Merge pull request #105 from intel/develop

Develop

bin/gen_layouts.pl

@@ -277,7 +277,7 @@ END
 
       # Creation.
       print " else if (ndims == $n && do_wrap == $wrap)\n",
-        "  gp = make_shared<YkElemGrid<$layout, $wrap>>(_dims, name, dims, _opts, &_ostr);\n";
+        "  gp = make_shared<YkElemGrid<$layout, $wrap>>(_dims, name, dims, &_opts, &_ostr);\n";
     }
   }
 

bin/yask_kernel_api_test.py

@@ -28,7 +28,7 @@
 import numpy as np
 import ctypes as ct
 import argparse
-import yask_kernel
+import yask_kernel as yk
 
 # Read data from grid using NumPy ndarray.
 def read_grid(grid, timestep) :
@@ -156,8 +156,8 @@ def init_grid(grid, timestep) :
 if __name__ == "__main__":
 
     # The factories from which all other kernel objects are made.
-    kfac = yask_kernel.yk_factory()
-    ofac = yask_kernel.yask_output_factory()
+    kfac = yk.yk_factory()
+    ofac = yk.yask_output_factory()
 
     # Initalize MPI, etc.
     env = kfac.new_env()
@@ -196,11 +196,13 @@ def init_grid(grid, timestep) :
         else :
             soln.set_block_size(dim_name, 32)
 
-    # Make a test fixed-size grid.
+    # Make a test fixed-size grid and set its NUMA preference.
     fgrid_sizes = ()
     for dim_name in soln_dims :
         fgrid_sizes += (5,)
     fgrid = soln.new_fixed_size_grid("fgrid", soln_dims, fgrid_sizes)
+    fgrid.set_numa_preferred(yk.cvar.yask_numa_local)
+    fgrid.alloc_storage()
 
     # Simple rank configuration in 1st dim only.
     # In production runs, the ranks would be distributed along

include/yask_kernel_api.hpp

@@ -47,12 +47,27 @@ namespace yask {
 #endif
 
     /// Allocate grids on local NUMA node.
+    /**
+       This is used in yk_solution::set_default_numa_preferred
+       and yk_grid::set_numa_preferred.
+       In Python, specify as `yask_kernel.cvar.yask_numa_local`. 
+    */
     const int yask_numa_local = -1;
 
     /// Allocate grids across all available NUMA nodes.
+    /**
+       This is used in yk_solution::set_default_numa_preferred
+       and yk_grid::set_numa_preferred.
+       In Python, specify as `yask_kernel.cvar.yask_numa_interleave`. 
+    */
     const int yask_numa_interleave = -2;
 
     /// Do not specify any NUMA binding.
+    /**
+       This is used in yk_solution::set_default_numa_preferred
+       and yk_grid::set_numa_preferred.
+       In Python, specify as `yask_kernel.cvar.yask_numa_none`. 
+    */
     const int yask_numa_none = -9;
 
     // Forward declarations of classes and pointers.
@@ -711,17 +726,21 @@ namespace yask {
            Instead of specifying a NUMA node, a special value may be used
            to specify another policy as listed.
            This setting may be overridden for any specific grid.
+           @returns `true` if NUMA preference was set;
+           `false` if NUMA preferences are not enabled.
         */
-        virtual void
+        virtual bool
         set_default_numa_preferred(int numa_node
                                    /**< [in] Preferred NUMA node for data
                                       allocation.  Alternatively, use
                                       `yask_numa_local` for explicit
                                       local-node allocation,
                                       `yask_numa_interleave` for
                                       interleaving pages across all nodes,
-                                      or `yask_numa_none` for no NUMA
-                                      policy. */) =0;
+                                      or `yask_numa_none` for no explicit NUMA
+                                      policy. These constants are defined in 
+                                      the _Variable Documentation_ section of
+                                      \ref yask_kernel_api.hpp. */) =0;
 
         /// **[Advanced]** Get the default preferred NUMA node on which to allocate data.
         /**
@@ -1441,11 +1460,15 @@ namespace yask {
         /// **[Advanced]** Set the default preferred NUMA node on which to allocate data.
         /**
            This value is used when allocating data for this grid.
+           Thus, the desired NUMA policy must be set before calling alloc_data()
+           or yk_solution::prepare_solution().
+           @returns `true` if NUMA preference was set;
+           `false` if NUMA preferences are not enabled.
         */
-        virtual void
+        virtual bool
         set_numa_preferred(int numa_node
                            /**< [in] Preferred NUMA node.
-                              See set_default_numa_preferred() for other options. */) =0;
+                              See yk_solution::set_default_numa_preferred() for other options. */) =0;
 
         /// **[Advanced]** Get the default preferred NUMA node on which to allocate data.
         /**

src/common/common_utils.cpp

@@ -41,7 +41,7 @@ namespace yask {
     // for numbers above 9 (at least up to 99).
 
     // Format: "major.minor.patch".
-    const string version = "2.05.06";
+    const string version = "2.05.08";
 
     string yask_get_version_string() {
         return version;

src/compiler/lib/YaskKernel.cpp

@@ -286,7 +286,7 @@ namespace yask {
             ctorCode += " " + grid + "_dim_names = {" +
                 gdims.makeDimStr(", ", "\"", "\"") + "};\n";
             string initCode = " " + grid + "_ptr = std::make_shared<" + typeDef +
-                ">(_dims, \"" + grid + "\", " + grid + "_dim_names, _opts, &_ostr);\n"
+                ">(_dims, \"" + grid + "\", " + grid + "_dim_names, &_opts, &_ostr);\n"
                 " assert(" + grid + "_ptr);\n";
 
             // Grid vars.
@@ -391,7 +391,7 @@ namespace yask {
                 if (!firstGrid)
                     newGridCode += " else";
                 newGridCode += " if (dims == " + grid + "_dim_names) gp = std::make_shared<" +
-                    typeDef + ">(_dims, name, dims, _opts, &_ostr);\n";
+                    typeDef + ">(_dims, name, dims, &_opts, &_ostr);\n";
             }
 
         } // grids.
@@ -416,7 +416,7 @@ namespace yask {
         os << "\n // Make a new grid iff its dims match any in the stencil.\n"
             " // Returns pointer to the new grid or nullptr if no match.\n"
             " virtual YkGridPtr newStencilGrid(const std::string& name,"
-            " const GridDimNames& dims, KernelSettingsPtr settings) {\n"
+            " const GridDimNames& dims) {\n"
             " YkGridPtr gp;\n" <<
             newGridCode <<
             " return gp;\n"

src/kernel/Makefile

@@ -31,6 +31,7 @@
 stencil		=	iso3dfd
 arch		=	snb
 mpi		=	1
+numa		=	1
 real_bytes	=	4
 radius		=	2
 ranks		= 	1
@@ -429,21 +430,26 @@ YK_LD		:=	$(YK_CXX)
 YK_LIBS		:=	-lrt
 YK_LFLAGS	:=	-Wl,-rpath=$(LIB_DIR) -L$(LIB_DIR) -l$(YK_BASE2)
 
+# Add options for NUMA.
+ifeq ($(numa),1)
+
+# Look for libnuma.
+# TODO: make this more portable.
+ifneq ($(wildcard /usr/lib64/libnuma.so),)
+ YK_LIBS	+=	-lnuma
+ MACROS		+=	USE_NUMA
+else ifneq ($(wildcard /usr/lib64/libnuma.so.1),)
+ YK_LIBS	+=	/usr/lib64/libnuma.so.1
+ MACROS		+=	USE_NUMA
+endif
+
 # Work-around missing numaif.h:
 # IF numaif.h is found in /usr/include,
 # THEN enable the macro to use it.
 ifneq ($(shell find /usr/include -name 'numaif.h' | wc -l),0)
  MACROS		+=	USE_NUMAIF_H
 endif
 
-# Work-around missing libnuma.so:
-# IF libnuma.so.1 exists AND "normal" libnuma can't be found,
-# THEN use hard-coded libnuma.so.1,
-# ELSE use "normal" libnuma.
-ifeq ($(and $(wildcard /usr/lib64/libnuma.so.1),$(shell whereis libnuma |wc -w)),1)
- YK_LIBS	+=	/usr/lib64/libnuma.so.1
-else
- YK_LIBS	+=	-lnuma
 endif
 
 # Tools.
@@ -738,9 +744,9 @@ yk-test-no-yc: kernel-only
 # run the tests from the top-level Makefile.
 all-tests:
 	$(MAKE) clean; $(MAKE) stencil=test_3d fold=x=4,y=2 cxx-yk-grid-test
-	$(MAKE) clean; $(MAKE) stencil=test_1d yc-and-yk-test
 	$(MAKE) clean; $(MAKE) stencil=iso3dfd real_bytes=8 cxx-yk-api-test
 	$(MAKE) clean; $(MAKE) stencil=iso3dfd py-yk-api-test
+	$(MAKE) clean; $(MAKE) stencil=test_1d yc-and-yk-test
 	$(MAKE) clean; $(MAKE) stencil=3axis fold=x=4,y=2 yc-and-yk-test
 	$(MAKE) clean; $(MAKE) stencil=9axis fold=z=2 yc-and-yk-test
 	$(MAKE) clean; $(MAKE) stencil=3plane fold=y=2,z=4 yc-and-yk-test

src/kernel/lib/context.cpp

@@ -1161,34 +1161,30 @@ namespace yask {
                                      const std::string& type) {
         ostream& os = get_ostr();
 
-        // Get default NUMA node from settings.
-        int numa_def = _opts->_numa_pref;
-
         for (const auto& i : nbytes) {
-            int np = i.first;
+            int numa_pref = i.first;
             size_t nb = i.second;
-            size_t ng = ngrids.at(np);
+            size_t ng = ngrids.at(numa_pref);
 
             // Don't need pad after last one.
             if (nb >= _data_buf_pad)
                 nb -= _data_buf_pad;
 
-            // What node?
-            int numa_pref = (np >= 0) ? np : numa_def;
-
             // Allocate data.
             os << "Allocating " << makeByteStr(nb) <<
                 " for " << ng << " " << type << "(s)";
+#ifdef USE_NUMA
             if (numa_pref >= 0)
                 os << " preferring NUMA node " << numa_pref;
             else
                 os << " using NUMA policy " << numa_pref;
+#endif
             os << "...\n" << flush;
             auto p = shared_numa_alloc<char>(nb, numa_pref);
             TRACE_MSG("Got memory at " << static_cast<void*>(p.get()));
 
             // Save using original key.
-            data_buf[np] = p;
+            data_buf[numa_pref] = p;
         }
     }
 

src/kernel/lib/context.hpp

@@ -540,8 +540,7 @@ namespace yask {
         // Make a new grid iff its dims match any in the stencil.
         // Returns pointer to the new grid or nullptr if no match.
         virtual YkGridPtr newStencilGrid (const std::string & name,
-                                          const GridDimNames & dims,
-                                          KernelSettingsPtr settings) =0;
+                                          const GridDimNames & dims) =0;
 
         // Make a new grid with 'name' and 'dims'.
         // Set sizes if 'sizes' is non-null.
@@ -654,8 +653,14 @@ namespace yask {
         virtual idx_t get_num_ranks(const std::string& dim) const;
         virtual idx_t get_rank_index(const std::string& dim) const;
         virtual std::string apply_command_line_options(const std::string& args);
-        virtual void set_default_numa_preferred(int numa_node) {
+        virtual bool set_default_numa_preferred(int numa_node) {
+#ifdef USE_NUMA
             _opts->_numa_pref = numa_node;
+            return true;
+#else
+            _opts->_numa_pref = yask_numa_none;
+            return numa_node == yask_numa_none;
+#endif
         }
         virtual int get_default_numa_preferred() const {
             return _opts->_numa_pref;

src/kernel/lib/generic_grids.cpp

@@ -32,7 +32,7 @@ namespace yask {
     GenericGridBase::GenericGridBase(string name,
                                      Layout& layout_base,
                                      const GridDimNames& dimNames,
-                                     KernelSettingsPtr settings,
+                                     KernelSettingsPtr* settings,
                                      ostream** ostr) :
         _name(name), _layout_base(&layout_base), _opts(settings), _ostr(ostr) {
         for (auto& dn : dimNames)
@@ -51,22 +51,21 @@ namespace yask {
         // Release any old data if last owner.
         release_storage();
 
-        // Get default NUMA node from settings.
-        int numa_def = _opts->_numa_pref;
-
         // What node?
-        int numa_pref = (_numa_pref >= 0) ? _numa_pref : numa_def;
+        int numa_pref = get_numa_pref();
 
         // Alloc required number of bytes.
         size_t sz = get_num_bytes();
         os << "Allocating " << makeByteStr(sz) <<
             " for grid '" << _name << "'";
+#ifdef USE_NUMA
         if (numa_pref >= 0)
             os << " preferring NUMA node " << numa_pref;
         else
             os << " on local NUMA node";
+#endif
         os << "...\n" << flush;
-        _base = shared_numa_alloc<char>(sz, _numa_pref);
+        _base = shared_numa_alloc<char>(sz, numa_pref);
 
         // No offset.
         _elems = _base.get();

src/kernel/lib/generic_grids.hpp

@@ -47,15 +47,16 @@ namespace yask {
         void* _elems = 0;          // actual data, which may be offset from _base.
 
         // Preferred NUMA node.
-        int _numa_pref = -1;   // -1 => use default.
+        const static int _numa_unset = -999;
+        int _numa_pref = _numa_unset; // use default from _opts.
 
         // Note that both _dims and *_layout_base hold dimensions unless this
         // is a scalar. For a scalar, _dims is empty and _layout_base = 0.
         IdxTuple _dims;         // names and lengths of grid dimensions.
         Layout* _layout_base = 0; // memory layout.
 
         // Command-line and env parameters.
-        KernelSettingsPtr _opts;
+        KernelSettingsPtr* _opts;
 
         // Output stream for messages.
         // Pointer-to-pointer to let it follow a parent's pointer.
@@ -76,7 +77,7 @@ namespace yask {
         GenericGridBase(std::string name,
                         Layout& layout_base,
                         const GridDimNames& dimNames,
-                        KernelSettingsPtr settings,
+                        KernelSettingsPtr* settings,
                         std::ostream** ostr);
 
         virtual ~GenericGridBase() { }
@@ -92,9 +93,20 @@ namespace yask {
         void set_name(const std::string& name) { _name = name; }
 
         // NUMA accessors.
-        virtual int get_numa_pref() const { return _numa_pref; }
-        virtual void set_numa_pref(int pref_numa_node) { _numa_pref = pref_numa_node; }
-
+        virtual int get_numa_pref() const {
+            return (_numa_pref != _numa_unset) ?
+                _numa_pref : (*_opts)->_numa_pref;
+        }
+        virtual bool set_numa_pref(int numa_node) {
+#ifdef USE_NUMA
+            _numa_pref = numa_node;
+            return true;
+#else
+            _numa_pref = yask_numa_none;
+            return numa_node == yask_numa_none;
+#endif
+        }        
+
         // Access dims.
         const IdxTuple& get_dims() const { return _dims; }
 
@@ -204,7 +216,7 @@ namespace yask {
         GenericGridTemplate(std::string name,
                             Layout& layout_base,
                             const GridDimNames& dimNames,
-                            KernelSettingsPtr settings,
+                            KernelSettingsPtr* settings,
                             std::ostream** ostr) :
             GenericGridBase(name, layout_base, dimNames, settings, ostr) { }
 
@@ -309,7 +321,7 @@ namespace yask {
         // Construct an unallocated grid.
         GenericGrid(std::string name,
                     const GridDimNames& dimNames,
-                    KernelSettingsPtr settings,
+                    KernelSettingsPtr* settings,
                     std::ostream** ostr) :
             GenericGridTemplate<T>(name, _layout, dimNames, settings, ostr) {
             assert(int(dimNames.size()) == _layout.get_num_sizes());

src/kernel/lib/new_grid.cpp

@@ -45,7 +45,7 @@ namespace yask {
 
         // First, try to make a grid that matches the layout in
         // the stencil.
-        YkGridPtr gp = newStencilGrid(name, dims, _opts);
+        YkGridPtr gp = newStencilGrid(name, dims);
 
         // If there was no match, use default layout.
         if (!gp) {
@@ -76,7 +76,7 @@ namespace yask {
 
             // Scalar?
             if (ndims == 0)
-                gp = make_shared<YkElemGrid<Layout_0d, false>>(_dims, name, dims, _opts, &_ostr);
+                gp = make_shared<YkElemGrid<Layout_0d, false>>(_dims, name, dims, &_opts, &_ostr);
 
             // Include auto-gen code for all other cases.
 #include "yask_grid_code.hpp"