From 5d1cdef530057f47678c6ccc26bdc3e1b8502eb9 Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 16 Oct 2012 12:54:25 +0100
Subject: [PATCH 1/4] STYLE: autoSnapDriver: unused var

---
 .../autoHexMesh/autoHexMeshDriver/autoSnapDriverFeature.C        | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/mesh/autoMesh/autoHexMesh/autoHexMeshDriver/autoSnapDriverFeature.C b/src/mesh/autoMesh/autoHexMesh/autoHexMeshDriver/autoSnapDriverFeature.C
index 828ee0e710..8bcd9c6270 100644
--- a/src/mesh/autoMesh/autoHexMesh/autoHexMeshDriver/autoSnapDriverFeature.C
+++ b/src/mesh/autoMesh/autoHexMesh/autoHexMeshDriver/autoSnapDriverFeature.C
@@ -2655,7 +2655,6 @@ Foam::vectorField Foam::autoSnapDriver::calcNearestSurfaceFeature
         }
 
         // Remove any meshed faces
-        PackedBoolList ppFaces(mesh.nFaces());
         forAll(pp.addressing(), i)
         {
             label meshFaceI = pp.addressing()[i];

From 9ff9a41b7b8d3b28ec1fc37467b06199e76fb56f Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 16 Oct 2012 12:54:58 +0100
Subject: [PATCH 2/4] BUG: inplaceExpand: update index after replacement

---
 src/OpenFOAM/primitives/strings/stringOps/stringOps.C | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/OpenFOAM/primitives/strings/stringOps/stringOps.C b/src/OpenFOAM/primitives/strings/stringOps/stringOps.C
index f44ffe3a6b..b7e11d644f 100644
--- a/src/OpenFOAM/primitives/strings/stringOps/stringOps.C
+++ b/src/OpenFOAM/primitives/strings/stringOps/stringOps.C
@@ -398,6 +398,8 @@ Foam::string& Foam::stringOps::inplaceExpand
                     begVar - stringStart + 1,
                     varValue
                 );
+
+                begVar = stringStart+varValue.size();
             }
             else
             {
@@ -744,8 +746,7 @@ Foam::string& Foam::stringOps::inplaceExpand
                     FatalErrorIn
                     (
                         "stringOps::inplaceExpand(string&, const bool)"
-                    )
-                        << "Unknown variable name '" << varName << "'"
+                    )   << "Unknown variable name '" << varName << "'"
                         << exit(FatalError);
                 }
             }

From e4f7c306ab8f28040a63866defafc9687fbb4a2d Mon Sep 17 00:00:00 2001
From: mattijs <mattijs>
Date: Tue, 16 Oct 2012 14:15:14 +0100
Subject: [PATCH 3/4] BUG: Time: have separate timer for secondary write
 interval

---
 src/OpenFOAM/db/Time/Time.C      | 44 +++++++++++++++++++++-----------
 src/OpenFOAM/db/Time/TimeIO.C    | 22 ++++++++++++++++
 src/OpenFOAM/db/Time/TimeState.C |  3 ++-
 src/OpenFOAM/db/Time/TimeState.H |  4 +--
 4 files changed, 55 insertions(+), 18 deletions(-)

diff --git a/src/OpenFOAM/db/Time/Time.C b/src/OpenFOAM/db/Time/Time.C
index 19a6c2b321..155c4c2eb4 100644
--- a/src/OpenFOAM/db/Time/Time.C
+++ b/src/OpenFOAM/db/Time/Time.C
@@ -79,21 +79,35 @@ Foam::word Foam::Time::controlDictName("controlDict");
 
 void Foam::Time::adjustDeltaT()
 {
+    bool adjustTime = false;
+    scalar timeToNextWrite = VGREAT;
+
     if (writeControl_ == wcAdjustableRunTime)
     {
-        scalar interval = writeInterval_;
-        if (secondaryWriteControl_ == wcAdjustableRunTime)
-        {
-            interval = min(interval, secondaryWriteInterval_);
-        }
-
-
-        scalar timeToNextWrite = max
+        adjustTime = true;
+        timeToNextWrite = max
         (
             0.0,
-            (outputTimeIndex_ + 1)*interval - (value() - startTime_)
+            (outputTimeIndex_ + 1)*writeInterval_ - (value() - startTime_)
         );
+    }
+    if (secondaryWriteControl_ == wcAdjustableRunTime)
+    {
+        adjustTime = true;
+        timeToNextWrite = max
+        (
+            0.0,
+            min
+            (
+                timeToNextWrite,
+                (secondaryOutputTimeIndex_ + 1)*secondaryWriteInterval_
+              - (value() - startTime_)
+            )
+        );
+    }
 
+    if (adjustTime)
+    {
         scalar nSteps = timeToNextWrite/deltaT_ - SMALL;
 
         // For tiny deltaT the label can overflow!
@@ -1130,10 +1144,10 @@ Foam::Time& Foam::Time::operator++()
                   / secondaryWriteInterval_
                 );
 
-                if (outputIndex > outputTimeIndex_)
+                if (outputIndex > secondaryOutputTimeIndex_)
                 {
                     outputTime_ = true;
-                    outputTimeIndex_ = outputIndex;
+                    secondaryOutputTimeIndex_ = outputIndex;
                 }
             }
             break;
@@ -1145,10 +1159,10 @@ Foam::Time& Foam::Time::operator++()
                     returnReduce(elapsedCpuTime(), maxOp<double>())
                   / secondaryWriteInterval_
                 );
-                if (outputIndex > outputTimeIndex_)
+                if (outputIndex > secondaryOutputTimeIndex_)
                 {
                     outputTime_ = true;
-                    outputTimeIndex_ = outputIndex;
+                    secondaryOutputTimeIndex_ = outputIndex;
                 }
             }
             break;
@@ -1160,10 +1174,10 @@ Foam::Time& Foam::Time::operator++()
                     returnReduce(label(elapsedClockTime()), maxOp<label>())
                   / secondaryWriteInterval_
                 );
-                if (outputIndex > outputTimeIndex_)
+                if (outputIndex > secondaryOutputTimeIndex_)
                 {
                     outputTime_ = true;
-                    outputTimeIndex_ = outputIndex;
+                    secondaryOutputTimeIndex_ = outputIndex;
                 }
             }
             break;
diff --git a/src/OpenFOAM/db/Time/TimeIO.C b/src/OpenFOAM/db/Time/TimeIO.C
index 00f1beefbe..6a80618404 100644
--- a/src/OpenFOAM/db/Time/TimeIO.C
+++ b/src/OpenFOAM/db/Time/TimeIO.C
@@ -51,6 +51,8 @@ void Foam::Time::readDict()
     }
 
     scalar oldWriteInterval = writeInterval_;
+    scalar oldSecondaryWriteInterval = secondaryWriteInterval_;
+
     if (controlDict_.readIfPresent("writeInterval", writeInterval_))
     {
         if (writeControl_ == wcTimeStep && label(writeInterval_) < 1)
@@ -124,6 +126,26 @@ void Foam::Time::readDict()
             break;
         }
     }
+    if (oldSecondaryWriteInterval != secondaryWriteInterval_)
+    {
+        switch (secondaryWriteControl_)
+        {
+            case wcRunTime:
+            case wcAdjustableRunTime:
+                // Recalculate secondaryOutputTimeIndex_ to be in units of
+                // current writeInterval.
+                secondaryOutputTimeIndex_ = label
+                (
+                    secondaryOutputTimeIndex_
+                  * oldSecondaryWriteInterval
+                  / secondaryWriteInterval_
+                );
+            break;
+
+            default:
+            break;
+        }
+    }
 
     if (controlDict_.readIfPresent("purgeWrite", purgeWrite_))
     {
diff --git a/src/OpenFOAM/db/Time/TimeState.C b/src/OpenFOAM/db/Time/TimeState.C
index b02b87bbfc..500ca47d43 100644
--- a/src/OpenFOAM/db/Time/TimeState.C
+++ b/src/OpenFOAM/db/Time/TimeState.C
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -37,6 +37,7 @@ Foam::TimeState::TimeState()
     deltaT0_(0),
     deltaTchanged_(false),
     outputTimeIndex_(0),
+    secondaryOutputTimeIndex_(0),
     outputTime_(false)
 {}
 
diff --git a/src/OpenFOAM/db/Time/TimeState.H b/src/OpenFOAM/db/Time/TimeState.H
index 1c59ca85a3..d721529480 100644
--- a/src/OpenFOAM/db/Time/TimeState.H
+++ b/src/OpenFOAM/db/Time/TimeState.H
@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2011 OpenFOAM Foundation
+    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -61,9 +61,9 @@ protected:
         bool deltaTchanged_;
 
         label outputTimeIndex_;
+        label secondaryOutputTimeIndex_;
         bool  outputTime_;
 
-
 public:
 
     // Constructors

From e4a3348ca2002c74ccd171e87cbe3bacbe11852e Mon Sep 17 00:00:00 2001
From: laurence <laurence>
Date: Tue, 16 Oct 2012 14:34:38 +0100
Subject: [PATCH 4/4] ENH: mpirunDebug: Add gperftools option

gperftools comes with a profiler. It should be installed in ThirdParty.
Then link the executable to libprofiler.so, run it and view the output
using kcachegrind.
---
 bin/mpirunDebug | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/bin/mpirunDebug b/bin/mpirunDebug
index a7a0cb32b0..7911e06e98 100755
--- a/bin/mpirunDebug
+++ b/bin/mpirunDebug
@@ -100,10 +100,10 @@ echo "run $args" > $PWD/gdbCommands
 echo "where" >> $PWD/gdbCommands
 echo "Constructed gdb initialization file $PWD/gdbCommands"
 
-$ECHO "Choose running method: 0)normal  1)gdb+xterm  2)gdb  3)log  4)log+xterm  5)xterm+valgrind: \c"
+$ECHO "Choose running method: 0)normal  1)gdb+xterm  2)gdb  3)log  4)log+xterm  5)xterm+valgrind  6)gperftools(callgrind): \c"
 read method
 case "$method" in
-0 | 1 | 2 | 3 | 4 | 5 )
+0 | 1 | 2 | 3 | 4 | 5 | 6)
     # okay
     ;;
 *)
@@ -199,6 +199,11 @@ do
         echo "$sourceFoam; cd $PWD; valgrind $exec $args; read dummy" >> $procCmdFile
         echo "${node}xterm -font fixed -title 'processor'$proc $geom -e $procCmdFile" >> $PWD/mpirun.schema
         ;;
+    6)
+        echo "$sourceFoam; cd $PWD; CPUPROFILE=log.profiler_$proc $exec $args; \
+             pprof --callgrind $exec log.profiler_$proc > log.profiler_$proc.callgrind;" >> $procCmdFile
+        echo "${node}$procCmdFile" >> $PWD/mpirun.schema
+        ;;
     esac
 
     chmod +x $procCmdFile