From 27c15c16b3c7a7b1ffb5b3c4aaf315837d9ee1af Mon Sep 17 00:00:00 2001
From: "Victor A. P. Magri" <paludettomag1@llnl.gov>
Date: Fri, 6 Dec 2024 00:12:13 -0500
Subject: [PATCH 1/7] Add timing statistics for output file writing

---
 .../fileIO/Outputs/OutputBase.cpp             | 22 +++++++++++++++++
 .../fileIO/Outputs/OutputBase.hpp             | 22 ++++++++++++++++-
 .../fileIO/Outputs/VTKOutput.cpp              | 24 ++++++++++++-------
 .../fileIO/Outputs/VTKOutput.hpp              |  3 +++
 4 files changed, 61 insertions(+), 10 deletions(-)

diff --git a/src/coreComponents/fileIO/Outputs/OutputBase.cpp b/src/coreComponents/fileIO/Outputs/OutputBase.cpp
index 0733dd38cc5..2f4f9940d39 100644
--- a/src/coreComponents/fileIO/Outputs/OutputBase.cpp
+++ b/src/coreComponents/fileIO/Outputs/OutputBase.cpp
@@ -18,6 +18,7 @@
  */
 
 #include "OutputBase.hpp"
+#include "common/Timer.hpp"
 #include "common/MpiWrapper.hpp"
 #include "functions/FunctionBase.hpp"
 
@@ -29,6 +30,7 @@ using namespace dataRepository;
 OutputBase::OutputBase( string const & name,
                         Group * const parent ):
   ExecutableGroup( name, parent ),
+  m_outputTimer(),
   m_childDirectory(),
   m_parallelThreads( 1 )
 {
@@ -43,6 +45,8 @@ OutputBase::OutputBase( string const & name,
     setInputFlag( InputFlags::OPTIONAL ).
     setDescription( "Number of plot files." );
 
+  // Add the Timers log level
+  addLogLevel< logInfo::OutputTimers >();
 }
 
 OutputBase::~OutputBase()
@@ -106,5 +110,23 @@ void OutputBase::setupDirectoryStructure()
   }
 }
 
+void OutputBase::cleanup( real64 const GEOS_UNUSED_PARAM( time_n ),
+                          integer const GEOS_UNUSED_PARAM( cycleNumber ),
+                          integer const GEOS_UNUSED_PARAM( eventCounter ),
+                          real64 const GEOS_UNUSED_PARAM( eventProgress ),
+                          DomainPartition & GEOS_UNUSED_PARAM( domain ) )
+{
+  // Report timing statistics
+  real64 const time = std::chrono::duration< double >( m_outputTimer ).count();
+  real64 const minTime = MpiWrapper::min( time );
+  real64 const maxTime = MpiWrapper::max( time );
+  if( maxTime > 0 )
+  {
+    GEOS_LOG_LEVEL_INFO_RANK_0( logInfo::OutputTimers,
+                               GEOS_FMT( "{}: file writing time = {} s (min), {} s (max)",
+                                        getName(), minTime, maxTime ) );
+  }
+}
+
 
 } /* namespace geos */
diff --git a/src/coreComponents/fileIO/Outputs/OutputBase.hpp b/src/coreComponents/fileIO/Outputs/OutputBase.hpp
index f4129433f7d..42580bae2ac 100644
--- a/src/coreComponents/fileIO/Outputs/OutputBase.hpp
+++ b/src/coreComponents/fileIO/Outputs/OutputBase.hpp
@@ -21,11 +21,21 @@
 
 #include "dataRepository/Group.hpp"
 #include "dataRepository/ExecutableGroup.hpp"
-
+#include "dataRepository/LogLevelsInfo.hpp"  // For logInfo namespace
+#include "common/Timer.hpp"
 
 namespace geos
 {
 
+namespace logInfo
+{
+struct OutputTimers
+{
+  static constexpr int getMinLogLevel() { return 1; }
+  static constexpr std::string_view getDescription() { return "Output timers information"; }
+};
+}
+
 /**
  * @class OutputBase
  *
@@ -102,6 +112,16 @@ class OutputBase : public ExecutableGroup
    **/
   virtual void initializePreSubGroups() override;
 
+  // Timer used to track duration of output operations
+  std::chrono::system_clock::duration m_outputTimer;
+
+  /// @copydoc geos::ExecutableGroup::cleanup
+  virtual void cleanup( real64 const time_n,
+                        integer const cycleNumber,
+                        integer const eventCounter,
+                        real64 const eventProgress,
+                        DomainPartition & domain ) override;
+
 private:
   string m_childDirectory;
   integer m_parallelThreads;
diff --git a/src/coreComponents/fileIO/Outputs/VTKOutput.cpp b/src/coreComponents/fileIO/Outputs/VTKOutput.cpp
index 15e4b1dac13..8b4ffec9fc1 100644
--- a/src/coreComponents/fileIO/Outputs/VTKOutput.cpp
+++ b/src/coreComponents/fileIO/Outputs/VTKOutput.cpp
@@ -80,7 +80,7 @@ VTKOutput::VTKOutput( string const & name,
   registerWrapper( viewKeysStruct::fieldNames, &m_fieldNames ).
     setRTTypeName( rtTypes::CustomTypes::groupNameRefArray ).
     setInputFlag( InputFlags::OPTIONAL ).
-    setDescription( "Names of the fields to output. If this attribute is specified, GEOSX outputs all the fields specified by the user, regardless of their `plotLevel`" );
+    setDescription( "Names of the fields to output. If this attribute is specified, GEOS outputs all the fields specified by the user, regardless of their `plotLevel`" );
 
   registerWrapper( viewKeysStruct::levelNames, &m_levelNames ).
     setInputFlag( InputFlags::OPTIONAL ).
@@ -159,14 +159,20 @@ bool VTKOutput::execute( real64 const time_n,
                          real64 const GEOS_UNUSED_PARAM ( eventProgress ),
                          DomainPartition & domain )
 {
-  GEOS_LOG_LEVEL_RANK_0( 1, GEOS_FMT( "{}: writing {} at time {} s (cycle number {})", getName(), m_fieldNames, time_n + dt, cycleNumber ));
-
-  m_writer.setWriteGhostCells( m_writeGhostCells );
-  m_writer.setWriteFaceElementsAs3D ( m_writeFaceElementsAs3D );
-  m_writer.setOutputMode( m_writeBinaryData );
-  m_writer.setOutputRegionType( m_outputRegionType );
-  m_writer.setPlotLevel( m_plotLevel );
-  m_writer.write( time_n, cycleNumber, domain );
+  GEOS_MARK_FUNCTION;
+
+  GEOS_LOG_LEVEL_RANK_0( 2, GEOS_FMT( "{}: writing {} at time {} s (cycle number {})", getName(), m_fieldNames, time_n + dt, cycleNumber ));
+
+  {
+    Timer timer( m_outputTimer );
+
+    m_writer.setWriteGhostCells( m_writeGhostCells );
+    m_writer.setWriteFaceElementsAs3D ( m_writeFaceElementsAs3D );
+    m_writer.setOutputMode( m_writeBinaryData );
+    m_writer.setOutputRegionType( m_outputRegionType );
+    m_writer.setPlotLevel( m_plotLevel );
+    m_writer.write( time_n, cycleNumber, domain );
+  }
 
   return false;
 }
diff --git a/src/coreComponents/fileIO/Outputs/VTKOutput.hpp b/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
index 5b167dc66d6..8778b722b6d 100644
--- a/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
@@ -77,6 +77,9 @@ class VTKOutput : public OutputBase
                         DomainPartition & domain ) override
   {
     execute( time_n, 0, cycleNumber, eventCounter, eventProgress, domain );
+
+    // Call parent class cleanup to get the timing statistics
+    OutputBase::cleanup(time_n, cycleNumber, eventCounter, eventProgress, domain);
   }
 
   /**

From fe465f2969e09f20feb65eb670a69506184a03c4 Mon Sep 17 00:00:00 2001
From: "Victor A. P. Magri" <50467563+victorapm@users.noreply.github.com>
Date: Thu, 5 Dec 2024 21:15:25 -0800
Subject: [PATCH 2/7] Remove redundant include

---
 src/coreComponents/fileIO/Outputs/OutputBase.cpp | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/coreComponents/fileIO/Outputs/OutputBase.cpp b/src/coreComponents/fileIO/Outputs/OutputBase.cpp
index 2f4f9940d39..15c6b894507 100644
--- a/src/coreComponents/fileIO/Outputs/OutputBase.cpp
+++ b/src/coreComponents/fileIO/Outputs/OutputBase.cpp
@@ -18,7 +18,6 @@
  */
 
 #include "OutputBase.hpp"
-#include "common/Timer.hpp"
 #include "common/MpiWrapper.hpp"
 #include "functions/FunctionBase.hpp"
 

From 5ca998ef71b0f2e53bbbb080937a2ac5d6dcfb63 Mon Sep 17 00:00:00 2001
From: "Victor A. P. Magri" <paludettomag1@llnl.gov>
Date: Fri, 6 Dec 2024 00:19:02 -0500
Subject: [PATCH 3/7] Style

---
 src/coreComponents/fileIO/Outputs/OutputBase.cpp | 4 ++--
 src/coreComponents/fileIO/Outputs/VTKOutput.hpp  | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/coreComponents/fileIO/Outputs/OutputBase.cpp b/src/coreComponents/fileIO/Outputs/OutputBase.cpp
index 2f4f9940d39..8f26401ad3a 100644
--- a/src/coreComponents/fileIO/Outputs/OutputBase.cpp
+++ b/src/coreComponents/fileIO/Outputs/OutputBase.cpp
@@ -123,8 +123,8 @@ void OutputBase::cleanup( real64 const GEOS_UNUSED_PARAM( time_n ),
   if( maxTime > 0 )
   {
     GEOS_LOG_LEVEL_INFO_RANK_0( logInfo::OutputTimers,
-                               GEOS_FMT( "{}: file writing time = {} s (min), {} s (max)",
-                                        getName(), minTime, maxTime ) );
+                                GEOS_FMT( "{}: file writing time = {} s (min), {} s (max)",
+                                          getName(), minTime, maxTime ) );
   }
 }
 
diff --git a/src/coreComponents/fileIO/Outputs/VTKOutput.hpp b/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
index 8778b722b6d..b53ff6c2c78 100644
--- a/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
@@ -79,7 +79,7 @@ class VTKOutput : public OutputBase
     execute( time_n, 0, cycleNumber, eventCounter, eventProgress, domain );
 
     // Call parent class cleanup to get the timing statistics
-    OutputBase::cleanup(time_n, cycleNumber, eventCounter, eventProgress, domain);
+    OutputBase::cleanup( time_n, cycleNumber, eventCounter, eventProgress, domain );
   }
 
   /**

From 1f6f99c3a2cee66b2c0565ab67552ddbe91d99f2 Mon Sep 17 00:00:00 2001
From: "Victor A. P. Magri" <paludettomag1@llnl.gov>
Date: Fri, 6 Dec 2024 00:24:05 -0500
Subject: [PATCH 4/7] Documentation

---
 src/coreComponents/fileIO/Outputs/OutputBase.hpp | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/coreComponents/fileIO/Outputs/OutputBase.hpp b/src/coreComponents/fileIO/Outputs/OutputBase.hpp
index 42580bae2ac..8c515688732 100644
--- a/src/coreComponents/fileIO/Outputs/OutputBase.hpp
+++ b/src/coreComponents/fileIO/Outputs/OutputBase.hpp
@@ -29,9 +29,22 @@ namespace geos
 
 namespace logInfo
 {
+/**
+ * @brief Log information structure for output timing data
+ * @details Provides configuration for logging output operation timing information
+ */
 struct OutputTimers
 {
+  /**
+   * @brief Get the minimum log level for output timing information
+   * @return The minimum log level
+   */
   static constexpr int getMinLogLevel() { return 1; }
+
+  /**
+   * @brief Get the description of this timing category
+   * @return Description string for output timing information
+   */
   static constexpr std::string_view getDescription() { return "Output timers information"; }
 };
 }
@@ -112,7 +125,7 @@ class OutputBase : public ExecutableGroup
    **/
   virtual void initializePreSubGroups() override;
 
-  // Timer used to track duration of output operations
+  /// Timer used to track duration of file writing operations
   std::chrono::system_clock::duration m_outputTimer;
 
   /// @copydoc geos::ExecutableGroup::cleanup

From 7d8677d89139f7d7c745c84ab91019eb1cdf8436 Mon Sep 17 00:00:00 2001
From: "Victor A. P. Magri" <paludettomag1@llnl.gov>
Date: Fri, 6 Dec 2024 11:10:32 -0500
Subject: [PATCH 5/7] Implement timers for all possible outputs

---
 .../fileIO/Outputs/BlueprintOutput.cpp        | 84 +++++++++++--------
 .../fileIO/Outputs/BlueprintOutput.hpp        |  3 +
 .../fileIO/Outputs/ChomboIO.cpp               | 14 ++++
 .../fileIO/Outputs/ChomboIO.hpp               |  3 +
 .../fileIO/Outputs/OutputBase.hpp             | 29 ++++---
 .../fileIO/Outputs/PythonOutput.cpp           | 14 ++++
 .../fileIO/Outputs/PythonOutput.hpp           |  3 +
 .../fileIO/Outputs/RestartOutput.cpp          | 29 +++++--
 .../fileIO/Outputs/RestartOutput.hpp          |  3 +
 .../fileIO/Outputs/SiloOutput.cpp             | 68 +++++++++------
 .../fileIO/Outputs/SiloOutput.hpp             |  3 +
 .../fileIO/Outputs/TimeHistoryOutput.cpp      | 28 ++++++-
 .../fileIO/Outputs/TimeHistoryOutput.hpp      |  3 +
 .../fileIO/Outputs/VTKOutput.cpp              | 14 ++++
 .../fileIO/Outputs/VTKOutput.hpp              |  3 +
 15 files changed, 219 insertions(+), 82 deletions(-)

diff --git a/src/coreComponents/fileIO/Outputs/BlueprintOutput.cpp b/src/coreComponents/fileIO/Outputs/BlueprintOutput.cpp
index 21457e7796e..cad26fcbb54 100644
--- a/src/coreComponents/fileIO/Outputs/BlueprintOutput.cpp
+++ b/src/coreComponents/fileIO/Outputs/BlueprintOutput.cpp
@@ -129,53 +129,57 @@ BlueprintOutput::BlueprintOutput( string const & name,
 }
 
 ///////////////////////////////////////////////////////////////////////////////////////////////////
-bool BlueprintOutput::execute( real64 const time,
-                               real64 const,
-                               integer const cycle,
-                               integer const,
-                               real64 const,
+bool BlueprintOutput::execute( real64 const time_n,
+                               real64 const GEOS_UNUSED_PARAM( dt ),
+                               integer const cycleNumber,
+                               integer const GEOS_UNUSED_PARAM( eventCounter ),
+                               real64 const GEOS_UNUSED_PARAM( eventProgress ),
                                DomainPartition & domain )
 {
   GEOS_MARK_FUNCTION;
 
-  MeshLevel const & meshLevel = domain.getMeshBody( 0 ).getBaseDiscretization();
+  {
+    Timer timer( m_outputTimer );
 
-  conduit::Node meshRoot;
-  conduit::Node & mesh = meshRoot[ "mesh" ];
-  conduit::Node & coordset = mesh[ "coordsets/nodes" ];
-  conduit::Node & topologies = mesh[ "topologies" ];
+    MeshLevel const & meshLevel = domain.getMeshBody( 0 ).getBaseDiscretization();
 
-  mesh[ "state/time" ] = time;
-  mesh[ "state/cycle" ] = cycle;
+    conduit::Node meshRoot;
+    conduit::Node & mesh = meshRoot[ "mesh" ];
+    conduit::Node & coordset = mesh[ "coordsets/nodes" ];
+    conduit::Node & topologies = mesh[ "topologies" ];
 
-  addNodalData( meshLevel.getNodeManager(), coordset, topologies, mesh[ "fields" ] );
+    mesh[ "state/time" ] = time_n;
+    mesh[ "state/cycle" ] = cycleNumber;
 
-  dataRepository::Group averagedElementData( "averagedElementData", this );
-  addElementData( meshLevel.getElemManager(), coordset, topologies, mesh[ "fields" ], averagedElementData );
+    addNodalData( meshLevel.getNodeManager(), coordset, topologies, mesh[ "fields" ] );
 
-  /// The Blueprint will complain if the fields node is present but empty.
-  if( mesh[ "fields" ].number_of_children() == 0 )
-  {
-    mesh.remove( "fields" );
-  }
+    dataRepository::Group averagedElementData( "averagedElementData", this );
+    addElementData( meshLevel.getElemManager(), coordset, topologies, mesh[ "fields" ], averagedElementData );
+
+    /// The Blueprint will complain if the fields node is present but empty.
+    if( mesh[ "fields" ].number_of_children() == 0 )
+    {
+      mesh.remove( "fields" );
+    }
 
-  /// Verify that the mesh conforms to the Blueprint.
-  conduit::Node info;
-  GEOS_ASSERT_MSG( conduit::blueprint::verify( "mesh", meshRoot, info ), info.to_json() );
+    /// Verify that the mesh conforms to the Blueprint.
+    conduit::Node info;
+    GEOS_ASSERT_MSG( conduit::blueprint::verify( "mesh", meshRoot, info ), info.to_json() );
 
-  /// Generate the Blueprint index.
-  conduit::Node fileRoot;
-  conduit::Node & index = fileRoot[ "blueprint_index/mesh" ];
-  conduit::blueprint::mesh::generate_index( mesh, "mesh", MpiWrapper::commSize(), index );
+    /// Generate the Blueprint index.
+    conduit::Node fileRoot;
+    conduit::Node & index = fileRoot[ "blueprint_index/mesh" ];
+    conduit::blueprint::mesh::generate_index( mesh, "mesh", MpiWrapper::commSize(), index );
 
-  /// Verify that the index conforms to the Blueprint.
-  info.reset();
-  GEOS_ASSERT_MSG( conduit::blueprint::mesh::index::verify( index, info ), info.to_json() );
+    /// Verify that the index conforms to the Blueprint.
+    info.reset();
+    GEOS_ASSERT_MSG( conduit::blueprint::mesh::index::verify( index, info ), info.to_json() );
 
-  /// Write out the root index file, then write out the mesh.
-  string const completePath = GEOS_FMT( "{}/blueprintFiles/cycle_{:07}", OutputBase::getOutputDirectory(), cycle );
-  string const filePathForRank = dataRepository::writeRootFile( fileRoot, completePath );
-  conduit::relay::io::save( meshRoot, filePathForRank, "hdf5" );
+    /// Write out the root index file, then write out the mesh.
+    string const completePath = GEOS_FMT( "{}/blueprintFiles/cycle_{:07}", OutputBase::getOutputDirectory(), cycleNumber );
+    string const filePathForRank = dataRepository::writeRootFile( fileRoot, completePath );
+    conduit::relay::io::save( meshRoot, filePathForRank, "hdf5" );
+  }
 
   return false;
 }
@@ -307,7 +311,19 @@ void BlueprintOutput::writeOutConstitutiveData( dataRepository::Group const & co
   } );
 }
 
+namespace logInfo
+{
+struct BlueprintOutputTimer : public OutputTimerBase
+{
+  std::string_view getDescription() const override { return "Blueprint output timing"; }
+};
+}
 
+logInfo::OutputTimerBase const & BlueprintOutput::getTimerCategory() const
+{
+  static logInfo::BlueprintOutputTimer timer;
+  return timer;
+}
 
 REGISTER_CATALOG_ENTRY( OutputBase, BlueprintOutput, string const &, dataRepository::Group * const )
 
diff --git a/src/coreComponents/fileIO/Outputs/BlueprintOutput.hpp b/src/coreComponents/fileIO/Outputs/BlueprintOutput.hpp
index 7d17570d47d..e8e8f558a24 100644
--- a/src/coreComponents/fileIO/Outputs/BlueprintOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/BlueprintOutput.hpp
@@ -36,6 +36,9 @@ class ElementRegionManager;
  */
 class BlueprintOutput : public OutputBase
 {
+protected:
+  logInfo::OutputTimerBase const & getTimerCategory() const override;
+
 public:
 
   /**
diff --git a/src/coreComponents/fileIO/Outputs/ChomboIO.cpp b/src/coreComponents/fileIO/Outputs/ChomboIO.cpp
index 674f1e4eace..26f73a9eb43 100644
--- a/src/coreComponents/fileIO/Outputs/ChomboIO.cpp
+++ b/src/coreComponents/fileIO/Outputs/ChomboIO.cpp
@@ -30,6 +30,20 @@ namespace geos
 
 using namespace dataRepository;
 
+namespace logInfo
+{
+struct ChomboOutputTimer : public OutputTimerBase
+{
+  std::string_view getDescription() const override { return "Chombo output timing"; }
+};
+}
+
+logInfo::OutputTimerBase const & ChomboIO::getTimerCategory() const
+{
+  static logInfo::ChomboOutputTimer timer;
+  return timer;
+}
+
 ChomboIO::ChomboIO( string const & name, Group * const parent ):
   OutputBase( name, parent ),
   m_coupler( nullptr ),
diff --git a/src/coreComponents/fileIO/Outputs/ChomboIO.hpp b/src/coreComponents/fileIO/Outputs/ChomboIO.hpp
index c483f066968..f9c331fb58c 100644
--- a/src/coreComponents/fileIO/Outputs/ChomboIO.hpp
+++ b/src/coreComponents/fileIO/Outputs/ChomboIO.hpp
@@ -89,6 +89,9 @@ class ChomboIO final : public OutputBase
   } viewKeys;
   /// @endcond
 
+protected:
+  logInfo::OutputTimerBase const & getTimerCategory() const override;
+
 private:
   ChomboCoupler * m_coupler;
   string m_outputPath;
diff --git a/src/coreComponents/fileIO/Outputs/OutputBase.hpp b/src/coreComponents/fileIO/Outputs/OutputBase.hpp
index 8c515688732..1146d8aef6c 100644
--- a/src/coreComponents/fileIO/Outputs/OutputBase.hpp
+++ b/src/coreComponents/fileIO/Outputs/OutputBase.hpp
@@ -30,22 +30,26 @@ namespace geos
 namespace logInfo
 {
 /**
- * @brief Log information structure for output timing data
+ * @brief Base timer category for output operations
  * @details Provides configuration for logging output operation timing information
  */
 struct OutputTimers
 {
-  /**
-   * @brief Get the minimum log level for output timing information
-   * @return The minimum log level
-   */
+  static std::string_view getDescription() { return "Output timing information"; }
   static constexpr int getMinLogLevel() { return 1; }
+};
 
-  /**
-   * @brief Get the description of this timing category
-   * @return Description string for output timing information
-   */
-  static constexpr std::string_view getDescription() { return "Output timers information"; }
+/**
+ * @brief Base interface for specific output type timers
+ * @details Each output type (VTK, Silo, etc.) implements this interface to provide
+ *          its own timing category. This is used in conjunction with OutputTimers:
+ *          - OutputTimerBase: For polymorphic behavior in derived output classes
+ *          - OutputTimers: For the general output timing logging infrastructure
+ */
+struct OutputTimerBase
+{
+  virtual std::string_view getDescription() const = 0;
+  virtual ~OutputTimerBase() = default;
 };
 }
 
@@ -125,9 +129,12 @@ class OutputBase : public ExecutableGroup
    **/
   virtual void initializePreSubGroups() override;
 
-  /// Timer used to track duration of file writing operations
+  /// Timer used to track duration of file writing operations for this specific output type
   std::chrono::system_clock::duration m_outputTimer;
 
+  /// Get the timer category for this specific output type
+  virtual logInfo::OutputTimerBase const & getTimerCategory() const = 0;
+
   /// @copydoc geos::ExecutableGroup::cleanup
   virtual void cleanup( real64 const time_n,
                         integer const cycleNumber,
diff --git a/src/coreComponents/fileIO/Outputs/PythonOutput.cpp b/src/coreComponents/fileIO/Outputs/PythonOutput.cpp
index e78f8835a06..5891fe55e26 100644
--- a/src/coreComponents/fileIO/Outputs/PythonOutput.cpp
+++ b/src/coreComponents/fileIO/Outputs/PythonOutput.cpp
@@ -18,6 +18,20 @@
 namespace geos
 {
 
+namespace logInfo
+{
+struct PythonOutputTimer : public OutputTimerBase
+{
+  std::string_view getDescription() const override { return "Python output timing"; }
+};
+}
+
+logInfo::OutputTimerBase const & PythonOutput::getTimerCategory() const
+{
+  static logInfo::PythonOutputTimer timer;
+  return timer;
+}
+
 REGISTER_CATALOG_ENTRY( OutputBase, PythonOutput, string const &, dataRepository::Group * const )
 
 } // namespace geos
diff --git a/src/coreComponents/fileIO/Outputs/PythonOutput.hpp b/src/coreComponents/fileIO/Outputs/PythonOutput.hpp
index 0e6c3cebb85..a73b6781654 100644
--- a/src/coreComponents/fileIO/Outputs/PythonOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/PythonOutput.hpp
@@ -75,6 +75,9 @@ class PythonOutput : public OutputBase
     GEOS_UNUSED_VAR( domain );
     return true;
   }
+
+protected:
+  logInfo::OutputTimerBase const & getTimerCategory() const override;
 };
 
 
diff --git a/src/coreComponents/fileIO/Outputs/RestartOutput.cpp b/src/coreComponents/fileIO/Outputs/RestartOutput.cpp
index 6fb7a2c6b19..6eb07281cf6 100644
--- a/src/coreComponents/fileIO/Outputs/RestartOutput.cpp
+++ b/src/coreComponents/fileIO/Outputs/RestartOutput.cpp
@@ -24,6 +24,14 @@ namespace geos
 
 using namespace dataRepository;
 
+namespace logInfo
+{
+struct RestartOutputTimer : public OutputTimerBase
+{
+  std::string_view getDescription() const override { return "Restart output timing"; }
+};
+}
+
 RestartOutput::RestartOutput( string const & name,
                               Group * const parent ):
   OutputBase( name, parent )
@@ -41,19 +49,24 @@ bool RestartOutput::execute( real64 const GEOS_UNUSED_PARAM( time_n ),
 {
   GEOS_MARK_FUNCTION;
 
-  Group & rootGroup = this->getGroupByPath( "/Problem" );
+  {
+    Timer timer( m_outputTimer );
 
-  // Ignoring the eventProgress indicator for now to be compliant with the integrated test repo
-  // integer const eventProgressPercent = static_cast<integer const>(eventProgress * 100.0);
-  string const fileName = GEOS_FMT( "{}_restart_{:09}", getFileNameRoot(), cycleNumber );
-
-  rootGroup.prepareToWrite();
-  writeTree( joinPath( OutputBase::getOutputDirectory(), fileName ), *(rootGroup.getConduitNode().parent()) );
-  rootGroup.finishWriting();
+    Group & rootGroup = this->getGroupByPath( "/Problem" );
+    string const fileName = GEOS_FMT( "{}_restart_{:09}", getFileNameRoot(), cycleNumber );
+    rootGroup.prepareToWrite();
+    writeTree( joinPath( OutputBase::getOutputDirectory(), fileName ), *(rootGroup.getConduitNode().parent()) );
+    rootGroup.finishWriting();
+  }
 
   return false;
 }
 
+logInfo::OutputTimerBase const & RestartOutput::getTimerCategory() const
+{
+  static logInfo::RestartOutputTimer timer;
+  return timer;
+}
 
 REGISTER_CATALOG_ENTRY( OutputBase, RestartOutput, string const &, Group * const )
 } /* namespace geos */
diff --git a/src/coreComponents/fileIO/Outputs/RestartOutput.hpp b/src/coreComponents/fileIO/Outputs/RestartOutput.hpp
index a2a12be781c..91c2fb2954f 100644
--- a/src/coreComponents/fileIO/Outputs/RestartOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/RestartOutput.hpp
@@ -78,6 +78,9 @@ class RestartOutput : public OutputBase
     dataRepository::ViewKey writeFEMFaces = { "writeFEMFaces" };
   } viewKeys;
   /// @endcond
+
+protected:
+  logInfo::OutputTimerBase const & getTimerCategory() const override;
 };
 
 
diff --git a/src/coreComponents/fileIO/Outputs/SiloOutput.cpp b/src/coreComponents/fileIO/Outputs/SiloOutput.cpp
index 756facc2da1..ba03ceead5f 100644
--- a/src/coreComponents/fileIO/Outputs/SiloOutput.cpp
+++ b/src/coreComponents/fileIO/Outputs/SiloOutput.cpp
@@ -28,6 +28,20 @@ namespace geos
 
 using namespace dataRepository;
 
+namespace logInfo
+{
+struct SiloOutputTimer : public OutputTimerBase
+{
+  std::string_view getDescription() const override { return "Silo output timing"; }
+};
+}
+
+logInfo::OutputTimerBase const & SiloOutput::getTimerCategory() const
+{
+  static logInfo::SiloOutputTimer timer;
+  return timer;
+}
+
 SiloOutput::SiloOutput( string const & name,
                         Group * const parent ):
   OutputBase( name, parent ),
@@ -122,31 +136,35 @@ bool SiloOutput::execute( real64 const time_n,
 {
   GEOS_MARK_FUNCTION;
 
-  SiloFile silo;
-
-  int const size = MpiWrapper::commSize( MPI_COMM_GEOS );
-  int const rank = MpiWrapper::commRank( MPI_COMM_GEOS );
-  MpiWrapper::barrier( MPI_COMM_GEOS );
-
-  integer const numFiles = parallelThreads() == 0 ? size : parallelThreads();
-
-  // TODO set this during initialization
-  //  silo.setOutputDirectory( getGlobalState().getCommandLineOptions().outputDirectory ),
-  silo.setOutputDirectory( getOutputDirectory() ),
-  silo.setPlotLevel( m_plotLevel );
-  silo.setWriteEdgeMesh( m_writeEdgeMesh );
-  silo.setWriteFaceMesh( m_writeFaceMesh );
-  silo.setWriteCellElementMesh( m_writeCellElementMesh );
-  silo.setWriteFaceElementMesh( m_writeFaceElementMesh );
-  silo.setOnlyPlotSpecifiedFieldNamesFlag( m_onlyPlotSpecifiedFieldNames );
-  silo.setFieldNames( m_fieldNames.toViewConst() );
-  silo.setPlotFileRoot( m_plotFileRoot );
-  silo.initialize( numFiles );
-  silo.waitForBatonWrite( rank, cycleNumber, eventCounter, false );
-  silo.writeDomainPartition( domain, cycleNumber, time_n + dt * eventProgress, 0 );
-  silo.handOffBaton();
-  silo.clearEmptiesFromMultiObjects( cycleNumber );
-  silo.finish();
+  {
+    Timer timer( m_outputTimer );
+
+    SiloFile silo;
+
+    int const size = MpiWrapper::commSize( MPI_COMM_GEOS );
+    int const rank = MpiWrapper::commRank( MPI_COMM_GEOS );
+    MpiWrapper::barrier( MPI_COMM_GEOS );
+
+    integer const numFiles = parallelThreads() == 0 ? size : parallelThreads();
+
+    // TODO set this during initialization
+    //  silo.setOutputDirectory( getGlobalState().getCommandLineOptions().outputDirectory ),
+    silo.setOutputDirectory( getOutputDirectory() ),
+    silo.setPlotLevel( m_plotLevel );
+    silo.setWriteEdgeMesh( m_writeEdgeMesh );
+    silo.setWriteFaceMesh( m_writeFaceMesh );
+    silo.setWriteCellElementMesh( m_writeCellElementMesh );
+    silo.setWriteFaceElementMesh( m_writeFaceElementMesh );
+    silo.setOnlyPlotSpecifiedFieldNamesFlag( m_onlyPlotSpecifiedFieldNames );
+    silo.setFieldNames( m_fieldNames.toViewConst() );
+    silo.setPlotFileRoot( m_plotFileRoot );
+    silo.initialize( numFiles );
+    silo.waitForBatonWrite( rank, cycleNumber, eventCounter, false );
+    silo.writeDomainPartition( domain, cycleNumber, time_n + dt * eventProgress, 0 );
+    silo.handOffBaton();
+    silo.clearEmptiesFromMultiObjects( cycleNumber );
+    silo.finish();
+  }
 
   return false;
 }
diff --git a/src/coreComponents/fileIO/Outputs/SiloOutput.hpp b/src/coreComponents/fileIO/Outputs/SiloOutput.hpp
index bb3574f3745..635ba196c98 100644
--- a/src/coreComponents/fileIO/Outputs/SiloOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/SiloOutput.hpp
@@ -85,6 +85,9 @@ class SiloOutput : public OutputBase
   } siloOutputViewKeys;
   /// @endcond
 
+protected:
+  logInfo::OutputTimerBase const & getTimerCategory() const override;
+
 private:
 
   void postInputInitialization() override;
diff --git a/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.cpp b/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.cpp
index d01edac3dcf..7e1299aac57 100644
--- a/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.cpp
+++ b/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.cpp
@@ -25,6 +25,20 @@ namespace geos
 {
 using namespace dataRepository;
 
+namespace logInfo
+{
+struct TimeHistoryOutputTimer : public OutputTimerBase
+{
+  std::string_view getDescription() const override { return "Time history output timing"; }
+};
+}
+
+logInfo::OutputTimerBase const & TimeHistoryOutput::getTimerCategory() const
+{
+  static logInfo::TimeHistoryOutputTimer timer;
+  return timer;
+}
+
 TimeHistoryOutput::TimeHistoryOutput( string const & name,
                                       Group * const parent ):
   OutputBase( name, parent ),
@@ -166,12 +180,18 @@ bool TimeHistoryOutput::execute( real64 const GEOS_UNUSED_PARAM( time_n ),
                                  DomainPartition & GEOS_UNUSED_PARAM( domain ) )
 {
   GEOS_MARK_FUNCTION;
-  localIndex newBuffered = m_io.front()->getBufferedCount( );
-  for( auto & th_io : m_io )
+
   {
-    th_io->write( );
+    Timer timer( m_outputTimer );
+
+    localIndex newBuffered = m_io.front()->getBufferedCount( );
+    for( auto & th_io : m_io )
+    {
+      th_io->write( );
+    }
+    m_recordCount += newBuffered;
   }
-  m_recordCount += newBuffered;
+
   return false;
 }
 
diff --git a/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.hpp b/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.hpp
index d7793943d9c..18230805668 100644
--- a/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.hpp
@@ -114,6 +114,9 @@ class TimeHistoryOutput : public OutputBase
   virtual PyTypeObject * getPythonType() const override;
 #endif
 
+protected:
+  logInfo::OutputTimerBase const & getTimerCategory() const override;
+
 private:
 
   /**
diff --git a/src/coreComponents/fileIO/Outputs/VTKOutput.cpp b/src/coreComponents/fileIO/Outputs/VTKOutput.cpp
index 8b4ffec9fc1..b6f4348899e 100644
--- a/src/coreComponents/fileIO/Outputs/VTKOutput.cpp
+++ b/src/coreComponents/fileIO/Outputs/VTKOutput.cpp
@@ -29,6 +29,20 @@ namespace geos
 
 using namespace dataRepository;
 
+namespace logInfo
+{
+struct VTKOutputTimer : public OutputTimerBase
+{
+  std::string_view getDescription() const override { return "VTK output timing"; }
+};
+}
+
+logInfo::OutputTimerBase const & VTKOutput::getTimerCategory() const
+{
+  static logInfo::VTKOutputTimer timer;
+  return timer;
+}
+
 VTKOutput::VTKOutput( string const & name,
                       Group * const parent ):
   OutputBase( name, parent ),
diff --git a/src/coreComponents/fileIO/Outputs/VTKOutput.hpp b/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
index b53ff6c2c78..0f112c6225e 100644
--- a/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
@@ -112,6 +112,9 @@ class VTKOutput : public OutputBase
   virtual PyTypeObject * getPythonType() const override;
 #endif
 
+protected:
+  logInfo::OutputTimerBase const & getTimerCategory() const override;
+
 private:
 
   string m_plotFileRoot;

From b528cb57868406227b38de89981fb69deef37b60 Mon Sep 17 00:00:00 2001
From: "Victor A. P. Magri" <paludettomag1@llnl.gov>
Date: Fri, 6 Dec 2024 11:20:46 -0500
Subject: [PATCH 6/7] Documentation

---
 .../fileIO/Outputs/BlueprintOutput.hpp        |  3 +++
 .../fileIO/Outputs/ChomboIO.hpp               |  3 +++
 .../fileIO/Outputs/OutputBase.hpp             | 19 +++++++++++++++++--
 .../fileIO/Outputs/RestartOutput.hpp          |  3 +++
 .../fileIO/Outputs/SiloOutput.hpp             |  3 +++
 .../fileIO/Outputs/TimeHistoryOutput.hpp      |  3 +++
 .../fileIO/Outputs/VTKOutput.hpp              |  3 +++
 7 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/src/coreComponents/fileIO/Outputs/BlueprintOutput.hpp b/src/coreComponents/fileIO/Outputs/BlueprintOutput.hpp
index e8e8f558a24..fd963698c3c 100644
--- a/src/coreComponents/fileIO/Outputs/BlueprintOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/BlueprintOutput.hpp
@@ -37,6 +37,9 @@ class ElementRegionManager;
 class BlueprintOutput : public OutputBase
 {
 protected:
+  /**
+   * @copydoc OutputBase::getTimerCategory
+   */
   logInfo::OutputTimerBase const & getTimerCategory() const override;
 
 public:
diff --git a/src/coreComponents/fileIO/Outputs/ChomboIO.hpp b/src/coreComponents/fileIO/Outputs/ChomboIO.hpp
index f9c331fb58c..c9e60cf2f79 100644
--- a/src/coreComponents/fileIO/Outputs/ChomboIO.hpp
+++ b/src/coreComponents/fileIO/Outputs/ChomboIO.hpp
@@ -90,6 +90,9 @@ class ChomboIO final : public OutputBase
   /// @endcond
 
 protected:
+  /**
+   * @copydoc OutputBase::getTimerCategory
+   */
   logInfo::OutputTimerBase const & getTimerCategory() const override;
 
 private:
diff --git a/src/coreComponents/fileIO/Outputs/OutputBase.hpp b/src/coreComponents/fileIO/Outputs/OutputBase.hpp
index 1146d8aef6c..ae957e22213 100644
--- a/src/coreComponents/fileIO/Outputs/OutputBase.hpp
+++ b/src/coreComponents/fileIO/Outputs/OutputBase.hpp
@@ -35,7 +35,16 @@ namespace logInfo
  */
 struct OutputTimers
 {
+  /**
+   * @brief Get the description of this timer
+   * @return String view containing the timer description
+   */
   static std::string_view getDescription() { return "Output timing information"; }
+
+  /**
+   * @brief Get the minimum log level for this timer
+   * @return Integer representing the minimum log level
+   */
   static constexpr int getMinLogLevel() { return 1; }
 };
 
@@ -48,8 +57,11 @@ struct OutputTimers
  */
 struct OutputTimerBase
 {
+  /**
+   * @brief Get the description of this timer
+   * @return String view containing the timer description
+   */
   virtual std::string_view getDescription() const = 0;
-  virtual ~OutputTimerBase() = default;
 };
 }
 
@@ -132,7 +144,10 @@ class OutputBase : public ExecutableGroup
   /// Timer used to track duration of file writing operations for this specific output type
   std::chrono::system_clock::duration m_outputTimer;
 
-  /// Get the timer category for this specific output type
+  /**
+   * @brief Get the timer category for this output type
+   * @return Reference to the output timer base for timing statistics
+   */
   virtual logInfo::OutputTimerBase const & getTimerCategory() const = 0;
 
   /// @copydoc geos::ExecutableGroup::cleanup
diff --git a/src/coreComponents/fileIO/Outputs/RestartOutput.hpp b/src/coreComponents/fileIO/Outputs/RestartOutput.hpp
index 91c2fb2954f..11c8715ed76 100644
--- a/src/coreComponents/fileIO/Outputs/RestartOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/RestartOutput.hpp
@@ -80,6 +80,9 @@ class RestartOutput : public OutputBase
   /// @endcond
 
 protected:
+  /**
+   * @copydoc OutputBase::getTimerCategory
+   */
   logInfo::OutputTimerBase const & getTimerCategory() const override;
 };
 
diff --git a/src/coreComponents/fileIO/Outputs/SiloOutput.hpp b/src/coreComponents/fileIO/Outputs/SiloOutput.hpp
index 635ba196c98..6b0a371974f 100644
--- a/src/coreComponents/fileIO/Outputs/SiloOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/SiloOutput.hpp
@@ -86,6 +86,9 @@ class SiloOutput : public OutputBase
   /// @endcond
 
 protected:
+  /**
+   * @copydoc OutputBase::getTimerCategory
+   */
   logInfo::OutputTimerBase const & getTimerCategory() const override;
 
 private:
diff --git a/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.hpp b/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.hpp
index 18230805668..e2846f7c312 100644
--- a/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/TimeHistoryOutput.hpp
@@ -115,6 +115,9 @@ class TimeHistoryOutput : public OutputBase
 #endif
 
 protected:
+  /**
+   * @copydoc OutputBase::getTimerCategory
+   */
   logInfo::OutputTimerBase const & getTimerCategory() const override;
 
 private:
diff --git a/src/coreComponents/fileIO/Outputs/VTKOutput.hpp b/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
index 0f112c6225e..bf36e900eaf 100644
--- a/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
+++ b/src/coreComponents/fileIO/Outputs/VTKOutput.hpp
@@ -113,6 +113,9 @@ class VTKOutput : public OutputBase
 #endif
 
 protected:
+  /**
+   * @copydoc OutputBase::getTimerCategory
+   */
   logInfo::OutputTimerBase const & getTimerCategory() const override;
 
 private:

From 01a009f5baec0f6f05d77b72013b42930cd57346 Mon Sep 17 00:00:00 2001
From: "Victor A. P. Magri" <50467563+victorapm@users.noreply.github.com>
Date: Fri, 6 Dec 2024 20:56:32 -0800
Subject: [PATCH 7/7] Update baselines

---
 .integrated_tests.yaml | 2 +-
 BASELINE_NOTES.md      | 4 ++++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.integrated_tests.yaml b/.integrated_tests.yaml
index 0ce10cbe33b..3aa31a7e4cb 100644
--- a/.integrated_tests.yaml
+++ b/.integrated_tests.yaml
@@ -1,6 +1,6 @@
 baselines:
   bucket: geosx
-  baseline: integratedTests/baseline_integratedTests-pr3467-9212-976cc3b
+  baseline: integratedTests/baseline_integratedTests-pr3480-9217-caaecb8
 allow_fail:
   all: ''
   streak: ''
diff --git a/BASELINE_NOTES.md b/BASELINE_NOTES.md
index 8f344877826..acbeb39e382 100644
--- a/BASELINE_NOTES.md
+++ b/BASELINE_NOTES.md
@@ -6,6 +6,10 @@ This file is designed to track changes to the integrated test baselines.
 Any developer who updates the baseline ID in the .integrated_tests.yaml file is expected to create an entry in this file with the pull request number, date, and their justification for rebaselining.
 These notes should be in reverse-chronological order, and use the following time format: (YYYY-MM-DD).
 
+PR #3480 (2024-12-06)
+=====================
+Add "logLevel" parameter under /Problem/Outputs in baseline files
+
 PR #3361 (2024-12-03)
 =====================
 Revert default gravity treatment to old version. Make the way introduced in #3337 optional.