Merge branch 'env-reporting' into 'development'
adjusting env reporting See merge request damask/DAMASK!375
This commit is contained in:
Francisco Jose Gallardo Basile
commit
c78b352956
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@ -30,7 +30,6 @@ PATH=${DAMASK_ROOT}/bin:$PATH
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SOLVER=$(type -p DAMASK_grid || true 2>/dev/null)
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[ "x$SOLVER" == "x" ] && SOLVER=$(blink 'Not found!')
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[ "x$OMP_NUM_THREADS" == "x" ] && OMP_NUM_THREADS=1
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# currently, there is no information that unlimited stack size causes problems
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# still, http://software.intel.com/en-us/forums/topic/501500 suggest to fix it
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@ -55,9 +54,8 @@ if [ ! -z "$PS1" ]; then
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[[ $(canonicalPath "$PETSC_DIR") == $PETSC_DIR ]] \
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|| echo " ~~> "$(canonicalPath "$PETSC_DIR")
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fi
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echo -n "MSC.Marc/Mentat "
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[ -d $MSC_ROOT ] && echo $MSC_ROOT || blink $MSC_ROOT
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echo
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[ "x$PETSC_ARCH" != "x" ] && echo "PETSc architecture $PETSC_ARCH"
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[ "x$OMP_NUM_THREADS" == "x" ] && export OMP_NUM_THREADS=4
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echo "Multithreading OMP_NUM_THREADS=$OMP_NUM_THREADS"
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echo -n "heap size "
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[[ "$(ulimit -d)" == "unlimited" ]] \
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@ -20,7 +20,6 @@ PATH=${DAMASK_ROOT}/bin:$PATH
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SOLVER=$(which DAMASK_grid || true 2>/dev/null)
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[[ "x$SOLVER" == "x" ]] && SOLVER=$(blink 'Not found!')
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[[ "x$OMP_NUM_THREADS" == "x" ]] && OMP_NUM_THREADS=1
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# currently, there is no information that unlimited stack size causes problems
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# still, http://software.intel.com/en-us/forums/topic/501500 suggest to fix it
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@ -45,11 +44,8 @@ if [ ! -z "$PS1" ]; then
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[[ $(canonicalPath "$PETSC_DIR") == $PETSC_DIR ]] \
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|| echo " ~~> "$(canonicalPath "$PETSC_DIR")
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fi
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[[ "x$PETSC_ARCH" == "x" ]] \
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|| echo "PETSc architecture $PETSC_ARCH"
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echo -n "MSC.Marc/Mentat "
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[ -d $MSC_ROOT ] && echo $MSC_ROOT || blink $MSC_ROOT
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echo
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[[ "x$PETSC_ARCH" != "x" ]] && echo "PETSc architecture $PETSC_ARCH"
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[[ "x$OMP_NUM_THREADS" == "x" ]] && export OMP_NUM_THREADS=4
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echo "Multithreading OMP_NUM_THREADS=$OMP_NUM_THREADS"
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echo -n "heap size "
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[[ "$(ulimit -d)" == "unlimited" ]] \
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@ -7,6 +7,11 @@ from pathlib import Path
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import damask
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def copy_and_replace(in_file,dst,msc_root,editor):
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with open(in_file) as f_in, open(dst/Path(in_file).name,'w') as f_out:
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f_out.write(f_in.read().replace('%INSTALLDIR%',msc_root).replace('%EDITOR%',editor))
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parser = argparse.ArgumentParser(
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description='Apply DAMASK modification to MSC.Marc/Mentat',
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prog = Path(__file__).name,
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@ -17,34 +22,25 @@ parser.add_argument('--editor', dest='editor', metavar='string', default='vi',
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parser.add_argument('--msc-root', dest='msc_root', metavar='string',
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default=damask.solver._marc._msc_root,
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help='MSC.Marc/Mentat root directory')
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parser.add_argument('--msc-version', dest='msc_version', metavar='string',
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parser.add_argument('--msc-version', dest='msc_version', type=float, metavar='float',
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default=damask.solver._marc._msc_version,
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help='MSC.Marc/Mentat version')
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parser.add_argument('--damask-root', dest='damask_root', type=float, metavar = 'float',
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parser.add_argument('--damask-root', dest='damask_root', metavar = 'string',
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default=damask.solver._marc._damask_root,
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help='DAMASK root directory')
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args = parser.parse_args()
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msc_root = Path(args.msc_root)
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damask_root = Path(args.damask_root)
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msc_version = args.msc_version
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def copy_and_replace(in_file,dst):
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with open(in_file) as f:
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content = f.read()
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content = content.replace('%INSTALLDIR%',str(msc_root))
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content = content.replace('%EDITOR%', args.editor)
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with open(dst/Path(in_file).name,'w') as f:
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f.write(content)
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print('adapting Marc tools...\n')
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src = damask_root/f'installation/mods_MarcMentat/{msc_version}/Marc_tools'
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dst = msc_root/f'marc{msc_version}/tools'
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for in_file in glob.glob(str(src/'*damask*')) + [str(src/'include_linux64')]:
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copy_and_replace(in_file,dst)
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copy_and_replace(in_file,dst,args.msc_root,args.editor)
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print('adapting Mentat scripts and menus...\n')
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@ -52,12 +48,12 @@ print('adapting Mentat scripts and menus...\n')
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src = damask_root/f'installation/mods_MarcMentat/{msc_version}/Mentat_bin'
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dst = msc_root/f'mentat{msc_version}/bin'
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for in_file in glob.glob(str(src/'*[!.original]')):
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copy_and_replace(in_file,dst)
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copy_and_replace(in_file,dst,args.msc_root,args.editor)
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src = damask_root/f'installation/mods_MarcMentat/{msc_version}/Mentat_menus'
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dst = msc_root/f'mentat{msc_version}/menus'
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for in_file in glob.glob(str(src/'job_run.ms')):
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copy_and_replace(in_file,dst)
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copy_and_replace(in_file,dst,args.msc_root,args.editor)
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print('compiling Mentat menu binaries...')
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@ -392,7 +392,7 @@ class Grid:
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seeds_p = seeds
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coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
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pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',1)))
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pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',4)))
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result = pool.map_async(partial(Grid._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
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pool.close()
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pool.join()
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@ -436,8 +436,12 @@ class Grid:
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"""
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coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
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KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
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devNull,material_ = KDTree.query(coords)
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tree = spatial.cKDTree(seeds,boxsize=size) if periodic else \
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spatial.cKDTree(seeds)
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try:
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material_ = tree.query(coords, workers = int(os.environ.get('OMP_NUM_THREADS',4)))[1]
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except TypeError:
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material_ = tree.query(coords, n_jobs = int(os.environ.get('OMP_NUM_THREADS',4)))[1] # scipy <1.6
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return Grid(material = (material_ if material is None else material[material_]).reshape(cells),
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size = size,
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@ -1179,7 +1179,7 @@ class Result:
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"""
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chunk_size = 1024**2//8
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pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',1)))
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pool = mp.Pool(int(os.environ.get('OMP_NUM_THREADS',4)))
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lock = mp.Manager().Lock()
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groups = []
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@ -78,7 +78,7 @@ def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,rng_seed=
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candidates = rng.random((N_candidates,3))*_np.broadcast_to(size,(N_candidates,3))
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tree = _spatial.cKDTree(coords[:s],boxsize=size) if periodic else \
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_spatial.cKDTree(coords[:s])
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distances, dev_null = tree.query(candidates)
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distances = tree.query(candidates)[0]
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best = distances.argmax()
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if distances[best] > distance: # require minimum separation
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coords[s] = candidates[best] # maximum separation to existing point cloud
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