Apply the changes that I accidentally submitted to the old server yesterday. Now...

git-svn-id: https://svn.dealii.org/trunk@18277 0785d39b-7218-0410-832d-ea1e28bc413d

diff --git a/deal.II/base/include/base/timer.h b/deal.II/base/include/base/timer.h
index 698c66438d55291877ec200dace8849e08cea294..ada33f40569a2a391c4d07897d20b6a9f2183a7d 100644 (file)
--- a/deal.II/base/include/base/timer.h
+++ b/deal.II/base/include/base/timer.h
@@ -16,6 +16,10 @@
 #include <base/config.h>
 #include <base/conditional_ostream.h>
 
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+#include <mpi.h>
+#endif
+
 #include <string>
 #include <list>
 #include <map>
@@ -73,6 +77,24 @@ class Timer
                                      */
     Timer ();
 
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+                                    /**
+                                     * Constructor that takes an MPI
+                                     * communicator as input. A timer
+                                     * constructed this way will sum up the
+                                     * CPU times over all processors in the
+                                     * MPI network when requested by the
+                                     * operator ().
+                                     * 
+                                     * Starts the timer at 0 sec.
+                                     *
+                                     * This constructor is only available
+                                     * if the deal.II compiler is an MPI
+                                     * compiler.
+                                     */
+    Timer (MPI_Comm mpi_communicator);
+#endif
+
                                     /**
                                      * Re-start the timer at the point where
                                      * it was stopped. This way a cumulative
@@ -170,6 +192,14 @@ class Timer
                                      * running.
                                      */
     bool                running;
+
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+                                    /**
+                                     * Store whether the timer is presently
+                                     * running.
+                                     */
+    MPI_Comm            mpi_communicator;
+#endif
 };
 
 
@@ -220,9 +250,43 @@ class TimerOutput
                                      * ConditionalOStream to write output to.
                                      */
     TimerOutput (ConditionalOStream        &stream, 
+                const enum OutputFrequency output_frequency,
+                const enum OutputType      output_type);
+    
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+                                    /**
+                                     * Constructor that takes an MPI
+                                     * communicator as input. A timer
+                                     * constructed this way will sum up the
+                                     * CPU times over all processors in the
+                                     * MPI network for calculating the CPU
+                                     * time.
+                                     *
+                                     * Meant for using std::cout as output
+                                     * stream.
+                                     */
+    TimerOutput (MPI_Comm                   mpi_comm,
+                std::ostream              &stream, 
                 const enum OutputFrequency output_frequency,
                 const enum OutputType      output_type);
 
+                                    /**
+                                     * Constructor that takes an MPI
+                                     * communicator as input. A timer
+                                     * constructed this way will sum up the
+                                     * CPU times over all processors in the
+                                     * MPI network for calculating the CPU
+                                     * time.
+                                     *
+                                     * Constructor that takes a
+                                     * ConditionalOStream to write output to.
+                                     */
+    TimerOutput (MPI_Comm                   mpi_comm,
+                ConditionalOStream        &stream, 
+                const enum OutputFrequency output_frequency,
+                const enum OutputType      output_type);
+#endif
+
                                     /**
                                      * Destructor. Calls print_summary() in
                                      * case the option for writing the
@@ -298,6 +362,14 @@ class TimerOutput
                                      * function.
                                      */
     std::list<std::string> active_sections;
+
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+                                    /**
+                                     * Store whether the timer is presently
+                                     * running.
+                                     */
+    MPI_Comm            mpi_communicator;
+#endif
 };
 
 DEAL_II_NAMESPACE_CLOSE

diff --git a/deal.II/base/source/timer.cc b/deal.II/base/source/timer.cc
index d0688febb145ea35d09b8ad21d1a75ea7bccb85e..81f4eaeae322b4020c1aa638f03f35f59ec6368b 100644 (file)
--- a/deal.II/base/source/timer.cc
+++ b/deal.II/base/source/timer.cc
@@ -22,9 +22,7 @@
 #include <sys/time.h>
 #include <sys/resource.h>
 
-#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
-#include <mpi.h>
-#endif
+#include <base/thread_management.h>
 
 
 // on SunOS 4.x, getrusage is stated in the man pages and exists, but
@@ -39,16 +37,37 @@ DEAL_II_NAMESPACE_OPEN
 
 
 
+                                  // in case we use an MPI compiler, need
+                                  // to create a communicator just for the
+                                  // current process
 Timer::Timer()
                 :
                 cumulative_time (0.),
                cumulative_wall_time (0.)
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+               , mpi_communicator (MPI_COMM_SELF)
+#endif
 {
   start();
 }
 
 
 
+                                  // in case we use an MPI compiler, use
+                                  // the communicator given from input
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+Timer::Timer(MPI_Comm mpi_communicator)
+                :
+                cumulative_time (0.),
+               cumulative_wall_time (0.),
+               mpi_communicator (mpi_communicator)
+{
+  start();
+}
+#endif
+
+
+
 void Timer::start ()
 {
   running    = true;
@@ -107,10 +126,52 @@ double Timer::operator() () const
       const double dtime_children =
        usage_children.ru_utime.tv_sec + 1.e-6 * usage_children.ru_utime.tv_usec;
 
+                                  // in case of MPI, need to get the time
+                                  // passed by summing the time over all
+                                  // processes in the network. works also
+                                  // in case we just want to have the time
+                                  // of a single thread, since then the
+                                  // communicator is MPI_COMM_SELF
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+      double local_time = dtime - start_time + dtime_children 
+       - start_time_children + cumulative_time;
+
+      int mpiInitialized;
+      MPI_Initialized(&mpiInitialized);
+
+      if ( mpiInitialized )
+       {
+         double global_time = 0.;
+         MPI_Allreduce (&local_time, &global_time, 1, MPI_DOUBLE, MPI_SUM, 
+                        mpi_communicator);
+         return global_time;
+       }
+      else
+       return local_time;
+#else
       return dtime - start_time + dtime_children - start_time_children + cumulative_time;
+#endif
     }
   else
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+    {
+      int mpiInitialized;
+      MPI_Initialized(&mpiInitialized);
+
+      if ( mpiInitialized )
+       {
+         double local_time = cumulative_time;
+         double global_time = 0.;
+         MPI_Allreduce (&local_time, &global_time, 1, MPI_DOUBLE, MPI_SUM, 
+                        mpi_communicator);
+         return global_time;
+       }
+      else
+       return cumulative_time;
+    }
+#else
     return cumulative_time;
+#endif
 }
 
 
@@ -148,6 +209,9 @@ TimerOutput::TimerOutput (std::ostream &stream,
                           output_frequency (output_frequency),
                          output_type (output_type),
                           out_stream (stream, true)
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+                         , mpi_communicator (MPI_COMM_SELF)
+#endif
 {}
 
 
@@ -159,8 +223,39 @@ TimerOutput::TimerOutput (ConditionalOStream &stream,
                           output_frequency (output_frequency),
                          output_type (output_type),
                           out_stream (stream)
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+                         , mpi_communicator (MPI_COMM_SELF)
+#endif
+{}
+
+
+#ifdef DEAL_II_COMPILER_SUPPORTS_MPI
+
+TimerOutput::TimerOutput (MPI_Comm      mpi_communicator,
+                         std::ostream &stream, 
+                         const enum OutputFrequency output_frequency,
+                         const enum OutputType output_type)
+                          :
+                          output_frequency (output_frequency),
+                         output_type (output_type),
+                          out_stream (stream, true), 
+                         mpi_communicator (mpi_communicator)
+{}
+
+
+
+TimerOutput::TimerOutput (MPI_Comm      mpi_communicator,
+                         ConditionalOStream &stream,
+                         const enum OutputFrequency output_frequency,
+                         const enum OutputType output_type)
+                          :
+                          output_frequency (output_frequency),
+                         output_type (output_type),
+                          out_stream (stream),
+                         mpi_communicator (mpi_communicator)
 {}
 
+#endif
 
 
 TimerOutput::~TimerOutput()
@@ -177,6 +272,9 @@ TimerOutput::~TimerOutput()
 void 
 TimerOutput::enter_section (const std::string &section_name)
 {
+  Threads::Mutex mutex;
+  Threads::Mutex::ScopedLock lock (mutex);
+
   Assert (section_name.empty() == false,
          ExcMessage ("Section string is empty."));
 
@@ -203,6 +301,9 @@ TimerOutput::enter_section (const std::string &section_name)
 void 
 TimerOutput::exit_section (const std::string &section_name)
 {
+  Threads::Mutex mutex;
+  Threads::Mutex::ScopedLock lock (mutex);
+
   if (section_name != "")
     {
       Assert (sections.find (section_name) != sections.end(),
@@ -222,13 +323,11 @@ TimerOutput::exit_section (const std::string &section_name)
   sections[actual_section_name].total_wall_time 
     += sections[actual_section_name].timer.wall_time();
 
-                                      // get cpu time. on MPI
-                                      // systems, add the local
-                                      // contributions.
-                                      // 
-                                      // TODO: this should rather be
-                                      // in the Timer class itself,
-                                      // shouldn't it?
+                                      // get cpu time. on MPI systems, add
+                                      // the local contributions. we could
+                                      // do that also in the Timer class
+                                      // itself, but we didn't initialize
+                                      // the Timers here according to that
   double cpu_time = sections[actual_section_name].timer();
   {
 
@@ -242,7 +341,7 @@ TimerOutput::exit_section (const std::string &section_name)
     if( mpiInitialized ) 
       {
        MPI_Allreduce (&cpu_time, &total_cpu_time, 1, MPI_DOUBLE, MPI_SUM, 
-                      MPI_COMM_WORLD);
+                      mpi_communicator);
        cpu_time = total_cpu_time;
       }
 #endif
@@ -294,8 +393,8 @@ TimerOutput::print_summary ()
 
        if( mpiInitialized ) 
          {
-           MPI_Allreduce (&my_cpu_time, &total_cpu_time, 1, MPI_DOUBLE, MPI_SUM, 
-                          MPI_COMM_WORLD);
+           MPI_Allreduce (&my_cpu_time, &total_cpu_time, 1, MPI_DOUBLE, 
+                          MPI_SUM, mpi_communicator);
          }
        else
          total_cpu_time = my_cpu_time;

diff --git a/deal.II/deal.II/source/fe/fe_values.cc b/deal.II/deal.II/source/fe/fe_values.cc
index 566ccff8311657b2c236954a772fe4002cbf9990..0f06613d7aa6d9a02bba84f43e0b6ad96a42ba35 100644 (file)
--- a/deal.II/deal.II/source/fe/fe_values.cc
+++ b/deal.II/deal.II/source/fe/fe_values.cc
@@ -255,6 +255,9 @@ namespace FEValuesViews
       if (shape_function_data[shape_function].is_nonzero_shape_function_component)
        {
          const double value = dof_values(shape_function);
+         if (value == 0.)
+           continue;
+
          const double * shape_value_ptr = 
            &fe_values.shape_values(shape_function_data[shape_function].row_index, 0);
          for (unsigned int q_point=0; q_point<fe_values.n_quadrature_points; ++q_point)
@@ -294,6 +297,9 @@ namespace FEValuesViews
       if (shape_function_data[shape_function].is_nonzero_shape_function_component)
        {
          const double value = dof_values(shape_function);
+         if (value == 0.)
+           continue;
+
          const Tensor<1,spacedim> * shape_gradient_ptr = 
            &fe_values.shape_gradients[shape_function_data[shape_function].
                                       row_index][0];
@@ -334,6 +340,9 @@ namespace FEValuesViews
       if (shape_function_data[shape_function].is_nonzero_shape_function_component)
        {
          const double value = dof_values(shape_function);
+         if (value == 0.)
+           continue;
+
          const Tensor<2,spacedim> * shape_hessian_ptr = 
            &fe_values.shape_hessians[shape_function_data[shape_function].
                                       row_index][0];
@@ -374,6 +383,9 @@ namespace FEValuesViews
       if (shape_function_data[shape_function].is_nonzero_shape_function_component)
        {
          const double value = dof_values(shape_function);
+         if (value == 0.)
+           continue;
+
          const unsigned int row_index = shape_function_data[shape_function].row_index;
          for (unsigned int q_point=0; q_point<fe_values.n_quadrature_points; ++q_point)
            laplacians[q_point] += 
@@ -419,6 +431,9 @@ namespace FEValuesViews
          continue;
 
        const double value = dof_values(shape_function);
+       if (value == 0.)
+         continue;
+
        if (snc != -1)
          {
            const unsigned int comp =
@@ -478,6 +493,9 @@ namespace FEValuesViews
          continue;
 
        const double value = dof_values(shape_function);
+       if (value == 0.)
+         continue;
+
        if (snc != -1)
          {
            const unsigned int comp = 
@@ -539,6 +557,9 @@ namespace FEValuesViews
          continue;
 
        const double value = dof_values(shape_function);
+       if (value == 0.)
+         continue;
+
        if (snc != -1)
          {
            const unsigned int comp = 
@@ -600,6 +621,9 @@ namespace FEValuesViews
          continue;
 
        const double value = dof_values(shape_function);
+       if (value == 0.)
+         continue;
+
        if (snc != -1)
          {
            const unsigned int comp = 
@@ -660,6 +684,9 @@ namespace FEValuesViews
          continue;
 
        const double value = dof_values(shape_function);
+       if (value == 0.)
+         continue;
+
        if (snc != -1)
          {
            const unsigned int comp = 
@@ -720,6 +747,9 @@ namespace FEValuesViews
          continue;
 
        const double value = dof_values(shape_function);
+       if (value == 0.)
+         continue;
+
        if (snc != -1)
          {
            const unsigned int comp =
@@ -1757,6 +1787,9 @@ void FEValuesBase<dim,spacedim>::get_function_values (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = dof_values(shape_func);
+      if (value == 0.)
+       continue;
+
       const double *shape_value_ptr = &this->shape_values(shape_func, 0);
       for (unsigned int point=0; point<n_quadrature_points; ++point)
        values[point] += value * *shape_value_ptr++;
@@ -1813,6 +1846,9 @@ void FEValuesBase<dim,spacedim>::get_function_values (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = fe_function(indices[shape_func]);
+      if (value == 0.)
+       continue;
+
       const double *shape_value_ptr = &this->shape_values(shape_func, 0);
       for (unsigned int point=0; point<n_quadrature_points; ++point)
        values[point] += value * *shape_value_ptr++;
@@ -1885,6 +1921,8 @@ void FEValuesBase<dim,spacedim>::get_function_values (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = dof_values(shape_func);
+      if (value == 0.)
+       continue;
 
       if (fe->is_primitive(shape_func))
        {
@@ -1987,6 +2025,8 @@ void FEValuesBase<dim,spacedim>::get_function_values (
     for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
       {
        const double value = fe_function(indices[shape_func+mc*dofs_per_cell]);
+       if (value == 0.)
+         continue;
 
        if (fe->is_primitive(shape_func))
          {
@@ -2089,6 +2129,8 @@ void FEValuesBase<dim,spacedim>::get_function_values (
     for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
       {
        const double value = fe_function(indices[shape_func+mc*dofs_per_cell]);
+       if (value == 0.)
+         continue;
 
        if (fe->is_primitive(shape_func))
          {
@@ -2187,9 +2229,11 @@ FEValuesBase<dim,spacedim>::get_function_gradients (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = dof_values(shape_func);
+      if (value == 0.)
+       continue;
+
       const Tensor<1,spacedim> *shape_gradient_ptr 
        = &this->shape_gradients[shape_func][0];
-
       for (unsigned int point=0; point<n_quadrature_points; ++point)
        gradients[point] += value * *shape_gradient_ptr++;
     }
@@ -2245,9 +2289,11 @@ void FEValuesBase<dim,spacedim>::get_function_gradients (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = fe_function(indices[shape_func]);
+      if (value == 0.)
+       continue;
+
       const Tensor<1,spacedim> *shape_gradient_ptr 
        = &this->shape_gradients[shape_func][0];
-
       for (unsigned int point=0; point<n_quadrature_points; ++point)
        gradients[point] += value * *shape_gradient_ptr++;
     }
@@ -2296,6 +2342,8 @@ FEValuesBase<dim,spacedim>::get_function_gradients (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = dof_values(shape_func);
+      if (value == 0.)
+       continue;
 
       if (fe->is_primitive(shape_func))
        {
@@ -2397,6 +2445,8 @@ void FEValuesBase<dim,spacedim>::get_function_gradients (
     for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
       {
        const double value = fe_function(indices[shape_func+mc*dofs_per_cell]);
+       if (value == 0.)
+         continue;
 
        if (fe->is_primitive(shape_func))
          {
@@ -2479,9 +2529,11 @@ get_function_hessians (const InputVector           &fe_function,
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = dof_values(shape_func);
+      if (value == 0.)
+       continue;
+
       const Tensor<2,spacedim> *shape_hessians_ptr 
        = &this->shape_hessians[shape_func][0];
-
       for (unsigned int point=0; point<n_quadrature_points; ++point)
        hessians[point] += value * *shape_hessians_ptr++;
     }
@@ -2521,9 +2573,11 @@ void FEValuesBase<dim,spacedim>::get_function_hessians (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = fe_function(indices[shape_func]);
+      if (value == 0.)
+       continue;
+
       const Tensor<2,spacedim> *shape_hessians_ptr 
        = &this->shape_hessians[shape_func][0];
-
       for (unsigned int point=0; point<n_quadrature_points; ++point)
        hessians[point] += value * *shape_hessians_ptr++;
     }
@@ -2569,6 +2623,8 @@ get_function_hessians (const InputVector                         &fe_function,
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = dof_values(shape_func);
+      if (value == 0.)
+       continue;
 
       if (fe->is_primitive(shape_func))
        {
@@ -2680,6 +2736,8 @@ void FEValuesBase<dim, spacedim>::get_function_hessians (
     for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
       {
        const double value = fe_function(indices[shape_func+mc*dofs_per_cell]);
+       if (value == 0.)
+         continue;
 
        if (fe->is_primitive(shape_func))
          {
@@ -2765,9 +2823,11 @@ void FEValuesBase<dim,spacedim>::get_function_laplacians (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = dof_values(shape_func);
+      if (value == 0.)
+       continue;
+
       const Tensor<2,spacedim> *shape_hessian_ptr 
        = &this->shape_hessians[shape_func][0];
-
       for (unsigned int point=0; point<n_quadrature_points; ++point)
        laplacians[point] += value * trace(*shape_hessian_ptr++);
     }
@@ -2810,9 +2870,11 @@ void FEValuesBase<dim,spacedim>::get_function_laplacians (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = fe_function(indices[shape_func]);
+      if (value == 0.)
+       continue;
+
       const Tensor<2,spacedim> *shape_hessian_ptr 
        = &this->shape_hessians[shape_func][0];
-
       for (unsigned int point=0; point<n_quadrature_points; ++point)
        laplacians[point] += value * trace(*shape_hessian_ptr++);
     }
@@ -2868,6 +2930,8 @@ void FEValuesBase<dim,spacedim>::get_function_laplacians (
   for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
     {
       const double value = dof_values(shape_func);
+      if (value == 0.)
+       continue;
 
       if (fe->is_primitive(shape_func))
        {
@@ -2958,6 +3022,8 @@ void FEValuesBase<dim,spacedim>::get_function_laplacians (
     for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
       {
        const double value = fe_function(indices[shape_func+mc*dofs_per_cell]);
+       if (value == 0.)
+         continue;
 
        if (fe->is_primitive(shape_func))
          {
@@ -3062,6 +3128,8 @@ void FEValuesBase<dim,spacedim>::get_function_laplacians (
     for (unsigned int shape_func=0; shape_func<dofs_per_cell; ++shape_func)
       {
        const double value = fe_function(indices[shape_func+mc*dofs_per_cell]);
+       if (value == 0.)
+         continue;
 
        if (fe->is_primitive(shape_func))
          {