Merge pull request #12751 from aeslaughter/vpp-csv-11087

Create FINAL and LATEST symlinks for VPP files

framework/include/outputs/CSV.h

@@ -97,6 +97,22 @@ class CSV : public TableOutput
 
   /// Flag indicating MOOSE is recovering via --recover command-line option
   bool _recovering;
+
+  /// Flag for creating a _FINAL symlink
+  bool _create_final_symlink;
+
+  /// Flag for creating a _LATEST symlink
+  bool _create_latest_symlink;
+
+  /// Current list of VPP filenames for creating _LATEST/_FINAL symlinks
+  // The pair is composed of the complete filename (foo_variable_0001.csv) and the incomplete name
+  // (foo_variable) to which the _FINAL or _LATEST is to be applied.
+  std::vector<std::pair<std::string, std::string>> _latest_vpp_filenames;
+
+  /**
+   * Returns the filename without the time/timestep information.
+   */
+  std::string getVectorPostprocessorFilePrefix(const std::string & vpp_name);
 };
 
 #endif /* CSV_H */

framework/include/utils/MooseUtils.h

@@ -517,6 +517,16 @@ template <>
 unsigned long long int convert<unsigned long long int>(const std::string & str,
                                                        bool throw_on_failure);
 
+/**
+ * Create a symbolic link, if the link already exists it is replaced.
+ */
+void createSymlink(const std::string & target, const std::string & link);
+
+/**
+ * Remove a symbolic link, if the given filename is a link.
+ */
+void clearSymlink(const std::string & link);
+
 /**
  * Convert supplied string to upper case.
  * @params name The string to convert upper case.

framework/src/outputs/CSV.C

@@ -30,6 +30,14 @@ validParams<CSV>()
       "Align the outputted csv data by padding the numbers with trailing whitespace");
   params.addParam<std::string>("delimiter", ",", "Assign the delimiter (default is ','");
   params.addParam<unsigned int>("precision", 14, "Set the output precision");
+  params.addParam<bool>("create_final_symlink",
+                        true,
+                        "Enable/disable the creation of a _FINAL symlink for vector postprocessor "
+                        "data with 'execute_on' includes 'FINAL'.");
+  params.addParam<bool>(
+      "create_latest_symlink",
+      true,
+      "Enable/disable the creation of a _LATEST symlink for vector postprocessor data.");
 
   // Suppress unused parameters
   params.suppressParameter<unsigned int>("padding");
@@ -46,7 +54,9 @@ CSV::CSV(const InputParameters & parameters)
     _write_all_table(false),
     _write_vector_table(false),
     _sort_columns(getParam<bool>("sort_columns")),
-    _recovering(_app.isRecovering())
+    _recovering(_app.isRecovering()),
+    _create_final_symlink(getParam<bool>("create_final_symlink")),
+    _create_latest_symlink(getParam<bool>("create_latest_symlink"))
 {
 }
 
@@ -64,6 +74,20 @@ CSV::initialSetup()
 
   if (_recovering)
     _all_data_table.append(true);
+
+  // Clear any existing symbolic links to LATEST and/or FINAL
+  if (processor_id() == 0)
+  {
+    const std::set<std::string> & out = getVectorPostprocessorOutput();
+    for (const auto & vpp_name : out)
+    {
+      std::string short_name = MooseUtils::shortName(vpp_name);
+      std::string out_latest = _file_base + "_" + short_name + "_LATEST.csv";
+      std::string out_final = _file_base + "_" + short_name + "_FINAL.csv";
+      MooseUtils::clearSymlink(out_latest);
+      MooseUtils::clearSymlink(out_final);
+    }
+  }
 }
 
 std::string
@@ -130,27 +154,54 @@ CSV::output(const ExecFlagType & type)
   // Output each VectorPostprocessor's data to a file
   if (_write_vector_table && processor_id() == 0)
   {
+
+    // The VPP table will not write the same data twice, so to get the symlinks correct
+    // for EXEC_FINAL (when other flags exist) whenever files are written the names must
+    // be stored. These stored names are then used outside of this loop when the EXEC_FINAL call is
+    // made.
+    _latest_vpp_filenames.clear();
+
     for (auto & it : _vector_postprocessor_tables)
     {
-      auto vpp_name = it.first;
+      const auto & vpp_name = it.first;
       it.second.setDelimiter(_delimiter);
       it.second.setPrecision(_precision);
       if (_sort_columns)
         it.second.sortColumns();
 
       auto include_time_suffix = !vpp_data.containsCompleteHistory(vpp_name);
+      std::string fname = getVectorPostprocessorFileName(vpp_name, include_time_suffix);
+      std::string fprefix = getVectorPostprocessorFilePrefix(vpp_name);
+      _latest_vpp_filenames.emplace_back(fname, fprefix);
+      it.second.printCSV(fname, 1, _align);
 
-      it.second.printCSV(getVectorPostprocessorFileName(vpp_name, include_time_suffix), 1, _align);
-
-      if (_time_data)
+      if (_create_latest_symlink)
       {
-        std::string file_name = _file_base + '_' + MooseUtils::shortName(vpp_name) + "_time.csv";
-        _vector_postprocessor_time_tables[vpp_name].printCSV(file_name);
+        std::string out_latest = fprefix + "_LATEST.csv";
+        MooseUtils::createSymlink(fname, out_latest);
       }
+
+      if (_time_data)
+        _vector_postprocessor_time_tables[vpp_name].printCSV(fprefix + "_time.csv");
+    }
+  }
+
+  if (type == EXEC_FINAL && _create_final_symlink && processor_id() == 0)
+  {
+    for (const auto & name_pair : _latest_vpp_filenames)
+    {
+      std::string out_final = name_pair.second + "_FINAL.csv";
+      MooseUtils::createSymlink(name_pair.first, out_final);
     }
   }
 
   // Re-set write flags
   _write_all_table = false;
   _write_vector_table = false;
 }
+
+std::string
+CSV::getVectorPostprocessorFilePrefix(const std::string & vpp_name)
+{
+  return _file_base + "_" + MooseUtils::shortName(vpp_name);
+}

framework/src/utils/MooseUtils.C

@@ -731,6 +731,7 @@ stringToInteger(const std::string & input, bool throw_on_failure)
 }
 
 void
+
 linearPartitionItems(dof_id_type num_items,
                      dof_id_type num_chunks,
                      dof_id_type chunk_id,
@@ -809,6 +810,26 @@ template std::string join<std::vector<MooseEnumItem>>(const std::vector<MooseEnu
 template std::string join<std::set<MooseEnumItem>>(const std::set<MooseEnumItem> &,
                                                    const std::string &);
 
+void
+createSymlink(const std::string & target, const std::string & link)
+{
+  clearSymlink(link);
+  int err = symlink(target.c_str(), link.c_str());
+  if (err != 0)
+    mooseError("Failed to create symbolic link (via 'symlink') from ", target, " to ", link);
+}
+
+void
+clearSymlink(const std::string & link)
+{
+  struct stat sbuf;
+  if (lstat(link.c_str(), &sbuf) == 0)
+  {
+    int err = unlink(link.c_str());
+    if (err != 0)
+      mooseError("Failed to remove symbolic link (via 'unlink') to ", link);
+  }
+}
 } // MooseUtils namespace
 
 std::string

test/tests/outputs/csv_final_and_latest/final.i

@@ -0,0 +1,68 @@
+[Mesh]
+  type = GeneratedMesh
+  dim = 2
+  nx = 10
+  ny = 10
+[]
+
+[Variables]
+  [./u]
+  [../]
+[]
+
+[Kernels]
+  [./diff]
+    type = CoefDiffusion
+    variable = u
+    coef = 0.1
+  [../]
+  [./time]
+    type = TimeDerivative
+    variable = u
+  [../]
+[]
+
+[BCs]
+  [./left]
+    type = DirichletBC
+    variable = u
+    boundary = left
+    value = 0
+  [../]
+  [./right]
+    type = DirichletBC
+    variable = u
+    boundary = right
+    value = 1
+  [../]
+[]
+
+[Executioner]
+  type = Transient
+  num_steps = 10
+  dt = 0.25
+  solve_type = PJFNK
+  petsc_options_iname = '-pc_type -pc_hypre_type'
+  petsc_options_value = 'hypre boomeramg'
+[]
+
+# Vector Postprocessor System
+[VectorPostprocessors]
+  [./line_sample]
+    type = LineValueSampler
+    execute_on = 'timestep_end final'
+    variable = 'u'
+    start_point = '0 0.5 0'
+    end_point = '1 0.5 0'
+    num_points = 11
+    sort_by = id
+  [../]
+[]
+
+[Outputs]
+  [./out]
+    type = CSV
+    execute_on = 'TIMESTEP_END FINAL'
+    create_latest_symlink = false
+  [../]
+[]

test/tests/outputs/csv_final_and_latest/gold/final_out_line_sample_FINAL.csv

@@ -0,0 +1,12 @@
+x,y,z,id,u
+0,0.5,0,0,0
+0.1,0.5,0,0.1,0.078663617984875
+0.2,0.5,0,0.2,0.15936788915787
+0.3,0.5,0,0.3,0.24397172256484
+0.4,0.5,0,0.4,0.33398168255287
+0.5,0.5,0,0.5,0.43040493832597
+0.6,0.5,0,0.6,0.53363981759493
+0.7,0.5,0,0.7,0.64341855974351
+0.8,0.5,0,0.8,0.75881470939601
+0.9,0.5,0,0.9,0.87832172561654
+1,0.5,0,1,1

test/tests/outputs/csv_final_and_latest/gold/latest_out_line_sample_LATEST.csv

@@ -0,0 +1 @@
+final_out_line_sample_FINAL.csv

test/tests/outputs/csv_final_and_latest/latest.i

@@ -0,0 +1,68 @@
+[Mesh]
+  type = GeneratedMesh
+  dim = 2
+  nx = 10
+  ny = 10
+[]
+
+[Variables]
+  [./u]
+  [../]
+[]
+
+[Kernels]
+  [./diff]
+    type = CoefDiffusion
+    variable = u
+    coef = 0.1
+  [../]
+  [./time]
+    type = TimeDerivative
+    variable = u
+  [../]
+[]
+
+[BCs]
+  [./left]
+    type = DirichletBC
+    variable = u
+    boundary = left
+    value = 0
+  [../]
+  [./right]
+    type = DirichletBC
+    variable = u
+    boundary = right
+    value = 1
+  [../]
+[]
+
+[Executioner]
+  type = Transient
+  num_steps = 10
+  dt = 0.25
+  solve_type = PJFNK
+  petsc_options_iname = '-pc_type -pc_hypre_type'
+  petsc_options_value = 'hypre boomeramg'
+[]
+
+# Vector Postprocessor System
+[VectorPostprocessors]
+  [./line_sample]
+    type = LineValueSampler
+    execute_on = 'timestep_end'
+    variable = 'u'
+    start_point = '0 0.5 0'
+    end_point = '1 0.5 0'
+    num_points = 11
+    sort_by = id
+  [../]
+[]
+
+[Outputs]
+  [./out]
+    type = CSV
+    execute_on = 'TIMESTEP_END'
+    create_final_symlink = false
+  [../]
+[]

test/tests/outputs/csv_final_and_latest/tests

@@ -0,0 +1,50 @@
+[Tests]
+  issues = "#11087"
+  design = "/VectorPostprocessors/index.md /CSV.md"
+  [final]
+    type = CSVDiff
+    input = final.i
+    csvdiff = final_out_line_sample_FINAL.csv
+    requirement = "The CSV output object shall create a symlink to the final output with "
+                  "with a '_FINAL' suffix for VectorPostprocessor data when there are execute flags "
+                  "in addition to FINAL."
+  []
+  [final_only]
+    type = CheckFiles
+    input = final.i
+    cli_args = Outputs/out/execute_on=FINAL
+    check_not_exists = 'final_out_line_sample_0009.csv'
+    check_files = 'final_out_line_sample_0011.csv final_out_line_sample_FINAL.csv'
+    requirement = "The CSV output object shall create a symlink to the final output with "
+                  "with a '_FINAL' suffix for VectorPostprocessor data when the execute flag is "
+                  "set to FINAL."
+    prereq = final
+  []
+  [no_link]
+    type = CheckFiles
+    input = final.i
+    cli_args = Outputs/out/create_final_symlink=false
+    delete_output_before_running = false
+    check_not_exists = 'final_out_line_sample_FINAL.csv'
+    requirement = "The CSV output object 'create_final_symlink' parameter shall be able to disable "
+                  "the creation of the final symlink."
+    prereq = final_only
+  []
+  [latest]
+    type = CSVDiff
+    input = latest.i
+    csvdiff = latest_out_line_sample_LATEST.csv
+    requirement = "The CSV output object shall create a symlink to the most recent output with "
+                  "with a '_LATEST' suffix for VectorPostprocessor data."
+  []
+  [no_latest]
+    type = CheckFiles
+    input = latest.i
+    delete_output_before_running = false
+    cli_args = Outputs/out/create_latest_symlink=false
+    check_not_exists = 'latest_out_line_sample_LATEST.csv'
+    requirement = "The CSV output object 'create_latest_symlink' parameter shall be able to disable "
+                  "the creation of the latest symlink."
+    prereq = latest
+  []
+[]