Merge branch 'development' into pretty-print-init

.gitlab-ci.yml

@@ -7,40 +7,33 @@ stages:
   - fortran
   - performance
   - deploy
-  - backup
   - update_master
-  - distclean
+
-  - clean
 
 ###################################################################################################
-before_script:
+default:
-  - if [ $(awk "/$CI_PIPELINE_ID/{print NR}" $LOCAL_HOME/GitLabCI.queue)x == 'x' ];
+  before_script:
-      then echo $CI_PIPELINE_ID >> $LOCAL_HOME/GitLabCI.queue;
+    - ${LOCAL_HOME}/bin/queue ${CI_JOB_ID}
-    fi
+    - source $DAMASKROOT/env/DAMASK.sh
-  - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $LOCAL_HOME/GitLabCI.queue) != 1 ];
+    - export PATH=${TESTROOT}/bin:$PATH
-      do sleep 5m;
+    - cd $DAMASKROOT/PRIVATE/testing
-      echo -e "Currently queued pipelines:\n$(cat $LOCAL_HOME/GitLabCI.queue)\n";
+    - echo Job start:" $(date)"
-    done
+  after_script:
-  - source $DAMASKROOT/env/DAMASK.sh
+    - echo Job end:" $(date)"
-  - cd $DAMASKROOT/PRIVATE/testing
-  - echo Job start:" $(date)"
 
-###################################################################################################
-after_script:
-  - echo Job end:" $(date)"
 
 ###################################################################################################
 variables:
   # ===============================================================================================
   # GitLab Settings
   # ===============================================================================================
-  GIT_SUBMODULE_STRATEGY: none
+  GIT_SUBMODULE_STRATEGY: normal
 
   # ===============================================================================================
   # Shortcut names
   # ===============================================================================================
+  TESTROOT:   "$LOCAL_HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID"
   DAMASKROOT: "$LOCAL_HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID/DAMASK"
-  TESTROOT:   "$LOCAL_HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID/tests"
 
   # ===============================================================================================
   # Names of module files to load
@@ -52,53 +45,42 @@ variables:
   MPI_Intel:      "MPI/Intel/19.1.2/IntelMPI/2019"
   MPI_GNU:        "MPI/GNU/10/OpenMPI/4.1.1"
   # ++++++++++++ PETSc ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-  PETSc_Intel:    "Libraries/PETSc/3.16.0/Intel-19.1.2-IntelMPI-2019"
+  PETSc_Intel:    "Libraries/PETSc/3.16.1/Intel-19.1.2-IntelMPI-2019"
-  PETSc_GNU:      "Libraries/PETSc/3.16.0/GNU-10-OpenMPI-4.1.1"
+  PETSc_GNU:      "Libraries/PETSc/3.16.1/GNU-10-OpenMPI-4.1.1"
   # ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   MSC:            "FEM/MSC/2021.2"
   IntelMarc:      "Compiler/Intel/19.1.2 Libraries/IMKL/2020"
   HDF5Marc:       "HDF5/1.12.1/Intel-19.1.2"
 
+
 ###################################################################################################
 checkout:
   stage: prepare
   before_script:
-    - echo $CI_PIPELINE_ID >> $LOCAL_HOME/GitLabCI.queue
+    - ${LOCAL_HOME}/bin/queue ${CI_JOB_ID}
-    - while [ $(awk "/$CI_PIPELINE_ID/{print NR}" $LOCAL_HOME/GitLabCI.queue) != 1 ];
+    - echo Job start:" $(date)"
-        do sleep 5m;
-        echo -e "Currently queued pipelines:\n$(cat $LOCAL_HOME/GitLabCI.queue)\n";
-      done
   script:
-    - mkdir -p $DAMASKROOT
+    - mkdir -p ${DAMASKROOT}
-    - mkdir -p $TESTROOT
+    - cd ${DAMASKROOT}
-    - cd $DAMASKROOT
     - git clone -q git@git.damask.mpie.de:damask/DAMASK.git .
-    - git checkout $CI_COMMIT_SHA
+    - git checkout ${CI_COMMIT_SHA}
     - git submodule update --init
-    - source env/DAMASK.sh
+
-  except:
-    - master
-    - release
 
 ###################################################################################################
 pytest:
   stage: python
   script:
-    - cd $DAMASKROOT/python
+    - PYTHONPATH=${CI_PROJECT_DIR}/python
-    - COLUMNS=256 pytest --basetemp=${TESTROOT}/python -v --cov --cov-report=term
+    - cd ${CI_PROJECT_DIR}/python
+    - pytest --basetemp ${TESTROOT}/python -v --cov --cov-report=term
     - coverage report --fail-under=90
-  except:
-    - master
-    - release
 
 mypy:
   stage: python
   script:
-    - cd $DAMASKROOT/python
+    - cd ${CI_PROJECT_DIR}/python
-    - mypy -m damask
+    - mypy damask
-  except:
-    - master
-    - release
 
 
 ###################################################################################################
@@ -107,50 +89,35 @@ compile_grid_Intel:
   script:
     - module load $IntelCompiler $MPI_Intel $PETSc_Intel
     - cd pytest
-    - COLUMNS=256 pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_Intel
+    - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_Intel
-  except:
-    - master
-    - release
 
 compile_mesh_Intel:
   stage: compile
   script:
     - module load $IntelCompiler $MPI_Intel $PETSc_Intel
     - cd pytest
-    - COLUMNS=256 pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_Intel
+    - pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_Intel
-  except:
-    - master
-    - release
 
 compile_grid_GNU:
   stage: compile
   script:
     - module load $GNUCompiler $MPI_GNU $PETSc_GNU
     - cd pytest
-    - COLUMNS=256 pytest -k 'compile and grid' --basetemp=${TESTROOT}/compile_grid_GNU
+    - pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_GNU
-  except:
-    - master
-    - release
 
 compile_mesh_GNU:
   stage: compile
   script:
     - module load $GNUCompiler $MPI_GNU $PETSc_GNU
     - cd pytest
-    - COLUMNS=256 pytest -k 'compile and mesh' --basetemp=${TESTROOT}/compile_mesh_GNU
+    - pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU
-  except:
-    - master
-    - release
 
 compile_Marc:
   stage: compile
   script:
     - module load $IntelMarc $HDF5Marc $MSC
     - cd pytest
-    - COLUMNS=256 pytest -k 'compile and Marc' --basetemp=${TESTROOT}/compile_Marc
+    - pytest -k 'compile and Marc' --basetemp ${TESTROOT}/compile_Marc
-  except:
-    - master
-    - release
 
 
 ###################################################################################################
@@ -158,25 +125,18 @@ setup_grid:
   stage: setup
   script:
     - module load $IntelCompiler $MPI_Intel $PETSc_Intel
-    - BUILD_DIR=$(mktemp -d)
+    - cd $(mktemp -d)
-    - cd ${BUILD_DIR}
+    - cmake -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${TESTROOT} ${CI_PROJECT_DIR}
-    - cmake -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${DAMASKROOT} ${DAMASKROOT}
     - make -j2 all install
-  except:
-    - master
-    - release
 
 setup_mesh:
   stage: setup
   script:
     - module load $IntelCompiler $MPI_Intel $PETSc_Intel
-    - BUILD_DIR=$(mktemp -d)
+    - cd $(mktemp -d)
-    - cd ${BUILD_DIR}
+    - cmake -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${TESTROOT} ${CI_PROJECT_DIR}
-    - cmake -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${DAMASKROOT} ${DAMASKROOT}
     - make -j2 all install
-  except:
+
-    - master
-    - release
 
 ###################################################################################################
 core:
@@ -184,67 +144,54 @@ core:
   script:
     - module load $IntelCompiler $MPI_Intel $PETSc_Intel
     - cd pytest
-    - COLUMNS=256 pytest -k 'not compile' --basetemp=${TESTROOT}/fortran -v
+    - pytest -k 'not compile' --basetemp ${TESTROOT}/fortran -v
-  except:
-    - master
-    - release
 
 # Needs closer look
 # Phenopowerlaw_singleSlip:
 #   stage: fortran
 #   script: Phenopowerlaw_singleSlip/test.py
-#   except:
+
-#     - master
-#     - release
 
 ###################################################################################################
-SpectralRuntime:
+grid_runtime:
   stage: performance
   script:
     - module load $IntelCompiler $MPI_Intel $PETSc_Intel
-    - cd $DAMASKROOT
+    - cd $(mktemp -d)
-    - make clean grid OPTIMIZATION=AGGRESSIVE
+    - cmake -DOPTIMIZATION=AGGRESSIVE -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${TESTROOT} ${CI_PROJECT_DIR}
-    - cd $LOCAL_HOME/performance                                                                    # location of old results
+    - make -j2 all install
-    - git checkout .                                                                                # undo any changes (i.e. run time data from non-development branch)
+    - cd $(mktemp -d)
-    - cd $DAMASKROOT/PRIVATE/testing
+    - git clone -q git@git.damask.mpie.de:damask/performance.git .
-    - ./runtime.py --results ${LOCAL_HOME}/performance --damask_root ${DAMASKROOT} --tag ${CI_COMMIT_SHA}
+    - ${DAMASKROOT}/PRIVATE/testing/runtime.py --input_dir $DAMASKROOT/examples/grid --output_dir . --tag ${CI_COMMIT_SHA}
-  except:
+    - if [ ${CI_COMMIT_BRANCH} == development ]; then git commit -am ${CI_PIPELINE_ID}_${CI_COMMIT_SHA}; git push; fi
-    - master
+  before_script:
-    - release
+    - ${LOCAL_HOME}/bin/queue ${CI_JOB_ID} --blocking
+    - source $DAMASKROOT/env/DAMASK.sh
+    - export PATH=${TESTROOT}/bin:$PATH
+    - echo Job start:" $(date)"
 
 ###################################################################################################
 source_distribution:
   stage: deploy
   script:
     - cd $(mktemp -d)
-    - $DAMASKROOT/PRIVATE/releasing/tar.xz/create.sh $DAMASKROOT $CI_COMMIT_SHA
+    - ${CI_PROJECT_DIR}/PRIVATE/releasing/tar.xz/create.sh ${CI_PROJECT_DIR} ${CI_COMMIT_SHA}
-  except:
-    - master
-    - release
 
-##################################################################################################
-backup_runtime_measurement:
-  stage: backup
-  script:
-    - cd $LOCAL_HOME/performance                                                                    # location of new runtime results
-    - git commit -am"${CI_PIPELINE_ID}_${CI_COMMIT_SHA}"
-    - git push
-  only:
-    - development
 
-##################################################################################################
+###################################################################################################
 merge_into_master:
   stage: update_master
   script:
-    - cd $DAMASKROOT
+    - cd ${DAMASKROOT}
     - export TESTEDREV=$(git describe)                                                              # might be detached from development branch
-    - echo $TESTEDREV > python/damask/VERSION
+    - echo ${TESTEDREV} > python/damask/VERSION
     - git add python/damask/VERSION
     - >
         git diff-index --quiet HEAD ||
         git commit -m "[skip ci] updated version information after successful test of $TESTEDREV"
     - export UPDATEDREV=$(git describe)                                                             # tested state + 1 commit
     - git checkout master
+    - git pull
     - git merge $UPDATEDREV -s recursive -X ours                                                    # conflicts occur only for inconsistent state
     - git push origin master                                                                        # master is now tested version and has updated VERSION file
     - git checkout development
@@ -253,26 +200,3 @@ merge_into_master:
     - git push origin development                                                                   # development is unchanged (as master is based on it) but has updated VERSION file
   only:
     - development
-
-###################################################################################################
-remove_data:
-  stage: distclean
-  before_script:
-    - echo "Removing data and lock of pipeline $CI_PIPELINE_ID"
-  script:
-    - rm -rf $LOCAL_HOME/GitLabCI_Pipeline_$CI_PIPELINE_ID
-    - sed -i "/$CI_PIPELINE_ID/d" $LOCAL_HOME/GitLabCI.queue                                        # in case pipeline was manually (web GUI) restarted and releaseLock was performed already
-  except:
-    - master
-    - release
-
-###################################################################################################
-remove_lock:
-  stage: clean
-  before_script:
-    - echo "Removing lock of pipeline $CI_PIPELINE_ID"
-  when: always
-  script: sed -i "/$CI_PIPELINE_ID/d" $LOCAL_HOME/GitLabCI.queue
-  except:
-    - master
-    - release

PRIVATE

@@ -1 +1 @@
-Subproject commit 5a769ec759d9dacc1866c35c6663cd0001e198c5
+Subproject commit f730bcb8ddd7224011e70c57d0a5c03068532d2d

python/damask/VERSION

@@ -1 +1 @@
-v3.0.0-alpha5-64-g8e08af31e
+v3.0.0-alpha5-90-gbb6655045

src/grid/discretization_grid.f90

@@ -215,7 +215,7 @@ subroutine readVTI(grid,geomSize,origin,material, &
           call cellsSizeOrigin(grid,geomSize,origin,fileContent(startPos:endPos))
         end if
       else
-        if (index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
+        if (index(fileContent(startPos:endPos),'<CellData',kind=pI64) /= 0_pI64) then
           gotCellData = .true.
           do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
             if (index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
@@ -379,12 +379,13 @@ subroutine readVTI(grid,geomSize,origin,material, &
     integer(pI64), dimension(:), allocatable :: temp, size_inflated, size_deflated
     integer(pI64) :: headerLen, nBlock, b,s,e
 
-    if    (headerType == 'UInt32') then
+
+    if      (headerType == 'UInt32') then
       temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64)
       nBlock = int(temp(1),pI64)
       headerLen = 4_pI64 * (3_pI64 + nBlock)
       temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
-    elseif (headerType == 'UInt64') then
+    else if (headerType == 'UInt64') then
       temp = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(:base64_nChar(8_pI64)))),pI64)
       nBlock = int(temp(1),pI64)
       headerLen = 8_pI64 * (3_pI64 + nBlock)
@@ -424,13 +425,13 @@ subroutine readVTI(grid,geomSize,origin,material, &
     allocate(bytes(0))
 
     s=0_pI64
-    if    (headerType == 'UInt32') then
+    if      (headerType == 'UInt32') then
       do while(s+base64_nChar(4_pI64)<(len(base64_str,pI64)))
         nByte = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64)))),pI64)
         bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64+nByte(1))),5_pI64)]
         s = s + base64_nChar(4_pI64+nByte(1))
       end do
-    elseif (headerType == 'UInt64') then
+    else if (headerType == 'UInt64') then
       do while(s+base64_nChar(8_pI64)<(len(base64_str,pI64)))
         nByte = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64)))),pI64)
         bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64+nByte(1))),9_pI64)]
@@ -510,6 +511,7 @@ function IPcoordinates0(grid,geomSize,grid3Offset)
     a,b,c, &
     i
 
+
   i = 0
   do c = 1, grid(3); do b = 1, grid(2); do a = 1, grid(1)
     i = i + 1
@@ -553,6 +555,7 @@ pure function cellSurfaceArea(geomSize,grid)
 
   real(pReal), dimension(6,1,product(grid)) :: cellSurfaceArea
 
+
   cellSurfaceArea(1:2,1,:) = geomSize(2)/real(grid(2)) * geomSize(3)/real(grid(3))
   cellSurfaceArea(3:4,1,:) = geomSize(3)/real(grid(3)) * geomSize(1)/real(grid(1))
   cellSurfaceArea(5:6,1,:) = geomSize(1)/real(grid(1)) * geomSize(2)/real(grid(2))

src/mesh/FEM_utilities.f90

@@ -123,9 +123,7 @@ subroutine FEM_utilities_init
   call PetscOptionsInsertString(PETSC_NULL_OPTIONS,'-mechanical_snes_type newtonls &
                                &-mechanical_snes_linesearch_type cp -mechanical_snes_ksp_ew &
                                &-mechanical_snes_ksp_ew_rtol0 0.01 -mechanical_snes_ksp_ew_rtolmax 0.01 &
-                               &-mechanical_ksp_type fgmres -mechanical_ksp_max_it 25 &
+                               &-mechanical_ksp_type fgmres -mechanical_ksp_max_it 25', ierr)
-                               &-mechanical_pc_type ml -mechanical_mg_levels_ksp_type chebyshev &
-                               &-mechanical_mg_levels_pc_type sor -mechanical_pc_ml_nullspace user',ierr)
   CHKERRQ(ierr)
   call PetscOptionsInsertString(PETSC_NULL_OPTIONS,num_mesh%get_asString('PETSc_options',defaultVal=''),ierr)
   CHKERRQ(ierr)
@@ -178,6 +176,7 @@ subroutine utilities_projectBCValues(localVec,section,field,comp,bcPointsIS,BCVa
   PetscScalar          :: BCValue,BCDotValue,timeinc
   PetscErrorCode       :: ierr
 
+
   call PetscSectionGetFieldComponents(section,field,numComp,ierr); CHKERRQ(ierr)
   call ISGetSize(bcPointsIS,nBcPoints,ierr); CHKERRQ(ierr)
   if (nBcPoints > 0) call ISGetIndicesF90(bcPointsIS,bcPoints,ierr)
@@ -189,8 +188,8 @@ subroutine utilities_projectBCValues(localVec,section,field,comp,bcPointsIS,BCVa
     CHKERRQ(ierr)
     do dof = offset+comp+1, offset+numDof, numComp
       localArray(dof) = localArray(dof) + BCValue + BCDotValue*timeinc
-    enddo
+    end do
-  enddo
+  end do
   call VecRestoreArrayF90(localVec,localArray,ierr); CHKERRQ(ierr)
   call VecAssemblyBegin(localVec, ierr); CHKERRQ(ierr)
   call VecAssemblyEnd  (localVec, ierr); CHKERRQ(ierr)

src/prec.f90

@@ -273,27 +273,27 @@ subroutine selfTest
 
 
   realloc_lhs_test = [1,2]
-  if (any(realloc_lhs_test/=[1,2]))        error stop 'LHS allocation'
+  if (any(realloc_lhs_test/=[1,2]))         error stop 'LHS allocation'
 
   call random_number(r)
   r = r/minval(r)
-  if(.not. all(dEq(r,r+PREAL_EPSILON)))    error stop 'dEq'
+  if (.not. all(dEq(r,r+PREAL_EPSILON)))    error stop 'dEq'
-  if(dEq(r(1),r(2)) .and. dNeq(r(1),r(2))) error stop 'dNeq'
+  if (dEq(r(1),r(2)) .and. dNeq(r(1),r(2))) error stop 'dNeq'
-  if(.not. all(dEq0(r-(r+PREAL_MIN))))     error stop 'dEq0'
+  if (.not. all(dEq0(r-(r+PREAL_MIN))))     error stop 'dEq0'
 
   ! https://www.binaryconvert.com
   ! https://www.rapidtables.com/convert/number/binary-to-decimal.html
   f = real(prec_bytesToC_FLOAT(int([-65,+11,-102,+75],C_SIGNED_CHAR)),pReal)
-  if(dNeq(f(1),20191102.0_pReal,0.0_pReal)) error stop 'prec_bytesToC_FLOAT'
+  if (dNeq(f(1),20191102.0_pReal,0.0_pReal)) error stop 'prec_bytesToC_FLOAT'
 
   f = real(prec_bytesToC_DOUBLE(int([0,0,0,-32,+119,+65,+115,65],C_SIGNED_CHAR)),pReal)
-  if(dNeq(f(1),20191102.0_pReal,0.0_pReal)) error stop 'prec_bytesToC_DOUBLE'
+  if (dNeq(f(1),20191102.0_pReal,0.0_pReal)) error stop 'prec_bytesToC_DOUBLE'
 
   i = int(prec_bytesToC_INT32_T(int([+126,+23,+52,+1],C_SIGNED_CHAR)),pInt)
-  if(i(1) /= 20191102_pInt)                 error stop 'prec_bytesToC_INT32_T'
+  if (i(1) /= 20191102_pInt)                 error stop 'prec_bytesToC_INT32_T'
 
   i = int(prec_bytesToC_INT64_T(int([+126,+23,+52,+1,0,0,0,0],C_SIGNED_CHAR)),pInt)
-  if(i(1) /= 20191102_pInt)                 error stop 'prec_bytesToC_INT64_T'
+  if (i(1) /= 20191102_pInt)                 error stop 'prec_bytesToC_INT64_T'
 
 end subroutine selfTest