Logger file improvements (#160)

* Switch to a setable UNIT number * Logging to file infastructure * Fixing of yaml logging * Explicit unit override * Linting * Update Fortran examples * Fixes for C++ interface to logger * Python examples updated * Better interface to the logger in c++ * yaml dependency for unit tests * linting * Simplified configuration on a Mac (#161) * Switch to a setable UNIT number * Logging to file infastructure * Fixing of yaml logging * Explicit unit override * Linting * Update Fortran examples * Fixes for C++ interface to logger * Python examples updated * Better interface to the logger in c++ * yaml dependency for unit tests * linting * Barrier in case that was messing with file system * Try to verify that it is in the reading * Output on failure * Spaces not tabs * It seems I needed to increase the integer print out size
william-dawson · Nov 16, 2020 · b833530 · b833530
1 parent 67d28ef
commit b833530
Show file tree

Hide file tree

Showing 45 changed files with 499 additions and 170 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -70,6 +70,7 @@ jobs:
     - name:               regression tests
       run:                |
         cd Build
+        export CTEST_OUTPUT_ON_FAILURE=1
         eval "$MAKETEST"
         cd ../
       env:

diff --git a/Examples/ComplexMatrix/main.cc b/Examples/ComplexMatrix/main.cc
@@ -7,6 +7,7 @@ using std::string;
 #include <sstream>
 using std::stringstream;
 #include "ExponentialSolvers.h"
+#include "Logging.h"
 #include "PSMatrix.h"
 #include "ProcessGrid.h"
 #include "SolverParameters.h"
@@ -96,6 +97,9 @@ int main(int argc, char *argv[]) {
   // Setup the process grid.
   NTPoly::ConstructGlobalProcessGrid(MPI_COMM_WORLD, process_rows,
                                      process_columns, process_slices, true);
+  if (NTPoly::GetGlobalIsRoot()) {
+    NTPoly::ActivateLogger();
+  }
 
   // Compute the Hermitian Matrix
   NTPoly::Matrix_ps InMat(input_file);
@@ -113,6 +117,9 @@ int main(int argc, char *argv[]) {
   OMat.WriteToMatrixMarket(exponential_file);
 
   // Cleanup
+  if (NTPoly::GetGlobalIsRoot()) {
+    NTPoly::DeactivateLogger();
+  }
   NTPoly::DestructGlobalProcessGrid();
   MPI_Finalize();
   return 0;

diff --git a/Examples/ComplexMatrix/main.f90 b/Examples/ComplexMatrix/main.f90
@@ -5,14 +5,16 @@
 PROGRAM ComplexMatrix
   USE DataTypesModule, ONLY : NTREAL, NTCOMPLEX
   USE ExponentialSolversModule, ONLY : ComputeExponential
-  USE LoggingModule, ONLY : EnterSubLog, ExitSubLog, WriteElement, WriteHeader
+  USE LoggingModule, ONLY : ActivateLogger, DeactivateLogger, EnterSubLog, &
+       & ExitSubLog, WriteElement, WriteHeader
   USE MatrixMarketModule, ONLY : MM_SYMMETRIC
   USE PSMatrixAlgebraModule, ONLY : IncrementMatrix, ScaleMatrix
   USE PSMatrixModule, ONLY : Matrix_ps, ConstructMatrixFromMatrixMarket, &
        & DestructMatrix, TransposeMatrix, GetMatrixTripletList, &
        & FillMatrixFromTripletList, ConstructEmptyMatrix, ConjugateMatrix, &
        & PrintMatrix, CopyMatrix, WriteMatrixToMatrixMarket
-  USE ProcessGridModule, ONLY : ConstructProcessGrid, DestructProcessGrid
+  USE ProcessGridModule, ONLY : ConstructProcessGrid, DestructProcessGrid, &
+       & IsRoot
   USE SolverParametersModule, ONLY : SolverParameters_t
   USE TripletListModule, ONLY : TripletList_r, DestructTripletList, &
        & GetTripletAt, TripletList_c, ConstructTripletList, &
@@ -40,7 +42,6 @@ PROGRAM ComplexMatrix
   CALL MPI_Init_thread(MPI_THREAD_SERIALIZED, provided, ierr)
 
   !! Process The Input
-  !! Process the input parameters.
   DO counter=1,COMMAND_ARGUMENT_COUNT(),2
      CALL GET_COMMAND_ARGUMENT(counter,argument)
      CALL GET_COMMAND_ARGUMENT(counter+1,argument_value)
@@ -64,6 +65,10 @@ PROGRAM ComplexMatrix
   CALL ConstructProcessGrid(MPI_COMM_WORLD, process_rows, process_columns, &
        & process_slices)
 
+  !! Write Out Parameters
+  IF (IsRoot()) THEN
+     CALL ActivateLogger
+  END IF
   CALL WriteHeader("Command Line Parameters")
   CALL EnterSubLog
   CALL WriteElement(key="input_file", VALUE=input_file)
@@ -89,6 +94,11 @@ PROGRAM ComplexMatrix
   !! Cleanup
   CALL DestructMatrix(InMat)
   CALL DestructMatrix(GMat)
+
+  !! Cleanup
+  IF (IsRoot()) THEN
+     CALL DeactivateLogger
+  END IF
   CALL DestructProcessGrid
   CALL MPI_Finalize(ierr)
 

diff --git a/Examples/ComplexMatrix/main.py b/Examples/ComplexMatrix/main.py
@@ -77,6 +77,8 @@ def ConstructGuoMatrix(InMat, OutMat):
     # Setup the process grid.
     nt.ConstructGlobalProcessGrid(
         process_rows, process_columns, process_slices)
+    if nt.GetGlobalIsRoot():
+        nt.ActivateLogger()
 
     # Construct The Hermitian Matrix
     InMat = nt.Matrix_ps(input_file)
@@ -92,4 +94,8 @@ def ConstructGuoMatrix(InMat, OutMat):
 
     # Write To File
     OMat.WriteToMatrixMarket(exponential_file)
+
+    # Cleanup
+    if nt.GetGlobalIsRoot():
+        nt.DeactivateLogger()
     nt.DestructGlobalProcessGrid()
diff --git a/Examples/GraphTheory/main.cc b/Examples/GraphTheory/main.cc
@@ -12,6 +12,7 @@ using std::vector;
 #include <iostream>
 // NTPoly Headers
 #include "InverseSolvers.h"
+#include "Logging.h"
 #include "PSMatrix.h"
 #include "ProcessGrid.h"
 #include "SolverParameters.h"
@@ -67,6 +68,10 @@ int main(int argc, char *argv[]) {
   // Setup the process grid.
   NTPoly::ConstructGlobalProcessGrid(MPI_COMM_WORLD, process_rows,
                                      process_columns, process_slices, true);
+  if (NTPoly::GetGlobalIsRoot()) {
+    NTPoly::ActivateLogger();
+  }
+
   // Set Up The Solver Parameters.
   NTPoly::SolverParameters solver_parameters;
   solver_parameters.SetConvergeDiff(convergence_threshold);
@@ -166,6 +171,9 @@ int main(int argc, char *argv[]) {
   ResultMat.WriteToMatrixMarket(output_file);
 
   // Cleanup
+  if (NTPoly::GetGlobalIsRoot()) {
+    NTPoly::DeactivateLogger();
+  }
   NTPoly::DestructGlobalProcessGrid();
   MPI_Finalize();
   return 0;

diff --git a/Examples/GraphTheory/main.f90 b/Examples/GraphTheory/main.f90
@@ -3,7 +3,10 @@
 PROGRAM GraphTheory
   USE DataTypesModule, ONLY : NTREAL
   USE InverseSolversModule, ONLY : Invert
-  USE ProcessGridModule, ONLY : ConstructProcessGrid, DestructProcessGrid
+  USE LoggingModule, ONLY : ActivateLogger, DeactivateLogger, WriteElement, &
+       & WriteHeader, EnterSubLog, ExitSubLog
+  USE ProcessGridModule, ONLY : ConstructProcessGrid, DestructProcessGrid, &
+       & IsRoot
   USE PSMatrixModule, ONLY : Matrix_ps, WriteMatrixToMatrixMarket, &
        & ConstructEmptyMatrix, FillMatrixFromTripletList, DestructMatrix, &
        & CopyMatrix, FillMatrixIdentity
@@ -76,6 +79,23 @@ PROGRAM GraphTheory
   CALL ConstructProcessGrid(MPI_COMM_WORLD, process_rows, process_columns, &
        & process_slices)
 
+  !! Write Out Parameters
+  IF (IsRoot()) THEN
+     CALL ActivateLogger
+  END IF
+  CALL WriteHeader("Command Line Parameters")
+  CALL EnterSubLog
+  CALL WriteElement(key="number_of_nodes", VALUE=number_of_nodes)
+  CALL WriteElement(key="extra_connections", VALUE=extra_connections)
+  CALL WriteElement(key="threshold", VALUE=threshold)
+  CALL WriteElement(key="convergence_threshold", VALUE=convergence_threshold)
+  CALL WriteElement(key="attenuation", VALUE=attenuation)
+  CALL WriteElement(key="process_rows", VALUE=process_rows)
+  CALL WriteElement(key="process_columns", VALUE=process_columns)
+  CALL WriteElement(key="process_slices", VALUE=process_slices)
+  CALL WriteElement(key="output_file", VALUE=output_file)
+  CALL ExitSubLog
+
   !! Set Up The Solver Parameters.
   solver_parameters = SolverParameters_t( be_verbose_in=.TRUE., &
        & converge_diff_in=convergence_threshold, threshold_in=threshold)
@@ -96,6 +116,11 @@ PROGRAM GraphTheory
   !! Cleanup
   CALL DestructMatrix(NetworkMat)
   CALL DestructMatrix(ResultMat)
+
+  !! Cleanup
+  IF (IsRoot()) THEN
+     CALL DeactivateLogger
+  END IF
   CALL DestructProcessGrid
   CALL MPI_Finalize(ierr)
 CONTAINS!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

diff --git a/Examples/GraphTheory/main.py b/Examples/GraphTheory/main.py
@@ -41,6 +41,8 @@
     # Setup the process grid.
     nt.ConstructGlobalProcessGrid(
         process_rows, process_columns, process_slices)
+    if nt.GetGlobalIsRoot():
+        nt.ActivateLogger()
 
     # Set Up The Solver Parameters.
     solver_parameters = nt.SolverParameters()
@@ -133,4 +135,8 @@
 
     # Print the density matrix to file.
     ResultMat.WriteToMatrixMarket(output_file)
+
+    # Cleanup
+    if nt.GetGlobalIsRoot():
+        nt.DeactivateLogger()
     nt.DestructGlobalProcessGrid()
diff --git a/Examples/HydrogenAtom/main.cc b/Examples/HydrogenAtom/main.cc
@@ -11,6 +11,7 @@ using std::vector;
 #include <iostream>
 // NTPoly Headers
 #include "DensityMatrixSolvers.h"
+#include "Logging.h"
 #include "PSMatrix.h"
 #include "ProcessGrid.h"
 #include "SolverParameters.h"
@@ -66,6 +67,10 @@ int main(int argc, char *argv[]) {
   // Setup the process grid.
   NTPoly::ConstructGlobalProcessGrid(MPI_COMM_WORLD, process_rows,
                                      process_columns, process_slices, true);
+  if (NTPoly::GetGlobalIsRoot()) {
+    NTPoly::ActivateLogger();
+  }
+
   // Set Up The Solver Parameters.
   NTPoly::SolverParameters solver_parameters;
   solver_parameters.SetConvergeDiff(convergence_threshold);
@@ -163,6 +168,9 @@ int main(int argc, char *argv[]) {
   Density.WriteToMatrixMarket(density_file_out);
 
   // Cleanup
+  if (NTPoly::GetGlobalIsRoot()) {
+    NTPoly::DeactivateLogger();
+  }
   NTPoly::DestructGlobalProcessGrid();
   MPI_Finalize();
   return 0;

diff --git a/Examples/HydrogenAtom/main.f90 b/Examples/HydrogenAtom/main.f90
@@ -3,7 +3,10 @@
 PROGRAM HydrogenAtom
   USE DataTypesModule, ONLY : NTREAL
   USE DensityMatrixSolversModule, ONLY : TRS2
-  USE ProcessGridModule, ONLY : ConstructProcessGrid, DestructProcessGrid
+  USE LoggingModule, ONLY : ActivateLogger, DeactivateLogger, WriteHeader, &
+       & WriteElement, EnterSubLog, ExitSubLog
+  USE ProcessGridModule, ONLY : ConstructProcessGrid, DestructProcessGrid, &
+       & IsRoot
   USE PSMatrixModule, ONLY : Matrix_ps, WriteMatrixToMatrixMarket, &
        & ConstructEmptyMatrix, FillMatrixFromTripletList, CopyMatrix, &
        & FillMatrixIdentity
@@ -76,6 +79,21 @@ PROGRAM HydrogenAtom
   CALL ConstructProcessGrid(MPI_COMM_WORLD, process_rows, process_columns, &
        & process_slices)
 
+  !! Write Out Parameters
+  IF (IsRoot()) THEN
+     CALL ActivateLogger
+  END IF
+  CALL WriteHeader("Command Line Parameters")
+  CALL EnterSubLog
+  CALL WriteElement(key="convergence_threshold", VALUE=convergence_threshold)
+  CALL WriteElement(key="grid_points", VALUE=grid_points)
+  CALL WriteElement(key="threshold", VALUE=threshold)
+  CALL WriteElement(key="process_rows", VALUE=process_rows)
+  CALL WriteElement(key="process_columns", VALUE=process_columns)
+  CALL WriteElement(key="process_slices", VALUE=process_slices)
+  CALL WriteElement(key="density_file_out", VALUE=density_file_out)
+  CALL ExitSubLog
+
   !! Set Up The Solver Parameters.
   solver_parameters = SolverParameters_t( be_verbose_in=.TRUE., &
        & converge_diff_in=convergence_threshold, threshold_in=threshold)
@@ -110,6 +128,9 @@ PROGRAM HydrogenAtom
   CALL WriteMatrixToMatrixMarket(Density,density_file_out)
 
   !! Cleanup
+  IF (IsRoot()) THEN
+     CALL DeactivateLogger
+  END IF
   CALL DestructProcessGrid
   CALL MPI_Finalize(ierr)
 CONTAINS!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

diff --git a/Examples/HydrogenAtom/main.py b/Examples/HydrogenAtom/main.py
@@ -39,6 +39,8 @@
     # Setup the process grid.
     nt.ConstructGlobalProcessGrid(
         process_rows, process_columns, process_slices)
+    if nt.GetGlobalIsRoot():
+        nt.ActivateLogger()
 
     # Set Up The Solver Parameters.
     solver_parameters = nt.SolverParameters()
@@ -121,4 +123,8 @@
 
     # Print the density matrix to file.
     Density.WriteToMatrixMarket(density_file_out)
+
+    # Cleanup
+    if nt.GetGlobalIsRoot():
+        nt.DeactivateLogger()
     nt.DestructGlobalProcessGrid()
diff --git a/Examples/MatrixMaps/main.cc b/Examples/MatrixMaps/main.cc
@@ -6,6 +6,7 @@ using std::string;
 #include <sstream>
 using std::stringstream;
 // NTPoly Headers
+#include "Logging.h"
 #include "MatrixMapper.h"
 #include "PSMatrix.h"
 #include "ProcessGrid.h"
@@ -53,6 +54,9 @@ int main(int argc, char *argv[]) {
 
   // Setup the process grid.
   NTPoly::ConstructGlobalProcessGrid(MPI_COMM_WORLD, process_slices, true);
+  if (NTPoly::GetGlobalIsRoot()) {
+    NTPoly::ActivateLogger();
+  }
 
   // Read in the matrices from file.
   NTPoly::Matrix_ps Input(input_file);
@@ -66,6 +70,9 @@ int main(int argc, char *argv[]) {
   Output.WriteToMatrixMarket(output_file);
 
   // Cleanup
+  if (NTPoly::GetGlobalIsRoot()) {
+    NTPoly::DeactivateLogger();
+  }
   NTPoly::DestructGlobalProcessGrid();
   MPI_Finalize();
   return 0;

diff --git a/Examples/MatrixMaps/main.f90 b/Examples/MatrixMaps/main.f90
@@ -2,9 +2,11 @@
 !> An example which shows how to use the matrix mapping feature of NTPoly.
 PROGRAM MatrixMapsProgram
   USE DataTypesModule, ONLY : NTREAL
-  USE LoggingModule, ONLY : EnterSubLog, ExitSubLog, WriteElement, WriteHeader
+  USE LoggingModule, ONLY : EnterSubLog, ExitSubLog, ActivateLogger, &
+       & DeactivateLogger, WriteElement, WriteHeader
   USE MatrixMapsModule, ONLY : MapMatrix_psr
-  USE ProcessGridModule, ONLY : ConstructProcessGrid, DestructProcessGrid
+  USE ProcessGridModule, ONLY : ConstructProcessGrid, DestructProcessGrid, &
+       & IsRoot
   USE PSMatrixModule, ONLY : Matrix_ps, ConstructMatrixFromMatrixMarket, &
        & DestructMatrix, WriteMatrixToMatrixMarket
   USE MPI
@@ -43,6 +45,9 @@ PROGRAM MatrixMapsProgram
   CALL ConstructProcessGrid(MPI_COMM_WORLD, process_slices)
 
   !! Print out parameters.
+  IF (IsRoot()) THEN
+     CALL ActivateLogger
+  END IF
   CALL WriteHeader("Command Line Parameters")
   CALL EnterSubLog
   CALL WriteElement(key="input_matrix", VALUE=input_matrix)
@@ -64,6 +69,9 @@ PROGRAM MatrixMapsProgram
   CALL DestructMatrix(OutMatrix)
 
   !! Cleanup
+  IF (IsRoot()) THEN
+     CALL DeactivateLogger
+  END IF
   CALL DestructProcessGrid
   CALL MPI_Finalize(ierr)
 CONTAINS!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

diff --git a/Examples/MatrixMaps/main.py b/Examples/MatrixMaps/main.py
@@ -37,6 +37,8 @@ def __call__(self):
 
     # Setup the process grid.
     nt.ConstructGlobalProcessGrid(process_slices)
+    if nt.GetGlobalIsRoot():
+        nt.ActivateLogger()
 
     # Read in the matrices from file.
     Input = nt.Matrix_ps(input_matrix)
@@ -48,4 +50,8 @@ def __call__(self):
 
     # Print the density matrix to file.
     Output.WriteToMatrixMarket(output_matrix)
+
+    # Cleanup
+    if nt.GetGlobalIsRoot():
+        nt.DeactivateLogger()
     nt.DestructGlobalProcessGrid()