Class: OodCore::Job::Adapters::Slurm::Batch Private

Inherits:
Object
  • Object
show all
Defined in:
lib/ood_core/job/adapters/slurm.rb

Overview

This class is part of a private API. You should avoid using this class if possible, as it may be removed or be changed in the future.

Object used for simplified communication with a Slurm batch server

Defined Under Namespace

Classes: Error, SlurmTimeoutError

Constant Summary collapse

UNIT_SEPARATOR =

This constant is part of a private API. You should avoid using this constant if possible, as it may be removed or be changed in the future. 

"\x1F"
RECORD_SEPARATOR =

This constant is part of a private API. You should avoid using this constant if possible, as it may be removed or be changed in the future. 

"\x1E"

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(cluster: nil, bin: nil, conf: nil, bin_overrides: {}, submit_host: "", strict_host_checking: true) ⇒ Batch

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Returns a new instance of Batch.

Parameters:

  • cluster (#to_s, nil) (defaults to: nil) —

    the cluster name

  • conf (#to_s, nil) (defaults to: nil) —

    path to the slurm conf

  • bin (#to_s) (defaults to: nil) —

    path to slurm installation binaries

  • bin_overrides (#to_h) (defaults to: {}) —

    a hash of bin ovverides to be used in job

  • submit_host (#to_s) (defaults to: "") —

    Submits the job on a login node via ssh

  • strict_host_checking (Bool) (defaults to: true) —

    Whether to use strict host checking when ssh to submit_host



100
101
102
103
104
105
106
107
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 100

def initialize(cluster: nil, bin: nil, conf: nil, bin_overrides: {}, submit_host: "", strict_host_checking: true)
  @cluster              = cluster && cluster.to_s
  @conf                 = conf    && Pathname.new(conf.to_s)
  @bin                  = Pathname.new(bin.to_s)
  @bin_overrides        = bin_overrides
  @submit_host          = submit_host.to_s
  @strict_host_checking = strict_host_checking
end

Instance Attribute Details

#bin ⇒ Pathname (readonly)

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

The path to the Slurm client installation binaries

Examples:

For Slurm 10.0.0

my_batch.bin.to_s #=> "/usr/local/slurm/10.0.0/bin

Returns:

  • (Pathname) —

    path to slurm binaries



69
70
71
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 69

def bin
  @bin
end

#bin_overrides ⇒ Object (readonly)

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Optional overrides for Slurm client executables

Examples:

{'sbatch' => '/usr/local/bin/sbatch'}


75
76
77
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 75

def bin_overrides
  @bin_overrides
end

#cluster ⇒ String? (readonly)

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

The cluster of the Slurm batch server

Examples:

CHPC's kingspeak cluster

my_batch.cluster #=> "kingspeak"

Returns:

  • (String, nil) —

    the cluster name



57
58
59
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 57

def cluster
  @cluster
end

#conf ⇒ Pathname? (readonly)

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

The path to the Slurm configuration file

Examples:

For Slurm 10.0.0

my_batch.conf.to_s #=> "/usr/local/slurm/10.0.0/etc/slurm.conf

Returns:

  • (Pathname, nil) —

    path to slurm conf



63
64
65
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 63

def conf
  @conf
end

#strict_host_checking ⇒ Bool (readonly)

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Wheter to use strict host checking when ssh to submit_host

Examples:

false

Returns:

  • (Bool) —

    ; true if empty



85
86
87
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 85

def strict_host_checking
  @strict_host_checking
end

#submit_host ⇒ String (readonly)

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

The login node where the job is submitted via ssh

Examples:

owens.osc.edu

Returns:

  • (String) —

    The login node



80
81
82
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 80

def submit_host
  @submit_host
end

Instance Method Details

#accounts ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 183

def accounts
  user = Etc.getlogin
  args = ['-nP', 'show', 'users', 'withassoc', 'format=account,cluster,partition,qos', 'where', "user=#{user}"]

  [].tap do |accts|
    call('sacctmgr', *args).each_line do |line|
      acct, cluster, queue, qos = line.split('|')
      next if acct.nil? || acct.chomp.empty?

      args = {
        name: acct,
        qos: qos.to_s.chomp.split(','),
        cluster: cluster,
        queue: queue.to_s.empty? ? nil : queue
      }
      info = OodCore::Job::AccountInfo.new(**args) unless acct.nil?
      accts << info unless acct.nil?
    end
  end
end

#all_sinfo_node_fields ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



376
377
378
379
380
381
382
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 376

def all_sinfo_node_fields
  {
    procs: '%c',
    name: '%n',
    features: '%f'
  }
end

#all_squeue_fields ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Fields requested from a formatted `squeue` call Note that the order of these fields is important



272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 272

def all_squeue_fields
  {
    account: "%a",
    job_id: "%A",
    exec_host: "%B",
    min_cpus: "%c",
    cpus: "%C",
    min_tmp_disk: "%d",
    nodes: "%D",
    end_time: "%e",
    dependency: "%E",
    features: "%f",
    array_job_id: "%F",
    group_name: "%g",
    group_id: "%G",
    over_subscribe: "%h",
    sockets_per_node: "%H",
    array_job_task_id: "%i",
    cores_per_socket: "%I",
    job_name: "%j",
    threads_per_core: "%J",
    comment: "%k",
    array_task_id: "%K",
    time_limit: "%l",
    time_left: "%L",
    min_memory: "%m",
    time_used: "%M",
    req_node: "%n",
    node_list: "%N",
    command: "%o",
    contiguous: "%O",
    qos: "%q",
    partition: "%P",
    priority: "%Q",
    reason: "%r",
    start_time: "%S",
    state_compact: "%t",
    state: "%T",
    user: "%u",
    user_id: "%U",
    reservation: "%v",
    submit_time: "%V",
    wckey: "%w",
    licenses: "%W",
    excluded_nodes: "%x",
    core_specialization: "%X",
    nice: "%y",
    scheduled_nodes: "%Y",
    sockets_cores_threads: "%z",
    work_dir: "%Z",
    gres: "%b",  # must come at the end to fix a bug with Slurm 18
  }
end

#delete_job(id) ⇒ void

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

This method returns an undefined value.

Delete a specified job from batch server

Examples:

Delete job “1234”

my_batch.delete_job("1234")

Parameters:

  • id (#to_s) —

    the id of the job

Raises:

  • (Error) —

    if `scancel` command exited unsuccessfully



254
255
256
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 254

def delete_job(id)
  call("scancel", id.to_s)
end

#get_cluster_info ⇒ ClusterInfo

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Get a ClusterInfo object containing information about the given cluster

Returns:



111
112
113
114
115
116
117
118
119
120
121
122
123
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 111

def get_cluster_info
  node_cpu_info = call("sinfo", "-aho %A/%D/%C").strip.split('/')
  gres_length = call("sinfo", "-o %G").lines.map(&:strip).map(&:length).max + 2
  gres_lines = call("sinfo", "-ahNO ,nodehost,gres:#{gres_length},gresused:#{gres_length}")
               .lines.uniq.map(&:split)
  ClusterInfo.new(active_nodes: node_cpu_info[0].to_i,
                  total_nodes: node_cpu_info[2].to_i,
                  active_processors: node_cpu_info[3].to_i,
                  total_processors: node_cpu_info[6].to_i,
                  active_gpus: gres_lines.sum { |line| Slurm.gpus_from_gres(line[2]) },
                  total_gpus: gres_lines.sum { |line| Slurm.gpus_from_gres(line[1]) }
  )
end

#get_jobs(id: "", owner: nil, attrs: nil) ⇒ Array<Hash>

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Get a list of hashes detailing each of the jobs on the batch server

Examples:

Status info for all jobs

my_batch.get_jobs
#=>
#[
#  {
#    :account => "account",
#    :job_id => "my_job",
#    ...
#  },
#  {
#    :account => "account",
#    :job_id => "my_other_job",
#    ...
#  },
#  ...
#]

Parameters:

  • id (#to_s) (defaults to: "") —

    the id of the job

  • owner (String) (defaults to: nil) —

    the owner(s) of the job

  • attrs (Array<Symbol>, nil) (defaults to: nil) —

    list of attributes request when calling squeue

Returns:

  • (Array<Hash>) —

    list of details for jobs

Raises:

  • (Error) —

    if `squeue` command exited unsuccessfully



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
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 147

def get_jobs(id: "", owner: nil, attrs: nil)
  fields = squeue_fields(attrs)
  args = squeue_args(id: id, owner: owner, options: fields.values)

  #TODO: switch mock of Open3 to be the squeue mock script
  # then you can use that for performance metrics
  StringIO.open(call("squeue", *args)) do |output|
    advance_past_squeue_header!(output)

    jobs = []
    output.each_line(RECORD_SEPARATOR) do |line|
      # TODO: once you can do performance metrics you can test zip against some other tools
      # or just small optimizations
      # for example, fields is ALREADY A HASH and we are setting the VALUES to
      # "line.strip.split(unit_separator)" array
      #
      # i.e. store keys in an array, do Hash[[keys, values].transpose]
      #
      # or
      #
      # job = {}
      # keys.each_with_index { |key, index| [key] = values[index] }
      # jobs << job
      #
      # assuming keys and values are same length! if not we have an error!
      line = line.encode('UTF-8', invalid: :replace, undef: :replace)
      values = line.chomp(RECORD_SEPARATOR).strip.split(UNIT_SEPARATOR)
      jobs << Hash[fields.keys.zip(values)] unless values.empty?
    end
    jobs
  end
rescue SlurmTimeoutError
  # TODO: could use a log entry here
  return [{ id: id, state: 'undetermined' }]
end

#hold_job(id) ⇒ void

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

This method returns an undefined value.

Put a specified job on hold

Examples:

Put job “1234” on hold

my_batch.hold_job("1234")

Parameters:

  • id (#to_s) —

    the id of the job

Raises:

  • (Error) —

    if `scontrol` command exited unsuccessfully



234
235
236
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 234

def hold_job(id)
  call("scontrol", "hold", id.to_s)
end

#nodes ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 384

def nodes
  args = all_sinfo_node_fields.values.join(UNIT_SEPARATOR)
  output = call('sinfo', '-ho', "#{RECORD_SEPARATOR}#{args}")

  output.each_line(RECORD_SEPARATOR).map do |line|
    values = line.chomp(RECORD_SEPARATOR).strip.split(UNIT_SEPARATOR)

    next if values.empty?

    data = Hash[all_sinfo_node_fields.keys.zip(values)]
    data[:name] = data[:name].to_s.split(',').first
    data[:features] = data[:features].to_s.split(',')
    NodeInfo.new(**data)
  end.compact
end

#queues ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



366
367
368
369
370
371
372
373
374
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 366

def queues
  info_raw = call('scontrol', 'show', 'part', '-o')

  [].tap do |ret_arr|
    info_raw.each_line do |line|
      ret_arr << str_to_queue_info(line)
    end
  end
end

#release_job(id) ⇒ void

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

This method returns an undefined value.

Release a specified job that is on hold

Examples:

Release job “1234” from on hold

my_batch.release_job("1234")

Parameters:

  • id (#to_s) —

    the id of the job

Raises:

  • (Error) —

    if `scontrol` command exited unsuccessfully



244
245
246
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 244

def release_job(id)
  call("scontrol", "release", id.to_s)
end

#sacct_info(job_ids, states, from, to, show_steps) ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 400

def sacct_info(job_ids, states, from, to, show_steps)
  # https://slurm.schedmd.com/sacct.html
  fields = sacct_info_fields
  args = ['-P'] # Output will be delimited
  args.concat ['--delimiter', UNIT_SEPARATOR]
  args.concat ['-n'] # No header
  args.concat ['--units', 'G'] # Memory units in GB
  args.concat ['--allocations'] unless show_steps # Show statistics relevant to the job, not taking steps into consideration
  args.concat ['-o', fields.values.join(',')] # Required data
  args.concat ['--state', states.join(',')] unless states.empty? # Filter by these states
  args.concat ['-j', job_ids.join(',')] unless job_ids.empty? # Filter by these job ids
  args.concat ['-S', from] if from # Filter from This date
  args.concat ['-E', to] if to # Filter until this date

  jobs_info = []
  StringIO.open(call('sacct', *args)) do |output|
    output.each_line do |line|
      # Replace blank values with nil
      values = line.strip.split(UNIT_SEPARATOR).map{ |value| value.to_s.empty? ? nil : value }
      jobs_info << Hash[fields.keys.zip(values)] unless values.empty?
    end
  end
  jobs_info
end

#sacct_info_fields ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Job info fields requested from a formatted `sacct` call



327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 327

def sacct_info_fields
  {
    # The user name of the user who ran the job.
    user: 'User',
    # The group name of the user who ran the job.
    group_name: 'Group',
    # Job Id for reference
    job_id: 'JobId',
    # The name of the job or job step
    job_name: 'JobName',
    # The job's elapsed time.
    elapsed: 'Elapsed',
    # Minimum required memory for the job
    req_mem: 'ReqMem',
    # Count of allocated CPUs
    alloc_cpus: 'AllocCPUS',
    # Number of requested CPUs.
    req_cpus: 'ReqCPUS',
    # What the timelimit was/is for the job
    time_limit: 'Timelimit',
    # Displays the job status, or state
    state: 'State',
    # The sum of the SystemCPU and UserCPU time used by the job or job step
    total_cpu: 'TotalCPU',
    # Maximum resident set size of all tasks in job.
    max_rss: 'MaxRSS',
    # Identifies the partition on which the job ran.
    partition: 'Partition',
    # The time the job was submitted. In the same format as End.
    submit_time: 'Submit',
    # Initiation time of the job. In the same format as End.
    start_time: 'Start',
    # Termination time of the job.
    end: 'End',
    # Trackable resources. These are the minimum resource counts requested by the job/step at submission time.
    gres: 'ReqTRES'
  }
end

#squeue_args(id: "", owner: nil, options: []) ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

TODO: write some barebones test for this? like 2 options and id or no id



220
221
222
223
224
225
226
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 220

def squeue_args(id: "", owner: nil, options: [])
  args  = ["--all", "--states=all", "--noconvert"]
  args.concat ["-o", "#{RECORD_SEPARATOR}#{options.join(UNIT_SEPARATOR)}"]
  args.concat ["-u", owner.to_s] unless owner.to_s.empty?
  args.concat ["-j", id.to_s] unless id.to_s.empty?
  args
end

#squeue_fields(attrs) ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



204
205
206
207
208
209
210
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 204

def squeue_fields(attrs)
  if attrs.nil?
    all_squeue_fields
  else
    all_squeue_fields.slice(*squeue_attrs_for_info_attrs(Array.wrap(attrs) + squeue_required_fields))
  end
end

#squeue_required_fields ⇒ Object

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future. 



212
213
214
215
216
217
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 212

def squeue_required_fields
  #TODO: does this need to include ::array_job_task_id?
  #TODO: does it matter that order of the output can vary depending on the arguments and if "squeue_required_fields" are included?
  # previously the order was "fields.keys"; i don't think it does
  [:job_id, :state_compact]
end

#submit_string(str, args: [], env: {}) ⇒ String

This method is part of a private API. You should avoid using this method if possible, as it may be removed or be changed in the future.

Submit a script expanded as a string to the batch server

Parameters:

  • str (#to_s) —

    script as a string

  • args (Array<#to_s>) (defaults to: []) —

    arguments passed to `sbatch` command

  • env (Hash{#to_s => #to_s}) (defaults to: {}) —

    environment variables set

Returns:

  • (String) —

    the id of the job that was created

Raises:

  • (Error) —

    if `sbatch` command exited unsuccessfully



264
265
266
267
268
 
# File 'lib/ood_core/job/adapters/slurm.rb', line 264

def submit_string(str, args: [], env: {})
  args = args.map(&:to_s) + ["--parsable"]
  env = env.to_h.each_with_object({}) { |(k, v), h| h[k.to_s] = v.to_s }
  call("sbatch", *args, env: env, stdin: str.to_s).strip.split(";").first
end