Module: Marenostrum::SLURM
- Defined in:
- lib/rbbt/hpc.rb
Constant Summary collapse
- TEMPLATE =
<<-EOF EOF
Class Method Summary collapse
- .done?(id, options = {}) ⇒ Boolean
- .gather(id, file = nil, options = {}) ⇒ Object
- .issue(cmd, name = nil, time = nil, options = {}) ⇒ Object
- .query(id, options = {}) ⇒ Object
- .run(cmd, name = nil, time = nil, options = {}) ⇒ Object
Class Method Details
.done?(id, options = {}) ⇒ Boolean
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# File 'lib/rbbt/hpc.rb', line 73 def self.done?(id, = {}) ! query(id, ).include? id end |
.gather(id, file = nil, options = {}) ⇒ Object
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# File 'lib/rbbt/hpc.rb', line 77 def self.gather(id, file = nil, = {}) key_file, user, workdir, output = .values_at :key_file, :user, :workdir, :output TmpFile.with_file do |result| begin cmd = "scp -i #{key_file} #{ user }@#{ SERVER }:'#{workdir}/#{output}' '#{ result }' " Log.debug cmd CMD.cmd(cmd) if file.nil? Open.read(result) else Misc.sensiblewrite(result, file) end rescue raise "Could not gather job: #{ id }: " << $!. end end end |
.issue(cmd, name = nil, time = nil, options = {}) ⇒ Object
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# File 'lib/rbbt/hpc.rb', line 11 def self.issue(cmd, name = nil, time = nil, = {}) name = "rbbt-job-" << rand(10000).to_s if name.nil? time = "00:00:10" if time.nil? workdir = "rbbt-workdir/" << name = Misc.add_defaults , "job-name" => name, "workdir" => workdir, "output" => "log", "error" => "log.err", "ntasks" => "1", "time" => time.to_s, "user" => ENV["USER"], "key_file" => File.join(ENV['HOME'], '.ssh/id_rsa.pub') .merge!() IndiferentHash.setup() key_file, user = .values_at :key_file, :user template = <<-EOF #!/bin/bash #{.collect do |name,value| next if name == 'user' next if name == 'key_file' name = "--" << name.to_s.sub(/^--/,'') [name, '"' << value << '"'] * "=" end.compact.collect{|str| "#SBATCH #{str}"} * "\n" } #{ cmd } EOF TmpFile.with_file do |slurm| res = nil begin Open.write(slurm, template) Log.medium("Issuing job:\n" + template) cmd = "ssh -i #{key_file} #{ user }@#{ SERVER } mkdir -p '#{ workdir }'; scp -i #{key_file} #{ slurm } #{ user }@#{ SERVER }:'#{ workdir }/#{ name }.slurm'; ssh -i #{key_file} #{ user }@#{ SERVER } sbatch #{ workdir }/#{ name }.slurm" Log.debug cmd res = CMD.cmd(cmd).read rescue raise "Could not issue job" end res.scan(/\d+/).first end end |
.query(id, options = {}) ⇒ Object
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# File 'lib/rbbt/hpc.rb', line 58 def self.query(id, = {}) key_file, user = .values_at :key_file, :user res = nil begin cmd = "ssh -i #{key_file} #{ user }@#{ SERVER } squeue |grep '#{id}\\|JOBID'" Log.debug cmd res = CMD.cmd(cmd).read rescue raise "Could not query job: #{ id }" << $!. end res end |
.run(cmd, name = nil, time = nil, options = {}) ⇒ Object
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# File 'lib/rbbt/hpc.rb', line 97 def self.run(cmd, name = nil, time = nil, = {}) sleep_time = Misc. , :sleep id = issue(cmd, name, time, ) if sleep_time.nil? times = [1,2,3,5,10,30] else times = Array === sleep_time ? sleep_time.dup : [sleep_time] end while not done?(id, ) Log.debug "Waiting on #{ id }" sleep_time = times.shift || sleep_time sleep sleep_time end gather(id, nil, ) end |