Merge commit 'v3.0.0-alpha3-22-gc0958a934'

.gitlab-ci.yml

@@ -207,7 +207,7 @@ J2_plasticBehavior:
   stage: fortran
   script:
     - module load $IntelMarc $HDF5Marc $MSC
-    - J2_plasticBehavior/test.py
+    - MSC_VERSION=2020 J2_plasticBehavior/test.py
   except:
     - master
     - release

env/CONFIG

@@ -1,5 +0,0 @@
-# "set"-syntax needed only for tcsh (but works with bash and zsh)
-set OMP_NUM_THREADS  = 4
-
-set MSC_ROOT         = /opt/msc
-set MSC_VERSION      = 2020

env/DAMASK.sh

@@ -19,17 +19,9 @@ fi
 
 DAMASK_ROOT=$(canonicalPath "$ENV_ROOT/../")
 
-
 # shorthand command to change to DAMASK_ROOT directory
 eval "function DAMASK_root() { cd $DAMASK_ROOT; }"
 
-# defining set() allows to source the same file for tcsh and bash, with and without space around =
-set() {
-    export $1$2$3
- }
-source $ENV_ROOT/CONFIG
-unset -f set
-
 # add BRANCH if DAMASK_ROOT is a git repository
 cd $DAMASK_ROOT >/dev/null; BRANCH=$(git branch 2>/dev/null| grep -E '^\* '); cd - >/dev/null
 
@@ -86,9 +78,6 @@ if [ ! -z "$PS1" ]; then
   echo
 fi
 
-export OMP_NUM_THREADS
-export MSC_ROOT
-export MSC_VERSION
 export DAMASK_ROOT
 export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH
 

env/DAMASK.zsh

@@ -12,16 +12,6 @@ function blink {
 ENV_ROOT=$(canonicalPath "${0:a:h}")
 DAMASK_ROOT=$(canonicalPath "${0:a:h}'/..")
 
-# shorthand command to change to DAMASK_ROOT directory
-eval "function DAMASK_root() { cd $DAMASK_ROOT; }"
-
-# defining set() allows to source the same file for tcsh and zsh, with and without space around =
-set() {
-    export $1$2$3
- }
-source $ENV_ROOT/CONFIG
-unset -f set
-
 # add BRANCH if DAMASK_ROOT is a git repository
 cd $DAMASK_ROOT >/dev/null; BRANCH=$(git branch 2>/dev/null| grep -E '^\* '); cd - >/dev/null
 
@@ -80,9 +70,6 @@ if [ ! -z "$PS1" ]; then
   echo
 fi
 
-export OMP_NUM_THREADS
-export MSC_ROOT
-export MSC_VERSION
 export DAMASK_ROOT
 export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH
 

installation/mods_MarcMentat/2020/Mentat_bin/submit4

@@ -4,7 +4,7 @@
 # Normal exit status is 0.
 #
 
-DIR=%INSTALLDIR%/marc%VERSION%
+DIR=%INSTALLDIR%/marc2020
 
 if test $MARCDIR1
 then

installation/mods_MarcMentat/2020/Mentat_bin/submit5

@@ -4,7 +4,7 @@
 # Normal exit status is 0.
 #
 
-DIR=%INSTALLDIR%/marc%VERSION%
+DIR=%INSTALLDIR%/marc2020
 
 if test $MARCDIR1
 then

installation/mods_MarcMentat/2020/Mentat_bin/submit6

@@ -4,7 +4,7 @@
 # Normal exit status is 0.
 #
 
-DIR=%INSTALLDIR%/marc%VERSION%
+DIR=%INSTALLDIR%/marc2020
 
 if test $MARCDIR1
 then

installation/mods_MarcMentat/apply_DAMASK_modifications.py

@@ -5,23 +5,36 @@ import glob
 import argparse
 from pathlib import Path
 
-msc_version = os.environ['MSC_VERSION']
-msc_root    = Path(os.environ['MSC_ROOT'])
-damask_root = Path(os.environ['DAMASK_ROOT'])
+import damask
 
 parser = argparse.ArgumentParser(
                   description='Apply DAMASK modification to MSC.Marc/Mentat',
-     epilog = f'MSC_ROOT={msc_root} and MSC_VERSION={msc_version} (from {damask_root}/env/CONFIG)')
+                  prog = Path(__file__).name,
+                  formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
 parser.add_argument('--editor', dest='editor', metavar='string', default='vi',
                     help='Name of the editor for MSC.Mentat (executable)')
+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',
+                    default=damask.solver._marc._msc_version,
+                    help='MSC.Marc/Mentat version')
+parser.add_argument('--damask-root', dest='damask_root', type=float, metavar = 'float',
+                    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('%VERSION%', msc_version)
-    content = content.replace('%EDITOR%', parser.parse_args().editor)
+    content = content.replace('%EDITOR%', args.editor)
     with open(dst/Path(in_file).name,'w') as f:
         f.write(content)
 

python/damask/solver/_marc.py

@@ -1,13 +1,16 @@
 import subprocess
 import shlex
 import re
-import os
 from pathlib import Path
 
+_msc_version = 2020
+_msc_root = '/opt/msc'
+_damask_root = str(Path(__file__).parents[3])
+
 class Marc:
     """Wrapper to run DAMASK with MSCMarc."""
 
-    def __init__(self,version=os.environ['MSC_VERSION']):
+    def __init__(self,msc_version=_msc_version,msc_root=_msc_root,damask_root=_damask_root):
         """
         Create a Marc solver object.
 
@@ -17,13 +20,14 @@ class Marc:
             Marc version
 
         """
-        self.solver  = 'Marc'
-        self.version = version
+        self.msc_version = msc_version
+        self.msc_root    = Path(msc_root)
+        self.damask_root = Path(damask_root)
 
     @property
     def library_path(self):
 
-        path_lib = Path(f'{os.environ["MSC_ROOT"]}/mentat{self.version}/shlib/linux64')
+        path_lib = self.msc_root/f'mentat{self.msc_version}/shlib/linux64'
         if not path_lib.is_dir():
             raise FileNotFoundError(f'library path "{path_lib}" not found')
 
@@ -33,7 +37,7 @@ class Marc:
     @property
     def tools_path(self):
 
-        path_tools = Path(f'{os.environ["MSC_ROOT"]}/marc{self.version}/tools')
+        path_tools = self.msc_root/f'marc{self.msc_version}/tools'
         if not path_tools.is_dir():
             raise FileNotFoundError(f'tools path "{path_tools}" not found')
 
@@ -44,7 +48,7 @@ class Marc:
                    compile      = False,
                    optimization = ''):
 
-        usersub = Path(os.environ['DAMASK_ROOT'])/'src/DAMASK_Marc'
+        usersub = self.damask_root/'src/DAMASK_Marc'
         usersub = usersub.parent/(usersub.name + ('.f90' if compile else '.marc'))
         if not usersub.is_file():
             raise FileNotFoundError(f'subroutine ({"source" if compile else "binary"}) "{usersub}" not found')

src/parallelization.f90

@@ -84,13 +84,13 @@ subroutine parallelization_init
 
 !$ call get_environment_variable(name='OMP_NUM_THREADS',value=NumThreadsString,STATUS=got_env)
 !$ if(got_env /= 0) then
-!$   print*, 'Could not determine value of $OMP_NUM_THREADS'
-!$   OMP_NUM_THREADS = 1_pI32
+!$   print*, 'Could not get $OMP_NUM_THREADS, using default'
+!$   OMP_NUM_THREADS = 4_pI32
 !$ else
 !$   read(NumThreadsString,'(i6)') OMP_NUM_THREADS
 !$   if (OMP_NUM_THREADS < 1_pI32) then
-!$     print*, 'Invalid OMP_NUM_THREADS: '//trim(NumThreadsString)
-!$     OMP_NUM_THREADS = 1_pI32
+!$     print*, 'Invalid OMP_NUM_THREADS: "'//trim(NumThreadsString)//'", using default'
+!$     OMP_NUM_THREADS = 4_pI32
 !$   endif
 !$ endif
 !$ print'(a,i2)',   ' OMP_NUM_THREADS: ',OMP_NUM_THREADS