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

fwk/wutils.py

@@ -90,25 +90,33 @@ def findbins(dirB=['build','wavesB']): # changer wavesB en autre chose !
 
 def initMKL(nthreads):
     import os
-    #os.environ['MKL_NUM_THREADS'] = '%d' % nthreads
-    #os.environ['MKL_DOMAIN_NUM_THREADS'] = 'MKL_BLAS=%d' % nthreads
-    #os.environ['OMP_NUM_THREADS'] = '1'  # tjs 1!
-    #os.environ['MKL_DYNAMIC'] = 'FALSE'
-    #os.environ['OMP_DYNAMIC'] = 'FALSE'
-    #print "nthreads(MKL)=%d" % nthreads
-    print "OMP environement"
-    print os.system('env | grep OMP')
-    print "MKL environement"
-    print os.system('env | grep MKL')
-    print "KMP environement"
-    print os.system('env | grep KMP')    
+    # we try to have full control over the threading environment
+    # => set MKL/OMP variables if (and only if) they are not set!
+    if not 'MKL_NUM_THREADS' in os.environ:
+        os.environ['MKL_NUM_THREADS'] = '%d' % nthreads
+    if not 'MKL_DOMAIN_NUM_THREADS' in os.environ:
+        os.environ['MKL_DOMAIN_NUM_THREADS'] = 'MKL_BLAS=%d' % nthreads
+    if not 'OMP_NUM_THREADS' in os.environ:
+        os.environ['OMP_NUM_THREADS'] = '1'
+    if not 'MKL_DYNAMIC' in os.environ:
+        os.environ['MKL_DYNAMIC'] = 'FALSE'
+    if not 'OMP_DYNAMIC' in os.environ:
+        os.environ['OMP_DYNAMIC'] = 'FALSE'
+    # display variables
+    for s in ['OMP_', 'MKL', 'KMP']:
+        print '* %s environment:' % s        
+        for key, value in os.environ.iteritems():
+            if s in key:
+                print '\t%s = %s' % (key, value)
+  
 # ------------------------------------------------------------------------------
 
-def mpi_setupwdir(testname):
+def setupwdir(testname):
     """
-    creates a working folder for each test
+    creates a single working folder for the given test
     """
     try:
+        # are we using MPI?
         import mpi4py.MPI as mpi
         comm = mpi.COMM_WORLD
         rank = comm.rank
@@ -120,51 +128,34 @@ def mpi_setupwdir(testname):
         rank = 0
         siz  = 1
         name = "noname"
-
     import os, os.path
+
+    # builds the name of the workspace folder       
     #print "__file__=",__file__
     dir1=os.path.abspath(os.path.dirname(__file__)+os.sep+"..")+os.sep
-    #print "dir1=",dir1
-    #print "testname=",testname
+    print "dir1=",dir1
+    print "testname=",testname
     common = os.path.commonprefix( (testname, dir1) )
     #print "common=", common
     resdir = testname[len(common):].replace(os.sep,"_")
     resdir = os.path.splitext(resdir)[0] # remove ".py"
     #print "resdir=", resdir
     wdir=os.path.join('workspace', resdir)
-    if rank == 0:
-        #if not os.path.isdir('workspace'):
-        #    os.makedirs('workspace')
 
+    if rank == 0:
+        # rank0 is in charge of creating the folder... 
         if not os.path.isdir(wdir):
+            print "creating", wdir
             os.makedirs(wdir)
-
-        for i in range(1,siz):
-            comm.send(1, dest=i, tag=11)
+        
+        if siz>1: # if multiple process => send sync to slaves. 
+            for i in range(1,siz):
+                comm.send(1, dest=i, tag=11)
     else:
-        data = comm.recv(source=0, tag=11)
-    os.chdir(wdir)
-
-# ------------------------------------------------------------------------------
-
-def setupwdir(testname):
-    """
-    creates a working folder for each test
-    """
-    import os, os.path
-    #print "__file__=",__file__
-    dir1=os.path.abspath(os.path.dirname(__file__)+os.sep+"..")+os.sep
-    print "dir1=",dir1
-    print "testname=",testname
-    common = os.path.commonprefix( (testname, dir1) )
-    #print "common=", common
-    resdir = testname[len(common):].replace(os.sep,"_")
-    resdir = os.path.splitext(resdir)[0] # remove ".py"
-    #print "resdir=", resdir
-    wdir=os.path.join('workspace', resdir)
-    if not os.path.isdir(wdir):
-        print "creating", wdir
-        os.makedirs(wdir)
+        # the others block and wait for rank0 ([RB] why not "mpi_barrier"????)
+        data = comm.recv(source=0, tag=11) 
+    
+    # we can now safely go into the new folder
     os.chdir(wdir)
 
 # ------------------------------------------------------------------------------