Module: HPC::PBS

Extended by:
Orchestration, TemplateGeneration
Defined in:
lib/rbbt/hpc/pbs.rb

Class Method Summary collapse

Methods included from TemplateGeneration

batch_dir_for_id, batch_options, batch_system_variables, cleanup_environment, coda, exec_cmd, execute, follow_job, header, hold_dependencies, job_queued, job_template, load_conda, load_modules, meta_data, prepare_environment, prepare_submision, rbbt_job_exec_cmd, run_job, sync_environment, wait_for_job

Methods included from Orchestration

accumulate_rules, add_batch_deps, add_config_keys, add_rules_and_consolidate, chain_batches, check_chains, get_chains, get_job_dependencies, get_recursive_job_dependencies, job_batches, job_chains, job_dependencies, job_rules, job_rules, job_workload, merge_rules, orchestrate_job, orchestration_rules, parse_chains, pb, piggyback, prepare_for_execution, task_specific_rules, workflow_rules, workload

Class Method Details

.batch_system ⇒ Object 



9
10
11
 
# File 'lib/rbbt/hpc/pbs.rb', line 9

def self.batch_system
  "PBS"
end

.batch_system_variables ⇒ Object 



13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
 
# File 'lib/rbbt/hpc/pbs.rb', line 13

def self.batch_system_variables
  <<-EOF
let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $PBS_CPUS_PER_TASK )"
MAX_MEMORY="$MAX_MEMORY_DEFAULT"
[ ! -z $PBS_MEM_PER_CPU ] && let MAX_MEMORY="$PBS_MEM_PER_CPU * $PBS_CPUS_PER_TASK" 
[ ! -z $PBS_MEM_PER_NODE ] && MAX_MEMORY="$PBS_MEM_PER_NODE"
export MAX_MEMORY_DEFAULT
export MAX_MEMORY
export BATCH_JOB_ID=$PBS_JOBID
export BATCH_SYSTEM=#{batch_system}

cd ${PBS_O_WORKDIR}
  EOF
end

.header(options = {}) ⇒ Object 



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
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
 
# File 'lib/rbbt/hpc/pbs.rb', line 29

def self.header(options = {})
  options = options.dup

  workdir    = Misc.process_options options, :workdir
  batch_dir  = Misc.process_options options, :batch_dir
  batch_name = Misc.process_options options, :batch_name

  queue      = Misc.process_options options, :queue
      = Misc.process_options options, :account
  time       = Misc.process_options options, :time
  nodes      = Misc.process_options options, :nodes

  # PBS 
  place      = Misc.process_options options, :place, :place => 'scatter'
  system     = Misc.process_options options, :partition
  filesystems = Misc.process_options options, :filesystems

  filesystems = "home" if filesystems.nil?

  filesystems = filesystems * "," if Array === filesystems

  # NOT USED 
  partition  = Misc.process_options options, :partition
  task_cpus  = Misc.process_options options, :task_cpus
  exclusive  = Misc.process_options options, :exclusive
  highmem    = Misc.process_options options, :highmem
  licenses   = Misc.process_options options, :licenses
  constraint = Misc.process_options options, :constraint
  gres       = Misc.process_options options, :gres

  constraint     = [constraint, "highmem"].compact * "&" if highmem

  mem            = Misc.process_options options, :mem
  mem_per_cpu    = Misc.process_options options, :mem_per_cpu

  fout       = File.join(batch_dir, 'std.out')
  ferr       = File.join(batch_dir, 'std.err')

  time = Misc.format_seconds Misc.timespan(time) unless time.include? ":"

  qsub_params = {  "-l filesystems=" => filesystems,
                   "-l system=" => system,
                   "-l select=" => nodes,
                   "-l place=" => place,
                   "-l walltime=" => time,
                   "-q " => queue,
                   "-A " => ,
                   "-o " => fout,
                   "-e " => ferr,
                   "-k doe" => true,
                   # "cpus-per-task" => task_cpus,
                   # "nodes" => nodes,
                   # "time" => time,
                   # "constraint" => constraint,
                   # "exclusive" => exclusive,
                   # "licenses" => licenses,
                   # "gres" => gres,
                   # "mem" => mem,
                   # "mem-per-cpu" => mem_per_cpu,
  }


  header =<<-EOF
#!/bin/bash
  EOF

  qsub_params.each do |name,value|
    next if value.nil? || value == ""
    if TrueClass === value
      header << "#PBS #{name}" << "\n"
    elsif Array === value
      value.each do |v|
        header << "#PBS #{name}\"#{v}\"" << "\n"
      end
    else
      header << "#PBS #{name}\"#{value}\"" << "\n"
    end
  end

  header
end

.job_status(job = nil) ⇒ Object 



165
166
167
168
169
170
171
172
173
174
175
 
# File 'lib/rbbt/hpc/pbs.rb', line 165

def self.job_status(job = nil)
  if job.nil?
    CMD.cmd("qstat").read
  else
    begin
      CMD.cmd("qstat #{job}").read
    rescue
      ""
    end
  end
end

.run_template(batch_dir, dry_run) ⇒ Object 



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
137
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
 
# File 'lib/rbbt/hpc/pbs.rb', line 111

def self.run_template(batch_dir, dry_run)

  fout   = File.join(batch_dir, 'std.out')
  ferr   = File.join(batch_dir, 'std.err')
  fjob   = File.join(batch_dir, 'job.id')
  fdep   = File.join(batch_dir, 'dependencies.list')
  fcfdep = File.join(batch_dir, 'canfail_dependencies.list')
  fexit  = File.join(batch_dir, 'exit.status')
  fsync  = File.join(batch_dir, 'sync.log')
  fcmd   = File.join(batch_dir, 'command.batch')

  return if Open.exists?(fexit)

  Log.info "Issuing PBS file: #{fcmd}"
  Log.debug Open.read(fcmd)

  if File.exist?(fjob)
    job = Open.read(fjob).to_i
  else

    dependencies = Open.read(fdep).split("\n") if File.exist? fdep
    canfail_dependencies = Open.read(fcfdep).split("\n") if File.exist? fcfdep

    normal_dep_str = dependencies && dependencies.any? ? "afterok:" + dependencies * ":" : nil
    canfail_dep_str = canfail_dependencies && canfail_dependencies.any? ? "afterany:" + canfail_dependencies * ":" : nil

    if normal_dep_str.nil? && canfail_dep_str.nil?
      dep_str = ""
    else
      dep_str = '-W depend=' + [normal_dep_str, canfail_dep_str].compact * ","
    end

    cmd = "qsub #{dep_str} '#{fcmd}'"

    if File.exist?(fout)
      return
    elsif dry_run
      STDERR.puts Log.color(:magenta, "To execute run: ") + Log.color(:blue, "squb '#{fcmd}'")
      STDERR.puts Log.color(:magenta, "To monitor progress run (needs local rbbt): ") + Log.color(:blue, "rbbt pbs tail '#{batch_dir}'")
      raise HPC::BATCH_DRY_RUN, batch_dir
    else
      Open.rm fsync
      Open.rm fexit
      Open.rm fout
      Open.rm ferr

      job = CMD.cmd(cmd).read.scan(/\d+/).first.to_i
      Log.debug "SBATCH job id: #{job}"
      Open.write(fjob, job.to_s)
      job
    end
  end
end