rbbt-util 5.30.13 → 5.31.0

data/share/rbbt_commands/slurm/orchestrate

@@ -1,48 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'rbbt/util/simpleopt'
-require 'rbbt/workflow'
-require 'rbbt/workflow/usage'
-require 'rbbt/hpc'
-require 'rbbt/hpc/orchestrate'
-require 'time'
-
-$slurm_options = SOPT.get <<EOF
--dr--dry_run Print only the template
--cj--clean_job Clean job
---drbbt* Use development version of rbbt 
--sing--singularity Use Singularity
--ug--user_group* Use alternative user group for group project directory
--c--contain* Contain in directory (using Singularity)
--s--sync* Contain in directory and sync jobs
--e--exclusive Make exclusive use of the node
--hm--highmem Make use of highmem cores
--wc--wipe_container* Wipe the jobs from the contain directory
--CS--contain_and_sync Contain and sync to default locations
--ci--copy_image When using a container directory, copy image there
--t--tail Tail the logs
--SPERF--SLURM_procpath* Save Procpath performance for SLURM job; specify only options
--q--queue* Queue
--t--task_cpus* Tasks
--W--workflows* Additional workflows
--tm--time* Time
--OR--orchestration_rules* Orchestration rules
--rmb--remove_slurm_basedir Remove the SLURM working directory (command, STDIN, exit status, ...)
-EOF
-
-class Step
-    def run(*args)
-        if done?
-            self.load
-        else
-            begin
-                Log.debug "Issuing SLURM job for #{self.path}"
-                HPC::SLURM.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
-            rescue HPC::SBATCH
-            end
-        end
-    end
-end
-
-ARGV.concat ["-W", $slurm_options[:workflows], '--detach'] if $slurm_options[:workflows]
-load Rbbt.share.rbbt_commands.workflow.task.find

data/share/rbbt_commands/slurm/task

@@ -1,46 +0,0 @@
-#!/usr/bin/env ruby
-
-require 'rbbt/util/simpleopt'
-require 'rbbt/workflow'
-require 'rbbt/workflow/usage'
-require 'rbbt/hpc'
-require 'time'
-
-$slurm_options = SOPT.get <<EOF
--dr--dry_run Print only the template
--cj--clean_job Clean job
---drbbt* Use development version of rbbt 
--sing--singularity Use Singularity
--ug--user_group* Use alternative user group for group project directory
--c--contain* Contain in directory (using Singularity)
--s--sync* Contain in directory and sync jobs
--e--exclusive Make exclusive use of the node
--hm--highmem Make use of highmem cores
--wc--wipe_container* Wipe the jobs from the contain directory
--CS--contain_and_sync Contain and sync to default locations
--ci--copy_image When using a container directory, copy image there
--t--tail Tail the logs
--SPERF--SLURM_procpath* Save Procpath performance for SLURM job; specify only options
--q--queue* Queue
--t--task_cpus* Tasks
--W--workflows* Additional workflows
--tm--time* Time
--rmb--remove_slurm_basedir Remove the SLURM working directory (command, STDIN, exit status, ...)
-EOF
-
-class Step
-    def run(*args)
-        if done?
-            self.load
-        else
-            begin
-                Log.debug "Issuing SLURM job for #{self.path}"
-                HPC::SLURM.run_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
-            rescue HPC::SBATCH
-            end
-        end
-    end
-end
-
-ARGV.concat ["-W", $slurm_options[:workflows]] if $slurm_options[:workflows]
-load Rbbt.share.rbbt_commands.workflow.task.find