qtools 0.4.0 → 0.4.1

checksums.yaml

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data/README.md

@@ -1,5 +1,7 @@
 # qtools
 
+[![Gem Version](https://badge.fury.io/rb/qtools.svg)](https://badge.fury.io/rb/qtools)
+
 `qtools` offers the shortcuts for some common procedures when working with the Open Grid Scheduler.
 
 
@@ -27,57 +29,37 @@ Usage:
 
 The command above will create a shell script file with the corresponding content and submit a job which will feature the name `my_name` and require `8gb` of memory.
 
-### qwatch
-
-Usage:
-
-    $ qwatch
+Available parameters:
 
-The command above is equivalent to running `watch -n1 -d "qstat -u $USER"`.
+- `-n`, `--name`   - job title
+- `-m`, `--memory` - memory (e.g., `80gb`)
+- `-q`, `--queue`  - queue title
+- `-t`, `--time`   - job time limit in hours (default is `24`)
+- `-c`, `--cpu`    - number of CPUs
 
-Flags:
+### qwatch
 
-  - `-n`, `--nodes` to show information on nodes too (`qstat -n1 -u $USER`)
+`qwatch` is equivalent to running `watch -n1 -d "qstat -u $USER"`. Use `-n` (`--nodes`) flag to show information on nodes too (`qstat -n1 -u $USER`)
 
 ### qclean
 
-Usage:
-
-    $ qclean
-
-The command above will run `rm *.[eo][0-9]*` in the current directory (if such files exist).
+`qclean` will run `rm *.[eo][0-9]*` in the current directory (if such files exist).
 
 ### qcount
 
-Usage:
-
-    $ qcount
-
-Count the number of jobs for the `$USER`. Running `qcount -a` will output the number of jobs for all the users.
+Use `qcount` to count the number of jobs for the `$USER`. Running `qcount -a` will output the number of jobs for all the users.
 
 ### qnode
 
-Usage:
-
-    $ qnode
-
-The command above will print the list of free nodes sorted by their `LOAD`. Use `qnode -m` to sort the list of free nodes by memory available and `qnode -c` to sort the list by the number of free cores.
+Run `qnode` to print the list of free nodes sorted by their `LOAD`. Use `qnode -m` to sort the list of free nodes by memory available and `qnode -c` to sort the list by the number of free cores.
 
 ### qundo
 
-Usage:
-
-    $ qundo
-
-The command above will try to run `qdel` for the last job submitted.
+`qundo` will try to run `qdel` for the last job submitted (for the current user).
 
 ### qless
 
-Usage:
-
-    $ qless
-
-The command above will try to read the last default error log `.e[0-9]*` in the current folder. Use `-o` flag to read the last default output file.
+Run `qless` to read the last default error log `.e[0-9]*` in the current folder. Use `-o` flag to read the last default output file.
 
 ## Contributing
 

data/bin/qcount

@@ -16,4 +16,4 @@ flags = []
 flags << '-u $USER' unless options[:all]
 flags_str = flags.join(' ')
  
-puts `qstat #{flags_str} | grep -c ^[0-9]`
+puts `qstat #{flags_str} | grep -c ^'\s'*[0-9]`

data/bin/qnode

@@ -27,5 +27,5 @@ else
   new_header = header.strip.gsub("CORES_TOTAL(USED)", "CORES_TOTAL\tCORES_USED") + "\tCORES_FREE"
   puts new_header
   puts `qhost | head -n2 | tail -n1`
-  puts `qhost | egrep 'free' | sort -k5nr | tr "(" "\t" | tr -d ")" | awk 'BEGIN {OFS="\t"}; {print $0, $2-$3}'`
+  puts `qhost | egrep 'free' | tr "(" "\t" | tr -d ")" | awk 'BEGIN {OFS="\t"}; {print $0, $2-$3}' | sort -k8nr`
 end

data/bin/qqsub

@@ -3,9 +3,9 @@
 require 'qtools'
 require 'optparse'
 
-Options = Struct.new(:name, :mem)
+Options = Struct.new(:name, :mem, :queue, :cpus, :time)
 
-args = Options.new(:name, :mem)
+args = Options.new
 OptionParser.new do |opts|
   opts.banner = "Usage: qtools 'python3 my_script.py ...' [options]"
 
@@ -15,6 +15,15 @@ OptionParser.new do |opts|
   opts.on("-m", "--memory MEMORY", "Memory for the job (e.g., 80gb)") do |m|
     args.mem = m
   end
+  opts.on("-q", "--queue QUEUE_TITLE", "Select a queue for the job") do |q|
+    args.queue = q
+  end
+  opts.on("-c", "--cpu NUMBER_OF_CORES", "Number of CPIs for the job (e.g., 8)") do |c|
+    args.cpus = c
+  end
+  opts.on("-t", "--time TIME_IN_HOURS", "Set the time limit for the job (default is 24 hours)") do |t|
+    args.time = t
+  end
 end.parse!
 
 command = ARGV
@@ -23,34 +32,56 @@ if command.empty?
   fail "Usage: qtools 'python3 my_script.py ...' [options]"
 end
 
-header_sge = <<-HEADER
-#!/bin/bash
 
-#$ -V
-#$ -cwd
-HEADER
+# Guess the scheduler (SGE or PBS)
+scheduler_temp = `pbs-config 2> /dev/null`
+SCHEDULER = (scheduler_temp.empty? or scheduler_temp.nil?) ? :sge : :pbs
+# puts "the scheduler is guessed to be #{SCHEDULER}"
 
 header_shell = "#!/bin/bash\n"
 
-header_pbs_tree = {}
-header_pbs_tree[:l] = ['walltime=24:00:00']
-header_pbs_tree[:d] = ['.']
+if SCHEDULER == :sge
+  header_tree = Hash.new
+  header_tree[:V] = []
+  header_tree[:cwd] = []
+  header_tree[:l] = []
+  header_tree[:l] << "h_rt=#{args.time ? args.time : '24'}:00:00"
+else
+  header_tree = Hash.new
+  header_tree[:l] = []
+  header_tree[:l] << "walltime=#{args.time ? args.time : '24'}:00:00"
+  header_tree[:d] = ['.']
+end
+
 
-unless args.name.is_a? Symbol
-  header_pbs_tree[:N] = [args.name]
+if args.name
+  header_tree[:N] = [args.name]
 end
 
-unless args.mem.is_a? Symbol
-  header_pbs_tree[:l] << "mem=#{args.mem}"
+if args.mem
+  header_tree[:l] << "#{SCHEDULER == :sge ? "h_vmem" : "mem"}=#{args.mem}"
+end
+
+if args.queue
+  header_tree[:q] = [args.queue]
+end
+
+if args.cpus
+  if SCHEDULER == :sge
+    header_tree[:pe] = "smp #{args.cpus}"
+  else
+    header_tree[:l] << "ncpus=#{args.cpus}"
+  end
 end
 
-header_pbs = header_pbs_tree.map { |k, v| "#PBS -#{k} #{v.join(',')}" }.join("\n")
+scheduler_prefix = SCHEDULER == :sge ? "$" : "PBS"
+header = header_tree.map { |k, v| "##{scheduler_prefix} -#{k} #{v.join(',')}" }.join("\n")
 
 sh_prefix_guess = (command[0].split[1].include?('.') or command[0].split.length == 1) ? command[0].split[1] : command[0].split[0]  # guess if script or executable
 sh_prefix = sh_prefix_guess.include?('.') ? sh_prefix_guess.match(/(.*)\.(.*?)/)[1] : sh_prefix_guess
-sh_name = (header_pbs_tree[:N] ? header_pbs_tree[:N][0] : sh_prefix) + '.sh'
+sh_name = (header_tree[:N] ? header_tree[:N][0] : sh_prefix) + '.sh'
 
-File.write(sh_name, [header_shell, header_pbs, "", command[0]].join("\n"))
+File.write(sh_name, [header_shell, header, "", command[0]].join("\n"))
 
 puts "-- Submit #{sh_name} for execution? [y/n]"
 answer = STDIN.gets.strip.downcase

data/bin/qundo

@@ -3,7 +3,7 @@
 require 'qtools'
 
 last_job = `qstat -u $USER | tail -n 1`
-last_job_id = `qstat -u $USER | tail -n 1 | sed -rn 's/(^[0-9]*).*/\1/p'`
+last_job_id = `qstat -u $USER | tail -n 1 | sed -rn 's/(^[0-9]*).*/\\1/p'`.strip
 
 unless last_job.empty?
   puts "-- The following job will be stopped:"

data/lib/qtools/version.rb

@@ -1,3 +1,3 @@
 module Qtools
-  VERSION = "0.4.0"
+  VERSION = "0.4.1"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: qtools
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.1
 platform: ruby
 authors:
 - Daniel
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-05-09 00:00:00.000000000 Z
+date: 2016-07-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler