#!/usr/bin/env ruby
+require 'trollop'
+
include Process
$warned = {}
end
end
+$trollopts = Trollop::options do
+ opt :use_env, "Pass selected environment variables (PATH, PYTHONPATH, RUBYLIB, GEM_PATH, PERLLIB) to crunch-job"
+end
+
ENV["RAILS_ENV"] = ARGV[0] || ENV["RAILS_ENV"] || "development"
require File.dirname(__FILE__) + '/../config/boot'
require File.dirname(__FILE__) + '/../config/environment'
require 'open3'
-$redis ||= Redis.new
-LOG_BUFFER_SIZE = 2**20
+LOG_BUFFER_SIZE = 4096
class Dispatcher
include ApplicationHelper
end
def refresh_todo
- @todo = Job.queue
+ @todo = Job.queue.select do |j| j.repository end
@todo_pipelines = PipelineInstance.queue
end
if Server::Application.config.crunch_job_user
cmd_args.unshift("sudo", "-E", "-u",
Server::Application.config.crunch_job_user,
- "PERLLIB=#{ENV['PERLLIB']}")
+ "PATH=#{ENV['PATH']}",
+ "PERLLIB=#{ENV['PERLLIB']}",
+ "PYTHONPATH=#{ENV['PYTHONPATH']}",
+ "RUBYLIB=#{ENV['RUBYLIB']}",
+ "GEM_PATH=#{ENV['GEM_PATH']}")
end
job_auth = ApiClientAuthorization.
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`
+ 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
+
+ unless src_repo
+ $stderr.puts "dispatch: #{File.join Rails.configuration.git_repositories_dir, job.repository} doesn't exist"
+ sleep 1
+ untake(job)
+ next
+ end
+
+ $stderr.puts `cd #{arvados_internal.shellescape} && git fetch --no-tags #{src_repo.shellescape} && git tag #{job.uuid.shellescape} #{job.script_version.shellescape}`
+
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
- commit = Commit.where(sha1: job.script_version).first
- if commit
- cmd_args << '--git-dir'
- if File.exists?(File.
- join(Rails.configuration.git_repositories_dir,
- commit.repository_name + '.git'))
- cmd_args << File.
- join(Rails.configuration.git_repositories_dir,
- commit.repository_name + '.git')
- else
- cmd_args << File.
- join(Rails.configuration.git_repositories_dir,
- commit.repository_name, '.git')
- end
- end
-
- $stderr.puts "dispatch: #{cmd_args.join ' '}"
+ $stderr.puts "dispatch: #{cmd_args}"
begin
- i, o, e, t = Open3.popen3(*cmd_args)
+ i, o, e, t = Open3.popen3({}, *cmd_args, { :unsetenv_others => true})
rescue
$stderr.puts "dispatch: popen3: #{$!}"
sleep 1
$stderr.puts "dispatch: job #{job.uuid}"
start_banner = "dispatch: child #{t.pid} start #{Time.now.ctime.to_s}"
$stderr.puts start_banner
- $redis.set job.uuid, start_banner + "\n"
- $redis.publish job.uuid, start_banner
- $redis.publish job.owner_uuid, start_banner
@running[job.uuid] = {
stdin: i,
stderr_buf: '',
started: false,
sent_int: 0,
- job_auth: job_auth
+ job_auth: job_auth,
+ stderr_buf_to_flush: '',
+ stderr_flushed_at: 0
}
i.close
end
lines.each do |line|
$stderr.print "#{job_uuid} ! " unless line.index(job_uuid)
$stderr.puts line
- pub_msg = "#{Time.now.ctime.to_s} #{line.strip}"
- $redis.publish job.owner_uuid, pub_msg
- $redis.publish job_uuid, pub_msg
- $redis.append job_uuid, pub_msg + "\n"
- if LOG_BUFFER_SIZE < $redis.strlen(job_uuid)
- $redis.set(job_uuid,
- $redis
- .getrange(job_uuid, (LOG_BUFFER_SIZE >> 1), -1)
- .sub(/^.*?\n/, ''))
- end
+ pub_msg = "#{Time.now.ctime.to_s} #{line.strip} \n"
+ j[:stderr_buf_to_flush] << pub_msg
+ end
+
+ if (LOG_BUFFER_SIZE < j[:stderr_buf_to_flush].size) || ((j[:stderr_flushed_at]+1) < Time.now.to_i)
+ write_log j
end
end
end
# 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"
end
j_done[:wait_thr].value
jobrecord = Job.find_by_uuid(job_done.uuid)
- jobrecord.running = false
- jobrecord.finished_at ||= Time.now,
- # Don't set 'jobrecord.success = false' because if the job failed to run due to an
- # issue with crunch-job or slurm, we want the job to stay in the queue.
- jobrecord.save!
+ if 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
+ 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
+ # issue with crunch-job or slurm, we want the job to stay in the
+ # queue.
+ end
# Invalidate the per-job auth token
j_done[:job_auth].update_attributes expires_at: Time.now
- $redis.publish job_done.uuid, "end"
-
@running.delete job_done.uuid
end
def update_pipelines
+ expire_tokens = @pipe_auth_tokens.dup
@todo_pipelines.each do |p|
- pipe_auth = ApiClientAuthorization.
- new(user: User.where('uuid=?', p.modified_by_user_uuid).first,
- api_client_id: 0)
- pipe_auth.save
-
+ 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}`
+ expire_tokens.delete p.uuid
+ end
+
+ expire_tokens.each do |k, v|
+ v.update_attributes expires_at: Time.now
+ @pipe_auth_tokens.delete k
end
end
def run
act_as_system_user
@running ||= {}
+ @pipe_auth_tokens ||= { }
$stderr.puts "dispatch: ready"
while !$signal[:term] or @running.size > 0
read_pipes
unless @todo.empty? or did_recently(:start_jobs, 1.0) or $signal[:term]
start_jobs
end
- unless @todo_pipelines.empty? or did_recently(:update_pipelines, 5.0)
+ unless (@todo_pipelines.empty? and @pipe_auth_tokens.empty?) or did_recently(:update_pipelines, 5.0)
update_pipelines
end
end
true
end
end
+
+ # 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] != '')
+ 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[:stderr_buf_to_flush] = ''
+ running_job[:stderr_flushed_at] = Time.now.to_i
+ 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
+ end
+ end
+
end
# This is how crunch-job child procs know where the "refresh" trigger file is
projects / arvados.git / blobdiff