Max number of threads is 8

spatialpy/Mesh.py

@@ -210,10 +210,10 @@ def read_msh_file(cls, filename):
             import pygmsh
         except ImportError as e:
             raise MeshError("The python package 'pygmsh' is not installed.")
-        try:
-            _ = pygmsh.get_gmsh_major_version()
-        except FileNotFoundError as e:
-            raise MeshError("The command line program 'gmsh' is not installed or is not found in the current PATH")
+       # try:
+       #     _ = pygmsh.get_gmsh_major_version()
+       # except FileNotFoundError as e:
+       #     raise MeshError("The command line program 'gmsh' is not installed or is not found in the current PATH")
 
         try:
             import meshio

spatialpy/Solver.py

@@ -53,7 +53,7 @@ def compile(self):
         """ Compile the model."""
 
         # Create a unique directory each time call to compile.
-        self.build_dir = tempfile.mkdtemp(dir=os.environ.get('SPATIALPY_TMPDIR'))
+        self.build_dir = tempfile.mkdtemp(prefix='spatialpy_build_',dir=os.environ.get('SPATIALPY_TMPDIR'))
 
         if self.report_level >= 1:
             print("Compiling Solver.  Build dir: {0}".format(self.build_dir))
@@ -114,7 +114,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None):
 
         # Execute the solver
         for run_ndx in range(number_of_trajectories):
-            outfile = tempfile.mkdtemp(dir=os.environ.get('SPATIALPY_TMPDIR'))
+            outfile = tempfile.mkdtemp(prefix='spatialpy_result_',dir=os.environ.get('SPATIALPY_TMPDIR'))
             result = Result(self.model, outfile)
             solver_cmd = 'cd {0}'.format(outfile) + ";" + os.path.join(self.build_dir, self.executable_name)
 

spatialpy/ssa_sdpd-c-simulation-engine/propensity_file_template.c

@@ -103,6 +103,7 @@ int main(int argc, char**argv){
         srand48((long int)time(NULL)+(long int)(1e9*clock()));
     }
     int num_threads = get_num_processors();
+    if(num_threads>8){ num_threads=8; }
     run_simulation(num_threads, system);
     exit(0);
 }