Merge Pull Request #7755 from trilinos/Trilinos/master_merge_20200731…

…_000610

Automatically Merged using Trilinos Master Merge AutoTester
PR Title: Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20200731_000610 branch to master
PR Author: trilinos-autotester

packages/amesos2/test/solvers/CMakeLists.txt

@@ -178,7 +178,7 @@ IF (${PACKAGE_NAME}_ENABLE_Cholmod)
 
   TRIBITS_COPY_FILES_TO_BINARY_DIR(SolverTestCholmodFiles
     SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}
-    SOURCE_FILES cholmod_test.xml
+    SOURCE_FILES cholmod_test.xml cholmod_int_test.xml
     EXEDEPS Solver_Test
     )
 
@@ -191,6 +191,15 @@ IF (${PACKAGE_NAME}_ENABLE_Cholmod)
     COMM serial mpi
     )
 
+  TRIBITS_ADD_TEST(
+    Solver_Test
+    NAME Cholmod_Int_Solver_Test
+    ARGS "--xml-params=cholmod_int_test.xml --filedir=${CMAKE_CURRENT_BINARY_DIR}/../matrices/ --multiple-solves --refactor"
+    STANDARD_PASS_OUTPUT
+    NUM_MPI_PROCS 1
+    COMM serial mpi
+    )
+
   IF (KokkosKernels_ENABLE_SUPERNODAL_SPTRSV AND KokkosKernels_ENABLE_TPL_CHOLMOD)
 
     TRIBITS_COPY_FILES_TO_BINARY_DIR(SolverTestCholmodTRSVFiles

packages/amesos2/test/solvers/cholmod_int_test.xml

@@ -0,0 +1,64 @@
+<ParameterList name="test_params">
+
+  <ParameterList name="tacho_test.mtx">
+
+    <!-- Optional parameter, used for debugging and for deciding whether to use epetra -->
+    <Parameter name="complex" type="bool" value="false"/>
+    <ParameterList name="Cholmod">
+
+      <!-- Test Epetra objects -->
+      <ParameterList name="epetra">
+        <!-- A non-list entry for epetra denotes a default run, name, type, and value are arbitrary -->
+        <Parameter name="defaultrun" type="bool" value="true"/>
+      </ParameterList>
+
+      <!-- Next test Tpetra objects -->
+      <ParameterList name="tpetra">
+        <!-- these `run*' sublist names are arbitrary -->
+        <!-- The `Node' parameter is not yet supported -->
+        <!-- Cholmod does not support float yet. -->
+
+        <ParameterList name="run_double_int">
+          <Parameter name="Scalar" type="string" value="double"/>
+          <Parameter name="LocalOrdinal" type="string" value="int"/>
+          <Parameter name="GlobalOrdinal" type="string" value="int"/>
+        </ParameterList>
+        <ParameterList name="run_double_long_long">
+          <Parameter name="Scalar" type="string" value="double"/>
+          <Parameter name="LocalOrdinal" type="string" value="int"/>
+          <Parameter name="GlobalOrdinal" type="string" value="long long int"/>
+        </ParameterList>
+      </ParameterList>
+
+        <!-- Next test Kokkos objects -->
+      <ParameterList name="kokkos">
+        <!-- these `run*' sublist names are arbitrary -->
+        <!-- Cholmod does not support float yet. -->
+        <ParameterList name="run_serial_double">
+          <Parameter name="Scalar" type="string" value="double"/>
+          <Parameter name="LocalOrdinal" type="string" value="int"/>
+          <Parameter name="Node" type="string" value="serial"/>
+        </ParameterList>
+        <ParameterList name="run_cuda_double">
+          <Parameter name="Scalar" type="string" value="double"/>
+          <Parameter name="LocalOrdinal" type="string" value="int"/>
+          <Parameter name="Node" type="string" value="cuda"/>
+        </ParameterList>
+        <ParameterList name="run_cudauvmoff_double">
+          <Parameter name="Scalar" type="string" value="double"/>
+          <Parameter name="LocalOrdinal" type="string" value="int"/>
+          <Parameter name="Node" type="string" value="cudauvmoff"/>
+        </ParameterList>
+      </ParameterList>
+
+      <ParameterList name="solver_params">
+        <Parameter name="CholmodInt" type="bool" value="true"/>
+        <!-- Cholmod cannot be GPU for int, though we can still run inputs with GPU as in the above tests,-->
+        <Parameter name="useGPU" type="int" value="0"/>
+      </ParameterList>
+    </ParameterList> <!-- end Cholmod -->
+    <ParameterList name="all_solver_params">
+    </ParameterList>
+  </ParameterList> <!-- end cholmod_test.mtx -->
+
+</ParameterList>

packages/shylu/shylu_node/tacho/cmake/Dependencies.cmake

@@ -1,6 +1,6 @@
 SET(LIB_REQUIRED_DEP_PACKAGES Kokkos)
-SET(LIB_OPTIONAL_DEP_PACKAGES TrilinosSS)
-SET(TEST_REQUIRED_DEP_PACKAGES Kokkos TrilinosSS Gtest)
+SET(LIB_OPTIONAL_DEP_PACKAGES)
+SET(TEST_REQUIRED_DEP_PACKAGES Kokkos KokkosAlgorithms Gtest)
 SET(TEST_OPTIONAL_DEP_PACKAGES)
 SET(LIB_REQUIRED_DEP_TPLS)
 SET(LIB_OPTIONAL_DEP_TPLS METIS Scotch Cholmod HWLOC HYPRE MKL LAPACK BLAS Pthread QTHREAD VTune CUSOLVER CUSPARSE CUBLAS CUDA)

packages/shylu/shylu_node/tacho/example/CMakeLists.txt

@@ -8,6 +8,13 @@ FILE(GLOB SOURCES *.cpp)
 
 SET(LIBRARIES tacho)
 
+TRIBITS_ADD_EXECUTABLE(
+  Tacho_ExampleCombineDataFileToMatrixMarketFile
+  NOEXEPREFIX
+  SOURCES Tacho_ExampleCombineDataFileToMatrixMarketFile.cpp
+  COMM serial mpi
+)
+
 IF (TACHO_HAVE_KOKKOS_TASK)
   #
   # Supernodes
@@ -199,7 +206,7 @@ IF (TACHO_HAVE_KOKKOS_TASK)
   ENDIF()
 
   TRIBITS_COPY_FILES_TO_BINARY_DIR(Tacho_SimpleSparseTest_File
-          SOURCE_FILES test.mtx
+          SOURCE_FILES test.mtx graph.dat weight.dat graph_test.mtx 
           SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}
           DEST_DIR ${CMAKE_CURRENT_BINARY_DIR}
   )

packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholCuSolver.cpp

@@ -73,8 +73,7 @@ int main (int argc, char *argv[]) {
 #if defined(TACHO_HAVE_METIS)
     typedef GraphTools_Metis graph_tools_type;
 #else
-    /// not recommend to use CAMD
-    typedef GraphTools_CAMD graph_tools_type;
+    typedef GraphTools graph_tools_type;    
 #endif
     Graph graph(h_A.NumRows(), h_A.NumNonZeros(), h_A.RowPtr(), h_A.Cols());
     graph_tools_type G(graph);

packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholLevelSet.cpp

@@ -118,7 +118,7 @@ int main (int argc, char *argv[]) {
 #elif defined(TACHO_HAVE_SCOTCH)
     Tacho::GraphTools_Scotch T(G);
 #else
-    Tacho::GraphTools_CAMD T(G);
+    Tacho::GraphTools T(G);
 #endif
     T.reorder(verbose);
 

packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholSupernodes.cpp

@@ -108,7 +108,7 @@ int main (int argc, char *argv[]) {
 #elif defined(TACHO_HAVE_SCOTCH)
     GraphTools_Scotch T(G);
 #else
-    GraphTools_CAMD T(G);
+    GraphTools T(G);
 #endif
     T.reorder(verbose);
 

packages/shylu/shylu_node/tacho/example/Tacho_ExampleCholTriSolve.cpp

@@ -107,7 +107,7 @@ int main (int argc, char *argv[]) {
 #elif defined(TACHO_HAVE_SCOTCH)
     Tacho::GraphTools_Scotch T(G);
 #else
-    Tacho::GraphTools_CAMD T(G);
+    Tacho::GraphTools T(G);
 #endif
     T.reorder(verbose);
 

packages/shylu/shylu_node/tacho/example/Tacho_ExampleCombineDataFileToMatrixMarketFile.cpp

@@ -0,0 +1,80 @@
+#include <Kokkos_Core.hpp>
+#include <Kokkos_Random.hpp>
+#include <impl/Kokkos_Timer.hpp>
+
+#include "Tacho_Internal.hpp"
+#include "Tacho_CommandLineParser.hpp"
+
+using namespace Tacho;
+
+int main (int argc, char *argv[]) {
+  CommandLineParser opts("This example program combines data file into a single matrix market file");
+
+  std::string graph_data_file = "graph.dat";
+  std::string value_data_file = "value.dat";
+  std::string matrix_market_file = "mm-out.mtx";
+
+  opts.set_option<std::string>("graph-file", "Input graph data file ", &graph_data_file);
+  opts.set_option<std::string>("value-file", "Input value data file ", &value_data_file);
+  opts.set_option<std::string>("matrix-market-file", "Output matrixmarket file", &matrix_market_file);
+
+  const bool r_parse = opts.parse(argc, argv);
+  if (r_parse) return 0; // print help return
+
+  Kokkos::initialize(argc, argv);
+
+  typedef Kokkos::DefaultHostExecutionSpace host_space;
+  {
+    typedef double value_type;
+    typedef CrsMatrixBase<value_type,host_space> CrsMatrixBaseTypeHost;
+
+    CrsMatrixBaseTypeHost A;
+    using ordinal_type_array = typename CrsMatrixBaseTypeHost::ordinal_type_array;
+    using size_type_array = typename CrsMatrixBaseTypeHost::size_type_array;
+    using value_type_array = typename CrsMatrixBaseTypeHost::value_type_array;
+
+    ordinal_type m(0), nnz(0);
+    size_type_array ap;
+    ordinal_type_array aj;
+    value_type_array ax;
+    {
+      std::ifstream in;
+      in.open(graph_data_file);
+      if (!in.good()) {
+        std::cout << "Failed in open the file: " << graph_data_file << std::endl;
+        return -1;
+      }
+
+      in >> m;
+      ap = size_type_array("ap", m+1);
+      for (ordinal_type i=0;i<(m+1);++i) 
+        in >> ap(i);
+
+      nnz = ap(m);
+      aj = ordinal_type_array("aj", nnz);
+      for (ordinal_type k=0;k<nnz;++k) 
+        in >> aj(k);
+    }
+    {
+      std::ifstream in;
+      in.open(value_data_file);
+      if (!in.good()) {
+        std::cout << "Failed in open the file: " << value_data_file << std::endl;
+        return -1;
+      }
+
+      ax = value_type_array("ax", nnz);
+      for (ordinal_type k=0;k<nnz;++k) 
+        in >> ax(k);
+    }
+
+    A.setExternalMatrix(m, m, nnz, ap, aj, ax);
+    {
+      std::ofstream out(matrix_market_file);
+      MatrixMarket<value_type>::write(out, A);
+    }
+  }
+  Kokkos::finalize();
+
+  return 0;
+}

packages/shylu/shylu_node/tacho/example/Tacho_ExampleExternalInterface.hpp

@@ -74,7 +74,11 @@ namespace tacho {
                    /// with TACHO_ENABLE_INT_INT, size_type is "int"
 		   int* rowBegin,
 		   int* columns,
-		   SX* values)
+		   SX* values,
+                   int numGraphRows = 0,
+                   int* graphRowBegin = nullptr,
+                   int* graphColumns = nullptr,
+                   int* graphWeights = nullptr)
     {
       m_numRows = numRows;
       if (m_numRows == 0) return 0;
@@ -83,6 +87,24 @@ namespace tacho {
       size_type_array_host    ap_host((size_type*)   rowBegin, numRows+1);
       ordinal_type_array_host aj_host((ordinal_type*)columns,  numTerms);
 
+      size_type_array_host graph_ap_host;
+      ordinal_type_array_host graph_aj_host;
+      ordinal_type_array_host graph_aw_host;
+
+      if (numGraphRows > 0) {
+        if (graphRowBegin == nullptr ||
+            graphColumns == nullptr ||
+            graphWeights == nullptr) {
+          std::cout << "ExternalInterface::Error, with non-zero numGraphRows, graph pointers should not be nullptr\n";
+          std::logic_error("Error: one of graph pointers is nullptr");
+        } else {
+          const size_type nnz_graph = graph_ap_host(numGraphRows);
+          graph_ap_host = size_type_array_host((size_type*)graphRowBegin, numGraphRows+1);
+          graph_aj_host = ordinal_type_array_host((ordinal_type*)graphColumns, nnz_graph);
+          graph_aw_host = ordinal_type_array_host((ordinal_type*)graphWeights, nnz_graph);
+        }
+      }
+
 #if defined (KOKKOS_ENABLE_CUDA)
       /// transfer A into device
       value_type_array ax(Kokkos::ViewAllocateWithoutInitializing("ax"), 
@@ -97,7 +119,12 @@ namespace tacho {
       Kokkos::Impl::Timer timer; 
       {
         timer.reset();
-	m_Solver.analyze(numRows, ap_host, aj_host);
+        if (numGraphRows > 0) {
+          m_Solver.analyze(numRows, ap_host, aj_host,
+                           numGraphRows, graph_ap_host, graph_aj_host, graph_aw_host);
+        } else {
+          m_Solver.analyze(numRows, ap_host, aj_host);
+        }
         const double t = timer.seconds();
         std::cout << "ExternalInterface:: analyze time " << t << std::endl;
       }

packages/shylu/shylu_node/tacho/example/Tacho_ExamplePerfTest.cpp

@@ -135,7 +135,7 @@ int main (int argc, char *argv[]) {
 #elif defined(TACHO_HAVE_SCOTCH)
     Tacho::GraphTools_Scotch G(graph);
 #else
-    Tacho::GraphTools_CAMD G(graph);
+    Tacho::GraphTools G(graph);
 #endif
     G.reorder(verbose);
 

packages/shylu/shylu_node/tacho/example/Tacho_ExampleSolver.hpp

@@ -29,6 +29,8 @@ int driver (int argc, char *argv[]) {
   bool verbose = true;
   bool sanitize = false;
   std::string file = "test.mtx";
+  std::string graph_file = "";
+  std::string weight_file = "";
   int nrhs = 1;
   int sym = 3;
   int posdef = 1;
@@ -53,6 +55,8 @@ int driver (int argc, char *argv[]) {
   opts.set_option<bool>("verbose", "Flag for verbose printing", &verbose);
   opts.set_option<bool>("sanitize", "Flag to sanitize input matrix (remove zeros)", &sanitize);
   opts.set_option<std::string>("file", "Input file (MatrixMarket SPD matrix)", &file);
+  opts.set_option<std::string>("graph", "Input condensed graph", &graph_file);
+  opts.set_option<std::string>("weight", "Input condensed graph weight", &weight_file);
   opts.set_option<int>("nrhs", "Number of RHS vectors", &nrhs);
   opts.set_option<int>("symmetric", "Symmetric type: 0 - unsym, 1 - structure sym, 2 - symmetric, 3 - hermitian", &sym);
   opts.set_option<int>("posdef", "Positive definite: 0 - indef, 1 - positive definite", &posdef);
@@ -105,6 +109,53 @@ int driver (int argc, char *argv[]) {
       }
       Tacho::MatrixMarket<value_type>::read(file, A, sanitize, verbose);
     }
+
+    /// read graph file if available
+    using size_type_array_host = typename CrsMatrixBaseTypeHost::size_type_array;
+    using ordinal_type_array_host = typename CrsMatrixBaseTypeHost::ordinal_type_array;
+
+    ordinal_type m_graph(0);
+    size_type_array_host ap_graph;
+    ordinal_type_array_host aw_graph, aj_graph;
+    {
+      if (graph_file.length() > 0 && weight_file.length() > 0) {
+        {
+          std::ifstream in;
+          in.open(graph_file);
+          if (!in.good()) {
+            std::cout << "Failed in open the file: " << graph_file << std::endl;
+            return -1;
+          }
+          in >> m_graph;
+
+          ap_graph = size_type_array_host("ap", m_graph+1);
+          for (ordinal_type i=0,iend=m_graph+1;i<iend;++i)
+            in >> ap_graph(i);
+
+          aj_graph = ordinal_type_array_host("aj", ap_graph(m_graph));
+          for (ordinal_type i=0;i<m_graph;++i) {
+            const ordinal_type jbeg = ap_graph(i), jend = ap_graph(i+1);
+            for (ordinal_type j=jbeg;j<jend;++j)
+              in >> aj_graph(j);
+          }
+        }
+
+        {
+          std::ifstream in;
+          in.open(weight_file);
+          if (!in.good()) {
+            std::cout << "Failed in open the file: " << weight_file << std::endl;
+            return -1;
+          }
+          ordinal_type m(0);
+          in >> m;
+          in >> m_graph;
+          aw_graph = ordinal_type_array_host("aw", m_graph);
+          for (ordinal_type i=0;i<m_graph;++i) 
+            in >> aw_graph(i);
+        }
+      }
+    }
 
     ///
     /// * to wrap triple pointers, declare following view types
@@ -149,9 +200,18 @@ int driver (int argc, char *argv[]) {
     Kokkos::deep_copy(values_on_device, A.Values());
 
     /// inputs are used for graph reordering and analysis
-    solver.analyze(A.NumRows(),
-                   A.RowPtr(),
-                   A.Cols());
+    if (m_graph > 0 && m_graph < A.NumRows())
+      solver.analyze(A.NumRows(),
+                     A.RowPtr(),
+                     A.Cols(),
+                     m_graph,
+                     ap_graph,
+                     aj_graph,
+                     aw_graph);
+    else 
+      solver.analyze(A.NumRows(),
+                     A.RowPtr(),
+                     A.Cols());
 
     /// create numeric tools and levelset tools
     solver.initialize();