Katropton: Add supports for Gmsh 4

As observed by @R.Boman, katropton was not working with MPI using Gmsh 4. This was due to the fact that Gmsh 4 does not save the ghost cells by default.

To save those cells, we have to use the option -part_ghosts as discussed in the Gmsh doc.

However, this option is not supported by Gmsh 3 (gmsh -h | grep "ghost" does not find any line). Therefore, to solve this issue, the code must test the version of Gmsh used and, if the major version is 4 or greater, must add the -part_ghosts argument.

This MR includes the correction of if statements in plat*.geo which prevented the use of newer Gmsh than 3.0.6.

katropton/utilities.py

@@ -16,22 +16,13 @@ import os
 import numpy as np
 from katropton.eigenvalues import *
 
+
 def get_gmsh_version():
-    command_line = 'gmsh --version'
-    tmp = shlex.split(command_line)
-    fileout = open('gmsh_version.log', 'w')
-    p = subprocess.Popen(tmp,
-                            stdin=subprocess.PIPE,
-                            stdout=fileout,
-                            stderr=fileout,
-                            env=os.environ,
-                            shell=False,
-                            close_fds=True)
-    retcode = p.wait()
-    fileout.close()
-    f = open('gmsh_version.log', 'r')
-    tmp = f.read().split('.')
-    return int(tmp[0]), int(tmp[1]), int(tmp[2])
+    tmp = subprocess.check_output(["gmsh", "--version"],
+                                  stderr=subprocess.STDOUT)
+    tmp2 = tmp.split('.')
+    return int(tmp2[0]), int(tmp2[1]), int(tmp2[2])
+
 
 def import_MPI():
     try:
@@ -261,16 +252,10 @@ def extract(msh,
         pos = msh.nodes[int(nodes[i])-1].pos
         x[i] = pos[which_pos]
 
-    #print x
-
     indices = np.argsort(x)
-    #print x
-
     for i in range(0, len(x)):
         x_sorted[i] = x[indices[i]]
         nodes_sorted[i] = nodes[indices[i]]
-    #print x_sorted
-    #print nodes_sorted
 
     with open(name_sol) as fp:
         for i, line in enumerate(fp):