Application.config.crunch_job_wrapper.to_s.match /^slurm/
-      @node_state ||= {}
-      node_seen = {}
+    return unless Server::Application.config.crunch_job_wrapper.to_s.match /^slurm/
+    @node_state ||= {}
+    slurm_status.each_pair do |hostname, slurmdata|
+      next if @node_state[hostname] == slurmdata
       begin
-        sinfo.split("\n").
-          each do |line|
-          re = line.match /(\S+?):+(idle|alloc|down)?/
-          next if !re
-
-          _, node_name, node_state = *re
-          node_state = 'down' unless %w(idle alloc down).include? node_state
-
-          # sinfo tells us about a node N times if it is shared by N partitions
-          next if node_seen[node_name]
-          node_seen[node_name] = true
-
-          # update our database (and cache) when a node's state changes
-          if @node_state[node_name] != node_state
-            @node_state[node_name] = node_state
-            node = Node.where('hostname=?', node_name).order(:last_ping_at).last
-            if node
-              $stderr.puts "dispatch: update #{node_name} state to #{node_state}"
-              node.info['slurm_state'] = node_state
-              if not node.save
-                $stderr.puts "dispatch: failed to update #{node.uuid}: #{node.errors.messages}"
-              end
-            elsif node_state != 'down'
-              $stderr.puts "dispatch: sinfo reports '#{node_name}' is not down, but no node has that name"
-            end
+        node = Node.where('hostname=?', hostname).order(:last_ping_at).last
+        if node
+          $stderr.puts "dispatch: update #{hostname} state to #{slurmdata}"
+          node.info["slurm_state"] = slurmdata[:state]
+          node.job_uuid = slurmdata[:job]
+          if node.save
+            @node_state[hostname] = slurmdata
+          else
+            $stderr.puts "dispatch: failed to update #{node.uuid}: #{node.errors.messages}"
           end
+        elsif slurmdata[:state] != 'down'
+          $stderr.puts "dispatch: SLURM reports '#{hostname}' is not down, but no node has that name"
         end
       rescue => error
-        $stderr.puts "dispatch: error updating node status: #{error}"
+        $stderr.puts "dispatch: error updating #{hostname} node status: #{error}"
       end
     end
   end
@@ -217,8 +222,6 @@ class Dispatcher
         raise "Unknown crunch_job_wrapper: #{Server::Application.config.crunch_job_wrapper}"
       end
 
-      next if !take(job)
-
       if Server::Application.config.crunch_job_user
         cmd_args.unshift("sudo", "-E", "-u",
                          Server::Application.config.crunch_job_user,
@@ -232,7 +235,10 @@ class Dispatcher
       job_auth = ApiClientAuthorization.
         new(user: User.where('uuid=?', job.modified_by_user_uuid).first,
             api_client_id: 0)
-      job_auth.save
+      if not job_auth.save
+        $stderr.puts "dispatch: job_auth.save failed"
+        next
+      end
 
       crunch_job_bin = (ENV['CRUNCH_JOB_BIN'] || `which arv-crunch-job`.strip)
       if crunch_job_bin == ''
@@ -246,17 +252,59 @@ class Dispatcher
         $stderr.puts `mkdir -p #{arvados_internal.shellescape} && cd #{arvados_internal.shellescape} && git init --bare`
       end
 
-      src_repo = File.join(Rails.configuration.git_repositories_dir, job.repository + '.git')
-      src_repo = File.join(Rails.configuration.git_repositories_dir, job.repository, '.git') unless File.exists? src_repo
+      repo_root = Rails.configuration.git_repositories_dir
+      src_repo = File.join(repo_root, job.repository + '.git')
+      if not File.exists? src_repo
+        src_repo = File.join(repo_root, job.repository, '.git')
+        if not File.exists? src_repo
+          $stderr.puts "dispatch: No #{job.repository}.git or #{job.repository}/.git at #{repo_root}"
+          sleep 1
+          next
+        end
+      end
 
-      unless src_repo
-        $stderr.puts "dispatch: #{File.join Rails.configuration.git_repositories_dir, job.repository} doesn't exist"
-        sleep 1
-        untake(job)
-        next
+      git = "git --git-dir=#{arvados_internal.shellescape}"
+
+      # check if the commit needs to be fetched or not
+      commit_rev = `#{git} rev-list -n1 #{job.script_version.shellescape} 2>/dev/null`.chomp
+      unless $? == 0 and commit_rev == job.script_version
+        # commit does not exist in internal repository, so import the source repository using git fetch-pack
+        cmd = "#{git} fetch-pack --no-progress --all #{src_repo.shellescape}"
+        $stderr.puts cmd
+        $stderr.puts `#{cmd}`
+        unless $? == 0
+          $stderr.puts "dispatch: git fetch-pack failed"
+          sleep 1
+          next
+        end
       end
 
-      $stderr.puts `cd #{arvados_internal.shellescape} && git fetch-pack --all #{src_repo.shellescape} && git tag #{job.uuid.shellescape} #{job.script_version.shellescape}`
+      # check if the commit needs to be tagged with this job uuid
+      tag_rev = `#{git} rev-list -n1 #{job.uuid.shellescape} 2>/dev/null`.chomp
+      if $? != 0
+        # no job tag found, so create one
+        cmd = "#{git} tag #{job.uuid.shellescape} #{job.script_version.shellescape}"
+        $stderr.puts cmd
+        $stderr.puts `#{cmd}`
+        unless $? == 0
+          $stderr.puts "dispatch: git tag failed"
+          sleep 1
+          next
+        end
+      else
+        # job tag found, check that it has the expected revision
+        unless tag_rev == job.script_version
+          # Uh oh, the tag doesn't point to the revision we were expecting.
+          # Someone has been monkeying with the job record and/or git.
+          $stderr.puts "dispatch: Already a tag #{job.script_version} pointing to commit #{tag_rev} but expected commit #{job.script_version}"
+          job.state = "Failed"
+          if not job.save
+            $stderr.puts "dispatch: job.save failed"
+            next
+          end
+          next
+        end
+      end
 
       cmd_args << crunch_job_bin
       cmd_args << '--job-api-token'
@@ -273,7 +321,6 @@ class Dispatcher
       rescue
         $stderr.puts "dispatch: popen3: #{$!}"
         sleep 1
-        untake(job)
         next
       end
 
@@ -287,70 +334,164 @@ class Dispatcher
         stderr: e,
         wait_thr: t,
         job: job,
-        stderr_buf: '',
+        buf: {stderr: '', stdout: ''},
         started: false,
         sent_int: 0,
         job_auth: job_auth,
         stderr_buf_to_flush: '',
-        stderr_flushed_at: 0,
+        stderr_flushed_at: Time.new(0),
         bytes_logged: 0,
         events_logged: 0,
-        log_truncated: false
+        log_throttle_is_open: true,
+        log_throttle_reset_time: Time.now + Rails.configuration.crunch_log_throttle_period,
+        log_throttle_bytes_so_far: 0,
+        log_throttle_lines_so_far: 0,
+        log_throttle_bytes_skipped: 0,
       }
       i.close
       update_node_status
     end
   end
 
-  def take(job)
-    # no-op -- let crunch-job take care of locking.
-    true
-  end
+  # Test for hard cap on total output and for log throttling.  Returns whether
+  # the log line should go to output or not.  Modifies "line" in place to
+  # replace it with an error if a logging limit is tripped.
+  def rate_limit running_job, line
+    message = false
+    linesize = line.size
+    if running_job[:log_throttle_is_open]
+      running_job[:log_throttle_lines_so_far] += 1
+      running_job[:log_throttle_bytes_so_far] += linesize
+      running_job[:bytes_logged] += linesize
+
+      if (running_job[:bytes_logged] >
+          Rails.configuration.crunch_limit_log_bytes_per_job)
+        message = "Exceeded log limit #{Rails.configuration.crunch_limit_log_bytes_per_job} bytes (crunch_limit_log_bytes_per_job). Log will be truncated."
+        running_job[:log_throttle_reset_time] = Time.now + 100.years
+        running_job[:log_throttle_is_open] = false
+
+      elsif (running_job[:log_throttle_bytes_so_far] >
+             Rails.configuration.crunch_log_throttle_bytes)
+        remaining_time = running_job[:log_throttle_reset_time] - Time.now
+        message = "Exceeded rate #{Rails.configuration.crunch_log_throttle_bytes} bytes per #{Rails.configuration.crunch_log_throttle_period} seconds (crunch_log_throttle_bytes). Logging will be silenced for the next #{remaining_time.round} seconds.\n"
+        running_job[:log_throttle_is_open] = false
+
+      elsif (running_job[:log_throttle_lines_so_far] >
+             Rails.configuration.crunch_log_throttle_lines)
+        remaining_time = running_job[:log_throttle_reset_time] - Time.now
+        message = "Exceeded rate #{Rails.configuration.crunch_log_throttle_lines} lines per #{Rails.configuration.crunch_log_throttle_period} seconds (crunch_log_throttle_lines), logging will be silenced for the next #{remaining_time.round} seconds.\n"
+        running_job[:log_throttle_is_open] = false
+      end
+    end
+
+    if not running_job[:log_throttle_is_open]
+      # Don't log anything if any limit has been exceeded. Just count lossage.
+      running_job[:log_throttle_bytes_skipped] += linesize
+    end
 
-  def untake(job)
-    # no-op -- let crunch-job take care of locking.
-    true
+    if message
+      # Yes, write to logs, but use our "rate exceeded" message
+      # instead of the log message that exceeded the limit.
+      line.replace message
+      true
+    else
+      running_job[:log_throttle_is_open]
+    end
   end
 
   def read_pipes
     @running.each do |job_uuid, j|
       job = j[:job]
 
-      # Throw away child stdout
-      begin
-        j[:stdout].read_nonblock(2**20)
-      rescue Errno::EAGAIN, EOFError
-      end
+      now = Time.now
+      if now > j[:log_throttle_reset_time]
+        # It has been more than throttle_period seconds since the last
+        # checkpoint so reset the throttle
+        if j[:log_throttle_bytes_skipped] > 0
+          message = "#{job_uuid} ! Skipped #{j[:log_throttle_bytes_skipped]} bytes of log"
+          $stderr.puts message
+          j[:stderr_buf_to_flush] << "#{Time.now.ctime.to_s} #{message}\n"
+        end
 
-      # Read whatever is available from child stderr
-      stderr_buf = false
-      begin
-        stderr_buf = j[:stderr].read_nonblock(2**20)
-      rescue Errno::EAGAIN, EOFError
+        j[:log_throttle_reset_time] = now + Rails.configuration.crunch_log_throttle_period
+        j[:log_throttle_bytes_so_far] = 0
+        j[:log_throttle_lines_so_far] = 0
+        j[:log_throttle_bytes_skipped] = 0
+        j[:log_throttle_is_open] = true
       end
 
-      if stderr_buf
-        j[:stderr_buf] << stderr_buf
-        if j[:stderr_buf].index "\n"
-          lines = j[:stderr_buf].lines("\n").to_a
-          if j[:stderr_buf][-1] == "\n"
-            j[:stderr_buf] = ''
-          else
-            j[:stderr_buf] = lines.pop
+      j[:buf].each do |stream, streambuf|
+        # Read some data from the child stream
+        buf = ''
+        begin
+          # It's important to use a big enough buffer here. When we're
+          # being flooded with logs, we must read and discard many
+          # bytes at once. Otherwise, we can easily peg a CPU with
+          # time-checking and other loop overhead. (Quick tests show a
+          # 1MiB buffer working 2.5x as fast as a 64 KiB buffer.)
+          #
+          # So don't reduce this buffer size!
+          buf = j[stream].read_nonblock(2**20)
+        rescue Errno::EAGAIN, EOFError
+        end
+
+        # Short circuit the counting code if we're just going to throw
+        # away the data anyway.
+        if not j[:log_throttle_is_open]
+          j[:log_throttle_bytes_skipped] += streambuf.size + buf.size
+          streambuf.replace ''
+          next
+        elsif buf == ''
+          next
+        end
+
+        # Append to incomplete line from previous read, if any
+        streambuf << buf
+
+        bufend = ''
+        streambuf.each_line do |line|
+          if not line.end_with? $/
+            if line.size > Rails.configuration.crunch_log_throttle_bytes
+              # Without a limit here, we'll use 2x an arbitrary amount
+              # of memory, and waste a lot of time copying strings
+              # around, all without providing any feedback to anyone
+              # about what's going on _or_ hitting any of our throttle
+              # limits.
+              #
+              # Here we leave "line" alone, knowing it will never be
+              # sent anywhere: rate_limit() will reach
+              # crunch_log_throttle_bytes immediately. However, we'll
+              # leave [...] in bufend: if the trailing end of the long
+              # line does end up getting sent anywhere, it will have
+              # some indication that it incomplete.
+              bufend = "[...]"
+            else
+              # If line length is sane, we'll wait for the rest of the
+              # line to appear in the next read_pipes() call.
+              bufend = line
+              break
+            end
           end
-          lines.each do |line|
+          # rate_limit returns true or false as to whether to actually log
+          # the line or not.  It also modifies "line" in place to replace
+          # it with an error if a logging limit is tripped.
+          if rate_limit j, line
             $stderr.print "#{job_uuid} ! " unless line.index(job_uuid)
             $stderr.puts line
-            pub_msg = "#{Time.now.ctime.to_s} #{line.strip} \n"
+            pub_msg = "#{Time.now.ctime.to_s} #{line.strip}\n"
             j[:stderr_buf_to_flush] << pub_msg
           end
-
-          if (Rails.configuration.crunch_log_bytes_per_event < j[:stderr_buf_to_flush].size or
-              (j[:stderr_flushed_at] + Rails.configuration.crunch_log_seconds_between_events < Time.now.to_i))
-            write_log j
-          end
         end
+
+        # Leave the trailing incomplete line (if any) in streambuf for
+        # next time.
+        streambuf.replace bufend
       end
+      # Flush buffered logs to the logs table, if appropriate. We have
+      # to do this even if we didn't collect any new logs this time:
+      # otherwise, buffered data older than seconds_between_events
+      # won't get flushed until new data arrives.
+      write_log j
     end
   end
 
@@ -393,27 +534,31 @@ class Dispatcher
     $stderr.puts "dispatch: child #{pid_done} exit"
     $stderr.puts "dispatch: job #{job_done.uuid} end"
 
-    # Ensure every last drop of stdout and stderr is consumed
+    # Ensure every last drop of stdout and stderr is consumed.
     read_pipes
-    write_log j_done # write any remaining logs
-
-    if j_done[:stderr_buf] and j_done[:stderr_buf] != ''
-      $stderr.puts j_done[:stderr_buf] + "\n"
+    # Reset flush timestamp to make sure log gets written.
+    j_done[:stderr_flushed_at] = Time.new(0)
+    # Write any remaining logs.
+    write_log j_done
+
+    j_done[:buf].each do |stream, streambuf|
+      if streambuf != ''
+        $stderr.puts streambuf + "\n"
+      end
     end
 
     # Wait the thread (returns a Process::Status)
-    exit_status = j_done[:wait_thr].value
+    exit_status = j_done[:wait_thr].value.exitstatus
 
     jobrecord = Job.find_by_uuid(job_done.uuid)
-    if exit_status.to_i != 75 and jobrecord.started_at
-      # Clean up state fields in case crunch-job exited without
-      # putting the job in a suitable "finished" state.
-      jobrecord.running = false
-      jobrecord.finished_at ||= Time.now
-      if jobrecord.success.nil?
-        jobrecord.success = false
+    if exit_status != 75 and jobrecord.state == "Running"
+      # crunch-job did not return exit code 75 (see below) and left the job in
+      # the "Running" state, which means there was an unhandled error.  Fail
+      # the job.
+      jobrecord.state = "Failed"
+      if not jobrecord.save
+        $stderr.puts "dispatch: jobrecord.save failed"
       end
-      jobrecord.save!
     else
       # Don't fail the job if crunch-job didn't even get as far as
       # starting it. If the job failed to run due to an infrastructure
@@ -444,7 +589,7 @@ class Dispatcher
       pipe_auth = (@pipe_auth_tokens[p.uuid] ||= ApiClientAuthorization.
                    create(user: User.where('uuid=?', p.modified_by_user_uuid).first,
                           api_client_id: 0))
-      puts `export ARVADOS_API_TOKEN=#{pipe_auth.api_token} && arv-run-pipeline-instance --run-here --no-wait --instance #{p.uuid}`
+      puts `export ARVADOS_API_TOKEN=#{pipe_auth.api_token} && arv-run-pipeline-instance --run-pipeline-here --no-wait --instance #{p.uuid}`
       expire_tokens.delete p.uuid
     end
 
@@ -491,15 +636,6 @@ class Dispatcher
 
   protected
 
-  def too_many_bytes_logged_for_job(j)
-    return (j[:bytes_logged] + j[:stderr_buf_to_flush].size >
-            Rails.configuration.crunch_limit_log_event_bytes_per_job)
-  end
-
-  def too_many_events_logged_for_job(j)
-    return (j[:events_logged] >= Rails.configuration.crunch_limit_log_events_per_job)
-  end
-
   def did_recently(thing, min_interval)
     @did_recently ||= {}
     if !@did_recently[thing] or @did_recently[thing] < Time.now - min_interval
@@ -512,38 +648,28 @@ class Dispatcher
 
   # send message to log table. we want these records to be transient
   def write_log running_job
-    begin
-      if (running_job && running_job[:stderr_buf_to_flush] != '')
-        # Truncate logs if they exceed crunch_limit_log_event_bytes_per_job
-        # or crunch_limit_log_events_per_job.
-        if (too_many_bytes_logged_for_job(running_job))
-          return if running_job[:log_truncated]
-          running_job[:log_truncated] = true
-          running_job[:stderr_buf_to_flush] =
-              "Server configured limit reached (crunch_limit_log_event_bytes_per_job: #{Rails.configuration.crunch_limit_log_event_bytes_per_job}). Subsequent logs truncated"
-        elsif (too_many_events_logged_for_job(running_job))
-          return if running_job[:log_truncated]
-          running_job[:log_truncated] = true
-          running_job[:stderr_buf_to_flush] =
-              "Server configured limit reached (crunch_limit_log_events_per_job: #{Rails.configuration.crunch_limit_log_events_per_job}). Subsequent logs truncated"
-        end
+    return if running_job[:stderr_buf_to_flush] == ''
+
+    # Send out to log event if buffer size exceeds the bytes per event or if
+    # it has been at least crunch_log_seconds_between_events seconds since
+    # the last flush.
+    if running_job[:stderr_buf_to_flush].size > Rails.configuration.crunch_log_bytes_per_event or
+        (Time.now - running_job[:stderr_flushed_at]) >= Rails.configuration.crunch_log_seconds_between_events
+      begin
         log = Log.new(object_uuid: running_job[:job].uuid,
                       event_type: 'stderr',
                       owner_uuid: running_job[:job].owner_uuid,
                       properties: {"text" => running_job[:stderr_buf_to_flush]})
         log.save!
-        running_job[:bytes_logged] += running_job[:stderr_buf_to_flush].size
         running_job[:events_logged] += 1
-        running_job[:stderr_buf_to_flush] = ''
-        running_job[:stderr_flushed_at] = Time.now.to_i
+      rescue => exception
+        $stderr.puts "Failed to write logs"
+        $stderr.puts exception.backtrace
       end
-    rescue
-      running_job[:stderr_buf] = "Failed to write logs \n"
       running_job[:stderr_buf_to_flush] = ''
-      running_job[:stderr_flushed_at] = Time.now.to_i
+      running_job[:stderr_flushed_at] = Time.now
     end
   end
-
 end
 
 # This is how crunch-job child procs know where the "refresh" trigger file is