Update libxml2 to 2.9.4.

Add test.xml stanza for Gaea. Disable garbage collection completely to avoid memory management bugs in libraries.
christopherwharrop · Aug 1, 2016 · aa8efb4 · aa8efb4
1 parent df994c9
commit aa8efb4
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Showing 12 changed files with 11 additions and 18 deletions.
diff --git a/INSTALL b/INSTALL
@@ -82,7 +82,7 @@ for file in `ls sbin | grep -v '\.sh'`; do
 done
 
 # Package versions
-LIBXML2_VERSION="2.9.3"
+LIBXML2_VERSION="2.9.4"
 LIBXML_RUBY_VERSION="2.8.0"
 SYSTEMTIMER_VERSION="1.2.3"
 SQLITE3_VERSION="autoconf-3120200"

diff --git a/lib/workflowmgr/cobaltbatchsystem.rb b/lib/workflowmgr/cobaltbatchsystem.rb
@@ -248,7 +248,6 @@ def refresh_jobqueue
 
 
       queued_jobs=nil
-      GC.start
 
     end  # job_queue
 

diff --git a/lib/workflowmgr/moabbatchsystem.rb b/lib/workflowmgr/moabbatchsystem.rb
@@ -244,7 +244,6 @@ def refresh_jobqueue
       }  #  queued_jobs.find
 
       queued_jobs=nil
-      GC.start
 
     end
 
@@ -319,7 +318,6 @@ def refresh_jobacct
       }
 
       recordxml=nil
-      GC.start
 
     end
 

diff --git a/lib/workflowmgr/moabtorquebatchsystem.rb b/lib/workflowmgr/moabtorquebatchsystem.rb
@@ -206,7 +206,6 @@ def refresh_jobqueue
       }  #  queued_jobs.find
 
       queued_jobs=nil
-      GC.start
 
     end
 
@@ -280,7 +279,6 @@ def refresh_jobacct
       }
 
       recordxml=nil
-      GC.start
 
     end
 

diff --git a/lib/workflowmgr/sgebatchsystem.rb b/lib/workflowmgr/sgebatchsystem.rb
@@ -353,7 +353,6 @@ def refresh_jobqueue
       }  #  queued_jobs.find
 
       queued_jobs=nil
-      GC.start
 
     end
 

diff --git a/lib/workflowmgr/torquebatchsystem.rb b/lib/workflowmgr/torquebatchsystem.rb
@@ -258,7 +258,6 @@ def refresh_jobqueue
       }  #  queued_jobs.find
 
       queued_jobs=nil
-      GC.start
 
     end  # job_queue
 

diff --git a/lib/workflowmgr/utilities.rb b/lib/workflowmgr/utilities.rb
@@ -263,8 +263,6 @@ def WorkflowMgr.run4(command,timeout=30)
     [output,error,exit_status]
 
   ensure
-    # Make sure we turn garbage collection back on!
-    GC.enable
 
   end
 

diff --git a/lib/workflowmgr/workflowdoc.rb b/lib/workflowmgr/workflowdoc.rb
@@ -732,10 +732,6 @@ def expand_metataskdeps
       @workflowdoc.root.each_element {|ch|
         if ch.name == "task"
 
-          # Initiate garbage collection to avoid seg faults resulting from LibXML
-          # memory management issues/bugs
-          GC.start
-
           # Find the metataskdep nodes
           metataskdeps=ch.find('.//metataskdep')
 
@@ -795,10 +791,6 @@ def expand_serialdeps
           depnode=nil
           andnode=nil
 
-          # Initiate garbage collection to avoid seg faults resulting from LibXML
-          # memory management issues/bugs
-          GC.start
-
           # Add dependencies for each serial metatask that this task is a member of
           metatasklist=ch.attributes["metatasks"]
           metatasklist.split(",").each_with_index do |m,idx|

diff --git a/lib/workflowmgr/workflowengine.rb b/lib/workflowmgr/workflowengine.rb
@@ -36,6 +36,9 @@ def initialize(options)
 
       begin
 
+        # Disable garbage collection
+	GC.disable
+
         # Turn on full program tracing for verbosity 1000+
         if WorkflowMgr::VERBOSE > 999
           set_trace_func proc { |event,file,line,id,binding,classname| printf "%10s %s:%-2d %10s %8s\n",event,file,line,id,classname }

diff --git a/tarfiles/libxml2-2.9.3.tar.gz b/tarfiles/libxml2-2.9.3.tar.gz
diff --git a/tarfiles/libxml2-2.9.4.tar.gz b/tarfiles/libxml2-2.9.4.tar.gz
diff --git a/test/test.xml b/test/test.xml
@@ -22,6 +22,13 @@
  <!ENTITY QUEUE "batch">
  <!ENTITY SCHED "moabtorque">
 
+<!--
+ <!ENTITY TEST_HOME "/autofs/mnt/ncrc-svm1_home1/Christopher.W.Harrop/opt/rocoto/master/test">
+ <!ENTITY DATA_HOME "/lustre/f1/Christopher.W.Harrop">
+ <!ENTITY PROJECT "esrl_bmcs">
+ <!ENTITY QUEUE "batch">
+ <!ENTITY SCHED "moab">
+-->
 <!--
  <!ENTITY TEST_HOME "/home/harrop/rocoto-devel/test">
  <!ENTITY DATA_HOME "/lfs1/jetmgmt/harrop/test">