Improving Skeletonize and id

.gitignore

@@ -1 +1,2 @@
+deps/
 build/

example/run_gofmm_userdefined.sh

@@ -39,8 +39,8 @@ then mpiexec="mpirun -n 4";
 else mpiexec=""; 
 fi
 if [ "${HMLP_USE_MPI}" = true ]; 
-then executable="./test_mpigofmm.x"
-else executable="./test_gofmm.x";
+then executable="./test_mpigofmm"
+else executable="./test_gofmm";
 fi
 echo "@PRIM"
 echo 'gofmm'

example/sbatch_gofmm_userdefine.sh

@@ -80,9 +80,9 @@ hiddenlayer="512-512-512"
 # ======= Do not change anything below this line ========
 mpiexec="ibrun tacc_affinity"
 #mpiexec="prun"
-#executable="./test_mpigofmm.x"
+#executable="./test_mpigofmm"
 #executable="gdb -ex run --args ./test_mpigofmm.x"
-executable="./test_gofmm.x"
+executable="./test_gofmm"
 
 
 echo "@PRIM"

frame/primitives/lowrank.hpp

@@ -201,33 +201,15 @@ void id
   jpvt.clear();
   jpvt.resize( n, 0 );
 
-  /** Traditional pivoting QR (GEQP3) */
-//#ifdef HMLP_USE_CUDA
-//  auto *dev = hmlp_get_device( 0 );
-//  cublasHandle_t &handle = 
-//      reinterpret_cast<hmlp::gpu::Nvidia*>( dev )->gethandle( 0 );
-//  hmlp::xgeqp3
-//  (
-//    handle,
-//    m, n, 
-//    A_tmp.data(), m,
-//    jpvt.data(), 
-//    tau.data(),
-//    work.data(), lwork
-//  );
-//#else
-  hmlp::xgeqp4
-  //hmlp::xgeqp3
-  (
-    m, n, 
-    A_tmp.data(), m,
-    jpvt.data(), 
-    tau.data(),
-    work.data(), lwork
-  );
-//#endif
-  //printf( "end xgeqp3\n" );
-
+  /** Pivoting QR (GEQP3 or GEQP4). */
+  if ( true )
+  {
+    hmlp::xgeqp4( m, n, A_tmp.data(), m, jpvt.data(), tau.data(), work.data(), lwork );
+  }
+  else
+  {
+    hmlp::xgeqp3( m, n, A_tmp.data(), m, jpvt.data(), tau.data(), work.data(), lwork );
+  }
   /** Shift jpvt from 1-base to 0-base index. */
   for ( int j = 0; j < jpvt.size(); j ++ ) 
   {
@@ -312,10 +294,10 @@ void id
         }
         else
         {
-	      proj[ j * s + i ] = A_tmp[ j * m + i ];
-	    }
-	  }
-	}
+          proj[ j * s + i ] = A_tmp[ j * m + i ];
+        }
+      }
+    }
   }
   else /** in the old version we use xgels, which is expensive */
   {

gofmm/gofmm.hpp

@@ -189,7 +189,7 @@ class CommandLineHelper
     /** (Default) user-defined approximation toleratnce and budget. */
     double stol = 1E-3;
     double budget = 0.0;
-    bool secure_accuracy = true;
+    bool secure_accuracy = false;
     /** (Default) geometric-oblivious scheme. */
     DistanceMetric metric = ANGLE_DISTANCE;
 
@@ -1197,48 +1197,28 @@ void Skeletonize( NODE *node )
 {
   /** Derive type T from NODE. */
   using T = typename NODE::T;
-  /** Early return if we do not need to skeletonize. */
-  if ( !node->parent ) return;
-
   /** Gather shared data and create reference. */
   auto &K   = *(node->setup->K);
-  auto &NN  = *(node->setup->NN);
   auto maxs = node->setup->MaximumRank();
   auto stol = node->setup->Tolerance();
   bool secure_accuracy = node->setup->SecureAccuracy();
   bool use_adaptive_ranks = node->setup->UseAdaptiveRanks();
-
   /** Gather per node data and create reference. */
   auto &data  = node->data;
   auto &skels = data.skels;
   auto &proj  = data.proj;
   auto &jpvt  = data.jpvt;
   auto &KIJ   = data.KIJ;
   auto &candidate_cols = data.candidate_cols;
-
   /** Interpolative decomposition (ID). */
   size_t N = K.col();
   size_t m = KIJ.row();
   size_t n = KIJ.col();
   size_t q = node->n;
-
-//  /* IMTODO: change this decision to a function call. */
-//  if ( secure_accuracy )
-//  {
-//    if ( !node->isleaf && ( !node->lchild->data.is_compressed || !node->rchild->data.is_compressed ) )
-//    {
-//      skels.clear();
-//      proj.resize( 0, 0 );
-//      data.is_compressed = false;
-//      return;
-//    }
-//  }
-
   /** Bill's l2 norm scaling factor. */
   T scaled_stol = std::sqrt( (T)n / q ) * std::sqrt( (T)m / (N - q) ) * stol;
-  /** Account for uniform sampling. */
-  scaled_stol *= std::sqrt( (T)q / N );
-
+  /** TODO: check if this is needed? Account for uniform sampling. */
+  if ( true ) scaled_stol *= std::sqrt( (T)q / N );
   /** Call adaptive interpolative decomposition primitive. */
   lowrank::id( use_adaptive_ranks, secure_accuracy,
     KIJ.row(), KIJ.col(), maxs, scaled_stol, KIJ, skels, proj, jpvt );
@@ -1249,13 +1229,6 @@ void Skeletonize( NODE *node )
   {
     skels[ i ] = candidate_cols[ skels[ i ] ];
   }
-
-//  /** Depending on the flag, decide is_compressed or not. */
-//  data.is_compressed = ( secure_accuracy ) ? skels.size() : true;
-//
-//  /** Sanity check. */
-//  if ( data.is_compressed ) assert( skels.size() && proj.size() && jpvt.size() );
-
 }; /* end Skeletonize() */
 
 
@@ -1309,6 +1282,8 @@ class SkeletonizeTask : public Task
 
     void Execute( Worker* user_worker ) 
     { 
+      /** Early return if we do not need to skeletonize. */
+      if ( !arg->parent ) return;
       /* Check if we need to secure the accuracy? */
       bool secure_accuracy = arg->setup->SecureAccuracy();
       /* Gather per node data and create reference. */
@@ -3661,7 +3636,8 @@ void SelfTesting( TREE &tree, size_t ntest, size_t nrhs )
   printf( "========================================================\n");
   for ( size_t i = 0; i < ntest; i ++ )
   {
-    size_t tar = i * n / ntest;
+    //size_t tar = i * n / ntest;
+    size_t tar = i * 1000;
     Data<T> potentials;
     /** ASKIT treecode with NN pruning. */
     Evaluate( tree, tar, potentials, EVALUATE_OPTION_NEIGHBOR_PRUNING );

gofmm/gofmm_mpi.hpp

@@ -3335,27 +3335,27 @@ class DistSkeletonKIJTask : public Task
 
 
 
-/**
- *  @brief Skeletonization with interpolative decomposition.
- */ 
-template<typename NODE, typename T>
-void DistSkeletonize_v2( NODE *node )
-{
-  /** Early return if we do not need to skeletonize. */
-  if ( !node->parent ) return;
-
-  /* Get the node communicator. */
-  mpi::Comm comm = arg->GetComm();
-
-  /* All children should have is_compressed properly set. Use a Reduce to AND all is_compressed. */
-
-
-
-  //if ( arg->GetCommRank() == 0 )
-  //    {
-  //      DistSkeletonize<NODE, T>( arg );
-  //    }
-};
+///**
+// *  @brief Skeletonization with interpolative decomposition.
+// */ 
+//template<typename NODE, typename T>
+//void DistSkeletonize_v2( NODE *node )
+//{
+//  /** Early return if we do not need to skeletonize. */
+//  if ( !node->parent ) return;
+//
+//  /* Get the node communicator. */
+//  mpi::Comm comm = arg->GetComm();
+//
+//  /* All children should have is_compressed properly set. Use a Reduce to AND all is_compressed. */
+//
+//
+//
+//  //if ( arg->GetCommRank() == 0 )
+//  //    {
+//  //      DistSkeletonize<NODE, T>( arg );
+//  //    }
+//};