reactDiff shell

exec/reactDiff/GNUmakefile

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+# AMREX_HOME defines the directory in which we will find all the AMReX code.
+# If you set AMREX_HOME as an environment variable, this line will be ignored
+AMREX_HOME ?= ../../../amrex/
+
+DEBUG     = FALSE
+USE_MPI   = TRUE
+USE_OMP   = FALSE
+USE_CUDA  = FALSE
+COMP      = gnu
+DIM       = 2
+MAX_SPEC  = 8
+
+TINY_PROFILE = FALSE
+
+include $(AMREX_HOME)/Tools/GNUMake/Make.defs
+
+# add this back on if we add any local files
+#include ./Make.package
+#VPATH_LOCATIONS   += .
+#INCLUDE_LOCATIONS += .
+
+#include ../../src_reactDiff/Make.package
+#VPATH_LOCATIONS   += ../../src_reactDiff/
+#INCLUDE_LOCATIONS += ../../src_reactDiff/
+
+include ../../src_analysis/Make.package
+VPATH_LOCATIONS   += ../../src_analysis/
+INCLUDE_LOCATIONS += ../../src_analysis/
+
+include ../../src_rng/Make.package
+VPATH_LOCATIONS   += ../../src_rng/
+INCLUDE_LOCATIONS += ../../src_rng/
+
+include ../../src_common/Make.package
+VPATH_LOCATIONS   += ../../src_common/
+INCLUDE_LOCATIONS += ../../src_common/
+
+include $(AMREX_HOME)/Src/Base/Make.package
+include $(AMREX_HOME)/Src/Boundary/Make.package
+include $(AMREX_HOME)/Src/LinearSolvers/MLMG/Make.package
+
+include $(AMREX_HOME)/Tools/GNUMake/Make.rules
+
+ifeq ($(findstring cgpu, $(HOST)), cgpu)
+  CXXFLAGS += $(FFTW)
+endif
+
+ifeq ($(USE_CUDA),TRUE)
+  LIBRARIES += -lcufft
+else
+  LIBRARIES += -L$(FFTW_DIR) -lfftw3_mpi -lfftw3
+endif
+
+MAXSPECIES := $(strip $(MAX_SPEC))
+DEFINES += -DMAX_SPECIES=$(MAXSPECIES)
+

exec/reactDiff/main_driver.cpp

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+
+#include "common_functions.H"
+
+#include <AMReX_VisMF.H>
+#include <AMReX_PlotFileUtil.H>
+#include <AMReX_ParallelDescriptor.H>
+#include <AMReX_MultiFabUtil.H>
+
+#include "chrono"
+
+using namespace std::chrono;
+using namespace amrex;
+
+// argv contains the name of the inputs file entered at the command line
+void main_driver(const char* argv)
+{
+
+    BL_PROFILE_VAR("main_driver()",main_driver);
+
+    // store the current time so we can later compute total run time.
+    Real strt_time = ParallelDescriptor::second();
+
+    std::string inputs_file = argv;
+
+    // Initialize variables in namespaces
+    InitializeCommonNamespace();
+
+    // is the problem periodic?
+    Vector<int> is_periodic(AMREX_SPACEDIM,0);  // set to 0 (not periodic) by default
+    for (int i=0; i<AMREX_SPACEDIM; ++i) {
+        if (bc_spec_lo[i] == -1 && bc_spec_hi[i] == -1) {
+            is_periodic[i] = 1;
+        }
+    }
+
+    // This defines the physical box, [-1,1] in each direction.
+    RealBox real_box({AMREX_D_DECL(prob_lo[0],prob_lo[1],prob_lo[2])},
+                     {AMREX_D_DECL(prob_hi[0],prob_hi[1],prob_hi[2])});
+
+    IntVect dom_lo(AMREX_D_DECL(           0,            0,            0));
+    IntVect dom_hi(AMREX_D_DECL(n_cells[0]-1, n_cells[1]-1, n_cells[2]-1));
+    Box domain(dom_lo, dom_hi);
+
+    Geometry geom(domain,&real_box,CoordSys::cartesian,is_periodic.data());
+
+    // BoxArray
+    BoxArray ba;
+
+    // how boxes are distrubuted among MPI processes
+    DistributionMapping dmap;
+
+    Real dt = fixed_dt;
+    const Real* dx = geom.CellSize();
+
+    /////////////////////////////////////////
+    //Initialise rngs
+    /////////////////////////////////////////
+    if (restart < 0) {
+
+        if (seed > 0) {
+            // initializes the seed for C++ random number calls
+            InitRandom(seed+ParallelDescriptor::MyProc(),
+                       ParallelDescriptor::NProcs(),
+                       seed+ParallelDescriptor::MyProc());
+        } else if (seed == 0) {
+            // initializes the seed for C++ random number calls based on the clock
+            auto now = time_point_cast<nanoseconds>(system_clock::now());
+            int randSeed = now.time_since_epoch().count();
+            // broadcast the same root seed to all processors
+            ParallelDescriptor::Bcast(&randSeed,1,ParallelDescriptor::IOProcessorNumber());
+            InitRandom(randSeed+ParallelDescriptor::MyProc(),
+                       ParallelDescriptor::NProcs(),
+                       randSeed+ParallelDescriptor::MyProc());
+        } else {
+            Abort("Must supply non-negative seed");
+        }
+
+    }
+
+    int step_start;
+    amrex::Real time;
+
+    // Initialize the boxarray "ba" from the single box "bx"
+    ba.define(domain);
+
+    // Break up boxarray "ba" into chunks no larger than "max_grid_size" along a direction
+    // note we are converting "Vector<int> max_grid_size" to an IntVect
+    ba.maxSize(IntVect(max_grid_size));
+
+    dmap.define(ba);
+
+
+
+
+
+
+
+    ///////////////////////////////////////////
+
+    // time step loop
+    for(int step=step_start;step<=max_step;++step) {
+
+
+        // MultiFab memory usage
+        const int IOProc = ParallelDescriptor::IOProcessorNumber();
+
+        amrex::Long min_fab_megabytes  = amrex::TotalBytesAllocatedInFabsHWM()/1048576;
+        amrex::Long max_fab_megabytes  = min_fab_megabytes;
+
+        ParallelDescriptor::ReduceLongMin(min_fab_megabytes, IOProc);
+        ParallelDescriptor::ReduceLongMax(max_fab_megabytes, IOProc);
+
+        amrex::Print() << "High-water FAB megabyte spread across MPI nodes: ["
+                       << min_fab_megabytes << " ... " << max_fab_megabytes << "]\n";
+
+        min_fab_megabytes  = amrex::TotalBytesAllocatedInFabs()/1048576;
+        max_fab_megabytes  = min_fab_megabytes;
+
+        ParallelDescriptor::ReduceLongMin(min_fab_megabytes, IOProc);
+        ParallelDescriptor::ReduceLongMax(max_fab_megabytes, IOProc);
+
+        amrex::Print() << "Curent     FAB megabyte spread across MPI nodes: ["
+                       << min_fab_megabytes << " ... " << max_fab_megabytes << "]\n";
+
+    }
+
+    // Call the timer again and compute the maximum difference between the start time
+    // and stop time over all processors
+    Real stop_time = ParallelDescriptor::second() - strt_time;
+    ParallelDescriptor::ReduceRealMax(stop_time);
+    amrex::Print() << "Run time = " << stop_time << std::endl;
+
+}