class WhRunPipelineInstance
end
-$application_version = 1.0
-
if RUBY_VERSION < '1.9.3' then
abort <<-EOS
#{$0.gsub(/^\.\//,'')} requires Ruby version 1.9.3 or higher.
suppress_warnings { OpenSSL::SSL::VERIFY_PEER = OpenSSL::SSL::VERIFY_NONE }
end
-class Google::APIClient
- def discovery_document(api, version)
- api = api.to_s
- return @discovery_documents["#{api}:#{version}"] ||=
- begin
- response = self.execute!(
- :http_method => :get,
- :uri => self.discovery_uri(api, version),
- :authenticated => false
- )
- response.body.class == String ? JSON.parse(response.body) : response.body
- end
- end
-end
-
# Parse command line options (the kind that control the behavior of
# this program, that is, not the pipeline component parameters).
:short => :none,
:type => :string)
opt(:submit,
- "Do not try to satisfy any components. Just create a pipeline instance and output its UUID.",
+ "Submit the pipeline instance to the server, and exit. Let the Crunch dispatch service satisfy the components by finding/running jobs.",
+ :short => :none,
+ :type => :boolean)
+ opt(:run_pipeline_here,
+ "Manage the pipeline instance in-process. Submit jobs to Crunch as needed. Do not exit until the pipeline finishes (or fails).",
+ :short => :none,
+ :type => :boolean)
+ opt(:run_jobs_here,
+ "Run jobs in the local terminal session instead of submitting them to Crunch. Implies --run-pipeline-here. Note: this results in a significantly different job execution environment, and some Crunch features are not supported. It can be necessary to modify a pipeline in order to make it run this way.",
:short => :none,
:type => :boolean)
opt(:run_here,
- "Manage the pipeline in process.",
+ "Synonym for --run-jobs-here.",
:short => :none,
:type => :boolean)
opt(:description,
end
$debuglevel = $options[:debug_level] || ($options[:debug] && 1) || 0
+$options[:run_jobs_here] ||= $options[:run_here] # old flag name
+$options[:run_pipeline_here] ||= $options[:run_jobs_here] # B requires A
+
if $options[:instance]
if $options[:template] or $options[:submit]
abort "#{$0}: syntax error: --instance cannot be combined with --template or --submit."
abort
end
-if $options[:run_here] == $options[:submit]
- abort "#{$0}: syntax error: you must supply either --run-here or --submit."
+if $options[:run_pipeline_here] == $options[:submit]
+ abort "#{$0}: error: you must supply --run-pipeline-here, --run-jobs-here, or --submit."
end
# Suppress SSL certificate checks if ARVADOS_API_HOST_INSECURE
# Set up the API client.
-$client ||= Google::APIClient.
- new(:host => $arvados_api_host,
- :application_name => File.split($0).last,
- :application_version => $application_version.to_s)
-$arvados = $client.discovered_api('arvados', $arvados_api_version)
$arv = Arvados.new api_version: 'v1'
-
+$client = $arv.client
+$arvados = $arv.arvados_api
class PipelineInstance
def self.find(uuid)
end
else
description = $options[:description]
- description = ("Created at #{Time.now.localtime}" + (@template[:name].andand.size>0 ? " using the pipeline template *#{@template[:name]}*" : "")) if !description
+ description = ("Created at #{Time.now.localtime}" + (@template[:name].andand.size.andand>0 ? " using the pipeline template *#{@template[:name]}*" : "")) if !description
@instance = PipelineInstance.
create(components: @components,
properties: {
# No job yet associated with this component and is component inputs
# are fully specified (any output_of script_parameters are resolved
# to real value)
+ my_submit_id = "instance #{@instance[:uuid]} rand #{rand(2**64).to_s(36)}"
job = JobCache.create(@instance, cname, {
:script => c[:script],
:script_parameters => c[:script_parameters],
:nondeterministic => c[:nondeterministic],
:runtime_constraints => c[:runtime_constraints],
:owner_uuid => owner_uuid,
+ :is_locked_by_uuid => (@options[:run_jobs_here] ? owner_uuid : nil),
+ :submit_id => my_submit_id,
}, {
# This is the right place to put these attributes when
# dealing with new API servers.
if job
debuglog "component #{cname} new job #{job[:uuid]}"
c[:job] = job
+ c[:run_in_process] = (@options[:run_jobs_here] and
+ job[:submit_id] == my_submit_id)
else
debuglog "component #{cname} new job failed", 0
job_creation_failed += 1
end
end
+ if c[:job] and c[:run_in_process] and c[:job][:success].nil?
+ report_status
+ begin
+ require 'open3'
+ Open3.popen3("arv-crunch-job", "--force-unlock",
+ "--job", c[:job][:uuid]) do |stdin, stdout, stderr, wait_thr|
+ debuglog "arv-crunch-job pid #{wait_thr.pid} started", 0
+ stdin.close
+ while true
+ rready, wready, = IO.select([stdout, stderr], [])
+ break if !rready[0]
+ begin
+ buf = rready[0].read_nonblock(2**20)
+ rescue EOFError
+ break
+ end
+ (rready[0] == stdout ? $stdout : $stderr).write(buf)
+ end
+ stdout.close
+ stderr.close
+ debuglog "arv-crunch-job pid #{wait_thr.pid} exit #{wait_thr.value.to_i}", 0
+ end
+ if not $arv.job.get(uuid: c[:job][:uuid])[:finished_at]
+ raise Exception.new("arv-crunch-job did not set finished_at.")
+ end
+ rescue Exception => e
+ debuglog "Interrupted (#{e}). Failing job.", 0
+ $arv.job.update(uuid: c[:job][:uuid],
+ job: {
+ finished_at: Time.now,
+ running: false,
+ success: false
+ })
+ end
+ end
+
if c[:job] and c[:job][:uuid]
if (c[:job][:running] or
not (c[:job][:finished_at] or c[:job][:cancelled_at]))
# succeeded. (At the top of this loop, I was still
# waiting for it to finish.)
- debuglog "names: #{@instance[:name]} #{@template[:name]}", 0
- if (not @instance[:name].nil?) and (not @instance[:name].empty?)
+ if @instance[:name].andand.length.andand > 0
pipeline_name = @instance[:name]
- else
- fetch_template(@instance[:pipeline_template_uuid])
+ elsif @template.andand[:name].andand.length.andand > 0
pipeline_name = @template[:name]
+ else
+ pipeline_name = @instance[:uuid]
end
if c[:output_name] != false
# Create a collection located in the same project as the pipeline with the contents of the output.
"failed #{c[:job][:finished_at]}"
elsif c[:job][:started_at]
"started #{c[:job][:started_at]}"
+ elsif c[:job][:is_locked_by_uuid]
+ "starting #{c[:job][:started_at]}"
else
"queued #{c[:job][:created_at]}"
end
projects / arvados.git / blobdiff