Module: CodeRunner::Slurm
Overview
A module to let CodeRunner run using the SLURM queue system, used on certain HPC systems.
Instance Method Summary collapse
- #batch_script ⇒ Object
- #batch_script_file ⇒ Object
- #cancel_job ⇒ Object
- #error_file ⇒ Object
- #execute ⇒ Object
- #get_run_status(job_no, current_status) ⇒ Object
- #max_ppn ⇒ Object
- #output_file ⇒ Object
- #queue_status ⇒ Object
- #run_command ⇒ Object
Instance Method Details
#batch_script ⇒ Object
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 78 79 80 81 82 83 84 |
# File 'lib/coderunner/system_modules/slurm.rb', line 50 def batch_script nodes, ppn = @nprocs.split(/x/) eputs "Warning: Underuse of nodes (#{ppn} cores per node instead of #{max_ppn})" if ppn.to_i < max_ppn raise "Error: cores per node cannot excede #{max_ppn}" if ppn.to_i > max_ppn # raise "Error: project (i.e. budget) not specified" unless @project ppn ||= max_ppn raise "Please specify wall minutes" unless @wall_mins if @wall_mins ep @wall_mins hours = (@wall_mins / 60).floor mins = @wall_mins.to_i % 60 secs = ((@wall_mins - @wall_mins.to_i) * 60).to_i end eputs "Allotted wall time is " + sprintf("%02d:%02d:%02d", hours, mins, secs) nprocstot = nodes.to_i * ppn.to_i <<EOF #!/bin/bash #SBATCH -J #{executable_name}.#{job_identifier} # jobname #SBATCH -N #{nodes.to_i} # number of nodes #SBATCH -n #{nprocstot} # number of tasks #SBATCH -o #{executable_name}.#{job_identifier}.o%j # strout filename (%j is jobid) #SBATCH -e #{executable_name}.#{job_identifier}.e%j # stderr filename (%j is jobid) #{@project ? "#SBATCH -A #@project # project to charge" : ""} #{@queue ? "#SBATCH -p #@queue # submission queue" : ""} #{@wall_mins ? "#SBATCH -t #{sprintf("%02d:%02d:%02d", hours, mins, secs)} # walltime" : ""} #{code_run_environment} echo "Submitting #{nodes}x#{ppn} job on #{CodeRunner::SYS} for project #@project..." EOF end |
#batch_script_file ⇒ Object
42 43 44 |
# File 'lib/coderunner/system_modules/slurm.rb', line 42 def batch_script_file "#{executable_name}.#{job_identifier}.sh" end |
#cancel_job ⇒ Object
86 87 88 89 90 91 92 93 |
# File 'lib/coderunner/system_modules/slurm.rb', line 86 def cancel_job if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false) fname = ENV['HOME'] + "/.coderunner_to_launch_#{prefix}/#{$$}.stop" File.open(fname, 'w'){|file| file.puts "\n"} else `scancel #{@job_no}` end end |
#error_file ⇒ Object
95 96 97 |
# File 'lib/coderunner/system_modules/slurm.rb', line 95 def error_file return "#{executable_name}.#{job_identifier}.e#@job_no" end |
#execute ⇒ Object
26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 |
# File 'lib/coderunner/system_modules/slurm.rb', line 26 def execute if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false) launch_id = "#{Time.now.to_i}#{$$}" fname = ENV['HOME'] + "/.coderunner_to_launch_#{prefix}/#{launch_id}" File.open(fname + '.start', 'w'){|file| file.puts "cd #{Dir.pwd};#{run_command}"} sleep 1 until FileTest.exist? fname + '.pid' pid = File.read(fname + '.pid').to_i FileUtils.rm fname + '.pid' return pid else File.open(batch_script_file, 'w'){|file| file.puts batch_script + run_command + "\n"} pid = %x[sbatch #{batch_script_file}].to_i return nil end end |
#get_run_status(job_no, current_status) ⇒ Object
103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 |
# File 'lib/coderunner/system_modules/slurm.rb', line 103 def get_run_status(job_no, current_status) if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false) return :Unknown end line = current_status.split(/\n/).grep(Regexp.new(job_no.to_s))[0] unless line return :Unknown else @running = true if line =~ /\sPD\s/ return :Queueing elsif line =~ /\sR\s/ return :Running elsif line =~ /\sC\s/ @running = false return :Unknown else ep 'line', line raise 'Could not get run status' end end end |
#max_ppn ⇒ Object
46 47 48 |
# File 'lib/coderunner/system_modules/slurm.rb', line 46 def max_ppn raise "Please define max_ppn for your system" end |
#output_file ⇒ Object
99 100 101 |
# File 'lib/coderunner/system_modules/slurm.rb', line 99 def output_file return "#{executable_name}.#{job_identifier}.o#@job_no" end |
#queue_status ⇒ Object
6 7 8 9 10 11 12 13 |
# File 'lib/coderunner/system_modules/slurm.rb', line 6 def queue_status if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false) %x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status.txt] + %x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status2.txt] else %x[squeue | grep #{ENV['USER'][0..7]}] end end |
#run_command ⇒ Object
15 16 17 18 19 20 21 22 23 24 |
# File 'lib/coderunner/system_modules/slurm.rb', line 15 def run_command # "qsub #{batch_script_file}" if (ENV['CODE_RUNNER_LAUNCHER'].size > 0 rescue false) return %[mpiexec -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}] else nodes, ppn = @nprocs.split(/x/) nprocstot = nodes.to_i * ppn.to_i "#@preamble mpirun -np #{nprocstot} #{executable_location}/#{executable_name} #{parameter_string}" end end |