Module: CodeRunner::Moab

Includes:
Launcher
Included in:
Archer, Dirac, Edison, Franklin, Hector, Hopper, Iridis, Loki
Defined in:
lib/coderunner/system_modules/moab.rb

Instance Method Summary collapse

Methods included from Launcher

#cancel_job_launcher, #error_file_launcher, #execute_launcher, #launcher_prefix, #output_file_launcher, #queue_status_launcher, #use_launcher

Instance Method Details

#batch_script ⇒ Object 



85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
 
# File 'lib/coderunner/system_modules/moab.rb', line 85

def batch_script
	ppn_checks
	hours, mins, secs = hours_minutes_seconds
<<EOF
#!/bin/bash --login 
#PBS -N #{executable_name}.#{job_identifier}
#PBS -l mppwidth=#{nprocstot}
#PBS -l mppnppn=#{ppn}
#PBS -l walltime=#{sprintf("%02d:%02d:%02d", hours, mins, secs)}
#{@project ? "#PBS -A #@project" : ""}
#{@queue ? "#PBS -q #@queue" : ""}

### start of jobscript 
cd $PBS_O_WORKDIR 
echo "workdir: $PBS_O_WORKDIR" 
#{code_run_environment}

echo "Submitting #{nodes}x#{ppn} job on #{CodeRunner::SYS} for project #@project..."
EOF
end

#batch_script_file ⇒ Object 



61
62
63
 
# File 'lib/coderunner/system_modules/moab.rb', line 61

def batch_script_file
	"#{executable_name}.#{job_identifier}.sh"
end

#cancel_job ⇒ Object 



106
107
108
 
# File 'lib/coderunner/system_modules/moab.rb', line 106

def cancel_job
	use_launcher ? cancel_job_launcher : `qdel #{@job_no}`
end

#error_file ⇒ Object 



110
111
112
113
 
# File 'lib/coderunner/system_modules/moab.rb', line 110

def error_file
	use_launcher ? error_file_launcher :
		"#{executable_name}.#{job_identifier}.e#@job_no"
end

#execute ⇒ Object 



52
53
54
55
56
57
58
59
 
# File 'lib/coderunner/system_modules/moab.rb', line 52

def execute
	if use_launcher
     return execute_launcher
	else
		File.open(batch_script_file, 'w'){|file| file.puts batch_script + run_command + "\n"}
		_pid = %x[qsub #{batch_script_file}].to_i
	end
end

#get_run_status(job_no, current_status) ⇒ Object 



120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
 
# File 'lib/coderunner/system_modules/moab.rb', line 120

def get_run_status(job_no, current_status)
  if use_launcher
    return :Unknown
  end
  line = current_status.split(/\n/).grep(Regexp.new(job_no.to_s))[0]
  unless line
    return :Unknown
  else 
    if line =~ /\sQ\s/
      return :Queueing
    elsif line =~ /\sR\s/
      return :Running
    elsif line =~ /\sH\s/
      return :Queueing
    elsif line =~ /\sC\s/
      @running=false
      return :Unknown
    else
      ep 'line', line
      raise 'Could not get run status'
    end
  end
end

#hours_minutes_seconds ⇒ Object 



69
70
71
72
73
74
75
76
77
78
79
80
 
# File 'lib/coderunner/system_modules/moab.rb', line 69

def hours_minutes_seconds
	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
	else
		raise "Please specify wall mins using the W flag"
	end
	eputs "Allotted wall time is " + sprintf("%02d:%02d:%02d", hours, mins, secs)
	return [hours, mins, secs]
end

#max_ppn ⇒ Object 



65
66
67
 
# File 'lib/coderunner/system_modules/moab.rb', line 65

def max_ppn
	raise "Please define max_ppn for your system"
end

#mpi_prog ⇒ Object 



25
26
27
 
# File 'lib/coderunner/system_modules/moab.rb', line 25

def mpi_prog
	"aprun -n #{nprocstot} -N #{ppn}"
end

#nodes ⇒ Object 



29
30
31
32
 
# File 'lib/coderunner/system_modules/moab.rb', line 29

def nodes
  nodes, _ppn = @nprocs.split(/:/)[0].split(/x/)
  nodes.to_i
end

#nprocstot ⇒ Object 



37
38
39
40
41
 
# File 'lib/coderunner/system_modules/moab.rb', line 37

def nprocstot
	
		#nodes, ppn = @nprocs.split(/x/)
		_nprocstot = nodes.to_i * ppn.to_i
end

#output_file ⇒ Object 



115
116
117
118
 
# File 'lib/coderunner/system_modules/moab.rb', line 115

def output_file
	use_launcher ? output_file_launcher :
		"#{executable_name}.#{job_identifier}.o#@job_no"
end

#ppn ⇒ Object 



33
34
35
36
 
# File 'lib/coderunner/system_modules/moab.rb', line 33

def ppn
		_nodes, ppn = @nprocs.split(/:/)[0].split(/x/)
		ppn.to_i
end

#ppn_checks ⇒ Object 



81
82
83
84
 
# File 'lib/coderunner/system_modules/moab.rb', line 81

def ppn_checks
	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
end

#queue_status ⇒ Object

Kernel.change_environment_with_shell_script(conf) end



17
18
19
20
21
22
23
 
# File 'lib/coderunner/system_modules/moab.rb', line 17

def queue_status
	if use_launcher
     queue_status_launcher
	else
		%x[qstat | grep $USER]
	end
end

#run_command ⇒ Object 



42
43
44
45
46
47
48
49
50
 
# File 'lib/coderunner/system_modules/moab.rb', line 42

def run_command
# 		"qsub #{batch_script_file}"
	if use_launcher
		return %[#{code_run_environment}
			#{mpi_prog} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
	else
		"#{mpi_prog}  #{executable_location}/#{executable_name} #{parameter_string}"
	end
end