Module: MiGA::Cli::Action::Init::DaemonHelper

Included in:
MiGA::Cli::Action::Init
Defined in:
lib/miga/cli/action/init/daemon_helper.rb

Overview

Helper module with daemon configuration functions for MiGA::Cli::Action::Init

Instance Method Summary collapse

Instance Method Details

#configure_bash_daemon(v) ⇒ Object 



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
 
# File 'lib/miga/cli/action/init/daemon_helper.rb', line 34

def configure_bash_daemon(v)
  v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '2').to_i
  v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '6').to_i
  v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
  v[:nodelist] = nil # <- To enable non-default with default SSH
  cli.puts 'Setting up internal daemon defaults.'
  cli.puts 'If you don\'t understand this just leave default values:'
  v[:cmd] = cli.ask_user(
    "How should I launch tasks?\n" \
      "  {{variables}}: script, vars, cpus, log, task_name, miga\n ",
    "{{vars}} {{miga}} run -r '{{script}}' -l '{{log}}' -e"
  )
  v[:var] = cli.ask_user(
    "How should I pass variables?\n" \
      "  {{variables}}: key, value\n ",
    "{{key}}={{value}}"
  )
  v[:varsep]  = cli.ask_user('What should I use to separate variables?', ' ')
  v[:alive]   = cli.ask_user(
    "How can I know that a process is still alive?\n" \
      "  Output should be 1 for running and 0 for non-running\n" \
      "  {{variables}}: pid\n ",
    "ps -p '{{pid}}' | tail -n +2 | wc -l"
  )
  v[:kill] = cli.ask_user(
    "How should I terminate tasks?\n" \
      "  {{variables}}: pid\n ",
    "kill -9 '{{pid}}'"
  )
  v
end

#configure_daemon ⇒ Object 



6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
 
# File 'lib/miga/cli/action/init/daemon_helper.rb', line 6

def configure_daemon
  cli.puts 'Default daemon configuration:'
  daemon_f = File.expand_path('.miga_daemon.json', ENV['MIGA_HOME'])
  unless File.exist?(daemon_f) and cli.ask_user(
    'A template daemon already exists, do you want to preserve it?',
    'yes', %w(yes no)
  ) == 'yes'
    v = { created: Time.now.to_s, updated: Time.now.to_s }
    v[:type] = cli.ask_user(
      'Please select the type of daemon you want to setup',
      cli[:dtype], %w(bash ssh qsub msub slurm)
    )
    case v[:type]
    when 'bash'
      v = configure_bash_daemon(v)
    when 'ssh'
      v = configure_ssh_daemon(v)
    when 'slurm'
      v = configure_slurm_daemon(v)
    else # [qm]sub
      v = configure_qsub_msub_daemon(v)
    end
    v[:format_version] = 1
    File.open(daemon_f, 'w') { |fh| fh.puts JSON.pretty_generate(v) }
  end
  cli.puts ''
end

#configure_qsub_msub_daemon(v) ⇒ Object 



138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
 
# File 'lib/miga/cli/action/init/daemon_helper.rb', line 138

def configure_qsub_msub_daemon(v)
  flavor      = v[:type] == 'msub' ? 'msub' :
                cli.ask_user('Select qsub flavor', 'torque', %w[torque sge])
  queue       = cli.ask_user('What queue should I use?', nil, nil, true)
  v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
  v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '300').to_i
  v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
  v[:nodelist] = nil # <- To enable non-default with default SSH
  cli.puts 'Setting up internal daemon defaults.'
  cli.puts 'If you don\'t understand this just leave default values:'
  if flavor == 'sge'
    v[:cmd] = cli.ask_user(
      "How should I launch tasks?\n" \
        "  {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
      "#{v[:type]} -q '#{queue}' -v '{{vars}}' -pe openmp {{cpus}} " \
        "-j y -o '{{log}}' -N '{{task_name_simple}}' -l h_vmem=9g " \
        "-l h_rt=12:00:00 '{{script}}' | grep . " \
        "| perl -pe 's/^Your job (\\S+) .*/$1/'"
    )
  else
    v[:cmd] = cli.ask_user(
      "How should I launch tasks?\n" \
        "  {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
      "#{v[:type]} -q '#{queue}' -v '{{vars}}' -l nodes=1:ppn={{cpus}} " \
        "-j oe -o '{{log}}' -N '{{task_name}}' -l mem=9g " \
        "-l walltime=12:00:00 '{{script}}' | grep ."
    )
  end
  v[:var] = cli.ask_user(
    "How should I pass variables?\n" \
      "  {{variables}}: key, value\n ",
    "{{key}}={{value}}"
  )
  v[:varsep] = cli.ask_user(
    'What should I use to separate variables?', ','
  )
  if v[:type] == 'qsub'
    if flavor == 'sge'
      v[:alive] = cli.ask_user(
        "How can I know that a process is still alive?\n" \
          "  Output should be 1 for running and 0 for non-running\n" \
          "  {{variables}}: pid\n ",
        "qstat -j '{{pid}}' -s pr 2>/dev/null | head -n 1 | wc -l " \
          "| awk '{print $1}'"
      )
    else
      v[:alive] = cli.ask_user(
        "How can I know that a process is still alive?\n" \
          "  Output should be 1 for running and 0 for non-running\n" \
          "  {{variables}}: pid\n ",
        "qstat -f '{{pid}}' | grep ' job_state =' | perl -pe 's/.*= //' " \
          "| grep '[^C]' | tail -n 1 | wc -l | awk '{print $1}'"
      )
    end
    v[:kill] = cli.ask_user(
      "How should I terminate tasks?\n" \
        "  {{variables}}: pid\n ",
      "qdel '{{pid}}'"
    )
  else # msub
    v[:alive] = cli.ask_user(
      "How can I know that a process is still alive?\n" \
        "  Output should be 1 for running and 0 for non-running\n" \
        "  {{variables}}: pid\n ",
      "checkjob '{{pid}}'|grep '^State:' | perl -pe 's/.*: //' " \
        "| grep 'Deferred\\|Hold\\|Idle\\|Starting\\|Running\\|Blocked'" \
        "| tail -n 1 | wc -l | awk '{print $1}'"
    )
    v[:kill] = cli.ask_user(
      "How should I terminate tasks?\n" \
        "  {{variables}}: pid\n ",
      "canceljob '{{pid}}'"
    )
  end
  v
end

#configure_slurm_daemon(v) ⇒ Object 



99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
 
# File 'lib/miga/cli/action/init/daemon_helper.rb', line 99

def configure_slurm_daemon(v)
  queue       = cli.ask_user('What queue should I use?', nil, nil, true)
  v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
  v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '300').to_i
  v[:ppn]     = cli.ask_user('How many CPUs can I use per job?', '2').to_i
  v[:nodelist] = nil # <- To enable non-default with default SSH
  cli.puts 'Setting up internal daemon defaults'
  cli.puts 'If you don\'t understand this just leave default values:'
  v[:cmd] = cli.ask_user(
    "How should I launch tasks?\n" \
      "  {{variables}}: script, vars, cpus, log, task_name, miga\n ",
    "{{vars}} sbatch --partition='#{queue}' --export=ALL " \
      "--nodes=1 --ntasks-per-node={{cpus}} --output='{{log}}' " \
      "--job-name='{{task_name}}' --mem=9G --time=12:00:00 {{script}} " \
      "| perl -pe 's/.* //'"
  )
  v[:var] = cli.ask_user(
    "How should I pass variables?\n" \
      "  {{variables}}: key, value\n ",
    "{{key}}={{value}}"
  )
  v[:varsep] = cli.ask_user(
    'What should I use to separate variables?', ' '
  )
  v[:alive] = cli.ask_user(
    "How can I know that a process is still alive?\n" \
      "  Output should be 1 for running and 0 for non-running\n" \
      "  {{variables}}: pid\n ",
    "squeue -h -o %t -j '{{pid}}' | grep '^PD\\|R\\|CF\\|CG$' " \
      "| tail -n 1 | wc -l"
  )
  v[:kill] = cli.ask_user(
    "How should I terminate tasks?\n" \
      "  {{variables}}: pid\n ",
    "scancel '{{pid}}'"
  )
  v
end

#configure_ssh_daemon(v) ⇒ Object 



66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
 
# File 'lib/miga/cli/action/init/daemon_helper.rb', line 66

def configure_ssh_daemon(v)
  v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '3').to_i
  v[:nodelist] = cli.ask_user(
    'What environmental variable points to node list?', '$MIGA_NODELIST'
  )
  v[:ppn] = cli.ask_user('How many CPUs can I use per job?', '2').to_i
  cli.puts 'Setting up internal daemon defaults.'
  cli.puts 'If you don\'t understand this just leave default values:'
  v[:cmd] = cli.ask_user(
    "How should I launch tasks?\n" \
      "  {{variables}}: script, vars, cpus, log, task_name, miga, host\n ",
    "{{vars}} {{miga}} run -r '{{script}}' -l '{{log}}' -R {{host}} -e"
  )
  v[:var] = cli.ask_user(
    "How should I pass variables?\n" \
      "  {{variables}}: key, value\n ",
    "{{key}}={{value}}"
  )
  v[:varsep]  = cli.ask_user('What should I use to separate variables?', ' ')
  v[:alive]   = cli.ask_user(
    "How can I know that a process is still alive?\n" \
      "  Output should be 1 for running and 0 for non-running\n" \
      "  {{variables}}: pid\n ",
    "ps -p '{{pid}}' | tail -n +2 | wc -l"
  )
  v[:kill] = cli.ask_user(
    "How should I terminate tasks?\n" \
      "  {{variables}}: pid\n ",
    "kill -9 '{{pid}}'"
  )
  v
end