diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/Makefile b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/Makefile
deleted file mode 100644
index f5c9d0d5..00000000
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/Makefile
+++ /dev/null
@@ -1,36 +0,0 @@
-CC = gcc
-C++ = g++
-CFLAGS = -c -std=c++14 -Wall -O3
-SIMFLAGS = -l. -std=c++14 -Wall -O3
-LFLAGS = -pthread -lm
-#INCDIR = "$(ROOTINC)/include/" "$(ROOTINC)/external/" "$(ROOTINC)/external/ANN/include/"
-#INCDIRPARAMS = $(INCDIR:%=-I%)
-INCDIRPARAMS  = -I$(ROOTINC)/include/ -I$(ROOTINC)/external/ -I$(ROOTINC)/external/ANN/include/
-OBJ = NRMConstant_v5.o particle.o simulate.o count_cores.o output.o simulate_rdme.o simulate_threads.o model.o pthread_barrier.o
-ANNOBJECTS = ANN.o brute.o kd_tree.o kd_util.o kd_split.o \
-	kd_dump.o kd_search.o kd_pr_search.o kd_fix_rad_search.o \
-	bd_tree.o bd_search.o bd_pr_search.o bd_fix_rad_search.o \
-	perf.o
-
-
-.PHONY: all
-
-all: ssa_sdpd
-
-
-CORE: $(OBJ)
-#this is now called directly, before this make command, in solver.py
-#	make -d -f $(ROOTINC_ESC)/external/ANN/src/Makefile.spatialpy ROOTINC=$(ROOTINC_ESC)
-
-main.o:
-	$(C++) -c $(GPROFFLAG) $(GDB_FLAG) -o main.o $(MODEL) $(INCDIRPARAMS) $(CFLAGS)
-
-%.o: $(ROOT)/src/%.cpp
-	$(C++) -c $(GPROFFLAG) $(GDB_FLAG) -o $@ "$<" $(INCDIRPARAMS) $(CFLAGS)
-
-%.o: $(ROOT)/src/%.c
-	$(CC) -c $(GPROFFLAG) $(GDB_FLAG) -o $@ "$<" $(INCDIRPARAMS) $(CFLAGS)
-
-ssa_sdpd: main.o 
-	$(C++) $(GPROFFLAG) $(GDB_FLAG) -o ssa_sdpd $(addprefix $(COREDIR)/,$(OBJ))  main.o $(addprefix $(COREDIR)/,$(ANNOBJECTS)) $(LFLAGS)
-
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/SConstruct b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/SConstruct
new file mode 100644
index 00000000..92b25a22
--- /dev/null
+++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/build/SConstruct
@@ -0,0 +1,34 @@
+import os
+
+model = ARGUMENTS.get('MODEL')
+root_dir = ARGUMENTS.get('ROOT')
+root_include_dir = ARGUMENTS.get('ROOTINC')
+core_dir = ARGUMENTS.get('COREDIR')
+build_dir = ARGUMENTS.get('BUILD')
+
+if core_dir is None:
+    core_dir = build_dir
+
+env = Environment(
+    tools=['default', 'mingw'],
+    CPPPATH=[
+        Dir(f'{root_include_dir}/include'),
+        Dir(f'{root_include_dir}/external/ANN/include'),
+    ],
+    LIBPATH=[
+        Dir(f'{core_dir}/lib'),
+    ],
+    ENV=os.environ,
+    # When MSVC (or any other compilers) are supported, update this to be a compiler-specific flag
+    CXXFLAGS=['-std=c++14'],
+)
+env.VariantDir(core_dir, f'{root_dir}/src', duplicate=False)
+env.VariantDir(f'{core_dir}/external/ANN', f'{root_dir}/external/ANN/src', duplicate=False)
+
+Export('env')
+ann = SConscript(f'{root_dir}/external/ANN/src/SConscript', variant_dir=f'{core_dir}/external/ANN', duplicate=False)
+core = SConscript(f'{root_dir}/src/SConscript', variant_dir=core_dir, duplicate=False)
+
+env.StaticLibrary(f'{core_dir}/lib/spatialpy-core', core)
+env.StaticLibrary(f'{core_dir}/lib/ANN', ann)
+env.Program('ssa_sdpd.exe', model, LIBS=['spatialpy-core', 'ANN', 'pthread'])
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/src/Makefile.spatialpy b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/src/Makefile.spatialpy
deleted file mode 100755
index 027ed9ac..00000000
--- a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/src/Makefile.spatialpy
+++ /dev/null
@@ -1,118 +0,0 @@
-#-----------------------------------------------------------------------------
-# Makefile for ANN library
-#----------------------------------------------------------------------
-# Copyright (c) 1997-2005 University of Maryland and Sunil Arya and
-# David Mount.  All Rights Reserved.
-# 
-# This software and related documentation is part of the Approximate
-# Nearest Neighbor Library (ANN).  This software is provided under
-# the provisions of the Lesser GNU Public License (LGPL).  See the
-# file ../ReadMe.txt for further information.
-# 
-# The University of Maryland (U.M.) and the authors make no
-# representations about the suitability or fitness of this software for
-# any purpose.  It is provided "as is" without express or implied
-# warranty.
-#----------------------------------------------------------------------
-# History:
-#	Revision 0.1  03/04/98
-#		Initial release
-#	Revision 1.0  04/01/05
-#		Renamed files from .cc to .cpp for Microsoft Visual C++
-#		Added kd_dump.cpp
-#	Revision 1.1  05/03/05
-#		Added kd_fix_rad_search.cpp and bd_fix_rad_search.cpp
-#----------------------------------------------------------------------
-
-#-----------------------------------------------------------------------------
-# Some basic definitions:
-#		BASEDIR		where include, src, lib, ... are
-#		INCLIB		include directory
-#		LIBLIB		library directory
-#-----------------------------------------------------------------------------
-BASEDIR	= ..
-C++ = g++
-CFLAGS = -c -std=c++14 -Wall -O3 -g
-INCDIR = $(ROOTINC)/external/ANN/include/
-LIBDIR	= $(BASEDIR)/lib
-
-SOURCES = ANN.cpp brute.cpp kd_tree.cpp kd_util.cpp kd_split.cpp \
-	kd_dump.cpp kd_search.cpp kd_pr_search.cpp kd_fix_rad_search.cpp \
-	bd_tree.cpp bd_search.cpp bd_pr_search.cpp bd_fix_rad_search.cpp \
-	perf.cpp
-
-HEADERS = kd_tree.h kd_split.h kd_util.h kd_search.h \
-	kd_pr_search.h kd_fix_rad_search.h perf.h pr_queue.h pr_queue_k.h
-
-OBJECTS = $(SOURCES:.cpp=.o)
-
-#-----------------------------------------------------------------------------
-# Make the library
-#-----------------------------------------------------------------------------
-
-default: spatialpy
-
-targets: $(LIBDIR)/$(ANNLIB)
-
-spatialpy: $(OBJECTS)
-
-$(LIBDIR)/$(ANNLIB): $(OBJECTS)
-	$(MAKELIB) $(ANNLIB) $(OBJECTS)
-	$(RANLIB) $(ANNLIB)
-	mv $(ANNLIB) $(LIBDIR)
-
-#-----------------------------------------------------------------------------
-# Make object files
-#-----------------------------------------------------------------------------
-
-ANN.o: $(ROOTINC)/external/ANN/src/ANN.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/ANN.cpp
-
-brute.o: $(ROOTINC)/external/ANN/src/brute.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/brute.cpp
-
-kd_tree.o: $(ROOTINC)/external/ANN/src/kd_tree.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/kd_tree.cpp
-
-kd_util.o: $(ROOTINC)/external/ANN/src/kd_util.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/kd_util.cpp
-
-kd_split.o: $(ROOTINC)/external/ANN/src/kd_split.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/kd_split.cpp
-
-kd_search.o: $(ROOTINC)/external/ANN/src/kd_search.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/kd_search.cpp
-
-kd_pr_search.o: $(ROOTINC)/external/ANN/src/kd_pr_search.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/kd_pr_search.cpp
-
-kd_fix_rad_search.o: $(ROOTINC)/external/ANN/src/kd_fix_rad_search.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/kd_fix_rad_search.cpp
-
-kd_dump.o: $(ROOTINC)/external/ANN/src/kd_dump.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/kd_dump.cpp
-
-bd_tree.o: $(ROOTINC)/external/ANN/src/bd_tree.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/bd_tree.cpp
-
-bd_search.o: $(ROOTINC)/external/ANN/src/bd_search.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/bd_search.cpp
-
-bd_pr_search.o: $(ROOTINC)/external/ANN/src/bd_pr_search.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/bd_pr_search.cpp
-
-bd_fix_rad_search.o: $(ROOTINC)/external/ANN/src/bd_fix_rad_search.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/bd_fix_rad_search.cpp
-
-perf.o: $(ROOTINC)/external/ANN/src/perf.cpp
-	$(C++) -c -I$(INCDIR) $(CFLAGS) $(ROOTINC)/external/ANN/src/perf.cpp
-
-#-----------------------------------------------------------------------------
-# Cleaning
-#-----------------------------------------------------------------------------
-
-clean:
-	-rm -f *.o core
-
-realclean: clean
-
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/src/SConscript b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/src/SConscript
new file mode 100644
index 00000000..8354d4c0
--- /dev/null
+++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/external/ANN/src/SConscript
@@ -0,0 +1,18 @@
+Import('env')
+libANN = env.Object([
+    'ANN.cpp',
+    'brute.cpp',
+    'kd_tree.cpp',
+    'kd_util.cpp',
+    'kd_split.cpp',
+    'kd_dump.cpp',
+    'kd_search.cpp',
+    'kd_pr_search.cpp',
+    'kd_fix_rad_search.cpp',
+    'bd_tree.cpp',
+    'bd_search.cpp',
+    'bd_pr_search.cpp',
+    'bd_fix_rad_search.cpp',
+    'perf.cpp'
+])
+Return('libANN')
diff --git a/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/SConscript b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/SConscript
new file mode 100644
index 00000000..c4a9a3c0
--- /dev/null
+++ b/spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/SConscript
@@ -0,0 +1,13 @@
+Import('env')
+libspatialpy_core = env.Object([
+    'count_cores.cpp',
+    'model.cpp',
+    'NRMConstant_v5.cpp',
+    'output.cpp',
+    'particle.cpp',
+    'pthread_barrier.cpp',
+    'simulate.cpp',
+    'simulate_rdme.cpp',
+    'simulate_threads.cpp'
+])
+Return('libspatialpy_core')
diff --git a/spatialpy/solvers/solver.py b/spatialpy/solvers/solver.py
index 6936f86e..c884a6f8 100644
--- a/spatialpy/solvers/solver.py
+++ b/spatialpy/solvers/solver.py
@@ -23,6 +23,7 @@
 import time
 import getpass
 import re
+import sys
 
 import numpy
 
@@ -66,7 +67,7 @@ def __init__(self, model, debug_level=0):
         self.build_dir = None
         self.propfilename = None
         self.prop_file_name = None
-        self.executable_name = 'ssa_sdpd'
+        self.executable_name = 'ssa_sdpd.exe'
         self.h = None  # basis function width
 
         self.spatialpy_root = os.path.dirname(
@@ -470,51 +471,35 @@ def compile(self, debug=False, profile=False):
         self.__create_propensity_file(stoich_matrix, dep_graph, file_name=self.prop_file_name)
 
         # Build the solver
-        for make_exe_location in ["make", "mingw32-make"]:
-            make_exe = shutil.which("make")
-            if make_exe is not None:
-                break
-        if make_exe is None:
-            raise SimulationError("Make executable could not be found")
-        makefile = self.spatialpy_rootdir+'/build/Makefile'
-        makefile_ann = self.spatialpy_rootdir+'/external/ANN/src/Makefile.spatialpy'
-
-        cmd_ann = [
-            make_exe, '-d', '-C', self.core_dir, '-f', makefile_ann,
-            f'ROOTINC={self.spatialpy_rootinc}',
-        ]
-        cmd_core = [
-            make_exe, '-d', '-C', self.core_dir, 'CORE', '-f',  makefile,
+        makefile = self.spatialpy_rootdir+'/build/SConstruct'
+        make_cmd = [
+            sys.executable, "-m", "SCons", f"-C{self.build_dir}", f"-f{makefile}",
             f'ROOT={self.spatialpy_rootparam}',
             f'ROOTINC={self.spatialpy_rootinc}',
-            f'BUILD={self.core_dir}',
-        ]
-        cmd_build = [
-            make_exe, '-d', '-C', self.build_dir, '-I', self.core_dir, '-f', makefile,
-            'ROOT=' + self.spatialpy_rootparam,
-            'ROOTINC=' + self.spatialpy_rootinc,
-            'COREDIR=' + self.core_dir,
-            'MODEL=' + self.prop_file_name, 'BUILD='+self.build_dir
+            f'COREDIR={self.core_dir}',
+            f'MODEL={self.prop_file_name}',
+            f'BUILD={self.build_dir}',
         ]
         if profile:
-            cmd_build.append('GPROFFLAG=-pg')
+            # TODO: add profile/debug targets to SConstruct file
+            make_cmd.append('GPROFFLAG=-pg')
         if profile or debug:
-            cmd_build.append('GDB_FLAG=-g')
+            make_cmd.append('GDB_FLAG=-g')
         if self.debug_level > 1:
-            cmd = " && ".join([*cmd_ann, *cmd_core, *cmd_build])
+            cmd = " ".join(make_cmd)
             print(f"cmd: {cmd}\n")
         try:
-            for cmd_target in [cmd_ann, cmd_core, cmd_build]:
-                result = subprocess.check_output(cmd_target, stderr=subprocess.STDOUT)
-                if self.debug_level > 1:
-                    print(result.stdout.decode("utf-8"))
+            result = subprocess.check_output(make_cmd, stderr=subprocess.STDOUT)
+            if self.debug_level > 1:
+                print(result)
         except subprocess.CalledProcessError as err:
             try:
                 print(err.stdout.decode("utf-8"))
             except Exception:
                 pass
-            raise SimulationError(f"Compilation of solver failed, return_code={result.return_code}")
+            raise SimulationError(f"Compilation of solver failed, return_code={err.returncode}")
         except OSError as err:
+            cmd = " ".join(make_cmd)
             print(f"Error, execution of compilation raised an exception: {err}")
             print(f"cmd = {cmd}")
             raise SimulationError("Compilation of solver failed") from err