rbbt-util 5.25.23 → 5.25.24
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +4 -2
- data/lib/rbbt/resource/util.rb +1 -1
- data/lib/rbbt/util/filecache.rb +5 -1
- data/lib/rbbt/workflow/step/run.rb +2 -0
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 97968ffcba988c2f18b367ca3e72dee52f05a31d
|
4
|
+
data.tar.gz: 3d0c7129ef2a0b4109590cc26ecb7e129e0a2879
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: bdffb227e99a0737cf89d7c195c326a10cddae2e00484b0a6a395ec1fb18567aa44f62cb4619672d0aa33f08e6bcba3cd333c5e4d055f31d6793b255d50db193
|
7
|
+
data.tar.gz: 1516e4382803e42abf12e3fc816304838e91b417ce88b18712bbd695dfb23e6b67aa988e5508793027d4721f686d20f262105f64ef9896a437174775c86f1829
|
data/lib/rbbt/hpc.rb
CHANGED
@@ -41,6 +41,7 @@ module Marenostrum
|
|
41
41
|
|
42
42
|
queue = options[:queue] || 'bsc_ls'
|
43
43
|
tasks = options[:tasks] || 1
|
44
|
+
nodes = options[:nodes] || 1
|
44
45
|
time = options[:time] || "0:00:10"
|
45
46
|
|
46
47
|
time = Misc.format_seconds Misc.timespan(time) unless time.include? ":"
|
@@ -69,6 +70,7 @@ module Marenostrum
|
|
69
70
|
#SBATCH --error="#{ferr}"
|
70
71
|
#SBATCH --ntasks="#{tasks}"
|
71
72
|
#SBATCH --time="#{time}"
|
73
|
+
#SBATCH --nodes="#{nodes}"
|
72
74
|
EOF
|
73
75
|
|
74
76
|
if highmem
|
@@ -282,7 +284,7 @@ EOF
|
|
282
284
|
ferr = File.join(workdir, 'std.err')
|
283
285
|
fstatus = File.join(workdir, 'job.status')
|
284
286
|
|
285
|
-
job = Open.read(fjob) if Open.exists?(fjob)
|
287
|
+
job = Open.read(fjob).strip if Open.exists?(fjob)
|
286
288
|
|
287
289
|
if job
|
288
290
|
status_txt = CMD.cmd("squeue --job #{job}").read
|
@@ -317,7 +319,7 @@ EOF
|
|
317
319
|
begin
|
318
320
|
CMD.cmd("squeue --job #{job} > #{fstatus}")
|
319
321
|
out = CMD.cmd("tail -f '#{fout}'", :pipe => true) if File.exists?(fout) and not tail == :STDERR
|
320
|
-
err = CMD.cmd("tail -f '#{ferr}'", :pipe => true) if File.exists?
|
322
|
+
err = CMD.cmd("tail -f '#{ferr}'", :pipe => true) if File.exists?(ferr)
|
321
323
|
|
322
324
|
Misc.consume_stream(err, true, STDERR) if err
|
323
325
|
Misc.consume_stream(out, true, STDOUT) if out
|
data/lib/rbbt/resource/util.rb
CHANGED
@@ -34,8 +34,8 @@ module Resource
|
|
34
34
|
software_dir.find_all.each do |software_dir|
|
35
35
|
next unless software_dir.exists?
|
36
36
|
software_dir = File.expand_path(software_dir)
|
37
|
-
bin_dir = File.join(software_dir, 'bin')
|
38
37
|
opt_dir = File.join(software_dir, 'opt')
|
38
|
+
bin_dir = File.join(opt_dir, 'bin')
|
39
39
|
|
40
40
|
Misc.env_add 'PATH', bin_dir
|
41
41
|
|
data/lib/rbbt/util/filecache.rb
CHANGED
@@ -4,7 +4,11 @@ require 'rbbt/util/misc'
|
|
4
4
|
# Provides caching functionality for files downloaded from the internet
|
5
5
|
module FileCache
|
6
6
|
CACHEDIR = "/tmp/rbbt_cache"
|
7
|
-
|
7
|
+
begin
|
8
|
+
FileUtils.mkdir(CACHEDIR)
|
9
|
+
rescue
|
10
|
+
end unless File.exist? CACHEDIR
|
11
|
+
|
8
12
|
|
9
13
|
def self.cachedir=(cachedir)
|
10
14
|
CACHEDIR.replace cachedir
|
@@ -1,4 +1,5 @@
|
|
1
1
|
require 'rbbt/workflow/step/dependencies'
|
2
|
+
require 'socket'
|
2
3
|
|
3
4
|
|
4
5
|
module StreamArray; end
|
@@ -224,6 +225,7 @@ class Step
|
|
224
225
|
:issued => (issue_time = Time.now),
|
225
226
|
:name => name,
|
226
227
|
:pid => Process.pid.to_s,
|
228
|
+
:pid_hostname => Socket.hostname,
|
227
229
|
:clean_name => clean_name,
|
228
230
|
:workflow => (@workflow || @task.workflow).to_s,
|
229
231
|
:task_name => @task.name,
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.25.
|
4
|
+
version: 5.25.24
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2019-01-
|
11
|
+
date: 2019-01-24 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|