params/mirrors cleaning + usable test suite (issues #11 and #10)

Context

This pull request solves:

• issue #11 : "The test suite lasts too long".
• issue #10 : "Several tests still display windows even with "nogui" option".

Modifications

root / fwk

• mpirun.py and run.py have been merged. These files were huge copy/paste of each other. The purpose was to be sure that the workspace folder was created by rank#0 process. Now, run.py checks whether MPI is used or not and does what is expected (automatically).
• wutils used setand grep unix command to display environment variables. This code has been rewritten in order to work also on windows.
• Variables such as OMP_NUM_THREADS or MKL_DYNAMIC are now set to predefined and controlled values if (and only if) they are not previously set by the user. For example OMP_NUM_THREADS is set to 1 if OMP_NUM_THREADS does not appear in the list of environment variables.

fdtd

• The tests named fdtd1d_1c and fdtd1d_1d have been modified in order to:
  • compute something even if --nogui is set.
  • completely hide matplotlib commands when --nogui is set (these tests failed if they were run in a ssh terminal without X display)

mirrors

• Some old files have been put in a new mirrors/attic folder: imported_10x10.py, imported_30x30.py, loop_old.py, loop_old2.py
• Some broken tests have been moved to mirrors/broken: NISP_Leg_cond.py (too old matplotlib), mirrors01.py, mirrors03.py, mirrors_test_battery.py (bad mesh with wrong normals)
• A folder named figs has been created for the scripts producing figures for reports: LSP*.py, numpy_matplotlib*
• mirrors/mirror_ss.py: the only working model for mirror! It has been cleaned. An "nogui" option has been added in the parameter list. Its defaut size has been decreased.
• mirror source code:
  • removal of unneeded header
  • basic code formatting
  • removal of unused code
  • additional comments/doc
• Tests:
  • mirrors02.py has been deleted (same as mirrors/mirror_ss.py and mirrors/tests/test1/simple.py )
  • mirrors/tests/test1/simple.py was moved to mirrors/tests
  • all loop*.py have been reduced in size so that they run in a few seconds.
  • all loop*.py can be run either with GUI or not with the desired result.

Test suite

• The test suite now runs in less than a minute (with 6 cores).
• It has been tested on ubuntu and windows

fdtd/tests/fdtd1d_1c.py

@@ -6,20 +6,18 @@ import numpy as np
 import matplotlib.pyplot as plt
 import matplotlib.animation as animation
 from fwk.wutils import parseargs
+args = parseargs()
 
-fig, ax = plt.subplots()
-
-SIZE=200
+SIZE = 200
 
 ez = np.zeros(SIZE, dtype=float)
 hy = np.zeros(SIZE, dtype=float)
 imp0 = 377.0
-maxTime = 1000
+maxTime = 300
 nloop = 1
 
-#
-args = parseargs()
 if not args.nogui:
+    fig, ax = plt.subplots()
     line, = plt.plot(ez)
     plt.title('Example p42')
     plt.xlabel('X')
@@ -28,6 +26,8 @@ if not args.nogui:
     plt.ylim(-1,1)
     plt.grid(True)
     plt.draw()
+else:
+    line = None
 
 qTime=0
 def animate(i): 
@@ -60,14 +60,17 @@ def animate(i):
         # correction for TFSF boundary
         ez[50] += np.exp(-(qTime+0.5- (-0.5) - 30.)*(qTime+0.5- (-0.5) - 30.)/100.)
 
+    if not args.nogui:
+        line.set_ydata(ez)
+        ax.set_title('time = %d' % qTime)
 
-    line.set_ydata(ez)
-    ax.set_title('time = %d' % qTime)  
     return line,
 
-#
-args = parseargs()
 if not args.nogui:
     ani = animation.FuncAnimation(fig, animate, maxTime // nloop, 
                                   interval=25, repeat=False)
-    plt.show()
\ No newline at end of file
+    plt.show()
+else:
+    # calls the loops without matplotlib
+    for i in xrange(maxTime // nloop):
+        animate(i)
\ No newline at end of file