rbbt-util 5.25.23 → 5.25.24

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: add6d584634f667abea0d292d96fb724b6f0bf8b
+  metadata.gz: 97968ffcba988c2f18b367ca3e72dee52f05a31d
+  data.tar.gz: 3d0c7129ef2a0b4109590cc26ecb7e129e0a2879
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+  data.tar.gz: 1516e4382803e42abf12e3fc816304838e91b417ce88b18712bbd695dfb23e6b67aa988e5508793027d4721f686d20f262105f64ef9896a437174775c86f1829

data/lib/rbbt/hpc.rb

@@ -41,6 +41,7 @@ module Marenostrum
 
       queue = options[:queue] || 'bsc_ls'
       tasks = options[:tasks] || 1
+      nodes = options[:nodes] || 1
       time = options[:time] || "0:00:10"
 
       time = Misc.format_seconds Misc.timespan(time) unless time.include? ":"
@@ -69,6 +70,7 @@ module Marenostrum
 #SBATCH --error="#{ferr}"
 #SBATCH --ntasks="#{tasks}"
 #SBATCH --time="#{time}"
+#SBATCH --nodes="#{nodes}"
       EOF
 
       if highmem
@@ -282,7 +284,7 @@ EOF
       ferr = File.join(workdir, 'std.err')
       fstatus = File.join(workdir, 'job.status')
 
-      job = Open.read(fjob) if Open.exists?(fjob)
+      job = Open.read(fjob).strip if Open.exists?(fjob)
 
       if job
         status_txt = CMD.cmd("squeue --job #{job}").read
@@ -317,7 +319,7 @@ EOF
         begin
           CMD.cmd("squeue --job #{job} > #{fstatus}")
           out = CMD.cmd("tail -f '#{fout}'", :pipe => true) if File.exists?(fout) and not tail == :STDERR
-          err = CMD.cmd("tail -f '#{ferr}'", :pipe => true) if File.exists? ferr
+          err = CMD.cmd("tail -f '#{ferr}'", :pipe => true) if File.exists?(ferr)
 
           Misc.consume_stream(err, true, STDERR) if err
           Misc.consume_stream(out, true, STDOUT) if out

data/lib/rbbt/resource/util.rb

@@ -34,8 +34,8 @@ module Resource
     software_dir.find_all.each do |software_dir|
       next unless software_dir.exists?
       software_dir = File.expand_path(software_dir)
-      bin_dir = File.join(software_dir, 'bin')
       opt_dir = File.join(software_dir, 'opt')
+      bin_dir = File.join(opt_dir, 'bin')
 
       Misc.env_add 'PATH', bin_dir
 

data/lib/rbbt/util/filecache.rb

@@ -4,7 +4,11 @@ require 'rbbt/util/misc'
 # Provides caching functionality for files downloaded from the internet
 module FileCache
   CACHEDIR = "/tmp/rbbt_cache" 
-  FileUtils.mkdir CACHEDIR unless File.exist? CACHEDIR
+  begin
+    FileUtils.mkdir(CACHEDIR)
+  rescue
+  end unless File.exist? CACHEDIR
+
 
   def self.cachedir=(cachedir)
     CACHEDIR.replace cachedir

data/lib/rbbt/workflow/step/run.rb

@@ -1,4 +1,5 @@
 require 'rbbt/workflow/step/dependencies'
+require 'socket'
 
 
 module StreamArray; end
@@ -224,6 +225,7 @@ class Step
             :issued => (issue_time = Time.now),
             :name => name,
             :pid => Process.pid.to_s,
+            :pid_hostname => Socket.hostname,
             :clean_name => clean_name,
             :workflow => (@workflow || @task.workflow).to_s,
             :task_name => @task.name,

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.23
+  version: 5.25.24
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-01-22 00:00:00.000000000 Z
+date: 2019-01-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake