Merge branch 'env-reporting' into 'development'

adjusting env reporting

See merge request damask/DAMASK!375

env/DAMASK.sh

@@ -30,7 +30,6 @@ PATH=${DAMASK_ROOT}/bin:$PATH
 SOLVER=$(type -p DAMASK_grid || true 2>/dev/null)
 [ "x$SOLVER" == "x" ] && SOLVER=$(blink 'Not found!')
 
-[ "x$OMP_NUM_THREADS" == "x" ] && OMP_NUM_THREADS=1
 
 # currently, there is no information that unlimited stack size causes problems
 # still, http://software.intel.com/en-us/forums/topic/501500 suggest to fix it
@@ -55,9 +54,8 @@ if [ ! -z "$PS1" ]; then
     [[ $(canonicalPath "$PETSC_DIR") == $PETSC_DIR ]] \
     || echo "               ~~> "$(canonicalPath "$PETSC_DIR")
   fi
-  echo -n "MSC.Marc/Mentat    "
+  [ "x$PETSC_ARCH" != "x" ] && echo "PETSc architecture $PETSC_ARCH"
-  [ -d $MSC_ROOT ] && echo $MSC_ROOT || blink $MSC_ROOT
+  [ "x$OMP_NUM_THREADS" == "x" ] && export OMP_NUM_THREADS=4
-  echo
   echo "Multithreading     OMP_NUM_THREADS=$OMP_NUM_THREADS"
   echo -n "heap  size         "
    [[ "$(ulimit -d)" == "unlimited" ]] \

env/DAMASK.zsh

@@ -20,7 +20,6 @@ PATH=${DAMASK_ROOT}/bin:$PATH
 SOLVER=$(which DAMASK_grid || true 2>/dev/null)
 [[ "x$SOLVER" == "x" ]] && SOLVER=$(blink 'Not found!')
 
-[[ "x$OMP_NUM_THREADS" == "x" ]] && OMP_NUM_THREADS=1
 
 # currently, there is no information that unlimited stack size causes problems
 # still, http://software.intel.com/en-us/forums/topic/501500 suggest to fix it
@@ -45,11 +44,8 @@ if [ ! -z "$PS1" ]; then
     [[ $(canonicalPath "$PETSC_DIR") == $PETSC_DIR ]] \
     || echo "               ~~> "$(canonicalPath "$PETSC_DIR")
   fi
-  [[ "x$PETSC_ARCH" == "x" ]] \
+  [[ "x$PETSC_ARCH" != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
-  || echo "PETSc architecture $PETSC_ARCH"
+  [[ "x$OMP_NUM_THREADS" == "x" ]] && export OMP_NUM_THREADS=4
-  echo -n "MSC.Marc/Mentat    "
-  [ -d $MSC_ROOT ] && echo $MSC_ROOT || blink $MSC_ROOT
-  echo
   echo "Multithreading     OMP_NUM_THREADS=$OMP_NUM_THREADS"
   echo -n "heap  size         "
    [[ "$(ulimit -d)" == "unlimited" ]] \

installation/mods_MarcMentat/apply_DAMASK_modifications.py

@@ -7,6 +7,11 @@ from pathlib import Path
 
 import damask
 
+def copy_and_replace(in_file,dst,msc_root,editor):
+    with open(in_file) as f_in, open(dst/Path(in_file).name,'w') as f_out:
+        f_out.write(f_in.read().replace('%INSTALLDIR%',msc_root).replace('%EDITOR%',editor))
+
+
 parser = argparse.ArgumentParser(
                   description='Apply DAMASK modification to MSC.Marc/Mentat',
                   prog = Path(__file__).name,
@@ -17,34 +22,25 @@ parser.add_argument('--editor', dest='editor', metavar='string', default='vi',
 parser.add_argument('--msc-root', dest='msc_root', metavar='string',
                     default=damask.solver._marc._msc_root,
                     help='MSC.Marc/Mentat root directory')
-parser.add_argument('--msc-version', dest='msc_version', metavar='string',
+parser.add_argument('--msc-version', dest='msc_version', type=float, metavar='float',
                     default=damask.solver._marc._msc_version,
                     help='MSC.Marc/Mentat version')
-parser.add_argument('--damask-root', dest='damask_root', type=float, metavar = 'float',
+parser.add_argument('--damask-root', dest='damask_root', metavar = 'string',
                     default=damask.solver._marc._damask_root,
                     help='DAMASK root directory')
 
-
 args = parser.parse_args()
 msc_root    = Path(args.msc_root)
 damask_root = Path(args.damask_root)
 msc_version = args.msc_version
 
-def copy_and_replace(in_file,dst):
-    with open(in_file) as f:
-        content = f.read()
-    content = content.replace('%INSTALLDIR%',str(msc_root))
-    content = content.replace('%EDITOR%', args.editor)
-    with open(dst/Path(in_file).name,'w') as f:
-        f.write(content)
-
 
 print('adapting Marc tools...\n')
 
 src = damask_root/f'installation/mods_MarcMentat/{msc_version}/Marc_tools'
 dst = msc_root/f'marc{msc_version}/tools'
 for in_file in glob.glob(str(src/'*damask*')) + [str(src/'include_linux64')]:
-    copy_and_replace(in_file,dst)
+    copy_and_replace(in_file,dst,args.msc_root,args.editor)
 
 
 print('adapting Mentat scripts and menus...\n')
@@ -52,12 +48,12 @@ print('adapting Mentat scripts and menus...\n')
 src = damask_root/f'installation/mods_MarcMentat/{msc_version}/Mentat_bin'
 dst = msc_root/f'mentat{msc_version}/bin'
 for in_file in glob.glob(str(src/'*[!.original]')):
-    copy_and_replace(in_file,dst)
+    copy_and_replace(in_file,dst,args.msc_root,args.editor)
 
 src = damask_root/f'installation/mods_MarcMentat/{msc_version}/Mentat_menus'
 dst = msc_root/f'mentat{msc_version}/menus'
 for in_file in glob.glob(str(src/'job_run.ms')):
-    copy_and_replace(in_file,dst)
+    copy_and_replace(in_file,dst,args.msc_root,args.editor)
 
 
 print('compiling Mentat menu binaries...')

python/damask/_grid.py

@@ -392,7 +392,7 @@ class Grid:
             seeds_p   = seeds
             coords    = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
 
-        pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',1)))
+        pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',4)))
         result = pool.map_async(partial(Grid._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
         pool.close()
         pool.join()
@@ -436,8 +436,12 @@ class Grid:
 
         """
         coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
-        KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
+        tree = spatial.cKDTree(seeds,boxsize=size) if periodic else \
-        devNull,material_ = KDTree.query(coords)
+               spatial.cKDTree(seeds)
+        try:
+            material_ = tree.query(coords, workers = int(os.environ.get('OMP_NUM_THREADS',4)))[1]
+        except TypeError:
+            material_ = tree.query(coords, n_jobs = int(os.environ.get('OMP_NUM_THREADS',4)))[1]    # scipy <1.6
 
         return Grid(material = (material_ if material is None else material[material_]).reshape(cells),
                     size     = size,

python/damask/_result.py

@@ -1179,7 +1179,7 @@ class Result:
 
         """
         chunk_size = 1024**2//8
-        pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',1)))
+        pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',4)))
         lock = mp.Manager().Lock()
 
         groups = []

python/damask/seeds.py

@@ -78,7 +78,7 @@ def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,rng_seed=
         candidates = rng.random((N_candidates,3))*_np.broadcast_to(size,(N_candidates,3))
         tree = _spatial.cKDTree(coords[:s],boxsize=size) if periodic else \
                _spatial.cKDTree(coords[:s])
-        distances, dev_null = tree.query(candidates)
+        distances = tree.query(candidates)[0]
         best = distances.argmax()
         if distances[best] > distance:                                                              # require minimum separation
             coords[s] = candidates[best]                                                            # maximum separation to existing point cloud