miga-base 1.2.5.3 → 1.2.6.2
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- checksums.yaml +4 -4
- data/lib/miga/cli/action/get_db.rb +14 -5
- data/lib/miga/cli/action/init/daemon_helper.rb +23 -7
- data/lib/miga/daemon.rb +1 -0
- data/lib/miga/version.rb +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
|
+
metadata.gz: 3dd2a47d0472b27985d65865358d2555f67f18e63143d41b62d2a36b83edddc6
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4
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+
data.tar.gz: b90dc62b2bddcd3903493abe84b663486b57170b7b4fd65a5f63d0bf36e747b2
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5
5
|
SHA512:
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6
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-
metadata.gz:
|
7
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-
data.tar.gz:
|
6
|
+
metadata.gz: f2b4507f9526471e64e17fc115918dcf880a0c4dfedebe111fcb98c24a7bede321b629809d8518f1bb93cb0d1c0f524bcb707309f891ee09569dd43ecc527f97
|
7
|
+
data.tar.gz: bf0f77f5d7879d27b5e1fb22b32a1ba42da8f41318ebdfefc92b35782ceb8538687de05647296afc6eb74d284729a73fba60520e288d33d049a7ece6e7d81de9
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@@ -12,6 +12,7 @@ class MiGA::Cli::Action::GetDb < MiGA::Cli::Action
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|
12
12
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local: File.expand_path('.miga_db', ENV['MIGA_HOME']),
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13
13
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host: MiGA::MiGA.known_hosts(:miga_db),
|
14
14
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pb: true,
|
15
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+
reuse_archive: false,
|
15
16
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overwrite: true
|
16
17
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}
|
17
18
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cli.parse do |opt|
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@@ -39,6 +40,10 @@ class MiGA::Cli::Action::GetDb < MiGA::Cli::Action
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|
39
40
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'--list-versions',
|
40
41
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'List available versions of the database and exit'
|
41
42
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) { |v| cli[:list_versions] = v }
|
43
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+
opt.on(
|
44
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+
'--reuse-archive',
|
45
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+
'Reuse a previously downloaded archive if available'
|
46
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+
) { |v| cli[:reuse_archive] = v }
|
42
47
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opt.on(
|
43
48
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'--no-overwrite',
|
44
49
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'Exit without downloading if the target database already exists'
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@@ -67,7 +72,7 @@ class MiGA::Cli::Action::GetDb < MiGA::Cli::Action
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67
72
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check_target and return
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68
73
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|
69
74
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# Download and expand
|
70
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-
file = download_file(@ftp, ver[:path])
|
75
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+
file = download_file(@ftp, ver[:path], cli[:reuse_archive])
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71
76
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check_digest(ver, file)
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72
77
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unarchive(file)
|
73
78
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register_database(manif, db, ver)
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@@ -89,13 +94,17 @@ class MiGA::Cli::Action::GetDb < MiGA::Cli::Action
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|
89
94
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MiGA::MiGA.remote_connection(cli[:host])
|
90
95
|
end
|
91
96
|
|
92
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-
def download_file(ftp, path)
|
97
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+
def download_file(ftp, path, reuse = false)
|
93
98
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cli.say "Downloading '#{path}'"
|
94
99
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file = File.expand_path(path, cli[:local])
|
95
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-
|
96
|
-
cli.
|
100
|
+
if reuse && File.exist?(file)
|
101
|
+
cli.say "Reusing #{file}"
|
102
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+
else
|
103
|
+
MiGA::MiGA.download_file_ftp(ftp, path, file) do |n, size|
|
104
|
+
cli.advance("#{path}:", n, size) if cli[:pb]
|
105
|
+
end
|
106
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+
cli.print "\n" if cli[:pb]
|
97
107
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end
|
98
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-
cli.print "\n" if cli[:pb]
|
99
108
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file
|
100
109
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end
|
101
110
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|
@@ -35,6 +35,7 @@ module MiGA::Cli::Action::Init::DaemonHelper
|
|
35
35
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v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '2').to_i
|
36
36
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v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '6').to_i
|
37
37
|
v[:ppn] = cli.ask_user('How many CPUs can I use per job?', '2').to_i
|
38
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+
v[:nodelist] = nil # <- To enable non-default with default SSH
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38
39
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cli.puts 'Setting up internal daemon defaults.'
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39
40
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cli.puts 'If you don\'t understand this just leave default values:'
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40
41
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v[:cmd] = cli.ask_user(
|
@@ -100,6 +101,7 @@ module MiGA::Cli::Action::Init::DaemonHelper
|
|
100
101
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v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
|
101
102
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v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '300').to_i
|
102
103
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v[:ppn] = cli.ask_user('How many CPUs can I use per job?', '2').to_i
|
104
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+
v[:nodelist] = nil # <- To enable non-default with default SSH
|
103
105
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cli.puts 'Setting up internal daemon defaults'
|
104
106
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cli.puts 'If you don\'t understand this just leave default values:'
|
105
107
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v[:cmd] = cli.ask_user(
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@@ -135,18 +137,32 @@ module MiGA::Cli::Action::Init::DaemonHelper
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135
137
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|
136
138
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def configure_qsub_msub_daemon(v)
|
137
139
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queue = cli.ask_user('What queue should I use?', nil, nil, true)
|
140
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+
flavor = v[:type] == 'msub' ? 'msub' :
|
141
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+
cli.ask_user('Select qsub flavor', 'torque', %w[torque sge])
|
138
142
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v[:latency] = cli.ask_user('How long should I sleep? (in secs)', '150').to_i
|
139
143
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v[:maxjobs] = cli.ask_user('How many jobs can I launch at once?', '300').to_i
|
140
144
|
v[:ppn] = cli.ask_user('How many CPUs can I use per job?', '2').to_i
|
145
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+
v[:nodelist] = nil # <- To enable non-default with default SSH
|
141
146
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cli.puts 'Setting up internal daemon defaults.'
|
142
147
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cli.puts 'If you don\'t understand this just leave default values:'
|
143
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-
|
144
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-
|
145
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-
"
|
146
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-
|
147
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-
"{
|
148
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-
|
149
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-
|
148
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+
if flavor == 'sge'
|
149
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+
v[:cmd] = cli.ask_user(
|
150
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+
"How should I launch tasks?\n" \
|
151
|
+
" {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
|
152
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+
"#{v[:type]} -q '#{queue}' -v '{{vars}}' -pe openmp {{cpus}} " \
|
153
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+
"-j y -o '{{log}}' -N '{{task_name_simple}}' -l h_vmem=9g " \
|
154
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+
"-l h_rt=walltime=12:00:00 '{{script}}' | grep . | " \
|
155
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+
"perl -pe 's/^Your job (\S+) .*/$1/'"
|
156
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+
)
|
157
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+
else
|
158
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+
v[:cmd] = cli.ask_user(
|
159
|
+
"How should I launch tasks?\n" \
|
160
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+
" {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
|
161
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+
"#{v[:type]} -q '#{queue}' -v '{{vars}}' -l nodes=1:ppn={{cpus}} " \
|
162
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+
"-j oe -o '{{log}}' -N '{{task_name}}' -l mem=9g " \
|
163
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+
"-l walltime=12:00:00 '{{script}}' | grep ."
|
164
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+
)
|
165
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+
end
|
150
166
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v[:var] = cli.ask_user(
|
151
167
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"How should I pass variables?\n" \
|
152
168
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" {{variables}}: key, value\n ",
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data/lib/miga/daemon.rb
CHANGED
@@ -257,6 +257,7 @@ class MiGA::Daemon < MiGA::MiGA
|
|
257
257
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cpus: ppn(what),
|
258
258
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log: File.join(log_dir, "#{to_run[:ds_name]}.log"),
|
259
259
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task_name: to_run[:task_name],
|
260
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+
task_name_simple: to_run[:task_name].gsub(/[^A-Za-z0-9_]/, '-'),
|
260
261
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miga: File.join(MiGA::MiGA.root_path, 'bin/miga').shellescape
|
261
262
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}
|
262
263
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runopts_for(:cmd, what).miga_variables(var_hsh)
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data/lib/miga/version.rb
CHANGED
@@ -12,7 +12,7 @@ module MiGA
|
|
12
12
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# - String indicating release status:
|
13
13
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# - rc* release candidate, not released as gem
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14
14
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# - [0-9]+ stable release, released as gem
|
15
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-
VERSION = [1.2,
|
15
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+
VERSION = [1.2, 6, 2].freeze
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16
16
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|
17
17
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##
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18
18
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# Nickname for the current major.minor version.
|
@@ -20,7 +20,7 @@ module MiGA
|
|
20
20
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|
21
21
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##
|
22
22
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# Date of the current gem relese.
|
23
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-
VERSION_DATE = Date.new(2022,
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23
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+
VERSION_DATE = Date.new(2022, 6, 24)
|
24
24
|
|
25
25
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##
|
26
26
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# References of MiGA
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: miga-base
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.2.
|
4
|
+
version: 1.2.6.2
|
5
5
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platform: ruby
|
6
6
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authors:
|
7
7
|
- Luis M. Rodriguez-R
|
8
8
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autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2022-
|
11
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+
date: 2022-06-24 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: daemons
|