#!/usr/bin/env ruby
+require 'shellwords'
include Process
$options = {}
require File.dirname(__FILE__) + '/../config/environment'
require 'open3'
+class LogTime < Time
+ def to_s
+ self.utc.strftime "%Y-%m-%d_%H:%M:%S"
+ end
+end
+
class Dispatcher
include ApplicationHelper
+ 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
+
+ @arvados_internal = Rails.configuration.git_internal_dir
+ if not File.exists? @arvados_internal
+ $stderr.puts `mkdir -p #{@arvados_internal.shellescape} && git init --bare #{@arvados_internal.shellescape}`
+ raise "No internal git repository available" unless ($? == 0)
+ end
+
+ @repo_root = Rails.configuration.git_repositories_dir
+ @authorizations = {}
+ @did_recently = {}
+ @fetched_commits = {}
+ @git_tags = {}
+ @node_state = {}
+ @pipe_auth_tokens = {}
+ @running = {}
+ @todo = []
+ @todo_pipelines = []
+ end
+
def sysuser
return act_as_system_user
end
def refresh_todo
- @todo = []
if $options[:jobs]
@todo = Job.queue.select(&:repository)
end
- @todo_pipelines = []
if $options[:pipelines]
@todo_pipelines = PipelineInstance.queue
end
def slurm_status
slurm_nodes = {}
each_slurm_line("sinfo", "%t") do |hostname, state|
+ # Treat nodes in idle* state as down, because the * means that slurm
+ # hasn't been able to communicate with it recently.
+ state.sub!(/^idle\*/, "down")
state.sub!(/\W+$/, "")
state = "down" unless %w(idle alloc down).include?(state)
slurm_nodes[hostname] = {state: state, job: nil}
def update_node_status
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
nodelist
end
+ def fail_job job, message
+ $stderr.puts "dispatch: #{job.uuid}: #{message}"
+ begin
+ Log.new(object_uuid: job.uuid,
+ event_type: 'dispatch',
+ owner_uuid: job.owner_uuid,
+ summary: message,
+ properties: {"text" => message}).save!
+ rescue
+ $stderr.puts "dispatch: log.create failed"
+ end
+
+ begin
+ job.lock @authorizations[job.uuid].user.uuid
+ job.state = "Failed"
+ if not job.save
+ $stderr.puts "dispatch: save failed setting job #{job.uuid} to failed"
+ end
+ rescue ArvadosModel::AlreadyLockedError
+ $stderr.puts "dispatch: tried to mark job #{job.uuid} as failed but it was already locked by someone else"
+ end
+ end
+
+ def stdout_s(cmd_a, opts={})
+ IO.popen(cmd_a, "r", opts) do |pipe|
+ return pipe.read.chomp
+ end
+ end
+
+ def git_cmd(*cmd_a)
+ ["git", "--git-dir=#{@arvados_internal}"] + cmd_a
+ end
+
+ def get_authorization(job)
+ if @authorizations[job.uuid] and
+ @authorizations[job.uuid].user.uuid != job.modified_by_user_uuid
+ # We already made a token for this job, but we need a new one
+ # because modified_by_user_uuid has changed (the job will run
+ # as a different user).
+ @authorizations[job.uuid].update_attributes expires_at: Time.now
+ @authorizations[job.uuid] = nil
+ end
+ if not @authorizations[job.uuid]
+ auth = ApiClientAuthorization.
+ new(user: User.where('uuid=?', job.modified_by_user_uuid).first,
+ api_client_id: 0)
+ if not auth.save
+ $stderr.puts "dispatch: auth.save failed for #{job.uuid}"
+ else
+ @authorizations[job.uuid] = auth
+ end
+ end
+ @authorizations[job.uuid]
+ end
+
+ def get_commit(repo_name, commit_hash)
+ # @fetched_commits[V]==true if we know commit V exists in the
+ # arvados_internal git repository.
+ if !@fetched_commits[commit_hash]
+ src_repo = File.join(@repo_root, "#{repo_name}.git")
+ if not File.exists? src_repo
+ src_repo = File.join(@repo_root, repo_name, '.git')
+ if not File.exists? src_repo
+ fail_job job, "No #{repo_name}.git or #{repo_name}/.git at #{@repo_root}"
+ return nil
+ end
+ end
+
+ # 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
+ end
+ @fetched_commits[commit_hash]
+ end
+
+ def tag_commit(commit_hash, tag_name)
+ # @git_tags[T]==V if we know commit V has been tagged T in the
+ # arvados_internal repository.
+ if not @git_tags[tag_name]
+ cmd = git_cmd("tag", tag_name, commit_hash)
+ $stderr.puts "dispatch: #{cmd}"
+ $stderr.puts(stdout_s(cmd, err: "/dev/null"))
+ unless $? == 0
+ # git tag failed. This may be because the tag already exists, so check for that.
+ tag_rev = stdout_s(git_cmd("rev-list", "-n1", tag_name))
+ if $? == 0
+ # We got a revision back
+ if tag_rev != commit_hash
+ # Uh oh, the tag doesn't point to the revision we were expecting.
+ # Someone has been monkeying with the job record and/or git.
+ fail_job job, "Existing tag #{tag_name} points to commit #{tag_rev} but expected commit #{commit_hash}"
+ return nil
+ end
+ # we're okay (fall through to setting @git_tags below)
+ else
+ # git rev-list failed for some reason.
+ fail_job job, "'git tag' for #{tag_name} failed but did not find any existing tag using 'git rev-list'"
+ return nil
+ end
+ end
+ # 'git tag' was successful, or there is an existing tag that points to the same revision.
+ @git_tags[tag_name] = commit_hash
+ elsif @git_tags[tag_name] != commit_hash
+ fail_job job, "Existing tag #{tag_name} points to commit #{@git_tags[tag_name]} but this job uses commit #{commit_hash}"
+ return nil
+ end
+ @git_tags[tag_name]
+ end
+
def start_jobs
@todo.each do |job|
next if @running[job.uuid]
"GEM_PATH=#{ENV['GEM_PATH']}")
end
- job_auth = ApiClientAuthorization.
- new(user: User.where('uuid=?', job.modified_by_user_uuid).first,
- api_client_id: 0)
- 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 == ''
- raise "No CRUNCH_JOB_BIN env var, and crunch-job not in path."
- end
-
- require 'shellwords'
-
- arvados_internal = Rails.configuration.git_internal_dir
- if not File.exists? arvados_internal
- $stderr.puts `mkdir -p #{arvados_internal.shellescape} && cd #{arvados_internal.shellescape} && git init --bare`
+ ready = (get_authorization(job) and
+ get_commit(job.repository, job.script_version) and
+ tag_commit(job.script_version, job.uuid))
+ if ready and job.arvados_sdk_version
+ ready = (get_commit("arvados", job.arvados_sdk_version) and
+ tag_commit(job.arvados_sdk_version, "#{job.uuid}-arvados-sdk"))
end
+ next unless ready
- 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
-
- 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
-
- # 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'
- cmd_args << job_auth.api_token
- cmd_args << '--job'
- cmd_args << job.uuid
- cmd_args << '--git-dir'
- cmd_args << arvados_internal
+ cmd_args += [@crunch_job_bin,
+ '--job-api-token', @authorizations[job.uuid].api_token,
+ '--job', job.uuid,
+ '--git-dir', @arvados_internal]
$stderr.puts "dispatch: #{cmd_args.join ' '}"
end
$stderr.puts "dispatch: job #{job.uuid}"
- start_banner = "dispatch: child #{t.pid} start #{Time.now.ctime.to_s}"
+ start_banner = "dispatch: child #{t.pid} start #{LogTime.now}"
$stderr.puts start_banner
@running[job.uuid] = {
buf: {stderr: '', stdout: ''},
started: false,
sent_int: 0,
- job_auth: job_auth,
+ job_auth: @authorizations[job.uuid],
stderr_buf_to_flush: '',
stderr_flushed_at: Time.new(0),
bytes_logged: 0,
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"
+ j[:stderr_buf_to_flush] << "#{LogTime.now} #{message}\n"
end
j[:log_throttle_reset_time] = now + Rails.configuration.crunch_log_throttle_period
if not j[:log_throttle_is_open]
j[:log_throttle_bytes_skipped] += streambuf.size + buf.size
streambuf.replace ''
+ next
elsif buf == ''
next
end
streambuf << buf
bufend = ''
- streambuf.lines("\n").each do |line|
- if not line.end_with? "\n"
+ 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
# 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.
+ # some indication that it is incomplete.
bufend = "[...]"
else
# If line length is sane, we'll wait for the rest of the
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 = "#{LogTime.now} #{line.strip}\n"
j[:stderr_buf_to_flush] << pub_msg
end
end
# fine.
end
- # Invalidate the per-job auth token
- j_done[:job_auth].update_attributes expires_at: Time.now
+ # Invalidate the per-job auth token, unless the job is still queued and we
+ # might want to try it again.
+ if jobrecord.state != "Queued"
+ j_done[:job_auth].update_attributes expires_at: Time.now
+ end
@running.delete job_done.uuid
end
def run
act_as_system_user
- @running ||= {}
- @pipe_auth_tokens ||= { }
$stderr.puts "dispatch: ready"
while !$signal[:term] or @running.size > 0
read_pipes
end
else
refresh_todo unless did_recently(:refresh_todo, 1.0)
- update_node_status
+ update_node_status unless did_recently(:update_node_status, 1.0)
unless @todo.empty? or did_recently(:start_jobs, 1.0) or $signal[:term]
start_jobs
end
protected
def did_recently(thing, min_interval)
- @did_recently ||= {}
if !@did_recently[thing] or @did_recently[thing] < Time.now - min_interval
@did_recently[thing] = Time.now
false
projects / arvados.git / blobdiff