added: ability to put terminal log in HDF5

src/IFEM.C

@@ -35,6 +35,7 @@ char** IFEM::argv = nullptr;
 SIMoptions IFEM::cmdOptions;
 ControlFIFO* IFEM::fifo = nullptr;
 utl::LogStream IFEM::cout(std::cout);
+std::shared_ptr<std::ostringstream> IFEM::memoryLog;
 
 
 int IFEM::Init (int arg_c, char** arg_v, const char* title)
@@ -52,6 +53,8 @@ int IFEM::Init (int arg_c, char** arg_v, const char* title)
       cmdOptions.parseOldOptions(argc,argv,i);
 
   cout.setPIDs(0,linalg.myPid);
+  memoryLog = std::make_shared<std::ostringstream>();
+  cout.addExtraLog(memoryLog);
 
   if (linalg.myPid != 0 || argc < 2)
     return linalg.myPid;
@@ -59,9 +62,9 @@ int IFEM::Init (int arg_c, char** arg_v, const char* title)
   if (title)
   {
     int i, nchar = 13 + strlen(title);
-    std::cout <<"\n >>> IFEM "<< title <<" <<<\n ";
+    IFEM::cout <<"\n >>> IFEM "<< title <<" <<<\n ";
     for (i = 0; i < nchar; i++) std::cout <<'=';
-    std::cout <<"\n\n Executing command:\n";
+    IFEM::cout <<"\n\n Executing command:\n";
 #ifdef HAVE_MPI
     int nProc = 1;
 #ifdef HAS_PETSC
@@ -70,91 +73,91 @@ int IFEM::Init (int arg_c, char** arg_v, const char* title)
     MPI_Comm_size(MPI_COMM_WORLD,&nProc);
 #endif
     if (nProc > 1)
-      std::cout <<" mpirun -np "<< nProc;
+      IFEM::cout <<" mpirun -np "<< nProc;
 #endif
     for (i = 0; i < argc; i++) IFEM::cout <<" "<< argv[i];
-    std::cout << std::endl;
+    IFEM::cout << std::endl;
   }
 
-  std::cout <<"\n ===== IFEM v"<< IFEM_VERSION_MAJOR <<"."
+  IFEM::cout <<"\n ===== IFEM v"<< IFEM_VERSION_MAJOR <<"."
-                               << IFEM_VERSION_MINOR <<"."
+                                << IFEM_VERSION_MINOR <<"."
-                               << IFEM_VERSION_PATCH <<" initialized =====";
+                                << IFEM_VERSION_PATCH <<" initialized =====";
 
-  std::cout <<"\n       HDF5 support: ";
+  IFEM::cout <<"\n       HDF5 support: ";
 #if HAS_HDF5
-  std::cout <<"enabled";
+  IFEM::cout <<"enabled";
 #else
-  std::cout <<"disabled";
+  IFEM::cout <<"disabled";
 #endif
 
-  std::cout <<"\n  LR spline support: ";
+  IFEM::cout <<"\n  LR spline support: ";
 #if HAS_LRSPLINE
-  std::cout <<"enabled";
+  IFEM::cout <<"enabled";
 #else
-  std::cout <<"disabled";
+  IFEM::cout <<"disabled";
 #endif
 
-  std::cout <<"\n     OpenMP support: ";
+  IFEM::cout <<"\n     OpenMP support: ";
 #if USE_OPENMP
-  std::cout <<"enabled";
+  IFEM::cout <<"enabled";
 #else
-  std::cout <<"disabled";
+  IFEM::cout <<"disabled";
 #endif
 
-  std::cout <<"\n        MPI support: ";
+  IFEM::cout <<"\n        MPI support: ";
 #ifdef HAVE_MPI
-  std::cout <<"enabled";
+  IFEM::cout <<"enabled";
 #else
-  std::cout <<"disabled";
+  IFEM::cout <<"disabled";
 #endif
 
-  std::cout <<"\n      PETSc support: ";
+  IFEM::cout <<"\n      PETSc support: ";
 #if HAS_PETSC
-  std::cout <<"enabled (v"<< PETSC_VERSION_MAJOR <<"."
+  IFEM::cout <<"enabled (v"<< PETSC_VERSION_MAJOR <<"."
-                          << PETSC_VERSION_MINOR <<"."
+                           << PETSC_VERSION_MINOR <<"."
-                          << PETSC_VERSION_SUBMINOR <<")";
+                           << PETSC_VERSION_SUBMINOR <<")";
 #else
-  std::cout <<"disabled";
+  IFEM::cout <<"disabled";
 #endif
 
-  std::cout <<"\n    SuperLU support: ";
+  IFEM::cout <<"\n    SuperLU support: ";
 #if HAS_SUPERLU
-  std::cout <<"enabled (serial)";
+  IFEM::cout <<"enabled (serial)";
 #elif HAS_SUPERLU_MT
-  std::cout <<"enabled (multi-threaded)";
+  IFEM::cout <<"enabled (multi-threaded)";
 #else
-  std::cout <<"disabled";
+  IFEM::cout <<"disabled";
 #endif
-  std::cout <<"\n    UMFPack support: ";
+  IFEM::cout <<"\n    UMFPack support: ";
 #if HAS_UMFPACK
-  std::cout <<"enabled (v" << UMFPACK_MAIN_VERSION <<"."
+  IFEM::cout <<"enabled (v" << UMFPACK_MAIN_VERSION <<"."
-                           << UMFPACK_SUB_VERSION <<"."
+                            << UMFPACK_SUB_VERSION <<"."
-                           << UMFPACK_SUBSUB_VERSION << ")";
+                            << UMFPACK_SUBSUB_VERSION << ")";
 #else
-  std::cout <<"disabled";
+  IFEM::cout <<"disabled";
 #endif
 
-  std::cout <<"\n       ISTL support: ";
+  IFEM::cout <<"\n       ISTL support: ";
 #if HAS_ISTL
-  std::cout <<"enabled (v"<< ISTL_VERSION <<")";
+  IFEM::cout <<"enabled (v"<< ISTL_VERSION <<")";
 #else
-  std::cout <<"disabled";
+  IFEM::cout <<"disabled";
 #endif
 
-  std::cout <<"\n        VTF support: ";
+  IFEM::cout <<"\n        VTF support: ";
 #if HAS_VTFAPI == 2
-  std::cout <<"enabled (v2)";
+  IFEM::cout <<"enabled (v2)";
 #elif HAS_VTFAPI == 1
-  std::cout <<"enabled (v1)";
+  IFEM::cout <<"enabled (v1)";
 #else
-  std::cout <<"disabled";
+  IFEM::cout <<"disabled";
 #endif
 
   if (enableController)
   {
     fifo = new ControlFIFO();
     if (fifo->open())
-      std::cout <<"\n        External controller enabled";
+      IFEM::cout <<"\n        External controller enabled";
     else
     {
       delete fifo;
@@ -162,7 +165,7 @@ int IFEM::Init (int arg_c, char** arg_v, const char* title)
     }
   }
 
-  std::cout << std::endl;
+  IFEM::cout << std::endl;
 
   return 0;
 }

src/IFEM.h.in

@@ -61,6 +61,8 @@ public:
 
   static utl::LogStream cout; //!< Combined standard out for parallel processes
 
+  static std::shared_ptr<std::ostringstream> memoryLog; //!< Logging data stored in memory
+
 private:
   static SIMoptions cmdOptions; //!< General input options
   static int argc;              //!< The number of command-line arguments

src/SIM/SIMoptions.C

@@ -44,7 +44,7 @@ SIMoptions::SIMoptions ()
   format  = -1;
   saveInc =  1;
   dtSave  =  0.0;
-  pSolOnly = saveNorms = false;
+  pSolOnly = saveNorms = saveLog = false;
   restartInc = 0;
   restartStep = -1;
 
@@ -182,6 +182,9 @@ bool SIMoptions::parseOutputTag (const TiXmlElement* elem)
   else if (!strcasecmp(elem->Value(),"saveNorms"))
     saveNorms = true;
 
+  else if (!strcasecmp(elem->Value(),"saveLog"))
+    saveLog = true;
+
   else if (!strcasecmp(elem->Value(),"projection")) {
     std::string type;
     if (utl::getAttribute(elem,"type",type))
@@ -248,7 +251,13 @@ bool SIMoptions::parseConsoleTag (const TiXmlElement* elem)
 
 bool SIMoptions::dumpHDF5 (const char* defaultName)
 {
-  if (hdf5.empty()) return false;
+  if (!saveLog) {
+    IFEM::cout.removeExtraLog(IFEM::memoryLog);
+    IFEM::memoryLog.reset();
+  }
+
+  if (hdf5.empty())
+    return false;
 
   if (hdf5 == "(default)") {
     hdf5 = defaultName;

src/SIM/SIMoptions.h

@@ -90,6 +90,7 @@ public:
   double dtSave; //!< Time interval between each result output
   bool pSolOnly; //!< If \e true, don't save secondary solution variables
   bool saveNorms;//!< If \e true, save element norms
+  bool saveLog;  //!< If \e true, export the log
 
   std::string hdf5; //!< Prefix for HDF5-file
   std::string vtf;  //!< Prefix for VTF-file

src/Utility/DataExporter.C

@@ -12,6 +12,7 @@
 //==============================================================================
 
 #include "DataExporter.h"
+#include "IFEM.h"
 #include "Utilities.h"
 #include "Profiler.h"
 #include "ProcessAdm.h"
@@ -35,6 +36,13 @@ DataWriter::DataWriter (const std::string& name,
 
 DataExporter::~DataExporter ()
 {
+  if (IFEM::memoryLog)
+    for (DataWriter* writer : m_writers) {
+      writer->openFile(0);
+      writer->writeLog(IFEM::memoryLog->str(), "cout");
+      writer->closeFile(0);
+    }
+
   if (m_delete)
     for (DataWriter* writer : m_writers)
       delete writer;

src/Utility/DataExporter.h

@@ -16,12 +16,16 @@
 
 #include "ControlFIFO.h"
 #include <map>
+#include <memory>
 #include <string>
 #include <vector>
 
 class DataWriter;
 class ProcessAdm;
 class TimeStep;
+namespace utl {
+class LogStream;
+}
 
 
 /*!
@@ -227,6 +231,10 @@ public:
   virtual bool writeTimeInfo(int level, int interval,
                              const TimeStep& tp) = 0;
 
+  //! \brief Write a log to output file.
+  //! \param name Name of log
+  virtual bool writeLog(const std::string& data, const std::string& name) = 0;
+
   //! \brief Sets the prefices used for norm output.
   void setNormPrefixes(const std::vector<std::string>& prefix) { m_prefix = prefix; }
 

src/Utility/HDF5Writer.C

@@ -727,3 +727,34 @@ void HDF5Writer::writeNodalForces(int level, const DataEntry& entry)
   std::cout << "HDF5Writer: compiled without HDF5 support, no data written" << std::endl;
 #endif
 }
+
+
+bool HDF5Writer::writeLog (const std::string& data, const std::string& name)
+{
+#ifdef HAS_HDF5
+  hid_t group;
+  if (checkGroupExistence(m_file,"/log"))
+    group = H5Gopen2(m_file,"/log",H5P_DEFAULT);
+  else
+    group = H5Gcreate2(m_file,"/log",0,H5P_DEFAULT,H5P_DEFAULT);
+
+  int rank = 0;
+  int size = 1;
+#ifdef HAVE_MPI
+  MPI_Comm_rank(*m_adm.getCommunicator(), &rank);
+  MPI_Comm_size(*m_adm.getCommunicator(), &size);
+#endif
+
+  for (int i = 0; i < size; ++i) {
+    if (rank == i)
+      writeArray(group, name.c_str(), i, data.size(), data.data(), H5T_NATIVE_CHAR);
+    else {
+      char dummy;
+      writeArray(group, name.c_str(), i, 0, &dummy, H5T_NATIVE_CHAR);
+    }
+  }
+  H5Gclose(group);
+
+  return true;
+#endif
+}

src/Utility/HDF5Writer.h

@@ -92,6 +92,11 @@ public:
   //! \param[in] tp The current time stepping info
   virtual bool writeTimeInfo(int level, int interval, const TimeStep& tp);
 
+  //! \brief Write a log to output file.
+  //! \param data Text to write
+  //! \param name Name of log
+  virtual bool writeLog(const std::string& data, const std::string& name);
+
 #ifdef HAS_HDF5
 protected:
   //! \brief Internal helper function writing a data array to file.

src/Utility/LogStream.C

@@ -13,6 +13,8 @@
 
 #include "LogStream.h"
 
+#include <algorithm>
+
 
 utl::LogStream::LogStream(std::ostream& out, int ppid, int mypid) :
   m_out(&out), m_ppid(ppid), m_pid(mypid)
@@ -59,6 +61,14 @@ void utl::LogStream::addExtraLog(std::shared_ptr<std::ostream> extra, bool clear
 }
 
 
+void utl::LogStream::removeExtraLog(std::shared_ptr<std::ostream> extra)
+{
+  auto it = std::find(m_extra.begin(), m_extra.end(), extra);
+  if (it != m_extra.end())
+    m_extra.erase(it);
+}
+
+
 int utl::LogStream::precision(int streamsize)
 {
   int result = streamsize;

src/Utility/LogStream.h

@@ -45,6 +45,8 @@ public:
   void addExtraLog(std::ostream* extra, bool clear = false);
   //! \brief Adds an extra logging stream.
   void addExtraLog(std::shared_ptr<std::ostream> extra, bool clear = false);
+  //! \brief Drop an extra logging stream.
+  void removeExtraLog(std::shared_ptr<std::ostream> extra);
 
   //! \brief Write data to stream
   template<typename T>