rbbt-util 5.31.15 → 5.32.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/hpc/lsf.rb +7 -4
- data/lib/rbbt/hpc/slurm.rb +2 -1
- data/lib/rbbt/workflow/step.rb +4 -0
- metadata +2 -2
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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3
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metadata.gz: ef9271207cbe69c725a4ab3a8553295d3b68e5f04ec1bfd25ad4654f162ed9cb
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4
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data.tar.gz: '087009c9ac6b4fee6d9fa7bceb003e050a0cc1e73f96987ec792c07388760633'
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SHA512:
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: b031c1143992b4c75eeeabcb231d656af2927a5bc46a0ea3527c4c90b7ffcc5eb44b0ec02ef9e31d4879fcf2b3192165ba5b22cd1978dc5250eec355f2556bdc
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7
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data.tar.gz: eb43875132a5f4ddc7ff9ae5dcaed7677c6bff84a4d61454cad9a83361d2a3dd63432cd5b28c656cd9e7bb589b8517bbdd3b57c0fa370527724d3ae55810b0cb
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data/lib/rbbt/hpc/lsf.rb
CHANGED
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@@ -7,10 +7,13 @@ module HPC
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def self.batch_system_variables
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<<-EOF
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-
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-
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-
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-
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let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
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let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $SLURM_CPUS_PER_TASK )"
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[ ! -z $LSB_MAX_MEM_RUSAGE ] && let MAX_MEMORY="$LSB_MAX_MEM_RUSAGE" || MAX_MEMORY="$MAX_MEMORY_DEFAULT"
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export MAX_MEMORY_DEFAULT
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export MAX_MEMORY
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export BATCH_JOB_ID=$LSF_JOBID
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export BATCH_SYSTEM=LSF
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EOF
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end
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data/lib/rbbt/hpc/slurm.rb
CHANGED
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@@ -8,7 +8,8 @@ module HPC
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def self.batch_system_variables
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<<-EOF
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-
let
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let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
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let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $SLURM_CPUS_PER_TASK )"
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[ ! -z $SLURM_MEM_PER_CPU ] && let MAX_MEMORY="$SLURM_MEM_PER_CPU * $SLURM_CPUS_PER_TASK" || MAX_MEMORY="$MAX_MEMORY_DEFAULT"
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export MAX_MEMORY_DEFAULT
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export MAX_MEMORY
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data/lib/rbbt/workflow/step.rb
CHANGED
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@@ -458,6 +458,10 @@ class Step
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end
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def clean
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if ! Open.exists?(info_file)
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Log.high "Refusing to clean step with no .info file: #{path}"
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return self
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end
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status = []
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status << "dirty" if done? && dirty?
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status << "not running" if ! done? && ! running?
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metadata
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: rbbt-util
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version: !ruby/object:Gem::Version
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version: 5.
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version: 5.32.0
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2021-04-
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date: 2021-04-15 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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