Work on padding cells

CMakeLists.txt

@@ -7,50 +7,52 @@ set(EMSCHUR3D_VERSION_NOQUOTES "${EMSCHUR3D_VERSION_MAJOR}.${EMSCHUR3D_VERSION_M
 
 option ( LEMMA_MODULE_EMSCHUR3D TRUE )
 
-find_package( SuperLU )
-if (SUPERLU_FOUND)
-	message( STATUS "SuperLU was found" )
-	add_compile_options(-DHAVE_SUPERLU)
-	INCLUDE_DIRECTORIES(${SUPERLU_INCLUDES})
+option ( LEMMA_USE_SUPERLU FALSE)
+if (LEMMA_USE_SUPERLU)
+	find_package( SuperLU )
+	if (SUPERLU_FOUND)
+		message( STATUS "SuperLU was found" )
+		add_compile_options(-DHAVE_SUPERLU)
+		INCLUDE_DIRECTORIES(${SUPERLU_INCLUDES})
+	endif()
 endif()
 
 #find_package( PaSTiX )
-find_package( PaSTiX COMPONENTS METIS SEQ )
-
-find_path(PASTIX_pastix_nompi.h_INCLUDE_DIRS
-  #NAMES pastix/nompi.h
-  NAMES pastix_nompi.h
-  HINTS ${PASTIX_INCLUDE_DIRS}
-)
-if (NOT PASTIX_pastix_nompi.h_INCLUDE_DIRS)
-  message(STATUS "A version of Pastix has been found but pastix_nompi.h does not exist in the include directory."
-                 " Because Eigen tests require a version without MPI, we disable the Pastix backend.")
-endif()
-if(PASTIX_FOUND AND PASTIX_pastix_nompi.h_INCLUDE_DIRS)
-  add_definitions("-DEIGEN_PASTIX_SUPPORT")
-  include_directories(${PASTIX_INCLUDE_DIRS_DEP})
-  if(SCOTCH_FOUND)
-    include_directories(${SCOTCH_INCLUDE_DIRS})
-    set(PASTIX_LIBRARIES ${PASTIX_LIBRARIES} ${SCOTCH_LIBRARIES})
-  elseif(METIS_FOUND)
-    include_directories(${METIS_INCLUDE_DIRS})
-    set(PASTIX_LIBRARIES ${PASTIX_LIBRARIES} ${METIS_LIBRARIES})
-  else(SCOTCH_FOUND)
+#find_package( PaSTiX COMPONENTS METIS SEQ )
+
+#find_path(PASTIX_pastix_nompi.h_INCLUDE_DIRS
+#  #NAMES pastix/nompi.h
+#  NAMES pastix_nompi.h
+#  HINTS ${PASTIX_INCLUDE_DIRS}
+#)
+#if (NOT PASTIX_pastix_nompi.h_INCLUDE_DIRS)
+#  message(STATUS "A version of Pastix has been found but pastix_nompi.h does not exist in the include directory."
+#                 " Because Eigen tests require a version without MPI, we disable the Pastix backend.")
+#endif()
+#if(PASTIX_FOUND AND PASTIX_pastix_nompi.h_INCLUDE_DIRS)
+#  add_definitions("-DEIGEN_PASTIX_SUPPORT")
+#  include_directories(${PASTIX_INCLUDE_DIRS_DEP})
+#  if(SCOTCH_FOUND)
+#    include_directories(${SCOTCH_INCLUDE_DIRS})
+#    set(PASTIX_LIBRARIES ${PASTIX_LIBRARIES} ${SCOTCH_LIBRARIES})
+#  elseif(METIS_FOUND)
+#    include_directories(${METIS_INCLUDE_DIRS})
+#    set(PASTIX_LIBRARIES ${PASTIX_LIBRARIES} ${METIS_LIBRARIES})
+#  else(SCOTCH_FOUND)
 #    ei_add_property(EIGEN_MISSING_BACKENDS  "PaStiX, ")
-  endif(SCOTCH_FOUND)
-  set(SPARSE_LIBS ${SPARSE_LIBS} ${PASTIX_LIBRARIES_DEP} ${ORDERING_LIBRARIES})
-  set(PASTIX_ALL_LIBS ${PASTIX_LIBRARIES_DEP})
+#  endif(SCOTCH_FOUND)
+#  set(SPARSE_LIBS ${SPARSE_LIBS} ${PASTIX_LIBRARIES_DEP} ${ORDERING_LIBRARIES})
+#  set(PASTIX_ALL_LIBS ${PASTIX_LIBRARIES_DEP})
 #  ei_add_property(EIGEN_TESTED_BACKENDS  "PaStiX, ")
-else()
+#else()
 #  ei_add_property(EIGEN_MISSING_BACKENDS  "PaStiX, ")
-endif()
-
-if ( PASTIX_FOUND )
-	message( STATUS "PaSTiX was found" )
-	add_compile_options(-DHAVE_PASTIX)
-	INCLUDE_DIRECTORIES(${PASTIX_INCLUDES})
-endif()
+#endif()
 
+#if ( PASTIX_FOUND )
+#	message( STATUS "PaSTiX was found" )
+#	add_compile_options(-DHAVE_PASTIX)
+#	INCLUDE_DIRECTORIES(${PASTIX_INCLUDES})
+#endif()
 
 
 find_package( Umfpack )
@@ -87,7 +89,18 @@ if ( LEMMA_VTK6_SUPPORT OR LEMMA_VTK7_SUPPORT OR LEMMA_VTK8_SUPPORT AND LEMMA_MO
 	#set (MKLLINK  "-L$MKLROOT/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -Wl,-rpath=$MKLROOT/lib/intel64")
         # OpenMP R3
         set (MKLLINK  "-L$MKLROOT/lib/intel64 -Wl,-rpath=$MKLROOT/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread")
+		add_compile_options( -DEIGEN_USE_MKL_ALL )
 		target_link_libraries(emschur3d "lemmacore" ${MKLLINK})
+	else()
+		find_library( PARDISO600 
+            NAMES pardiso600 libpardiso600.so libpardiso600-GNU800-X86-64.so 
+        	HINTS $(CMAKE_INSTALL_PREFIX)
+			PATH_SUFFIXES lib
+        )
+		if (PARDISO600)
+			add_compile_options(-DHAVE_PARDISO -mkl) # -mkl ONLY WORKS WITH INTEL, but academic pardiso doesn't include headers...
+			target_link_libraries( emschur3d "lemmacore" )
+		endif()
 	endif()
 
 	# Linking

examples/CMakeLists.txt

@@ -15,6 +15,7 @@ install ( DIRECTORY mod  DESTINATION ${CMAKE_INSTALL_PREFIX}/share/EMSchur3D/ )
 install ( DIRECTORY grd  DESTINATION ${CMAKE_INSTALL_PREFIX}/share/EMSchur3D/ ) 
 install ( DIRECTORY src  DESTINATION ${CMAKE_INSTALL_PREFIX}/share/EMSchur3D/ ) 
 install ( FILES block.sh  DESTINATION ${CMAKE_INSTALL_PREFIX}/share/EMSchur3D/ ) 
+install ( FILES block2.sh  DESTINATION ${CMAKE_INSTALL_PREFIX}/share/EMSchur3D/ ) 
 install ( FILES block.py  DESTINATION ${CMAKE_INSTALL_PREFIX}/share/EMSchur3D/ ) 
 
 INSTALL_TARGETS( "/share/EMSchur3D/"

examples/EMSchur3D.cpp

@@ -10,7 +10,6 @@
 /**
  * @file
  * @date      01/04/2018 04:34:54 PM
- * @version   $Id$
  * @author    Trevor Irons (ti)
  * @email     tirons@egi.utah.edu
  * @copyright Copyright (c) 2018, University of Utah
@@ -28,18 +27,19 @@ using namespace Lemma;
 
 int main( int argc, char** argv ) {
 
-    // BiCGSTAB Diagonal preconditioner
-    auto EM3D = EMSchur3D< Eigen::BiCGSTAB<Eigen::SparseMatrix<Complex, SPARSEMAJOR>, Eigen::IncompleteLUT<Complex> > >::NewSP();
+    // BiCGSTAB ILU preconditioner
+    //auto EM3D = EMSchur3D< Eigen::BiCGSTAB<Eigen::SparseMatrix<Complex, SPARSEMAJOR>, Eigen::IncompleteLUT<Complex> > >::NewSP();
 
     //auto EM3D = EMSchur3D< Eigen::BiCGSTAB<Eigen::SparseMatrix<Complex, SPARSEMAJOR> > >::NewSP();
 
     // SUPERLU
     //auto EM3D = EMSchur3D< Eigen::SuperLU<Eigen::SparseMatrix<Complex, SPARSEMAJOR> > >::NewSP();
 
-    //auto EM3D = EMSchur3D< Eigen::PardisoLU<Eigen::SparseMatrix<Complex, SPARSEMAJOR> > >::NewSP();
+    // Pardiso
+    auto EM3D = EMSchur3D< Eigen::PardisoLU<Eigen::SparseMatrix<Complex, SPARSEMAJOR> > >::NewSP();
     //auto EM3D = EMSchur3D< Eigen::PardisoLDLT<Eigen::SparseMatrix<Complex, SPARSEMAJOR>, Eigen::Symmetric&Eigen::Lower > >::NewSP();
 
-    // Eigen built-in
+    // Eigen LU
     //auto EM3D = EMSchur3D< Eigen::SparseLU<Eigen::SparseMatrix<Complex, SPARSEMAJOR> > >::NewSP();
 
     // UmfPack

include/EMSchur3D.h

@@ -10,7 +10,6 @@
 /**
  * @file
  * @date      02/19/2015 01:10:39 PM
- * @version   $Id$
  * @author    Trevor Irons (ti)
  * @email     Trevor.Irons@Lemmasoftware.org
  * @copyright Copyright (c) 2015, XRI Geophysics, LLC
@@ -282,7 +281,6 @@ namespace Lemma {
 
 
         /* Restart if necessary */
-/*
         int nrestart(1);
         // TODO send MAC to implicitbicgstab?
         while (success == 2 && nrestart < 18 && iter_done > 1) {
@@ -290,7 +288,6 @@ namespace Lemma {
             //Phi.array() *= MAC.array().cast<Complex>(); // remove phi from air regions
             nrestart += 1;
         }
-*/
 
         logio << "Implicit BiCGStab solution in " << iter_done << " iterations."
                 << " with error " << std::setprecision(8) << std::scientific << errorn << std::endl;
@@ -478,14 +475,16 @@ namespace Lemma {
             /*  Complex system */
             std::cout << "PardisoLU pattern analyzing C_" << iw << ",";
             std::cout.flush();
-            CSolver[iw].analyzePattern( Cvec[iw].selfadjointView< Eigen::Lower>() );
+            //CSolver[iw].analyzePattern( Cvec[iw].selfadjointView< Eigen::Lower>() );
+            CSolver[iw].analyzePattern( Cvec[iw] );
             std::cout << " done in " << timer.end() / 60. << " [m]" << std::endl;
 
             // factorize
             timer.begin();
             std::cout << "PardisoLU factorising C_" << iw << ", ";
             std::cout.flush();
-            CSolver[iw].factorize( Cvec[iw].selfadjointView< Eigen::Lower>() );
+            //CSolver[iw].factorize( Cvec[iw].selfadjointView< Eigen::Lower>() );
+            CSolver[iw].factorize( Cvec[iw] );
             std::cout << " done in " << timer.end() / 60. << " [m]" << std::endl;
         }
     }