Module: RemoteWorkflow::SSH
- Defined in:
- lib/rbbt/workflow/remote_workflow/driver/ssh.rb
Class Method Summary collapse
- .clean(url, input_id, jobname = nil) ⇒ Object
- .get_json(url, params = {}) ⇒ Object
- .get_raw(url, params) ⇒ Object
- .job_script(inputs_id, jobname = nil) ⇒ Object
- .missing_dep_inputs(job) ⇒ Object
- .orchestrate_slurm_job(url, input_id, jobname = nil, slurm_options = {}) ⇒ Object
-
.parse_url(url) ⇒ Object
def self.run_log(server, script) Log.debug “Run and monitor ssh script in #server:n#script” CMD.cmd(“ssh ‘#server’ ‘shopt -s expand_aliases; bash -ic "ruby"’ ”, :in => script, :log => true) end.
- .path_script(path) ⇒ Object
- .post_job(url, inputs_id, jobname = nil) ⇒ Object
- .relay(workflow, task, jobname, inputs, server, options = {}) ⇒ Object
- .relay_job(job, server, options = {}) ⇒ Object
- .run_job(url, input_id, jobname = nil) ⇒ Object
- .run_slurm_job(url, input_id, jobname = nil, slurm_options = {}) ⇒ Object
-
.upload_dependencies(job, server, search_path = 'user', produce_dependencies = false) ⇒ Object
remote = RemoteWorkflow.new(“ssh://#server:#workflowworkflow.to_s”, “#workflowworkflow.to_s”) rjob = remote.job(task, jobname, {}) rjob.override_dependencies = override_dependencies rjob.run end.
- .upload_inputs(server, inputs, input_types, input_id) ⇒ Object
Instance Method Summary collapse
- #documentation ⇒ Object
- #init_remote_tasks ⇒ Object
- #task_dependencies ⇒ Object
- #task_info(task) ⇒ Object
- #tasks ⇒ Object
- #workflow_description ⇒ Object
Class Method Details
.clean(url, input_id, jobname = nil) ⇒ Object
171 172 173 174 175 176 177 178 179 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 171 def self.clean(url, input_id, jobname = nil) server, path = parse_url(url) script = path_script(path) script +=<<-EOF job.clean EOF Misc.ssh_run(server, script) end |
.get_json(url, params = {}) ⇒ Object
89 90 91 92 93 94 95 96 97 98 99 100 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 89 def self.get_json(url, params = {}) server, path = parse_url(url) script = path_script(path) script +=<<-EOF STDOUT.write res.to_json EOF json = Misc.ssh_run(server, script) Log.debug "JSON (#{ url }): #{json}" if RBBT_DEBUG_REMOTE_JSON JSON.parse(json) end |
.get_raw(url, params) ⇒ Object
102 103 104 105 106 107 108 109 110 111 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 102 def self.get_raw(url, params) server, path = parse_url(url) script = path_script(path) script +=<<-EOF STDOUT.write res EOF Misc.ssh_run(server, script) end |
.job_script(inputs_id, jobname = nil) ⇒ Object
79 80 81 82 83 84 85 86 87 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 79 def self.job_script(inputs_id, jobname = nil) script =<<-EOF jobname = #{jobname.nil? ? 'nil' : "'#{jobname}'"} path = File.join(ENV["HOME"], '.rbbt/tmp/tmp-ssh_job_inputs/#{inputs_id}') job_inputs = Workflow.load_inputs(path, task_info[:inputs], task_info[:input_types]) job = wf.job(task, jobname, job_inputs) EOF script end |
.missing_dep_inputs(job) ⇒ Object
241 242 243 244 245 246 247 248 249 250 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 241 def self.missing_dep_inputs(job) inputs = job.inputs.to_hash.slice(*job.real_inputs.map{|i| i.to_s}) job.dependencies.each do |dep| next if dep.done? iif [dep, dep.inputs, dep.real_inputs] inputs = dep.inputs.to_hash.slice(*dep.real_inputs.map{|i| i.to_s}).merge(inputs) inputs = missing_dep_inputs(dep).merge(inputs) end inputs end |
.orchestrate_slurm_job(url, input_id, jobname = nil, slurm_options = {}) ⇒ Object
155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 155 def self.orchestrate_slurm_job(url, input_id, jobname = nil, = {}) server, path = parse_url(url) script = path_script(path) script += job_script(input_id, jobname) script +=<<-EOF require 'rbbt/hpc' HPC::BATCH_MODULE = HPC.batch_system "SLURM" slurm_options = JSON.parse(%q(#{.to_json})) job.clean if job.error? and job.recoverable_error? HPC::BATCH_MODULE.orchestrate_job(job, slurm_options) unless job.done? || job.error? STDOUT.write job.path EOF Misc.ssh_run(server, script) end |
.parse_url(url) ⇒ Object
15 16 17 18 19 20 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 15 def self.parse_url(url) m = url.match(/ssh:\/\/([^:]+):(.*)/) server = m.captures[0] path = m.captures[1] [server, path] end |
.path_script(path) ⇒ Object
22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 22 def self.path_script(path) workflow, task, job, *rest = path.split("/") workflow_name = begin wf = Kernel.const_get(workflow) if String === workflow && ! workflow.empty? wf.respond_to?(:complete_name) ? (wf.complete_name || workflow) : workflow rescue workflow end script =<<-EOF require 'rbbt/workflow' wf = Workflow.require_workflow "#{workflow_name}" EOF case task when nil script +=<<-EOF task_info = {} wf.tasks.keys.each do |task| task_info[task] = wf.task_info(task) end res = task_info EOF when 'documentation' script +=<<-EOF res = documentation = wf.documentation EOF else if job.nil? script +=<<-EOF task = '#{task}' res = task_info = wf.task_info(task) EOF else case rest.first when nil script +=<<-EOF task = '#{task}' jobname = '#{job}' res = job = wf.fast_load_id(File.join(task, jobname)) EOF when "info" script +=<<-EOF task = '#{task}' jobname = '#{job}' job = wf.fast_load_id(File.join(task, jobname)) res = job_info = job.info EOF else raise "Unkown path: #{[path, rest].inspect}" end end end end |
.post_job(url, inputs_id, jobname = nil) ⇒ Object
113 114 115 116 117 118 119 120 121 122 123 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 113 def self.post_job(url, inputs_id, jobname = nil) server, path = parse_url(url) script = path_script(path) script += job_script(inputs_id, jobname) script +=<<-EOF job.init_info STDOUT.write job.path EOF Misc.ssh_run(server, script) end |
.relay(workflow, task, jobname, inputs, server, options = {}) ⇒ Object
282 283 284 285 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 282 def self.relay(workflow, task, jobname, inputs, server, = {}) job = workflow.job(task, jobname, inputs) relay_job(job, server, ) end |
.relay_job(job, server, options = {}) ⇒ Object
252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 252 def self.relay_job(job, server, = {}) migrate, produce, produce_dependencies, search_path, run_type, = Misc. .dup, :migrate, :produce, :produce_dependencies, :search_path, :run_type, :slurm_options search_path ||= 'user' produce = true if migrate workflow_name = job.workflow.to_s remote_workflow = RemoteWorkflow.new("ssh://#{server}:#{workflow_name}", "#{workflow_name}") inputs = job.recursive_inputs.to_hash.slice(*job.real_inputs.map{|i| i.to_s}) Log.medium "Relaying dependency #{job.workflow}:#{job.short_path} to #{server} (#{inputs.keys * ", "})" upload_dependencies(job, server, search_path, [:produce_dependencies]) rjob = remote_workflow.job(job.task_name.to_s, job.clean_name, inputs) override_dependencies = job.rec_dependencies.select{|dep| dep.done? }.collect{|dep| [dep.workflow.to_s, dep.task_name.to_s] * "#" << "=" << Rbbt.identify(dep.path)} rjob.override_dependencies = override_dependencies rjob.run_type = run_type rjob. = || {} if [:migrate] rjob.produce Step.migrate(Rbbt.identify(job.path), 'user', :source => server) end rjob end |
.run_job(url, input_id, jobname = nil) ⇒ Object
125 126 127 128 129 130 131 132 133 134 135 136 137 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 125 def self.run_job(url, input_id, jobname = nil) server, path = parse_url(url) script = path_script(path) script += job_script(input_id, jobname) script +=<<-EOF ENV["RBBT_UPDATE"]="#{(ENV["RBBT_UPDATE"] || false).to_s}" job.clean if job.error? and job.recoverable_error? job.run unless job.done? || job.error? STDOUT.write job.path EOF Misc.ssh_run(server, script) end |
.run_slurm_job(url, input_id, jobname = nil, slurm_options = {}) ⇒ Object
139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 139 def self.run_slurm_job(url, input_id, jobname = nil, = {}) server, path = parse_url(url) script = path_script(path) script += job_script(input_id, jobname) script +=<<-EOF require 'rbbt/hpc' HPC::BATCH_MODULE = HPC.batch_system "SLURM" slurm_options = JSON.parse(%q(#{.to_json})) job.clean if job.error? and job.recoverable_error? HPC::BATCH_MODULE.run_job(job, slurm_options) unless job.done? || job.error? STDOUT.write job.path EOF Misc.ssh_run(server, script) end |
.upload_dependencies(job, server, search_path = 'user', produce_dependencies = false) ⇒ Object
remote = RemoteWorkflow.new(“ssh://#server:#workflowworkflow.to_s”, “#workflowworkflow.to_s”)
rjob = remote.job(task, jobname, {})
rjob.override_dependencies = override_dependencies
rjob.run
end
223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 223 def self.upload_dependencies(job, server, search_path = 'user', produce_dependencies = false) server, path = parse_url(server) if server =~ /^ssh:\/\// job.dependencies.each do |dep| Log.medium "Producing #{dep.workflow}:#{dep.short_path} dependency for #{job.workflow}:#{job.short_path}" dep.produce end if produce_dependencies job.input_dependencies.each do |dep| Log.medium "Producing #{dep.workflow}:#{dep.short_path} dependency for #{job.workflow}:#{job.short_path}" dep.produce end migrate_dependencies = job.rec_dependencies.select{|d| d.done? }.collect{|d| d.path } migrate_dependencies += job.input_dependencies.select{|d| d.done? }.collect{|d| d.path } Log.medium "Migrating #{migrate_dependencies.length} dependencies from #{job.path} to #{ server }" Step.migrate(migrate_dependencies, search_path, :target => server) if migrate_dependencies.any? end |
.upload_inputs(server, inputs, input_types, input_id) ⇒ Object
181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 181 def self.upload_inputs(server, inputs, input_types, input_id) TmpFile.with_file do |dir| if Step.save_inputs(inputs, input_types, dir) # Dir.glob(File.join(dir, "*.as_step")).each do |file| # Log.medium "Migrating Step input #{file} #{ server }" # path = Open.read(file).strip # new = Step.migrate(path, :user, :target => server) # Open.write(file, new) # end files = Dir.glob(File.join(dir, "*.as_step")) paths = files.collect{|f| Open.read(f).strip } new = Step.migrate(paths, :user, :target => server) files.zip(new).each{|file,new| Open.write(file, new) } CMD.cmd_log("ssh '#{server}' mkdir -p .rbbt/tmp/tmp-ssh_job_inputs/; scp -r '#{dir}' #{server}:.rbbt/tmp/tmp-ssh_job_inputs/#{input_id}") end end end |
Instance Method Details
#documentation ⇒ Object
291 292 293 294 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 291 def documentation @documention ||= IndiferentHash.setup(RemoteWorkflow::SSH.get_json(File.join(url, "documentation"))) @documention end |
#init_remote_tasks ⇒ Object
336 337 338 339 340 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 336 def init_remote_tasks @task_info = IndiferentHash.setup(RemoteWorkflow::SSH.get_json(url)) @exec_exports = @stream_exports = @synchronous_exports = [] @asynchronous_exports = @task_info.keys end |
#task_dependencies ⇒ Object
326 327 328 329 330 331 332 333 334 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 326 def task_dependencies @task_dependencies ||= Hash.new do |hash,task| hash[task] = if exported_tasks.include? task RemoteWorkflow::SSH.get_json(File.join(url, task.to_s, 'dependencies')) else [] end end end |
#task_info(task) ⇒ Object
296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 296 def task_info(task) @task_info ||= IndiferentHash.setup({}) if @task_info[task].nil? task_info = RemoteWorkflow::SSH.get_json(File.join(@base_url || @url, task.to_s)) task_info = RemoteWorkflow::SSH.fix_hash(task_info) task_info[:result_type] = task_info[:result_type].to_sym if task_info[:result_type] task_info[:export] = task_info[:export].to_sym if task_info[:export] task_info[:input_types] = RemoteWorkflow::SSH.fix_hash(task_info[:input_types], true) task_info[:inputs] = task_info[:inputs].collect{|input| input.to_sym } @task_info[task] = IndiferentHash.setup(task_info) end IndiferentHash.setup(@task_info[task]) end |
#tasks ⇒ Object
314 315 316 317 318 319 320 321 322 323 324 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 314 def tasks @tasks ||= Hash.new do |hash,task_name| raise Workflow::TaskNotFoundException, "Task #{task_name} not found in workflow #{self.to_s}" unless @task_info.include?(task_name) info = @task_info[task_name] task = Task.setup info do |*args| raise "This is a remote task" end task.name = task_name.to_sym hash[task_name] = task end end |
#workflow_description ⇒ Object
287 288 289 |
# File 'lib/rbbt/workflow/remote_workflow/driver/ssh.rb', line 287 def workflow_description RemoteWorkflow::SSH.get_raw(File.join(url, 'description')) end |