rbbt-util 5.34.15 → 5.34.16
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc/slurm.rb +3 -1
- data/lib/rbbt/persist.rb +2 -0
- data/lib/rbbt/tsv/parser.rb +1 -1
- data/lib/rbbt/tsv.rb +2 -2
- data/lib/rbbt/util/cmd.rb +2 -1
- data/lib/rbbt/util/misc/math.rb +3 -3
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 5b76f18c79a3b52708203f69eb7cd9baff8cb07feb2a4b26850094cfda9b9edc
|
4
|
+
data.tar.gz: 8511317ae202283e8138746485e74d39b28881b78b85539c521e94309337782e
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 71dd9c6806e8129fa08b466ddd3e8ea7172a0938000f399b030ef89a5f40321b08f24f6b98ba823ac72317460f45dbc9a8fc88c65899582766a542fde55adb24
|
7
|
+
data.tar.gz: 0b6d4b0aea41c92161193ffb379ee86e44715298ebf6d26d585ffb6292ae89a77e82a9764f07630106510c45bc5b56193b716de9edd71ed52cb4046f711d2e24
|
data/lib/rbbt/hpc/slurm.rb
CHANGED
@@ -10,7 +10,9 @@ module HPC
|
|
10
10
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<<-EOF
|
11
11
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let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
|
12
12
|
let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $SLURM_CPUS_PER_TASK )"
|
13
|
-
|
13
|
+
MAX_MEMORY="$MAX_MEMORY_DEFAULT"
|
14
|
+
[ ! -z $SLURM_MEM_PER_CPU ] && let MAX_MEMORY="$SLURM_MEM_PER_CPU * $SLURM_CPUS_PER_TASK"
|
15
|
+
[ ! -z $SLURM_MEM_PER_NODE ] && MAX_MEMORY="$SLURM_MEM_PER_NODE"
|
14
16
|
export MAX_MEMORY_DEFAULT
|
15
17
|
export MAX_MEMORY
|
16
18
|
export BATCH_JOB_ID=$SLURM_JOB_ID
|
data/lib/rbbt/persist.rb
CHANGED
data/lib/rbbt/tsv/parser.rb
CHANGED
@@ -135,7 +135,7 @@ module TSV
|
|
135
135
|
[]
|
136
136
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else
|
137
137
|
parts.values_at *field_positions
|
138
|
-
end.collect{|value| (value.
|
138
|
+
end.collect{|value| (value.nil? || value.empty?) ? [] : value.split(@sep2, -1) }
|
139
139
|
[keys, values]
|
140
140
|
end
|
141
141
|
|
data/lib/rbbt/tsv.rb
CHANGED
@@ -137,12 +137,12 @@ module TSV
|
|
137
137
|
case
|
138
138
|
when Path === stream
|
139
139
|
stream.open do |f|
|
140
|
-
f.no_fail =
|
140
|
+
f.no_fail = true if ConcurrentStream === f
|
141
141
|
Parser.new f, options
|
142
142
|
end
|
143
143
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when (String === stream and stream.length < 300 and (Open.exists? stream or Open.remote? stream))
|
144
144
|
Open.open(stream) do |f|
|
145
|
-
f.no_fail =
|
145
|
+
f.no_fail = true if ConcurrentStream === f
|
146
146
|
Parser.new f, options
|
147
147
|
end
|
148
148
|
else
|
data/lib/rbbt/util/cmd.rb
CHANGED
@@ -163,6 +163,7 @@ module CMD
|
|
163
163
|
|
164
164
|
if in_content.respond_to?(:read)
|
165
165
|
in_thread = Thread.new(Thread.current) do |parent|
|
166
|
+
Thread.current.report_on_exception = false if no_fail
|
166
167
|
begin
|
167
168
|
begin
|
168
169
|
while c = in_content.readpartial(Misc::BLOCK_SIZE)
|
@@ -177,7 +178,7 @@ module CMD
|
|
177
178
|
in_content.join if in_content.respond_to? :join
|
178
179
|
end
|
179
180
|
rescue
|
180
|
-
Log.error "Error in CMD [#{pid}] #{cmd}: #{$!.message}"
|
181
|
+
Log.error "Error in CMD [#{pid}] #{cmd}: #{$!.message}" unless no_fail
|
181
182
|
raise $!
|
182
183
|
end
|
183
184
|
end
|
data/lib/rbbt/util/misc/math.rb
CHANGED
@@ -39,17 +39,17 @@ module Misc
|
|
39
39
|
end
|
40
40
|
|
41
41
|
def self.sum(list)
|
42
|
-
list.compact.inject(0.0){|acc,e| acc += e}
|
42
|
+
list.compact.inject(0.0){|acc,e| acc += e }
|
43
43
|
end
|
44
44
|
|
45
45
|
def self.mean(list)
|
46
|
-
sum(list
|
46
|
+
sum(list.compact.collect{|v| v.to_f } ) / list.compact.length
|
47
47
|
end
|
48
48
|
|
49
49
|
def self.median(array)
|
50
50
|
sorted = array.sort
|
51
51
|
len = sorted.length
|
52
|
-
(sorted[(len - 1) / 2] + sorted[len / 2]) / 2
|
52
|
+
(sorted[(len - 1) / 2] + sorted[len / 2]).to_f / 2
|
53
53
|
end
|
54
54
|
|
55
55
|
def self.variance(list)
|
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: 5.34.
|
4
|
+
version: 5.34.16
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2022-10-
|
11
|
+
date: 2022-10-05 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|