Removing HDF5.

TPLsList.cmake

@@ -10,9 +10,7 @@
 #
 #   Trilinos/cmake/TrilinosTPLs.cmake
 #
-SET(ProfugusMC_TPLS_FINDMODS_CLASSIFICATIONS
-  HDF5   "cmake/TPLs/"   SS
-  )
+SET(ProfugusMC_TPLS_FINDMODS_CLASSIFICATIONS)
 
 ##---------------------------------------------------------------------------##
 ## end of TPLsList.cmake

cmake/TPLs/FindTPLHDF5.cmake

-
-SET(LIBS_NAMES hdf5_hl hdf5)
-
-IF( ${PROJECT_NAME}_ENABLE_VERAIn )
-  APPEND_SET(LIBS_NAMES hdf5_fortran)
-ENDIF()
-
-TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( HDF5
-  REQUIRED_HEADERS hdf5.h
-  REQUIRED_LIBS_NAMES ${LIBS_NAMES} z
-  )

cmake/TPLs/FindTPLSILO.cmake

-
-IF(NOT TPL_ENABLE_HDF5)
-  MESSAGE(FATAL_ERROR "\nSILO TPL requires that HDF5 support is enabled.\n\n")
-ELSE()
-  TRIBITS_TPL_FIND_INCLUDE_DIRS_AND_LIBRARIES( SILO
-    REQUIRED_HEADERS silo.h
-    REQUIRED_LIBS_NAMES siloh5
-    )
-ENDIF()

install/cmake_cpu.sh

@@ -10,10 +10,9 @@ cmake \
     -DCMAKE_CXX_COMPILER="mpicxx" \
     -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL} \
     -DBUILD_SHARED_LIBS:BOOL=ON \
-    -DProfugus_ENABLE_CXX11:BOOL=ON \
+    -DProfugusMC_ENABLE_CXX11:BOOL=ON \
     -DTPL_ENABLE_MPI:BOOL=ON \
-    -DTPL_ENABLE_HDF5:BOOL=ON \
-    -DProfugus_ENABLE_MC:BOOL=ON \
-    -DProfugus_ENABLE_TESTS:BOOL=OFF \
+    -DProfugusMC_ENABLE_MC:BOOL=ON \
+    -DProfugusMC_ENABLE_TESTS:BOOL=OFF \
     ${SOURCE}
     

install/cmake_cuda.sh

@@ -11,14 +11,13 @@ cmake \
     -DCMAKE_CXX_COMPILER="mpicxx" \
     -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL} \
     -DBUILD_SHARED_LIBS:BOOL=ON \
-    -DProfugus_ENABLE_CXX11:BOOL=ON \
+    -DProfugusMC_ENABLE_CXX11:BOOL=ON \
     -DTPL_ENABLE_MPI:BOOL=ON \
-    -DTPL_ENABLE_HDF5:BOOL=ON \
     -DTPL_ENABLE_CUDA:BOOL=ON \
-    -DProfugus_ENABLE_CUDA:BOOL=ON \
+    -DProfugusMC_ENABLE_CUDA:BOOL=ON \
     -DCUDA_PROPAGATE_HOST_FLAGS:BOOL=OFF \
     -DCUDA_NVCC_FLAGS:STRING="--std=c++11;-arch=sm_35;-Xptxas=-dlcm=cg" \
-    -DProfugus_ENABLE_MC:BOOL=ON \
-    -DProfugus_ENABLE_TESTS:BOOL=OFF \
+    -DProfugusMC_ENABLE_MC:BOOL=ON \
+    -DProfugusMC_ENABLE_TESTS:BOOL=OFF \
     ${SOURCE}
     

packages/MC/cuda_mc/Cell_Tally.cuh

@@ -142,9 +142,6 @@ class Cell_Tally_DMM : public cuda::Device_Memory_Manager<Cell_Tally<Geometry>>
     std::vector<double> d_tally_sum_sq;
     std::vector<double> d_batch_np;
 
-    // Prefix for hdf5 filename
-    std::string d_file_prefix;
-
   public:
 
     // Constructor.

packages/MC/cuda_mc/Cell_Tally.t.cuh

@@ -16,7 +16,6 @@
 
 #include "Utils/comm/global.hh"
 #include "Utils/utils/View_Field.hh"
-#include "Utils/utils/Serial_HDF5_Writer.hh"
 
 #include "cuda_utils/Launch_Args.t.cuh"
 
@@ -42,9 +41,6 @@ Cell_Tally_DMM<Geometry>::Cell_Tally_DMM(RCP_Std_DB   db,
     REQUIRE(d_geometry.get_device_ptr());
     REQUIRE(d_physics.get_host_ptr());
     REQUIRE(d_physics.get_device_ptr());
-    d_file_prefix = "cell_tally";
-    if (db->isType<std::string>("problem_name"))
-        d_file_prefix = db->get<std::string>("problem_name");
 }
 
 //---------------------------------------------------------------------------//
@@ -149,20 +145,6 @@ void Cell_Tally_DMM<Geometry>::finalize(double num_particles)
         d_host_tally[cell] = tally_mean / vol;
         d_host_std_dev[cell] = std::sqrt(var) / vol;
     }
-
-#ifdef USE_HDF5
-    // Open file for writing
-    std::string filename = d_file_prefix + "_flux.h5";
-    profugus::Serial_HDF5_Writer writer;
-    writer.open(filename);
-
-    // Write data
-    writer.write("cells",d_host_cells);
-    writer.write("flux_mean",d_host_tally);
-    writer.write("flux_std_dev",d_host_std_dev);
-
-    writer.close();
-#endif
 }
 
 //---------------------------------------------------------------------------//

packages/MC/cuda_mc/Manager_Cuda.hh

@@ -101,9 +101,6 @@ class Manager_Cuda : public mc::Manager_Base
     // Solve the problem.
     void solve();
 
-    // Output.
-    void output();
-
   protected:
 
     // Get keff

packages/MC/cuda_mc/Manager_Cuda.t.cuh

@@ -20,8 +20,6 @@
 #include "comm/global.hh"
 #include "xs/XS_Builder.hh"
 #include "utils/String_Functions.hh"
-#include "utils/Serial_HDF5_Writer.hh"
-#include "utils/Parallel_HDF5_Writer.hh"
 #include "cuda_geometry/Mesh_Geometry.hh"
 #include "Uniform_Source.cuh"
 #include "Tallier.cuh"
@@ -232,67 +230,6 @@ void Manager_Cuda<Geometry_DMM>::solve()
     }
 }
 
-//---------------------------------------------------------------------------//
-/*!
- * \brief Do output.
- */
-template <class Geometry_DMM>
-void Manager_Cuda<Geometry_DMM>::output()
-{
-    using std::string;
-
-    SCOPED_TIMER("Manager_Cuda.output");
-
-    SCREEN_MSG("Outputting data");
-
-    // >>> OUTPUT FINAL DATABASE
-
-    // output the final database
-    if (d_node == 0)
-    {
-        std::ostringstream m;
-        m << d_problem_name << "_db.xml";
-        Teuchos::writeParameterListToXmlFile(*d_db, m.str());
-    }
-
-    profugus::global_barrier();
-
-    // >>> OUTPUT SOLUTION (only available if HDF5 is on)
-#ifdef USE_HDF5
-
-    // Output filename
-    std::ostringstream m;
-    m << d_problem_name << "_output.h5";
-    string outfile = m.str();
-
-    // scalar output for kcode
-    if (d_keff_solver)
-    {
-        // get the kcode tally
-        auto keff = d_keff_solver->keff_tally();
-        CHECK(keff);
-
-        // make the hdf5 file
-        profugus::Serial_HDF5_Writer writer;
-        writer.open(outfile);
-
-        // output scalar quantities
-        writer.begin_group("keff");
-
-        writer.write(string("mean"), keff->mean());
-        writer.write(string("variance"), keff->variance());
-        writer.write(string("num_active_cycles"),
-                     static_cast<int>(keff->cycle_count()));
-        writer.write(string("cycle_estimates"), keff->all_keff());
-
-        writer.end_group();
-
-        writer.close();
-    }
-
-#endif // USE_HDF5
-}
-
 //---------------------------------------------------------------------------//
 /*!
  * \brief Build mesh geometry

packages/MC/mc/Cell_Tally.t.hh

@@ -16,7 +16,6 @@
 
 #include "Utils/comm/global.hh"
 #include "Cell_Tally.hh"
-#include "utils/Serial_HDF5_Writer.hh"
 
 namespace profugus
 {
@@ -160,7 +159,7 @@ void Cell_Tally<Geometry>::finalize(double num_particles)
         // Store the error of the sample mean
         moments.second = std::sqrt(var * inv_N);
 
-        // Store values back into vectors for HDF5 writing
+        // Store values back into vectors
         first[ctr]  = moments.first;
         second[ctr] = moments.second;
 
@@ -195,18 +194,6 @@ void Cell_Tally<Geometry>::finalize(double num_particles)
             second[i] = tmp_second[ind];
         }
     }
-
-#ifdef USE_HDF5
-    REQUIRE( d_db->isType<std::string>("problem_name") );
-    std::string filename = d_db->get<std::string>("problem_name") + "_flux.h5";
-
-    Serial_HDF5_Writer writer;
-    writer.open(filename);
-    writer.write("cells",cells);
-    writer.write("flux_mean",first);
-    writer.write("flux_std_dev",second);
-    writer.close();
-#endif
 }
 
 //---------------------------------------------------------------------------//

packages/MC/mc/Source_Diagnostic_Tally.hh

@@ -18,7 +18,6 @@
 #include "Teuchos_RCP.hpp"
 #include "Teuchos_ParameterList.hpp"
 
-#include "utils/Serial_HDF5_Writer.hh"
 #include "geometry/Mesh_Geometry.hh"
 #include "Tally.hh"
 
@@ -99,9 +98,8 @@ class Source_Diagnostic_Tally : public Source_Tally<Geometry>
   private:
     // >>> IMPLEMENTATION
 
-    // Output file name and hdf5 writer.
+    // Output file name
     std::string        d_filename;
-    Serial_HDF5_Writer d_writer;
 
     // Cycle counter.
     int d_cycle_ctr;

packages/MC/mc/Source_Diagnostic_Tally.t.hh

@@ -52,33 +52,8 @@ Source_Diagnostic_Tally<Geometry>::Source_Diagnostic_Tally(
     // set the name
     Base::set_name("fission_source");
 
-#ifndef USE_HDF5
     ADD_WARNING("HDF5 not available in this build, turning source diagnostic"
                 << " tally off");
-#else
-
-    // make the source diagnostic output file
-    d_filename = db->get<std::string>("problem_name") + "_fs.h5";
-
-    // make the initial file
-    d_writer.open(d_filename);
-
-    // write the mesh
-    d_writer.begin_group("mesh");
-
-    // get the underlying cartesian mesh
-    const auto &cart_mesh = d_mesh->mesh();
-
-    // write the edges
-    d_writer.write("x", cart_mesh.edges(def::X));
-    d_writer.write("y", cart_mesh.edges(def::Y));
-    d_writer.write("z", cart_mesh.edges(def::Z));
-
-    d_writer.end_group();
-
-    d_writer.close();
-
-#endif
 }
 
 //---------------------------------------------------------------------------//
@@ -90,25 +65,6 @@ Source_Diagnostic_Tally<Geometry>::Source_Diagnostic_Tally(
 template <class Geometry>
 void Source_Diagnostic_Tally<Geometry>::birth(const Particle_t &p)
 {
-#ifdef USE_HDF5
-    // get the particle's geometric state
-    const auto &geo_state = p.geo_state();
-
-    // initialize the particle in the fission-matrix mesh
-    d_mesh->initialize(d_geometry->position(geo_state),
-                       d_geometry->direction(geo_state),
-                       d_state);
-
-    // determine the birth cell in the fission matrix mesh
-    auto mesh_idx = d_mesh->cell(d_state);
-    CHECK(mesh_idx >= 0 && mesh_idx < d_mesh->num_cells());
-
-    // tally the source (particle) density
-    d_source_density[mesh_idx] += p.wt();
-
-    // count up the particles in this cycle
-    ++d_num_per_cycle;
-#endif
 }
 
 //---------------------------------------------------------------------------//
@@ -118,59 +74,6 @@ void Source_Diagnostic_Tally<Geometry>::birth(const Particle_t &p)
 template <class Geometry>
 void Source_Diagnostic_Tally<Geometry>::end_cycle(double num_particles)
 {
-#ifdef USE_HDF5
-    REQUIRE(d_source_density.size() == d_mesh->num_cells());
-
-    // reduce the tally across all sets
-    profugus::global_sum(d_source_density.data(), d_source_density.size());
-
-    // get the underlying cartesian mesh
-    const auto &cart_mesh = d_mesh->mesh();
-    CHECK(cart_mesh.num_cells() == d_mesh->num_cells());
-
-    // normalize so that s\dot s = 1
-    double norm = 0.0;
-    for (int cell = 0; cell < d_source_density.size(); ++cell)
-    {
-        d_source_density[cell] /= cart_mesh.volume(cell);
-        norm += d_source_density[cell] * d_source_density[cell];
-    }
-
-    // calculate the normalization
-    norm = 1.0 / std::sqrt(norm);
-
-    // apply the normalization
-    for (auto &s : d_source_density)
-    {
-        s *= norm;
-    }
-
-    // open the file - writing is only on proc 0
-    d_writer.open(d_filename, HDF5_IO::APPEND, 0);
-
-    // make the cycle group
-    std::ostringstream m;
-    m << "cycle_" << d_cycle_ctr;
-    d_writer.begin_group(m.str());
-
-    // write the number of particles
-    profugus::global_sum(&d_num_per_cycle, 1);
-    d_writer.write("num_particles", d_num_per_cycle);
-
-    // write the normalized source
-    d_writer.write("source_density", d_source_density);
-
-    // end the group and close
-    d_writer.end_group();
-    d_writer.close();
-
-    // reset the source tally for the next cycle
-    reset();
-
-    // update the cycle counter
-    ++d_cycle_ctr;
-
-#endif
 }
 
 //---------------------------------------------------------------------------//

packages/MC/mc_driver/Manager.hh

@@ -92,9 +92,6 @@ class Manager : public Manager_Base
                         double      k_std_ref,
                         std::string flux_file);
 
-    // Output.
-    void output();
-
   protected:
 
     // Get keff

packages/MC/mc_driver/Manager.t.hh

@@ -14,15 +14,13 @@
 #include <sstream>
 #include <fstream>
 #include <iostream>
-//#include <iomanip>
+#include <iomanip>
 
 #include "Teuchos_XMLParameterListHelpers.hpp"
 
 #include "harness/DBC.hh"
 #include "comm/Timing.hh"
 #include "comm/global.hh"
-#include "utils/Serial_HDF5_Writer.hh"
-#include "utils/Parallel_HDF5_Writer.hh"
 #include "mc/Fission_Source.hh"
 #include "mc/Uniform_Source.hh"
 #include "mc/KCode_Solver.hh"
@@ -263,67 +261,6 @@ void Manager<Geometry>::get_keff(double& keff_mean, double& keff_var)
     keff_var  = keff_tally->variance();
 }
 
-//---------------------------------------------------------------------------//
-/*!
- * \brief Do output.
- */
-template <class Geometry>
-void Manager<Geometry>::output()
-{
-    using std::string;
-
-    SCOPED_TIMER("Manager.output");
-
-    SCREEN_MSG("Outputting data");
-
-    // >>> OUTPUT FINAL DATABASE
-
-    // output the final database
-    if (d_node == 0)
-    {
-        std::ostringstream m;
-        m << d_problem_name << "_db.xml";
-        Teuchos::writeParameterListToXmlFile(*d_db, m.str());
-    }
-
-    profugus::global_barrier();
-
-    // >>> OUTPUT SOLUTION (only available if HDF5 is on)
-#ifdef USE_HDF5
-
-    // Output filename
-    std::ostringstream m;
-    m << d_problem_name << "_output.h5";
-    string outfile = m.str();
-
-    // scalar output for kcode
-    if (d_keff_solver)
-    {
-        // get the kcode tally
-        auto keff = d_keff_solver->keff_tally();
-        CHECK(keff);
-
-        // make the hdf5 file
-        profugus::Serial_HDF5_Writer writer;
-        writer.open(outfile);
-
-        // output scalar quantities
-        writer.begin_group("keff");
-
-        writer.write(string("mean"), keff->mean());
-        writer.write(string("variance"), keff->variance());
-        writer.write(string("num_active_cycles"),
-                     static_cast<int>(keff->cycle_count()));
-        writer.write(string("cycle_estimates"), keff->all_keff());
-
-        writer.end_group();
-
-        writer.close();
-    }
-
-#endif // USE_HDF5
-}
-
 } // end namespace mc
 
 #endif // mc_driver_Manager_t_hh

packages/MC/mc_driver/Manager_Base.hh

@@ -48,9 +48,6 @@ class Manager_Base
           double      k_std_ref,
           std::string flux_file);
 
-      // Output data.
-      virtual void output() = 0;
-
   protected:
 
       // Get keff

packages/MC/mc_driver/mc.cc

@@ -129,9 +129,6 @@ int main(int argc, char *argv[])
 
         // solve the problem
         manager->solve();
-
-        // output
-        manager->output();
     }
     catch (const profugus::assertion &a)
     {

packages/MC/mc_driver/profugus.cc

@@ -184,9 +184,6 @@ int main(int argc, char *argv[])
         double k_std_ref = 6.131761e-06;
         std::string flux_file = data_dir + "c5g7_flux_ref.txt";
         manager->check_solution(k_ref, k_std_ref, flux_file);
-
-        // output
-        manager->output();
     }
     catch (const profugus::assertion &a)
     {

packages/Utils/CMakeLists.txt

@@ -202,14 +202,6 @@ IF(SPRNG_BigEndian)
   SET(SPRNG_LittleEndian OFF)
 ENDIF()
 
-##---------------------------------------------------------------------------##
-## Optional TPLs
-
-IF (TPL_ENABLE_HDF5)
-  MESSAGE(STATUS "Building Utils with HDF5 support")
-  SET(USE_HDF5 ON)
-ENDIF()
-
 ##---------------------------------------------------------------------------##
 # C) Process the subpackages
 ##---------------------------------------------------------------------------##
@@ -260,20 +252,9 @@ INSTALL(FILES ${COMM_HEADERS} DESTINATION include/Utils/comm)
 FILE(GLOB UTILS_HEADERS utils/*.hh)
 SET(UTILS_SOURCES
   utils/Hash_Functions.cc
-  utils/String_Functions.cc)
-
-IF(TPL_ENABLE_HDF5)
-  APPEND_SET(UTILS_SOURCES
-    utils/HDF5_IO.cc
-    utils/HDF5_Reader.cc
-    utils/Hash_Functions.cc
-    utils/Member_Manager.cc
-    utils/Parallel_HDF5_Writer.cc
-    utils/Serial_HDF5_Writer.cc
-    utils/String_Functions.cc
-    utils/Vector_Functions.cc
-    )
-ENDIF()
+  utils/Member_Manager.cc
+  utils/String_Functions.cc
+  utils/Vector_Functions.cc)
 
 LIST(APPEND HEADERS ${UTILS_HEADERS})
 LIST(APPEND SOURCES ${UTILS_SOURCES})

packages/Utils/cmake/Dependencies.cmake

@@ -13,7 +13,7 @@ SET(LIB_OPTIONAL_DEP_PACKAGES)
 SET(TEST_REQUIRED_DEP_PACKAGES)
 SET(TEST_OPTIONAL_DEP_PACKAGES)
 SET(LIB_REQUIRED_DEP_TPLS)
-SET(LIB_OPTIONAL_DEP_TPLS HDF5)
+SET(LIB_OPTIONAL_DEP_TPLS)
 SET(TEST_REQUIRED_DEP_TPLS)
 SET(TEST_OPTIONAL_DEP_TPLS)
 

packages/Utils/cmake/config.h.in

@@ -144,9 +144,6 @@
 /* C++11 settings */
 #cmakedefine01 GTEST_LANG_CXX11
 
-/* USE HDF5 OUTPUT FUNCTIONS */
-#cmakedefine USE_HDF5
-
 #cmakedefine CMAKE_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@"
 
 /* >>> RNG VARIABLES */