Merge remote-tracking branch 'upstream/master' into ltarchive_updates

Make sure the ltarchive_updates branch is up-to-date with the master.
CESM-Development · Nov 22, 2015 · fddbba4 · fddbba4
2 parents e99dda1 + c6c789f
commit fddbba4
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Showing 18 changed files with 117 additions and 105 deletions.
diff --git a/cime_config/cesm/machines/config_compilers.xml b/cime_config/cesm/machines/config_compilers.xml
@@ -105,7 +105,7 @@ for mct, etc.
   <FIXEDFLAGS>  -qsuffix=f=f -qfixed=132 </FIXEDFLAGS>
   <FREEFLAGS> -qsuffix=f=f90:cpp=F90  </FREEFLAGS>
   <FFLAGS> -g -qfullpath -qmaxmem=-1 </FFLAGS>
-  <ADD_FFLAGS DEBUG="FALSE"> -O2 -qstrict -Q </ADD_FFLAGS>
+  <ADD_FFLAGS DEBUG="FALSE"> -O2 -qstrict -qinline=auto </ADD_FFLAGS>
   <ADD_CFLAGS DEBUG="FALSE"> -O3  </ADD_CFLAGS>
   <ADD_FFLAGS compile_threaded="true"> -qsmp=omp </ADD_FFLAGS>
   <ADD_CFLAGS compile_threaded="true"> -qsmp=omp </ADD_CFLAGS>
@@ -598,7 +598,7 @@ for mct, etc.
   <SCC> blrts_xlc </SCC>
   <MPICC> blrts_xlc </MPICC>
   <CFLAGS> -O3 -qstrict </CFLAGS>
-  <ADD_FFLAGS DEBUG="FALSE"> -O3 -qstrict -Q </ADD_FFLAGS>
+  <ADD_FFLAGS DEBUG="FALSE"> -O3 -qstrict -qinline=auto </ADD_FFLAGS>
   <ADD_FFLAGS DEBUG="TRUE"> -qinitauto=FF911299 -qflttrap=ov:zero:inv:en </ADD_FFLAGS>
   <MLIBS> -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts </MLIBS>
   <ADD_CPPDEFS> -DLINUX -DnoI8 </ADD_CPPDEFS>
@@ -619,7 +619,7 @@ for mct, etc.
 
 <compiler COMPILER="ibm" OS="BGQ">
   <FFLAGS> -g -qfullpath -qmaxmem=-1 -qspillsize=2500 -qextname=flush </FFLAGS>
-  <ADD_FFLAGS DEBUG="FALSE"> -O3 -qstrict -Q </ADD_FFLAGS>
+  <ADD_FFLAGS DEBUG="FALSE"> -O3 -qstrict -qinline=auto </ADD_FFLAGS>
   <ADD_FFLAGS DEBUG="FALSE" compile_threaded="true"> -qsmp=omp </ADD_FFLAGS>
   <ADD_FFLAGS DEBUG="TRUE" compile_threaded="true"> -qsmp=omp:noopt </ADD_FFLAGS>
   <ADD_CPPDEFS> -DLINUX  </ADD_CPPDEFS>

diff --git a/cime_config/cesm/machines/config_machines.xml b/cime_config/cesm/machines/config_machines.xml
@@ -498,10 +498,10 @@
 	<command name="use">/global/project/projectdirs/ccsm1/modulefiles/cori</command>
       </modules>
       <modules compiler="intel" mpilib="!mpi-serial" >
-	<command name="load">esmf/6.3.0rp1-defio-intel2016-mpi-0</command>
+	<command name="load">esmf/6.3.0rp1-defio-intel2016-mpi-O</command>
       </modules>
       <modules compiler="intel" mpilib="mpi-serial" >
-        <command name="load">esmf/6.3.0rp1-defio-intel2016-mpiuni-0</command>
+        <command name="load">esmf/6.3.0rp1-defio-intel2016-mpiuni-O</command>
       </modules>
 
       <modules compiler="cray">
@@ -1139,7 +1139,7 @@
     <BATCHQUERY>qstat</BATCHQUERY>
     <BATCHSUBMIT>qsub</BATCHSUBMIT>
     <BATCHREDIRECT></BATCHREDIRECT>
-    <SUPPORTED_BY>   mickelso -at- mcs.anl.gov</SUPPORTED_BY>
+    <SUPPORTED_BY> cseg </SUPPORTED_BY>
     <GMAKE_J>4</GMAKE_J>
     <MAX_TASKS_PER_NODE>64</MAX_TASKS_PER_NODE>
     <PES_PER_NODE>8</PES_PER_NODE>

diff --git a/cime_config/cesm/machines/template.cesmrun b/cime_config/cesm/machines/template.cesmrun
@@ -209,7 +209,7 @@ sub doPreRunChecks()
     $logger->info(" - To prestage restarts, untar a restart.tar file into $config{'RUNDIR'}");
 
     # Run preview namelists.. should turn this into a module at some point..
-    system("./preview_namelists -loglevel $opts{loglevel}");
+    system("./preview_namelists -loglevel $opts{loglevel} ");
 
     if($?)
     {
@@ -248,7 +248,7 @@ sub checkInputData()
         $out.="expected location, and are not from the input data repository.\n";
         $out.="This is informational only.\n";
 	$logger->warn($out);
-	system("./check_input_data -inputdata $config{'DIN_LOC_ROOT'} -check -loglevel $opts{loglevel}");
+	system("./check_input_data -inputdata $config{'DIN_LOC_ROOT'} -check -loglevel $opts{loglevel} ");
     }
 
     if(@missing)
@@ -446,7 +446,7 @@ sub postRun()
         }
 
         $logger->debug("lid: $LID");
-	foreach my $comp (qw(atm cpl ocn wav glc ice rof lnd)){
+	foreach my $comp (qw(atm cpl ocn wav glc ice rof lnd cesm)){
 	    disposeLog($config{RUNDIR},$config{CASEROOT}, $comp ,$LID,$config{LOGDIR});
 	}
     }
@@ -490,7 +490,7 @@ sub resubmitCheck()
 	my $submitscript = "$config{'CASEROOT'}/case.submit";
 	my $cwd = getcwd;
 	chdir $config{'CASEROOT'};
-	my $resubmitcommand = "$submitscript -resubmit -scriptname case. -loglevel $opts{loglevel}";
+	my $resubmitcommand = "$submitscript -resubmit -scriptname case.";
 
 	if(defined $config{TESTCASE} && $config{TESTCASE} eq "ERR"){
 	    $resubmitcommand .= "test"; 

diff --git a/cime_config/cesm/machines/template.st_archive b/cime_config/cesm/machines/template.st_archive
@@ -3,7 +3,7 @@
 # Batch system directives
 #------------------------------------------------------------------------------
 {{ batchdirectives }}
-
+use strict;
 if(! -e "./xmlquery" and defined $ENV{'PBS_O_WORKDIR'})
 {
 	chdir $ENV{'PBS_O_WORKDIR'};
@@ -21,7 +21,7 @@ require Batch::BatchUtils;
 use Cwd;
 require Log::Log4perl;
 
-my $level = Log::Log4perl::Level::to_priority("DEBUG");
+my $level = Log::Log4perl::Level::to_priority("INFO");
 Log::Log4perl->easy_init({level=>$level,
 			  layout=>'%m%n'});
 
@@ -63,7 +63,7 @@ sub resubmitCheck()
 	my $submitscript = "$config{'CASEROOT'}/case.submit";
 	my $cwd = getcwd;
 	chdir $config{CASEROOT};
-	my $resubmitcommand = "$submitscript -resubmit -scriptname case.st_archive -loglevel $opts{loglevel}";
+	my $resubmitcommand = "$submitscript  -resubmit -scriptname case.st_archive";
 	$logger->debug( "running resubmit check $resubmitcommand");
 	if(-e $testlog){
 	    open(TL,">>$testlog");

diff --git a/driver_cpl/shr/seq_flds_mod.F90 b/driver_cpl/shr/seq_flds_mod.F90
@@ -2051,8 +2051,7 @@ subroutine seq_flds_set(nmlfile, ID)
         longname = 'Volumetric soil water'
         stdname  = 'soil_water'
         units    = 'm3/m3'
-        attname = trim(carma_fields)
-        call metadata_set(attname, longname, stdname, units)
+        call metadata_set(carma_fields, longname, stdname, units)
      endif
 
      !-----------------------------------------------------------------------------
@@ -2068,8 +2067,7 @@ subroutine seq_flds_set(nmlfile, ID)
         longname = 'MEGAN emission fluxes'
         stdname  = 'megan_fluxes'
         units    = 'molecules/m2/sec'
-        attname = trim(megan_voc_fields)
-        call metadata_set(attname, longname, stdname, units)
+        call metadata_set(megan_voc_fields, longname, stdname, units)
      endif
 
      !-----------------------------------------------------------------------------
@@ -2085,16 +2083,15 @@ subroutine seq_flds_set(nmlfile, ID)
         longname = 'wild fire emission fluxes'
         stdname  = 'fire_emis'
         units    = 'kg/m2/sec'
-        attname = trim(fire_emis_fields)
-        call metadata_set(attname, longname, stdname, units)
+        call metadata_set(fire_emis_fields, longname, stdname, units)
 
         call seq_flds_add(l2x_states, trim(shr_fire_emis_ztop_token))
         call seq_flds_add(x2a_states, trim(shr_fire_emis_ztop_token))
         longname = 'wild fire plume height'
         stdname  = 'fire_plume_top'
         units    = 'm'
-        attname = trim(shr_fire_emis_ztop_token)
-        call metadata_set(attname, longname, stdname, units)
+
+        call metadata_set(shr_fire_emis_ztop_token, longname, stdname, units)
 
      endif
 
@@ -2109,13 +2106,13 @@ subroutine seq_flds_set(nmlfile, ID)
 
      call seq_drydep_readnl(nlfilename="drv_flds_in", ID=ID, seq_drydep_fields=seq_drydep_fields)
      if ( lnd_drydep ) then
-        attname = trim(seq_drydep_fields)
-        call seq_flds_add(l2x_states, attname)
-        call seq_flds_add(x2a_states, attname)
-        longname = 'dry deposition velocities'
+        call seq_flds_add(l2x_states, seq_drydep_fields)
+        call seq_flds_add(x2a_states, seq_drydep_fields)
+
+        longname = 'dry deposition velocity'
         stdname  = 'drydep_vel'
         units    = 'cm/sec'
-        call metadata_set(attname, longname, stdname, units)
+        call metadata_set(seq_drydep_fields, longname, stdname, units)
 
      endif
      call seq_drydep_init( )
@@ -2368,7 +2365,8 @@ subroutine seq_flds_getField(outfield, nfld, cstring)
    end subroutine seq_flds_getField
 
    !===============================================================================
-
+! If the attname passed in contains colons it is assumed to be a list of fields 
+! all of which have the same names and units
    subroutine metadata_set(attname , longname, stdname , units   )
 
      ! !USES:
@@ -2382,19 +2380,35 @@ subroutine metadata_set(attname , longname, stdname , units   )
 
      !EOP
      character(len=*),parameter :: subname = '(seq_flds_metadata_set) '
-
+     integer :: i, j
+
+     i = index(attname,':')
+     j=1
+
+     do while(i>j .and. i<=len_trim(attname))
+        n_entries = n_entries + 1
+        lookup_entry(n_entries,1) = attname(j:i-1) 
+        lookup_entry(n_entries,2) = trim(longname)
+        lookup_entry(n_entries,3) = trim(stdname )
+        lookup_entry(n_entries,4) = trim(units   )
+        j=i+1
+        i =  index(attname(j:),':') + j - 1
+     enddo
      n_entries = n_entries + 1
-     if (n_entries > nmax) then
-        write(logunit,*)'n_entries= ',n_entries,' nmax = ',nmax,' attname= ',trim(attname)
-        call shr_sys_abort(subname//'ERROR: nmax fields in lookup_entry table exceeded') 
-     end if
-
-     lookup_entry(n_entries,1) = trim(attname )
+     i = len_trim(attname)
+     lookup_entry(n_entries,1) = attname(j:i)
      lookup_entry(n_entries,2) = trim(longname)
      lookup_entry(n_entries,3) = trim(stdname )
      lookup_entry(n_entries,4) = trim(units   )
 
 
+
+
+     if (n_entries .ge. nmax) then
+        write(logunit,*)'n_entries= ',n_entries,' nmax = ',nmax,' attname= ',trim(attname)
+        call shr_sys_abort(subname//'ERROR: nmax fields in lookup_entry table exceeded') 
+     end if
+
    end subroutine metadata_set
 
    !===============================================================================

diff --git a/scripts/Tools/cs.status b/scripts/Tools/cs.status
@@ -133,7 +133,7 @@ sub getTestStatus
 	my $testxml = $parser->parse_file($testlist);
 	@xfailnodes = $testxml->findnodes("//entry");
 	foreach my $xfailnode (@xfailnodes) {
-	    my @xfailchild_nodes = $xfailnode->childNodes();
+	    my @xfailchild_nodes = $xfailnode->findnodes(".//");
 	}
     }
 

diff --git a/scripts/Tools/xmlchange b/scripts/Tools/xmlchange
@@ -197,7 +197,7 @@ foreach my $id ( keys(%idlist) )
 	    # Do error checking for requested change
 	    my $value = $node->getAttribute('value');
 	    my($type, $valid_values, $is_list_value);
-	    foreach my $childnode ($node->childNodes()) 
+	    foreach my $childnode ($node->findnodes(".//*")) 
 	    {
 		if ($childnode->nodeName() eq 'type') {
 		    $type = $childnode->textContent();

diff --git a/scripts/create_test b/scripts/create_test
@@ -865,11 +865,11 @@ sub ExpandXmlList
     foreach my $compset_elem (@compset_elems) {
 	my $compset_val = $compset_elem->getAttribute('name');
 
-	my @grid_elems = $compset_elem->childNodes();
+	my @grid_elems = $compset_elem->findnodes(".//grid");
 	foreach my $grid_elem (@grid_elems) {
 	    my $grid_val  = $grid_elem->getAttribute('name');
 
-	    my @test_elems = $grid_elem->childNodes();
+	    my @test_elems = $grid_elem->findnodes(".//test");
 	    foreach my $test_elem (@test_elems) {
 		my $test_val  = $test_elem->getAttribute('name');
 		if ($opts{'nlcompareonly'}) {
@@ -881,7 +881,7 @@ sub ExpandXmlList
 		    }
 		}
 
-		my @mach_elems = $test_elem->childNodes();
+		my @mach_elems = $test_elem->findnodes(".//machine");
 		foreach my $mach_elem (@mach_elems) {
 		    my $machine_val  = $mach_elem->textContent();
 		    my $testtype_val = $mach_elem->getAttribute('testtype');

diff --git a/scripts/manage_case b/scripts/manage_case
@@ -304,7 +304,7 @@ sub _queryGrids
 	    print " component grid: $name \n";
 	}	    
 	my $support; my $nx; my $ny; my $desc;
-	foreach my $child_node ($node->childNodes()) {
+	foreach my $child_node ($node->findnodes(".//*")) {
 	    my $name  = $child_node->nodeName();
 	    my $value = $child_node->textContent();
 	    if ($name eq 'support') {$support= $value;}

diff --git a/scripts/manage_pes b/scripts/manage_pes
@@ -443,7 +443,7 @@ sub formattedOutput {
 	       }
 	       foreach my $element ('ntasks','nthrds','rootpe') {
 		   foreach my $node_ntasks ($pes_node->findnodes("./$element")) {
-		       my @child_nodes = $node_ntasks->childNodes();
+		       my @child_nodes = $node_ntasks->findnodes(".//");
 		       foreach my $child_node (@child_nodes) {
 			   my $name  = $child_node->nodeName();
 			   my $value = $child_node->textContent();

diff --git a/utils/perl5lib/Batch/BatchMaker.pm b/utils/perl5lib/Batch/BatchMaker.pm
@@ -513,6 +513,11 @@ sub setQueue()
     # Get the queue from env_batch.xml if its defined there
     # otherwise get the default from config_machines.xml
     # and set it in env_batch.xml
+    if(! defined $self->{envBatch}){
+	$logger->logdie("envBatch not defined");
+    }elsif(! defined $self->{job}){
+	$logger->logdie("job not defined");
+    }
 
     my $queue = $self->{envBatch}{$self->{job}}{JOB_QUEUE};
 

diff --git a/utils/perl5lib/Config/ConfigCase.pm b/utils/perl5lib/Config/ConfigCase.pm
@@ -110,32 +110,33 @@ sub add_config_variables
     foreach my $node (@nodes) 
     {
 	my $id = $node->getAttribute('id');
-	foreach my $define_node ($node->childNodes()) 
+	foreach my $define_node ($node->findnodes(".//*")) 
 	{
 	    my $node_name  = $define_node->nodeName();
 	    #
             # This creates a hash of values with attribute name and id as keys
             #
 	    if($node_name eq "values"){
-		foreach my $val_node ($define_node->childNodes()){
+		foreach my $val_node ($define_node->findnodes(".//value")){
                     if($val_node->hasAttributes()){		 
-                    my @att = $val_node->attributes();
-		    foreach my $attstr (@att){
-			$attstr =~ /(\w+)=\"(.*)\"/;
-	                my $att = $1;
-	                my $att_val = $2;
-			my $val =  $val_node->textContent();		
-			$val =~ s/\$MODEL/$model/;
-			$val =~ s/\$CIMEROOT/$cimeroot/;
-			if (-d $srcroot) {
-			    $val =~ s/\$SRCROOT/$srcroot/;
-			}			
-			$self->{$id}{$att}{$att_val} = $val;
+			my @att = $val_node->attributes();
+			foreach my $attstr (@att){
+			    my $att = $attstr->nodeName();
+			    my $att_val = $attstr->getValue();
+			    my $val =  $val_node->textContent();		
+			    $val =~ s/\$MODEL/$model/;
+			    $val =~ s/\$CIMEROOT/$cimeroot/;
+			    if (-d $srcroot) {
+				$val =~ s/\$SRCROOT/$srcroot/;
+			    }			
+			    $self->{$id}{$att}{$att_val} = $val;
+			}
 		    }
-}
 		}
 
 	    }else{
+		# we want to avoid the 'value' nodes which are children of 'values'
+		next if($node_name eq 'value' and $define_node->parentNode() ne $node);
 		my $node_value = $define_node->textContent();
 		if (defined $node_value) {
 		    $node_value =~ s/\$MODEL/$model/;

diff --git a/utils/perl5lib/Config/ConfigCompsetGrid.pm b/utils/perl5lib/Config/ConfigCompsetGrid.pm
@@ -72,12 +72,9 @@ sub getCompsetLongname
 
 		$logger->logdie ("ERROR create_newcase: more than one match for compset alias $input_compset in file $file ");
 	    } else {
-		my @name_nodes = $alias_nodes[0]->childNodes();
+		my @name_nodes = $alias_nodes[0]->findnodes(".//lname");
 		foreach my $name_node (@name_nodes) {
-		    my $debug = $name_node->nodeName();
-		    if ($name_node->nodeName() eq 'lname') {
-			$compset_longname = $name_node->textContent();
-		    }		    
+		    $compset_longname = $name_node->textContent();
 		}
 	    }
 	    $pes_setby = $node_file->getAttribute('component');
@@ -93,12 +90,9 @@ sub getCompsetLongname
 	    if ($#lname_nodes > 0) {
 		die "ERROR create_newcase: more than one match for lname element in file $file \n";
 	    } else {
-		my @name_nodes = $lname_nodes[0]->childNodes();
+		my @name_nodes = $lname_nodes[0]->findnodes(".//lname");
 		foreach my $name_node (@name_nodes) {
-		    my $debug = $name_node->nodeName();
-		    if ($name_node->nodeName() eq 'lname') {
-			$compset_longname = $name_node->textContent();
-		    }		    
+		    $compset_longname = $name_node->textContent();
 		}
 	    }
 	    $pes_setby = $node_file->getAttribute('component');
@@ -194,7 +188,7 @@ sub getGridLongname
     }
 
     # set the compset grid alias and longname
-    foreach my $node ($grid_node->childNodes()) {
+    foreach my $node ($grid_node->findnodes(".//*")) {
 	my $name = $node->nodeName();
 	my $value = $node->textContent();
 	if ($name eq 'lname') {$grid_longname   = $node->textContent();}

diff --git a/utils/perl5lib/Config/ConfigPes.pm b/utils/perl5lib/Config/ConfigPes.pm
@@ -278,7 +278,7 @@ sub _setPESsettings
 
     foreach my $pes (@pes_ntasks, @pes_nthrds, @pes_rootpe) {
 	next if($pes->nodeType == XML_COMMENT_NODE);
-	my @children = $pes ->childNodes();
+	my @children = $pes ->findnodes(".//*");
 	foreach my $child (@children) {
 	    next if($child->nodeType == XML_COMMENT_NODE);
 	    my $name  = uc $child->nodeName();