rbbt-util 5.29.2 → 5.30.3
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc/orchestrate.rb +12 -1
- data/lib/rbbt/hpc/slurm.rb +56 -24
- data/lib/rbbt/persist.rb +4 -0
- data/lib/rbbt/persist/tsv/adapter.rb +44 -13
- data/lib/rbbt/tsv.rb +3 -2
- data/lib/rbbt/util/cmd.rb +6 -1
- data/lib/rbbt/util/misc/options.rb +0 -42
- data/lib/rbbt/util/procpath.rb +49 -0
- data/lib/rbbt/workflow/step/accessor.rb +3 -4
- data/lib/rbbt/workflow/step/run.rb +2 -4
- data/lib/rbbt/workflow/usage.rb +1 -1
- data/share/rbbt_commands/slurm/clean +165 -0
- data/share/rbbt_commands/slurm/list +174 -95
- data/share/rbbt_commands/slurm/orchestrate +3 -2
- data/share/rbbt_commands/slurm/task +1 -0
- data/share/rbbt_commands/tsv/slice +3 -3
- data/share/rbbt_commands/workflow/info +1 -1
- data/share/rbbt_commands/workflow/task +27 -7
- data/share/rbbt_commands/workflow/write_info +52 -0
- data/test/rbbt/util/test_procpath.rb +23 -0
- metadata +7 -2
@@ -0,0 +1,49 @@
|
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1
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+
require 'rbbt/util/cmd'
|
2
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+
module ProcPath
|
3
|
+
CMD.tool :procpath do
|
4
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+
'pip install procpath'
|
5
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+
end
|
6
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+
|
7
|
+
def self.record(pid, path, options = {})
|
8
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+
IndiferentHash.setup(options)
|
9
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+
options = Misc.add_defaults options, "interval" => 30
|
10
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+
|
11
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+
cmd_options = %w(interval recnum reevalnum).inject({}){|acc,k| acc[k] = options[k]; acc}
|
12
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+
|
13
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+
Log.debug "ProcPath recording #{pid} in #{path} (#{Misc.fingerprint options})"
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14
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+
procpath_thread = Thread.new do
|
15
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+
begin
|
16
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+
procpath_pid = CMD.cmd_pid(:procpath, "record --database-file '#{path}' '$..children[?(@.stat.pid == #{pid})]'", cmd_options.merge(:nofail => true, :add_option_dashes => true))
|
17
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+
rescue Exception
|
18
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+
Log.exceptions $!
|
19
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+
Process.kill "INT", procpath_pid
|
20
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+
end
|
21
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+
end
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22
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+
|
23
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+
procpath_thread.report_on_exception = false
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24
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+
|
25
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+
Process.wait pid.to_i
|
26
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+
procpath_thread.raise Interrupt
|
27
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+
end
|
28
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+
|
29
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+
def self.plot(path, output, options = {})
|
30
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+
IndiferentHash.setup(options)
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31
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+
options = Misc.add_defaults options, "query-name" => 'rss', 'epsilon' => 0.5, "moving-average-window" => 10
|
32
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+
|
33
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+
cmd_options = %w(query-name epsilon monitor-average-window title logarithmic after before custom-query-file custom-value-expr).inject({}){|acc,k| acc[k] = options[k]; acc}
|
34
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+
CMD.cmd_log(:procpath, "plot --database-file '#{path}' --plot-file '#{output}' ", cmd_options.merge(:nofail => true, :add_option_dashes => true))
|
35
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+
end
|
36
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+
|
37
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+
def self.monitor(pid, path)
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38
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+
database, options_str = path.split("#")
|
39
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+
options = options_str.nil? ? {} : Misc.string2hash(options_str)
|
40
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+
|
41
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+
database = File.expand_path database
|
42
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+
Log.low "ProcPath monitor #{pid} in #{database} (#{Misc.fingerprint options})"
|
43
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+
|
44
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+
ProcPath.record(pid, database + '.sqlite3', options)
|
45
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+
ProcPath.plot(database + '.sqlite3', database + '.cpu.svg', options.merge("query-name" => 'cpu'))
|
46
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+
ProcPath.plot(database + '.sqlite3', database + '.rss.svg', options.merge("query-name" => 'rss'))
|
47
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+
end
|
48
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+
end
|
49
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+
|
@@ -505,8 +505,8 @@ class Step
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505
505
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|
506
506
|
def running?
|
507
507
|
return false if ! (started? || status == :ending)
|
508
|
-
|
509
|
-
|
508
|
+
return nil unless Open.exist?(self.pid_file)
|
509
|
+
pid = Open.read(self.pid_file).to_i
|
510
510
|
|
511
511
|
return false if done? or error? or aborted?
|
512
512
|
|
@@ -530,8 +530,7 @@ class Step
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|
530
530
|
end
|
531
531
|
|
532
532
|
def nopid?
|
533
|
-
|
534
|
-
! pid && ! (status.nil? || status == :aborted || status == :done || status == :error || status == :cleaned)
|
533
|
+
! Open.exists?(pid_file) && ! (status.nil? || status == :aborted || status == :done || status == :error || status == :cleaned)
|
535
534
|
end
|
536
535
|
|
537
536
|
def aborted?
|
@@ -373,7 +373,6 @@ class Step
|
|
373
373
|
Log.exception $!
|
374
374
|
ensure
|
375
375
|
Step.purge_stream_cache
|
376
|
-
set_info :pid, nil
|
377
376
|
Open.rm pid_file if Open.exist?(pid_file)
|
378
377
|
end
|
379
378
|
end
|
@@ -388,7 +387,6 @@ class Step
|
|
388
387
|
_clean_finished
|
389
388
|
rescue
|
390
389
|
stop_dependencies
|
391
|
-
set_info :pid, nil
|
392
390
|
Open.rm pid_file if Open.exist?(pid_file)
|
393
391
|
end
|
394
392
|
end
|
@@ -449,7 +447,7 @@ class Step
|
|
449
447
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ensure
|
450
448
|
no_load = false unless IO === result
|
451
449
|
Open.rm pid_file if Open.exist?(pid_file) unless no_load
|
452
|
-
set_info :pid, nil unless no_load
|
450
|
+
#set_info :pid, nil unless no_load
|
453
451
|
end
|
454
452
|
end
|
455
453
|
|
@@ -559,7 +557,7 @@ class Step
|
|
559
557
|
RbbtSemaphore.post_semaphore(semaphore) if semaphore
|
560
558
|
Kernel.exit! -1
|
561
559
|
end
|
562
|
-
set_info :pid, nil
|
560
|
+
#set_info :pid, nil
|
563
561
|
ensure
|
564
562
|
RbbtSemaphore.post_semaphore(semaphore) if semaphore
|
565
563
|
end
|
data/lib/rbbt/workflow/usage.rb
CHANGED
@@ -57,7 +57,7 @@ module Task
|
|
57
57
|
puts Log.color(:magenta, "Input select options")
|
58
58
|
puts
|
59
59
|
selects.collect{|p| p}.uniq.each do |input,options|
|
60
|
-
puts Log.color(:blue, input.to_s + ": ") << Misc.format_paragraph(options.collect{|o| o.to_s} * ", ") << "\n"
|
60
|
+
puts Log.color(:blue, input.to_s + ": ") << Misc.format_paragraph(options.collect{|o| Array === o ? o.first.to_s : o.to_s} * ", ") << "\n"
|
61
61
|
puts unless Log.compact
|
62
62
|
end
|
63
63
|
puts
|
@@ -0,0 +1,165 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
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+
|
3
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+
require 'rbbt-util'
|
4
|
+
require 'rbbt/util/simpleopt'
|
5
|
+
|
6
|
+
#$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
|
7
|
+
|
8
|
+
options = SOPT.setup <<EOF
|
9
|
+
|
10
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+
Clean error or aborted jobs
|
11
|
+
|
12
|
+
$ rbbt mnl [options]
|
13
|
+
|
14
|
+
-h--help Print this help
|
15
|
+
-d--done Done jobs only
|
16
|
+
-e--error Error jobs only
|
17
|
+
-a--aborted SLURM aboted jobs
|
18
|
+
-j--job* Job ids
|
19
|
+
-s--search* Regular expression
|
20
|
+
-t--tail* Show the last lines of the STDERR
|
21
|
+
-SBP--sbatch_parameters show sbatch parameters
|
22
|
+
-dr--dry_run Do not erase anything
|
23
|
+
EOF
|
24
|
+
|
25
|
+
if options[:help]
|
26
|
+
if defined? rbbt_usage
|
27
|
+
rbbt_usage
|
28
|
+
else
|
29
|
+
puts SOPT.doc
|
30
|
+
end
|
31
|
+
exit 0
|
32
|
+
end
|
33
|
+
|
34
|
+
Log.severity = 4
|
35
|
+
done, error, aborted, jobid, search, tail, sbatch_parameters, dry_run = options.values_at :done, :error, :aborted, :job, :search, :tail, :sbatch_parameters, :dry_run
|
36
|
+
|
37
|
+
workdir = File.expand_path('~/rbbt-slurm')
|
38
|
+
Path.setup(workdir)
|
39
|
+
|
40
|
+
running_jobs = begin
|
41
|
+
squeue_txt = CMD.cmd('squeue').read
|
42
|
+
squeue_txt.split("\n").collect{|l| l.to_i.to_s}
|
43
|
+
rescue
|
44
|
+
Log.warn "Cannot determine if jobs are running, they will seem to be all alive (Job ID in green)"
|
45
|
+
squeue_txt = nil
|
46
|
+
$norunningjobs = true
|
47
|
+
[]
|
48
|
+
end
|
49
|
+
|
50
|
+
if squeue_txt
|
51
|
+
job_nodes = {}
|
52
|
+
squeue_txt.split("\n").each do |line|
|
53
|
+
parts = line.strip.split(/\s+/)
|
54
|
+
job_nodes[parts.first] = parts.last.split(",")
|
55
|
+
end
|
56
|
+
else
|
57
|
+
job_nodes = nil
|
58
|
+
end
|
59
|
+
|
60
|
+
count = 0
|
61
|
+
workdir.glob("**/command.slurm").sort_by{|f| File.mtime(f)}.each do |fcmd|
|
62
|
+
dir = File.dirname(fcmd)
|
63
|
+
|
64
|
+
if m = Open.read(fcmd).match(/#CMD: (.*)/)
|
65
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+
cmd = m[1]
|
66
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+
else
|
67
|
+
cmd = nil
|
68
|
+
end
|
69
|
+
|
70
|
+
if m = Open.read(fcmd).match(/# Run command\n(.*?)\n/im)
|
71
|
+
exe = m[1]
|
72
|
+
else
|
73
|
+
exe = nil
|
74
|
+
end
|
75
|
+
|
76
|
+
if m = Open.read(fcmd).match(/^CONTAINER_DIR=(.*)/)
|
77
|
+
container_home = m[1]
|
78
|
+
else
|
79
|
+
container_home = nil
|
80
|
+
end
|
81
|
+
|
82
|
+
|
83
|
+
if File.exists?(fid = File.join(dir, 'job.id'))
|
84
|
+
id = Open.read(fid).chomp
|
85
|
+
else
|
86
|
+
id = nil
|
87
|
+
end
|
88
|
+
|
89
|
+
if File.exists?(fstatus = File.join(dir, 'exit.status'))
|
90
|
+
exit_status = Open.read(fstatus).to_i
|
91
|
+
else
|
92
|
+
exit_status = nil
|
93
|
+
end
|
94
|
+
|
95
|
+
if File.exists?(fstatus = File.join(dir, 'job.status'))
|
96
|
+
nodes = Open.read(fstatus).split("\n").last.split(/\s+/).last.split(",")
|
97
|
+
elsif job_nodes[id]
|
98
|
+
nodes = job_nodes[id]
|
99
|
+
else
|
100
|
+
nodes = []
|
101
|
+
end
|
102
|
+
|
103
|
+
if File.exists?(File.join(dir, 'std.out'))
|
104
|
+
outt = File.mtime File.join(dir, 'std.out')
|
105
|
+
errt = File.mtime File.join(dir, 'std.err')
|
106
|
+
time_diff = Time.now - [outt, errt].max
|
107
|
+
end
|
108
|
+
|
109
|
+
fdep = File.join(dir, 'dependencies.list')
|
110
|
+
deps = Open.read(fdep).split("\n") if File.exists?(fdep)
|
111
|
+
|
112
|
+
fcadep = File.join(dir, 'canfail_dependencies.list')
|
113
|
+
cadeps = Open.read(fcadep).split("\n") if File.exists?(fcadep)
|
114
|
+
|
115
|
+
aborted = error = true if aborted.nil? && error.nil?
|
116
|
+
if done || error || aborted || running || queued || jobid || search
|
117
|
+
select = false
|
118
|
+
select = true if done && exit_status && exit_status.to_i == 0
|
119
|
+
select = true if error && exit_status && exit_status.to_i != 0
|
120
|
+
select = true if aborted && (exit_status.nil? && ! running_jobs.include?(id))
|
121
|
+
select = select && jobid.split(",").include?(id) if jobid
|
122
|
+
select = select && cmd.match(/#{search}/) if search
|
123
|
+
next unless select
|
124
|
+
end
|
125
|
+
|
126
|
+
|
127
|
+
puts Log.color(:yellow, "**ERASING**")
|
128
|
+
puts Log.color :blue, dir
|
129
|
+
puts Log.color(:magenta, "Creation: ") << File.mtime(File.join(dir, 'command.slurm')).to_s
|
130
|
+
puts Log.color(:magenta, "Done: ") << File.mtime(File.join(dir, 'exit.status')).to_s if File.exist?(File.join(dir, 'exit.status'))
|
131
|
+
puts Log.color(:magenta, "Exec: ") << (exe || "Missing")
|
132
|
+
puts Log.color(:magenta, "CMD: ") << (Log.color(:yellow, cmd) || "Missing")
|
133
|
+
puts Log.color(:magenta, "HOME: ") << Log.color(:yellow, container_home) if container_home
|
134
|
+
puts Log.color(:magenta, "Job ID: ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" : (running_jobs.include?(id) || $norunningjobs ? Log.color(:green, id) : Log.color(:red, id) ))
|
135
|
+
puts Log.color(:magenta, "Dependencies: ") << deps * ", " if deps
|
136
|
+
puts Log.color(:magenta, "Dependencies (can fail): ") << cadeps * ", " if cadeps
|
137
|
+
puts Log.color(:magenta, "Nodes: ") << nodes * ", "
|
138
|
+
puts Log.color(:magenta, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)")
|
139
|
+
|
140
|
+
if options[:sbatch_parameters]
|
141
|
+
puts Log.color(:magenta, "SBATCH parameters: ")
|
142
|
+
puts Log.color :blue, CMD.cmd('grep "^#SBATCH" |tail -n +6', :in => Open.read(fcmd)).read.strip
|
143
|
+
end
|
144
|
+
|
145
|
+
if tail && File.exists?(File.join(dir, 'std.err'))
|
146
|
+
if exit_status && exit_status != 0
|
147
|
+
puts Log.color(:magenta, "First error or exception found: ")
|
148
|
+
puts CMD.cmd("grep -i -w 'error\\|[a-z]*exception' #{File.join(dir, 'std.err')} -A #{tail.to_i} |head -n #{tail.to_i}", :no_fail => true).read
|
149
|
+
elsif exit_status
|
150
|
+
puts Log.color(:magenta, "Completed jobs: ")
|
151
|
+
puts CMD.cmd("grep -i -w 'Completed step' #{File.join(dir, 'std.err')} | grep -v 'Retrying dep.' | tail -n #{tail.to_i}", :no_fail => true).read
|
152
|
+
else
|
153
|
+
puts Log.color(:magenta, "Log tail: ")
|
154
|
+
puts CMD.cmd("tail -n #{tail.to_i} #{File.join(dir, 'std.err')}").read
|
155
|
+
end
|
156
|
+
end
|
157
|
+
|
158
|
+
count += 1
|
159
|
+
|
160
|
+
Open.rm_rf dir unless dry_run
|
161
|
+
end
|
162
|
+
|
163
|
+
puts
|
164
|
+
puts "Found #{count} jobs"
|
165
|
+
|
@@ -20,15 +20,18 @@ $ rbbt mnl [options]
|
|
20
20
|
-j--job* Job ids
|
21
21
|
-s--search* Regular expression
|
22
22
|
-t--tail* Show the last lines of the STDERR
|
23
|
+
-SBP--sbatch_parameters show sbatch parameters
|
24
|
+
-PERF--procpath_performance show Procpath performance summary
|
25
|
+
-sacct--sacct_peformance show sacct performance summary
|
23
26
|
EOF
|
24
27
|
|
25
28
|
if options[:help]
|
26
|
-
|
27
|
-
|
28
|
-
|
29
|
-
|
30
|
-
|
31
|
-
|
29
|
+
if defined? rbbt_usage
|
30
|
+
rbbt_usage
|
31
|
+
else
|
32
|
+
puts SOPT.doc
|
33
|
+
end
|
34
|
+
exit 0
|
32
35
|
end
|
33
36
|
|
34
37
|
Log.severity = 4
|
@@ -38,101 +41,177 @@ workdir = File.expand_path('~/rbbt-slurm')
|
|
38
41
|
Path.setup(workdir)
|
39
42
|
|
40
43
|
running_jobs = begin
|
41
|
-
|
44
|
+
squeue_txt = CMD.cmd('squeue').read
|
45
|
+
squeue_txt.split("\n").collect{|l| l.to_i.to_s}
|
42
46
|
rescue
|
43
|
-
|
44
|
-
|
45
|
-
|
47
|
+
Log.warn "Cannot determine if jobs are running, they will seem to be all alive (Job ID in green)"
|
48
|
+
squeue_txt = nil
|
49
|
+
$norunningjobs = true
|
50
|
+
[]
|
46
51
|
end
|
47
52
|
|
53
|
+
if squeue_txt
|
54
|
+
job_nodes = {}
|
55
|
+
squeue_txt.split("\n").each do |line|
|
56
|
+
parts = line.strip.split(/\s+/)
|
57
|
+
job_nodes[parts.first] = parts.last.split(",")
|
58
|
+
end
|
59
|
+
else
|
60
|
+
job_nodes = nil
|
61
|
+
end
|
62
|
+
|
48
63
|
count = 0
|
49
64
|
workdir.glob("**/command.slurm").sort_by{|f| File.mtime(f)}.each do |fcmd|
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
65
|
+
dir = File.dirname(fcmd)
|
66
|
+
|
67
|
+
if m = Open.read(fcmd).match(/#CMD: (.*)/)
|
68
|
+
cmd = m[1]
|
69
|
+
else
|
70
|
+
cmd = nil
|
71
|
+
end
|
72
|
+
|
73
|
+
if m = Open.read(fcmd).match(/# Run command\n(.*?)\n/im)
|
74
|
+
exe = m[1].sub('step_path=$(','')
|
75
|
+
else
|
76
|
+
exe = nil
|
77
|
+
end
|
78
|
+
|
79
|
+
if m = Open.read(fcmd).match(/^CONTAINER_DIR=(.*)/)
|
80
|
+
container_home = m[1]
|
81
|
+
else
|
82
|
+
container_home = nil
|
83
|
+
end
|
84
|
+
|
85
|
+
|
86
|
+
if File.exists?(fid = File.join(dir, 'job.id'))
|
87
|
+
id = Open.read(fid).chomp
|
88
|
+
else
|
89
|
+
id = nil
|
90
|
+
end
|
91
|
+
|
92
|
+
if File.exists?(fstatus = File.join(dir, 'exit.status'))
|
93
|
+
exit_status = Open.read(fstatus).to_i
|
94
|
+
else
|
95
|
+
exit_status = nil
|
96
|
+
end
|
97
|
+
|
98
|
+
if File.exists?(fstatus = File.join(dir, 'job.status'))
|
99
|
+
nodes = Open.read(fstatus).split("\n").last.split(/\s+/).last.split(",")
|
100
|
+
elsif job_nodes[id]
|
101
|
+
nodes = job_nodes[id]
|
102
|
+
else
|
103
|
+
nodes = []
|
104
|
+
end
|
105
|
+
|
106
|
+
if File.exists?(File.join(dir, 'std.out'))
|
107
|
+
outt = File.mtime File.join(dir, 'std.out')
|
108
|
+
errt = File.mtime File.join(dir, 'std.err')
|
109
|
+
time_diff = Time.now - [outt, errt].max
|
110
|
+
end
|
111
|
+
|
112
|
+
fdep = File.join(dir, 'dependencies.list')
|
113
|
+
deps = Open.read(fdep).split("\n") if File.exists?(fdep)
|
114
|
+
|
115
|
+
fcadep = File.join(dir, 'canfail_dependencies.list')
|
116
|
+
cadeps = Open.read(fcadep).split("\n") if File.exists?(fcadep)
|
117
|
+
|
118
|
+
if done || error || aborted || running || queued || jobid || search
|
119
|
+
select = false
|
120
|
+
select = true if done && exit_status == 0
|
121
|
+
select = true if error && exit_status && exit_status != 0
|
122
|
+
select = true if aborted && (exit_status.nil? && ! running_jobs.include?(id))
|
123
|
+
select = true if queued && deps && (running_jobs & deps).any?
|
124
|
+
select = true if running && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
|
125
|
+
select = true if jobid && jobid.split(",").include?(id)
|
126
|
+
select = true if search && cmd.match(/#{search}/)
|
127
|
+
next unless select
|
128
|
+
end
|
129
|
+
|
130
|
+
|
131
|
+
puts Log.color :blue, dir
|
132
|
+
puts Log.color(:magenta, "Creation: ") << File.mtime(File.join(dir, 'command.slurm')).to_s
|
133
|
+
puts Log.color(:magenta, "Done: ") << File.mtime(File.join(dir, 'exit.status')).to_s if File.exist?(File.join(dir, 'exit.status'))
|
134
|
+
puts Log.color(:magenta, "Exec: ") << (exe || "Missing")
|
135
|
+
puts Log.color(:magenta, "CMD: ") << (Log.color(:yellow, cmd) || "Missing")
|
136
|
+
puts Log.color(:magenta, "HOME: ") << Log.color(:yellow, container_home) if container_home
|
137
|
+
puts Log.color(:magenta, "Job ID: ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) + " (#{ id })" : (running_jobs.include?(id) || $norunningjobs ? Log.color(:green, id) : Log.color(:red, id) ))
|
138
|
+
puts Log.color(:magenta, "Dependencies: ") << deps * ", " if deps
|
139
|
+
puts Log.color(:magenta, "Dependencies (can fail): ") << cadeps * ", " if cadeps
|
140
|
+
puts Log.color(:magenta, "Nodes: ") << nodes * ", "
|
141
|
+
puts Log.color(:magenta, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)")
|
142
|
+
|
143
|
+
if options[:sbatch_parameters]
|
144
|
+
puts Log.color(:magenta, "SBATCH parameters: ")
|
145
|
+
text = CMD.cmd('grep "^#SBATCH" |tail -n +6', :in => Open.read(fcmd)).read.strip
|
146
|
+
lines = text.split("\n").collect{|line| header, _sep, value = line.partition(/\s+/); Log.color(:yellow, header + ": ") + value}
|
147
|
+
puts Log.color :yellow, lines * "\n"
|
148
|
+
end
|
149
|
+
|
150
|
+
fprocpath = File.join(dir, 'procpath.sqlite3')
|
151
|
+
if options[:procpath_performance] && Open.exists?(fprocpath)
|
152
|
+
puts Log.color(:magenta, "Procpath summary: ")
|
153
|
+
require 'rbbt/tsv/csv'
|
154
|
+
meta = TSV.csv(CMD.cmd("sqlite3 -header -csv #{fprocpath} 'select * from meta;' "))
|
155
|
+
perf = TSV.csv(CMD.cmd("sqlite3 -header -csv #{fprocpath} 'select * from record;' "))
|
156
|
+
|
157
|
+
page_size = meta["page_size"].first.to_f
|
158
|
+
clock_ticks = meta["clock_ticks"].first.to_f
|
159
|
+
|
160
|
+
cpu_average = {}
|
161
|
+
rss_average = {}
|
162
|
+
perf.through :key, ["ts", 'stat_pid', "stat_utime", "stat_stime", "stat_cutime", "stat_cstime", "stat_rss"] do |k, values|
|
163
|
+
time, stat_pid, ucpu, scpu, ccpu, cscpu, rss = values
|
164
|
+
time = time.to_f
|
165
|
+
|
166
|
+
cpu = Misc.sum([ucpu, scpu].collect{|v| v.to_f})
|
167
|
+
cpu_average[stat_pid] ||= {}
|
168
|
+
cpu_average[stat_pid][time] ||= []
|
169
|
+
cpu_average[stat_pid][time] << cpu.to_f
|
170
|
+
rss_average[time] ||= []
|
171
|
+
rss_average[time] << rss.to_f * page_size
|
172
|
+
end
|
173
|
+
|
174
|
+
ticks = 0
|
175
|
+
cpu_average.each do |stat_pid, cpu_average_pid|
|
176
|
+
start = cpu_average_pid.keys.sort.first
|
177
|
+
eend = cpu_average_pid.keys.sort.last
|
178
|
+
ticks += Misc.sum(cpu_average_pid[eend]) - Misc.sum(cpu_average_pid[start])
|
179
|
+
end
|
180
|
+
start = rss_average.keys.sort.first
|
181
|
+
eend = rss_average.keys.sort.last
|
182
|
+
time_elapsed = eend - start
|
183
|
+
puts Log.color(:yellow, "CPU average: ") + "%.2f" % ( ticks / clock_ticks / time_elapsed * 100).to_s
|
184
|
+
puts Log.color(:yellow, "RSS average: ") + "%.2f GB" % Misc.mean(rss_average.collect{|t,l| Misc.sum(l) / (1024 * 1024 * 1024)}).to_s
|
185
|
+
|
186
|
+
end
|
187
|
+
|
188
|
+
if options[:sacct_peformance]
|
189
|
+
begin
|
190
|
+
tsv = TSV.open(CMD.cmd("sacct -j #{id} -o 'jobid,AveRSS,MaxRSS,MaxDiskRead,MaxDiskWrite' -P|grep 'JobID\\|\.batch'"), :header_hash => '', :sep => "|", :type => :list)
|
191
|
+
values = tsv[tsv.keys.first]
|
192
|
+
if values.compact.any?
|
193
|
+
puts Log.color(:magenta, "SACCT performance: ")
|
194
|
+
puts values.zip(values.fields).collect{|v,t| Log.color(:yellow, t + ": ") + v.to_s } * "\n"
|
56
195
|
end
|
57
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
66
|
-
|
67
|
-
|
68
|
-
|
69
|
-
|
70
|
-
|
71
|
-
|
72
|
-
|
73
|
-
|
74
|
-
|
75
|
-
|
76
|
-
|
77
|
-
if File.exists?(fstatus = File.join(dir, 'exit.status'))
|
78
|
-
exit_status = Open.read(fstatus).to_i
|
79
|
-
else
|
80
|
-
exit_status = nil
|
81
|
-
end
|
82
|
-
|
83
|
-
if File.exists?(fstatus = File.join(dir, 'job.status'))
|
84
|
-
nodes = Open.read(fstatus).split("\n").last.split(/\s+/).last.split(",")
|
85
|
-
else
|
86
|
-
nodes = []
|
87
|
-
end
|
88
|
-
|
89
|
-
if File.exists?(File.join(dir, 'std.out'))
|
90
|
-
outt = File.mtime File.join(dir, 'std.out')
|
91
|
-
errt = File.mtime File.join(dir, 'std.err')
|
92
|
-
time_diff = Time.now - [outt, errt].max
|
93
|
-
end
|
94
|
-
|
95
|
-
fdep = File.join(dir, 'dependencies.list')
|
96
|
-
deps = Open.read(fdep).split("\n") if File.exists?(fdep)
|
97
|
-
|
98
|
-
if done || error || aborted || running || queued || jobid || search
|
99
|
-
select = false
|
100
|
-
select = true if done && exit_status == 0
|
101
|
-
select = true if error && exit_status && exit_status != 0
|
102
|
-
select = true if aborted && (exit_status.nil? && ! running_jobs.include?(id))
|
103
|
-
select = true if queued && deps && (running_jobs & deps).any?
|
104
|
-
select = true if running && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
|
105
|
-
select = true if jobid && jobid.split(",").include?(id)
|
106
|
-
select = true if search && cmd.match(/#{search}/)
|
107
|
-
next unless select
|
108
|
-
end
|
109
|
-
|
110
|
-
|
111
|
-
puts Log.color :blue, dir
|
112
|
-
puts Log.color(:magenta, "Creation: ") << File.mtime(File.join(dir, 'command.slurm')).to_s
|
113
|
-
puts Log.color(:magenta, "Done: ") << File.mtime(File.join(dir, 'exit.status')).to_s if File.exist?(File.join(dir, 'exit.status'))
|
114
|
-
puts Log.color(:magenta, "Exec: ") << (exe || "Missing")
|
115
|
-
puts Log.color(:magenta, "CMD: ") << (Log.color(:yellow, cmd) || "Missing")
|
116
|
-
puts Log.color(:magenta, "HOME: ") << Log.color(:yellow, container_home) if container_home
|
117
|
-
puts Log.color(:magenta, "Job ID: ") << (exit_status ? (exit_status == 0 ? Log.color(:green, "Done") : Log.color(:red, "Error")) : (running_jobs.include?(id) || $norunningjobs ? Log.color(:green, id) : Log.color(:red, id) ))
|
118
|
-
puts Log.color(:magenta, "Dependencies: ") << deps * ", " if deps
|
119
|
-
puts Log.color(:magenta, "Nodes: ") << nodes * ", "
|
120
|
-
puts Log.color(:magenta, "Output: ") << File.exists?(File.join(dir, 'std.out')).to_s << (id.nil? ? "" : " (last update " + Misc.format_seconds(time_diff) + " ago)")
|
121
|
-
|
122
|
-
if tail && File.exists?(File.join(dir, 'std.err'))
|
123
|
-
if exit_status && exit_status != 0
|
124
|
-
puts Log.color(:magenta, "First error or exception found: ")
|
125
|
-
puts CMD.cmd("grep -i -w 'error\\|[a-z]*exception' #{File.join(dir, 'std.err')} -A #{tail.to_i} |head -n #{tail.to_i}", :no_fail => true).read
|
126
|
-
elsif exit_status
|
127
|
-
puts Log.color(:magenta, "Completed jobs: ")
|
128
|
-
puts CMD.cmd("grep -i -w 'Completed step' #{File.join(dir, 'std.err')} | grep -v 'Retrying dep.' | tail -n #{tail.to_i}", :no_fail => true).read
|
129
|
-
else
|
130
|
-
puts Log.color(:magenta, "Log tail: ")
|
131
|
-
puts CMD.cmd("tail -n #{tail.to_i} #{File.join(dir, 'std.err')}").read
|
132
|
-
end
|
133
|
-
end
|
134
|
-
|
135
|
-
count += 1
|
196
|
+
rescue
|
197
|
+
end
|
198
|
+
end
|
199
|
+
|
200
|
+
|
201
|
+
if tail && File.exists?(File.join(dir, 'std.err'))
|
202
|
+
if exit_status && exit_status != 0
|
203
|
+
puts Log.color(:magenta, "First error or exception found: ")
|
204
|
+
puts CMD.cmd("grep -i -w 'error\\|[a-z]*exception' #{File.join(dir, 'std.err')} -A #{tail.to_i} |head -n #{tail.to_i}", :no_fail => true).read
|
205
|
+
elsif exit_status
|
206
|
+
puts Log.color(:magenta, "Completed jobs: ")
|
207
|
+
puts CMD.cmd("grep -i -w 'Completed step' #{File.join(dir, 'std.err')} | grep -v 'Retrying dep.' | tail -n #{tail.to_i}", :no_fail => true).read
|
208
|
+
else
|
209
|
+
puts Log.color(:magenta, "Log tail: ")
|
210
|
+
puts CMD.cmd("tail -n #{tail.to_i} #{File.join(dir, 'std.err')}").read
|
211
|
+
end
|
212
|
+
end
|
213
|
+
|
214
|
+
count += 1
|
136
215
|
|
137
216
|
end
|
138
217
|
|