Update Kokkos library in LAMMPS to v3.0
This commit is contained in:
Stan Moore
@ -1,13 +1,14 @@
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/*
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//@HEADER
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// ************************************************************************
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//
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// Kokkos v. 2.0
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// Copyright (2014) Sandia Corporation
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//
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// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
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//
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// Kokkos v. 3.0
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// Copyright (2020) National Technology & Engineering
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// Solutions of Sandia, LLC (NTESS).
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//
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// Under the terms of Contract DE-NA0003525 with NTESS,
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// the U.S. Government retains certain rights in this software.
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//
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//
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// Redistribution and use in source and binary forms, with or without
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// modification, are permitted provided that the following conditions are
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// met:
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@ -23,10 +24,10 @@
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// contributors may be used to endorse or promote products derived from
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// this software without specific prior written permission.
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//
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// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
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// THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
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// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
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// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
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// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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@ -36,7 +37,7 @@
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// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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//
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// Questions? Contact Christian R. Trott (crtrott@sandia.gov)
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//
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//
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// ************************************************************************
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//@HEADER
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*/
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@ -55,131 +56,105 @@ namespace Test {
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// Reduction : result = dot( Q(:,j) , Q(:,j) );
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// PostProcess : R(j,j) = result ; inv = 1 / result ;
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template< class VectorView , class ValueView >
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struct InvNorm2 : public Kokkos::DotSingle< VectorView > {
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template <class VectorView, class ValueView>
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struct InvNorm2 : public Kokkos::DotSingle<VectorView> {
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typedef typename Kokkos::DotSingle<VectorView>::value_type value_type;
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typedef typename Kokkos::DotSingle< VectorView >::value_type value_type ;
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ValueView Rjj;
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ValueView inv;
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ValueView Rjj ;
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ValueView inv ;
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InvNorm2( const VectorView & argX ,
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const ValueView & argR ,
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const ValueView & argInv )
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: Kokkos::DotSingle< VectorView >( argX )
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, Rjj( argR )
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, inv( argInv )
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{}
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InvNorm2(const VectorView& argX, const ValueView& argR,
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const ValueView& argInv)
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: Kokkos::DotSingle<VectorView>(argX), Rjj(argR), inv(argInv) {}
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KOKKOS_INLINE_FUNCTION
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void final( value_type & result ) const
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{
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result = std::sqrt( result );
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Rjj() = result ;
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inv() = ( 0 < result ) ? 1.0 / result : 0 ;
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void final(value_type& result) const {
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result = std::sqrt(result);
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Rjj() = result;
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inv() = (0 < result) ? 1.0 / result : 0;
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}
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};
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template< class VectorView , class ValueView >
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inline
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void invnorm2( const VectorView & x ,
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const ValueView & r ,
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const ValueView & r_inv )
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{
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Kokkos::parallel_reduce( x.extent(0) , InvNorm2< VectorView , ValueView >( x , r , r_inv ) );
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template <class VectorView, class ValueView>
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inline void invnorm2(const VectorView& x, const ValueView& r,
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const ValueView& r_inv) {
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Kokkos::parallel_reduce(x.extent(0),
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InvNorm2<VectorView, ValueView>(x, r, r_inv));
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}
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// PostProcess : tmp = - ( R(j,k) = result );
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template< class VectorView , class ValueView >
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struct DotM : public Kokkos::Dot< VectorView > {
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template <class VectorView, class ValueView>
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struct DotM : public Kokkos::Dot<VectorView> {
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typedef typename Kokkos::Dot<VectorView>::value_type value_type;
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typedef typename Kokkos::Dot< VectorView >::value_type value_type ;
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ValueView Rjk;
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ValueView tmp;
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ValueView Rjk ;
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ValueView tmp ;
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DotM( const VectorView & argX ,
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const VectorView & argY ,
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const ValueView & argR ,
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const ValueView & argTmp )
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: Kokkos::Dot< VectorView >( argX , argY )
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, Rjk( argR )
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, tmp( argTmp )
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{}
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DotM(const VectorView& argX, const VectorView& argY, const ValueView& argR,
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const ValueView& argTmp)
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: Kokkos::Dot<VectorView>(argX, argY), Rjk(argR), tmp(argTmp) {}
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KOKKOS_INLINE_FUNCTION
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void final( value_type & result ) const
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{
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Rjk() = result ;
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tmp() = - result ;
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void final(value_type& result) const {
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Rjk() = result;
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tmp() = -result;
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}
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};
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template< class VectorView , class ValueView >
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inline
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void dot_neg( const VectorView & x ,
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const VectorView & y ,
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const ValueView & r ,
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const ValueView & r_neg )
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{
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Kokkos::parallel_reduce( x.extent(0) , DotM< VectorView , ValueView >( x , y , r , r_neg ) );
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template <class VectorView, class ValueView>
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inline void dot_neg(const VectorView& x, const VectorView& y,
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const ValueView& r, const ValueView& r_neg) {
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Kokkos::parallel_reduce(x.extent(0),
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DotM<VectorView, ValueView>(x, y, r, r_neg));
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}
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template <typename Scalar, class DeviceType>
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struct ModifiedGramSchmidt {
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typedef DeviceType execution_space;
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typedef typename execution_space::size_type size_type;
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template< typename Scalar , class DeviceType >
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struct ModifiedGramSchmidt
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{
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typedef DeviceType execution_space ;
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typedef typename execution_space::size_type size_type ;
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typedef Kokkos::View<Scalar**, Kokkos::LayoutLeft, execution_space>
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multivector_type;
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typedef Kokkos::View< Scalar** ,
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Kokkos::LayoutLeft ,
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execution_space > multivector_type ;
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typedef Kokkos::View<Scalar*, Kokkos::LayoutLeft, execution_space>
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vector_type;
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typedef Kokkos::View< Scalar* ,
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Kokkos::LayoutLeft ,
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execution_space > vector_type ;
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typedef Kokkos::View<Scalar, Kokkos::LayoutLeft, execution_space> value_view;
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typedef Kokkos::View< Scalar ,
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Kokkos::LayoutLeft ,
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execution_space > value_view ;
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multivector_type Q;
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multivector_type R;
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multivector_type Q ;
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multivector_type R ;
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static double factorization( const multivector_type Q_ ,
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const multivector_type R_ )
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{
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const size_type count = Q_.extent(1);
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static double factorization(const multivector_type Q_,
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const multivector_type R_) {
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const size_type count = Q_.extent(1);
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value_view tmp("tmp");
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value_view one("one");
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Kokkos::deep_copy( one , (Scalar) 1 );
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Kokkos::deep_copy(one, (Scalar)1);
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Kokkos::Timer timer ;
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Kokkos::Timer timer;
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for ( size_type j = 0 ; j < count ; ++j ) {
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for (size_type j = 0; j < count; ++j) {
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// Reduction : tmp = dot( Q(:,j) , Q(:,j) );
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// PostProcess : tmp = std::sqrt( tmp ); R(j,j) = tmp ; tmp = 1 / tmp ;
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const vector_type Qj = Kokkos::subview( Q_ , Kokkos::ALL() , j );
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const value_view Rjj = Kokkos::subview( R_ , j , j );
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const vector_type Qj = Kokkos::subview(Q_, Kokkos::ALL(), j);
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const value_view Rjj = Kokkos::subview(R_, j, j);
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invnorm2( Qj , Rjj , tmp );
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invnorm2(Qj, Rjj, tmp);
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// Q(:,j) *= ( 1 / R(j,j) ); => Q(:,j) *= tmp ;
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Kokkos::scale( tmp , Qj );
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Kokkos::scale(tmp, Qj);
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for ( size_t k = j + 1 ; k < count ; ++k ) {
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const vector_type Qk = Kokkos::subview( Q_ , Kokkos::ALL() , k );
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const value_view Rjk = Kokkos::subview( R_ , j , k );
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for (size_t k = j + 1; k < count; ++k) {
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const vector_type Qk = Kokkos::subview(Q_, Kokkos::ALL(), k);
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const value_view Rjk = Kokkos::subview(R_, j, k);
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// Reduction : R(j,k) = dot( Q(:,j) , Q(:,k) );
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// PostProcess : tmp = - R(j,k);
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dot_neg( Qj , Qk , Rjk , tmp );
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dot_neg(Qj, Qk, Rjk, tmp);
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// Q(:,k) -= R(j,k) * Q(:,j); => Q(:,k) += tmp * Q(:,j)
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Kokkos::axpby( tmp , Qj , one , Qk );
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Kokkos::axpby(tmp, Qj, one, Qk);
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}
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}
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@ -190,94 +165,87 @@ struct ModifiedGramSchmidt
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//--------------------------------------------------------------------------
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static double test( const size_t length ,
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const size_t count ,
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const size_t iter = 1 )
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{
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multivector_type Q_( "Q" , length , count );
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multivector_type R_( "R" , count , count );
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static double test(const size_t length, const size_t count,
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const size_t iter = 1) {
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multivector_type Q_("Q", length, count);
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multivector_type R_("R", count, count);
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typename multivector_type::HostMirror A =
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Kokkos::create_mirror( Q_ );
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typename multivector_type::HostMirror A = Kokkos::create_mirror(Q_);
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// Create and fill A on the host
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for ( size_type j = 0 ; j < count ; ++j ) {
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for ( size_type i = 0 ; i < length ; ++i ) {
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A(i,j) = ( i + 1 ) * ( j + 1 );
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for (size_type j = 0; j < count; ++j) {
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for (size_type i = 0; i < length; ++i) {
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A(i, j) = (i + 1) * (j + 1);
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}
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}
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double dt_min = 0 ;
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double dt_min = 0;
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for ( size_t i = 0 ; i < iter ; ++i ) {
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Kokkos::deep_copy( Q_ , A );
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for (size_t i = 0; i < iter; ++i) {
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Kokkos::deep_copy(Q_, A);
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// A = Q * R
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const double dt = factorization( Q_ , R_ );
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const double dt = factorization(Q_, R_);
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if ( 0 == i ) dt_min = dt ;
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else dt_min = dt < dt_min ? dt : dt_min ;
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if (0 == i)
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dt_min = dt;
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else
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dt_min = dt < dt_min ? dt : dt_min;
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}
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return dt_min ;
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return dt_min;
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}
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};
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template< class DeviceType >
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void run_test_gramschmidt( int exp_beg , int exp_end, int num_trials, const char deviceTypeName[] )
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{
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std::string label_gramschmidt ;
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label_gramschmidt.append( "\"GramSchmidt< double , " );
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label_gramschmidt.append( deviceTypeName );
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label_gramschmidt.append( " >\"" );
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template <class DeviceType>
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void run_test_gramschmidt(int exp_beg, int exp_end, int num_trials,
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const char deviceTypeName[]) {
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std::string label_gramschmidt;
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label_gramschmidt.append("\"GramSchmidt< double , ");
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label_gramschmidt.append(deviceTypeName);
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label_gramschmidt.append(" >\"");
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for (int i = exp_beg ; i < exp_end ; ++i) {
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double min_seconds = 0.0 ;
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double max_seconds = 0.0 ;
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double avg_seconds = 0.0 ;
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for (int i = exp_beg; i < exp_end; ++i) {
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double min_seconds = 0.0;
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double max_seconds = 0.0;
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double avg_seconds = 0.0;
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const int parallel_work_length = 1<<i;
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const int parallel_work_length = 1 << i;
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for ( int j = 0 ; j < num_trials ; ++j ) {
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const double seconds = ModifiedGramSchmidt< double , DeviceType >::test(parallel_work_length, 32 ) ;
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for (int j = 0; j < num_trials; ++j) {
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const double seconds = ModifiedGramSchmidt<double, DeviceType>::test(
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parallel_work_length, 32);
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if ( 0 == j ) {
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min_seconds = seconds ;
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max_seconds = seconds ;
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if (0 == j) {
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min_seconds = seconds;
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max_seconds = seconds;
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} else {
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if (seconds < min_seconds) min_seconds = seconds;
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if (seconds > max_seconds) max_seconds = seconds;
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}
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else {
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if ( seconds < min_seconds ) min_seconds = seconds ;
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if ( seconds > max_seconds ) max_seconds = seconds ;
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}
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avg_seconds += seconds ;
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avg_seconds += seconds;
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}
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avg_seconds /= num_trials ;
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avg_seconds /= num_trials;
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std::cout << label_gramschmidt
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<< " , " << parallel_work_length
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<< " , " << min_seconds
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<< " , " << ( min_seconds / parallel_work_length )
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<< std::endl ;
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std::cout << label_gramschmidt << " , " << parallel_work_length << " , "
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<< min_seconds << " , " << (min_seconds / parallel_work_length)
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<< std::endl;
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}
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}
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TEST_F( default_exec, gramschmidt ) {
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int exp_beg = 10;
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int exp_end = 20;
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TEST(default_exec, gramschmidt) {
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int exp_beg = 10;
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int exp_end = 20;
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int num_trials = 5;
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if(command_line_num_args()>1)
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exp_beg = atoi(command_line_arg(1));
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if(command_line_num_args()>2)
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exp_end = atoi(command_line_arg(2));
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if(command_line_num_args()>3)
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num_trials = atoi(command_line_arg(3));
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EXPECT_NO_THROW(run_test_gramschmidt< Kokkos::DefaultExecutionSpace>( exp_beg, exp_end, num_trials, Kokkos::DefaultExecutionSpace::name() ));
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}
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if (command_line_num_args() > 1) exp_beg = atoi(command_line_arg(1));
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if (command_line_num_args() > 2) exp_end = atoi(command_line_arg(2));
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if (command_line_num_args() > 3) num_trials = atoi(command_line_arg(3));
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EXPECT_NO_THROW(run_test_gramschmidt<Kokkos::DefaultExecutionSpace>(
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exp_beg, exp_end, num_trials, Kokkos::DefaultExecutionSpace::name()));
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}
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} // namespace Test
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