From ce8eb6ed51e6906b27facdb6b9a4183f6654faea Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Wed, 20 Dec 2017 12:12:46 +0100
Subject: [PATCH] benchmark paper with C++ macro for fast stencil
---
.../3_gray_scott_3d_vectorization/Makefile | 2 +-
.../3_gray_scott_3d_vectorization/main.cpp | 65 ++++++++++++-------
.../Iterators/grid_dist_id_iterator_sub.hpp | 35 ++++++++++
3 files changed, 76 insertions(+), 26 deletions(-)
diff --git a/example/Grid/3_gray_scott_3d_vectorization/Makefile b/example/Grid/3_gray_scott_3d_vectorization/Makefile
index 68d37df8c..9488bea01 100644
--- a/example/Grid/3_gray_scott_3d_vectorization/Makefile
+++ b/example/Grid/3_gray_scott_3d_vectorization/Makefile
@@ -10,7 +10,7 @@ OBJ = main.o update_new.o
mpif90 -ffree-line-length-none -fno-range-check -fno-second-underscore -fimplicit-none -mavx -O3 -c -g -o $@ $<
%.o: %.cpp
- $(CC) -O3 -mavx -g -c --std=c++11 -Wno-ignored-attributes -o $@ $< $(INCLUDE_PATH) -I/scratch/p_ppm/VCDEVEL/include
+ $(CC) -O3 -mavx -g -c --std=c++11 -Wno-ignored-attributes -o $@ $< $(INCLUDE_PATH) -I/home/i-bird/VC/include
gray_scott: $(OBJ)
$(CC) -o $@ $^ $(CFLAGS) $(LIBS_PATH) $(LIBS) -L/home/i-bird/VC/lib -lVc
diff --git a/example/Grid/3_gray_scott_3d_vectorization/main.cpp b/example/Grid/3_gray_scott_3d_vectorization/main.cpp
index d99e431b0..db8f5ea04 100644
--- a/example/Grid/3_gray_scott_3d_vectorization/main.cpp
+++ b/example/Grid/3_gray_scott_3d_vectorization/main.cpp
@@ -36,7 +36,7 @@
//! \cond [constants] \endcond
-#define FORTRAN_UPDATE
+//#define FORTRAN_UPDATE
constexpr int x = 0;
constexpr int y = 1;
@@ -111,18 +111,17 @@ void step(grid_dist_id<3, double, aggregate<double>> & OldU,
Vc::double_v uFactor, Vc::double_v vFactor, double deltaT, double F, double K)
{
#ifndef FORTRAN_UPDATE
- for (size_t i = 0 ; i < OldU.getN_loc_grid() ; i++)
- {
- auto & U_old = OldU.get_loc_grid(i);
- auto & V_old = OldV.get_loc_grid(i);
- auto & U_new = NewU.get_loc_grid(i);
- auto & V_new = NewV.get_loc_grid(i);
+ //! \cond [cpp_update] \endcond
- auto it = OldU.get_loc_grid_iterator_stencil(i,star_stencil_3D);
+ WHILE_M(OldU,star_stencil_3D)
+ auto & U_old = GET_GRID_M(OldU);
+ auto & V_old = GET_GRID_M(OldV);
+
+ auto & U_new = GET_GRID_M(NewU);
+ auto & V_new = GET_GRID_M(NewV);
+ ITERATE_3D_M
- while (it.isNext())
- {
// center point
auto Cp = it.getStencil<0>();
@@ -168,13 +167,14 @@ void step(grid_dist_id<3, double, aggregate<double>> & OldU,
out1.store(&U_new.get<0>(Cp),Vc::Unaligned);
out2.store(&V_new.get<0>(Cp),Vc::Unaligned);
+ END_LOOP_M
+
+ //! \cond [cpp_update] \endcond
- // Next point in the grid
- it += Vc::double_v::Size;
- }
- }
#else
+ //! \cond [fort_update] \endcond
+
double uFactor_s = uFactor[0];
double vFactor_s = vFactor[0];
@@ -209,6 +209,8 @@ void step(grid_dist_id<3, double, aggregate<double>> & OldU,
&deltaT, &uFactor_s, &vFactor_s,&F,&K);
}
+ //! \cond [fort_update] \endcond
+
#endif
}
@@ -306,19 +308,30 @@ int main(int argc, char* argv[])
* \page Grid_3_gs_3D_vector Gray Scott in 3D fast implementation with vectorization
*
* Alternate New and Old field to run one step, switch between old and new if the iteration
- * is even or odd. The function step is nothing else than the the implementation of Gray-Scott
- * 3D in the previous example.
+ * is even or odd. The function step is nothing else than the implementation of Gray-Scott
+ * 3D in the previous example but in a more optimized way.
*
* \snippet Grid/3_gray_scott_3d_vectorization/main.cpp alternate
*
+ * In this function we show two methods to optimize this function.
*
- * The function has two main changes. The first is that we iterate
- * across local grids rather than a performance improvement is a convenient way
- * in case we have a lot of grid in this case we moved from 3 grid Old and New
- * to 4 grids. The second improvement is using Vc::double_v instead of double to
- * vectorize the code.
+ * * We can use the macro **WHILE_M** passing the stencil definition, **ITERATE_3D** to define the loop,
+ * **END_LOOP** to close the loop, and use the function
+ * function **getStencil<0>()** to retrieve the stencil points. Additionaly we can use Vc::double_v instead
+ * of double to vectorize the code. This method give the advantage to keep all the
+ * code in C++.
*
- * \snippet Grid/3_gray_scott_3d_vectorization/main.cpp vectorization
+ * \snippet Grid/3_gray_scott_3d_vectorization/main.cpp cpp_update
+ *
+ * * Another possibility is to use FORTRAN. Because FORTRAN has better
+ * support for multi dimensional array another possibility is to process each local grid using
+ * FORTRAN, this also give us the opportunity to show hybrid code. We can switch between
+ * one and the other method commenting
+ * and uncommeting the line #define FORTRAN_UPDATE in the code.
+ *
+ * \snippet Grid/3_gray_scott_3d_vectorization/main.cpp fort_update
+ *
+ * \include Grid/3_gray_scott_3d_vectorization/update_new.f90
*
*/
@@ -352,10 +365,10 @@ int main(int argc, char* argv[])
//! \cond [save hdf5] \endcond
- // Every 500 time step we output the configuration on hdf5
+ // Every 2000 time step we output the configuration on hdf5
if (i % 2000 == 0)
{
-// OldU.save("output_u_" + std::to_string(count));
+ OldU.save("output_u_" + std::to_string(count));
OldV.save("output_v_" + std::to_string(count));
count++;
}
@@ -364,7 +377,9 @@ int main(int argc, char* argv[])
}
tot_sim.stop();
- std::cout << "Total simulation: " << tot_sim.getwct() << std::endl;
+
+ if (create_vcluster().rank() == 0)
+ {std::cout << "Total simulation: " << tot_sim.getwct() << std::endl;}
// We frite the final configuration
OldV.write("final");
diff --git a/src/Grid/Iterators/grid_dist_id_iterator_sub.hpp b/src/Grid/Iterators/grid_dist_id_iterator_sub.hpp
index a1730e5dc..c249787f2 100644
--- a/src/Grid/Iterators/grid_dist_id_iterator_sub.hpp
+++ b/src/Grid/Iterators/grid_dist_id_iterator_sub.hpp
@@ -249,6 +249,41 @@ class grid_dist_iterator_sub
{
return stop;
}
+
+ /*! \brief Return the number of local grids
+ *
+ *
+ */
+ inline size_t N_loc_grid()
+ {
+ return gList.size();
+ }
+
+ /*! \brief Return the component j of the starting point (P1) of the domain part
+ * for the local grid i
+ *
+ * \param i local grid
+ * \param j dimension
+ *
+ *
+ */
+ inline size_t loc_grid_info_start(size_t i,size_t j)
+ {
+ return gdb_ext.get(i).DBox.getLow(i);
+ }
+
+ /*! \brief Return the component j of the stop point (P2) of the domain part
+ * for the local grid i
+ *
+ * \param i local grid
+ * \param j dimension
+ *
+ *
+ */
+ inline size_t loc_grid_info_size(size_t i,size_t j)
+ {
+ return gdb_ext.get(i).GDBox.getHigh(i);
+ }
};
#endif /* SRC_GRID_GRID_DIST_ID_ITERATOR_SUB_HPP_ */
--
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