X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/379717415ec5f772ab2f54e263c2c3f44d77f70f..6207681aa301ad12d164aab24f52a210945af04b:/services/api/script/crunch-dispatch.rb

diff --git a/services/api/script/crunch-dispatch.rb b/services/api/script/crunch-dispatch.rb
index 249582ec6a..9fb25664a4 100755
--- a/services/api/script/crunch-dispatch.rb
+++ b/services/api/script/crunch-dispatch.rb
@@ -1,5 +1,9 @@
 #!/usr/bin/env ruby
 
+# We want files written by crunch-dispatch to be writable by other processes
+# with the same GID, see bug #7228
+File.umask(0002)
+
 require 'shellwords'
 include Process
 
@@ -53,12 +57,18 @@ end
 class Dispatcher
   include ApplicationHelper
 
+  EXIT_TEMPFAIL = 75
+  EXIT_RETRY_UNLOCKED = 93
+  RETRY_UNLOCKED_LIMIT = 3
+
   def initialize
     @crunch_job_bin = (ENV['CRUNCH_JOB_BIN'] || `which arv-crunch-job`.strip)
     if @crunch_job_bin.empty?
       raise "No CRUNCH_JOB_BIN env var, and crunch-job not in path."
     end
 
+    @docker_bin = ENV['CRUNCH_JOB_DOCKER_BIN']
+
     @arvados_internal = Rails.configuration.git_internal_dir
     if not File.exists? @arvados_internal
       $stderr.puts `mkdir -p #{@arvados_internal.shellescape} && git init --bare #{@arvados_internal.shellescape}`
@@ -75,6 +85,8 @@ class Dispatcher
     @pipe_auth_tokens = {}
     @running = {}
     @todo = []
+    @todo_job_retries = {}
+    @job_retry_counts = Hash.new(0)
     @todo_pipelines = []
   end
 
@@ -84,7 +96,7 @@ class Dispatcher
 
   def refresh_todo
     if $options[:jobs]
-      @todo = Job.queue.select(&:repository)
+      @todo = @todo_job_retries.values + Job.queue.select(&:repository)
     end
     if $options[:pipelines]
       @todo_pipelines = PipelineInstance.queue
@@ -182,7 +194,7 @@ class Dispatcher
     # Otherwise, return nil.
     need_procs = NODE_CONSTRAINT_MAP.each_pair.map do |job_key, node_key|
       Proc.new do |node|
-        positive_int(node.info[node_key], 0) >=
+        positive_int(node.properties[node_key], 0) >=
           positive_int(job.runtime_constraints[job_key], 0)
       end
     end
@@ -277,26 +289,24 @@ class Dispatcher
     @authorizations[job.uuid]
   end
 
-  def get_commit(src_repo, commit_hash)
-    # @fetched_commits[V]==true if we know commit V exists in the
-    # arvados_internal git repository.
-    if !@fetched_commits[commit_hash]
-      # check if the commit needs to be fetched or not
-      commit_rev = stdout_s(git_cmd("rev-list", "-n1", commit_hash),
-                            err: "/dev/null")
-      unless $? == 0 and commit_rev == commit_hash
-        # commit does not exist in internal repository, so import the source repository using git fetch-pack
-        cmd = git_cmd("fetch-pack", "--no-progress", "--all", src_repo)
-        $stderr.puts "dispatch: #{cmd}"
-        $stderr.puts(stdout_s(cmd))
-        unless $? == 0
-          fail_job job, "git fetch-pack failed"
-          return nil
-        end
-      end
-      @fetched_commits[commit_hash] = true
+  def internal_repo_has_commit? sha1
+    if (not @fetched_commits[sha1] and
+        sha1 == stdout_s(git_cmd("rev-list", "-n1", sha1), err: "/dev/null") and
+        $? == 0)
+      @fetched_commits[sha1] = true
     end
-    @fetched_commits[commit_hash]
+    return @fetched_commits[sha1]
+  end
+
+  def get_commit src_repo, sha1
+    return true if internal_repo_has_commit? sha1
+
+    # commit does not exist in internal repository, so import the
+    # source repository using git fetch-pack
+    cmd = git_cmd("fetch-pack", "--no-progress", "--all", src_repo)
+    $stderr.puts "dispatch: #{cmd}"
+    $stderr.puts(stdout_s(cmd))
+    @fetched_commits[sha1] = ($? == 0)
   end
 
   def tag_commit(commit_hash, tag_name)
@@ -368,6 +378,7 @@ class Dispatcher
       if Server::Application.config.crunch_job_user
         cmd_args.unshift("sudo", "-E", "-u",
                          Server::Application.config.crunch_job_user,
+                         "LD_LIBRARY_PATH=#{ENV['LD_LIBRARY_PATH']}",
                          "PATH=#{ENV['PATH']}",
                          "PERLLIB=#{ENV['PERLLIB']}",
                          "PYTHONPATH=#{ENV['PYTHONPATH']}",
@@ -375,26 +386,56 @@ class Dispatcher
                          "GEM_PATH=#{ENV['GEM_PATH']}")
       end
 
-      repo = Repository.where(name: job.repository).first
-      if repo.nil? or repo.server_path.nil?
-        fail_job "Repository #{job.repository} not found under #{@repo_root}"
-        next
+      next unless get_authorization job
+
+      ready = internal_repo_has_commit? job.script_version
+
+      if not ready
+        # Import the commit from the specified repository into the
+        # internal repository. This should have been done already when
+        # the job was created/updated; this code is obsolete except to
+        # avoid deployment races. Failing the job would be a
+        # reasonable thing to do at this point.
+        repo = Repository.where(name: job.repository).first
+        if repo.nil? or repo.server_path.nil?
+          fail_job "Repository #{job.repository} not found under #{@repo_root}"
+          next
+        end
+        ready &&= get_commit repo.server_path, job.script_version
+        ready &&= tag_commit job.script_version, job.uuid
+      end
+
+      # This should be unnecessary, because API server does it during
+      # job create/update, but it's still not a bad idea to verify the
+      # tag is correct before starting the job:
+      ready &&= tag_commit job.script_version, job.uuid
+
+      # The arvados_sdk_version doesn't support use of arbitrary
+      # remote URLs, so the requested version isn't necessarily copied
+      # into the internal repository yet.
+      if job.arvados_sdk_version
+        ready &&= get_commit @arvados_repo_path, job.arvados_sdk_version
+        ready &&= tag_commit job.arvados_sdk_version, "#{job.uuid}-arvados-sdk"
       end
 
-      ready = (get_authorization(job) and
-               get_commit(repo.server_path, job.script_version) and
-               tag_commit(job.script_version, job.uuid))
-      if ready and job.arvados_sdk_version
-        ready = (get_commit(@arvados_repo_path, job.arvados_sdk_version) and
-                 tag_commit(job.arvados_sdk_version, "#{job.uuid}-arvados-sdk"))
+      if not ready
+        fail_job job, "commit not present in internal repository"
+        next
       end
-      next unless ready
 
       cmd_args += [@crunch_job_bin,
                    '--job-api-token', @authorizations[job.uuid].api_token,
                    '--job', job.uuid,
                    '--git-dir', @arvados_internal]
 
+      if @docker_bin
+        cmd_args += ['--docker-bin', @docker_bin]
+      end
+
+      if @todo_job_retries.include?(job.uuid)
+        cmd_args << "--force-unlock"
+      end
+
       $stderr.puts "dispatch: #{cmd_args.join ' '}"
 
       begin
@@ -430,6 +471,7 @@ class Dispatcher
         log_throttle_bytes_skipped: 0,
       }
       i.close
+      @todo_job_retries.delete(job.uuid)
       update_node_status
     end
   end
@@ -612,8 +654,6 @@ class Dispatcher
     return if !pid_done
 
     job_done = j_done[:job]
-    $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.
     read_pipes
@@ -630,23 +670,49 @@ class Dispatcher
 
     # Wait the thread (returns a Process::Status)
     exit_status = j_done[:wait_thr].value.exitstatus
+    exit_tempfail = exit_status == EXIT_TEMPFAIL
+
+    $stderr.puts "dispatch: child #{pid_done} exit #{exit_status}"
+    $stderr.puts "dispatch: job #{job_done.uuid} end"
 
     jobrecord = Job.find_by_uuid(job_done.uuid)
-    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"
+
+    if exit_status == EXIT_RETRY_UNLOCKED
+      # The job failed because all of the nodes allocated to it
+      # failed.  Only this crunch-dispatch process can retry the job:
+      # it's already locked, and there's no way to put it back in the
+      # Queued state.  Put it in our internal todo list unless the job
+      # has failed this way excessively.
+      @job_retry_counts[jobrecord.uuid] += 1
+      exit_tempfail = @job_retry_counts[jobrecord.uuid] <= RETRY_UNLOCKED_LIMIT
+      if exit_tempfail
+        @todo_job_retries[jobrecord.uuid] = jobrecord
+      else
+        $stderr.puts("dispatch: job #{jobrecord.uuid} exceeded node failure retry limit -- giving up")
+      end
+    end
+
+    if !exit_tempfail
+      @job_retry_counts.delete(jobrecord.uuid)
+      if jobrecord.state == "Running"
+        # Apparently there was an unhandled error.  That could potentially
+        # include "all allocated nodes failed" when we don't to retry
+        # because the job has already been retried RETRY_UNLOCKED_LIMIT
+        # times.  Fail the job.
+        jobrecord.state = "Failed"
+        if not jobrecord.save
+          $stderr.puts "dispatch: jobrecord.save failed"
+        end
       end
     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
+      # If the job failed to run due to an infrastructure
       # issue with crunch-job or slurm, we want the job to stay in the
       # queue. If crunch-job exited after losing a race to another
       # crunch-job process, it exits 75 and we should leave the job
-      # record alone so the winner of the race do its thing.
+      # record alone so the winner of the race can do its thing.
+      # If crunch-job exited after all of its allocated nodes failed,
+      # it exits 93, and we want to retry it later (see the
+      # EXIT_RETRY_UNLOCKED `if` block).
       #
       # There is still an unhandled race condition: If our crunch-job
       # process is about to lose a race with another crunch-job
@@ -660,7 +726,7 @@ class Dispatcher
 
     # Invalidate the per-job auth token, unless the job is still queued and we
     # might want to try it again.
-    if jobrecord.state != "Queued"
+    if jobrecord.state != "Queued" and !@todo_job_retries.include?(jobrecord.uuid)
       j_done[:job_auth].update_attributes expires_at: Time.now
     end
 
@@ -685,6 +751,7 @@ class Dispatcher
 
   def run
     act_as_system_user
+    User.first.group_permissions
     $stderr.puts "dispatch: ready"
     while !$signal[:term] or @running.size > 0
       read_pipes
@@ -714,6 +781,14 @@ class Dispatcher
       select(@running.values.collect { |j| [j[:stdout], j[:stderr]] }.flatten,
              [], [], 1)
     end
+    # If there are jobs we wanted to retry, we have to mark them as failed now.
+    # Other dispatchers can't pick them up because we hold their lock.
+    @todo_job_retries.each_key do |job_uuid|
+      job = Job.find_by_uuid(job_uuid)
+      if job.state == "Running"
+        fail_job(job, "crunch-dispatch was stopped during job's tempfail retry loop")
+      end
+    end
   end
 
   protected
@@ -756,4 +831,10 @@ end
 # This is how crunch-job child procs know where the "refresh" trigger file is
 ENV["CRUNCH_REFRESH_TRIGGER"] = Rails.configuration.crunch_refresh_trigger
 
+# If salloc can't allocate resources immediately, make it use our temporary
+# failure exit code.  This ensures crunch-dispatch won't mark a job failed
+# because of an issue with node allocation.  This often happens when
+# another dispatcher wins the race to allocate nodes.
+ENV["SLURM_EXIT_IMMEDIATE"] = Dispatcher::EXIT_TEMPFAIL.to_s
+
 Dispatcher.new.run