Merge remote-tracking branch 'origin/development' into YAML-bug-fix

cmake/Compiler-GNU.cmake

@@ -12,9 +12,9 @@ endif ()
 if (OPTIMIZATION STREQUAL "OFF")
   set (OPTIMIZATION_FLAGS "-O0")
 elseif (OPTIMIZATION STREQUAL "DEFENSIVE")
-  set (OPTIMIZATION_FLAGS "-O2")
+  set (OPTIMIZATION_FLAGS "-O2 -mtune=generic")
 elseif (OPTIMIZATION STREQUAL "AGGRESSIVE")
-  set (OPTIMIZATION_FLAGS "-O3 -ffast-math -funroll-loops -ftree-vectorize")
+  set (OPTIMIZATION_FLAGS "-O3 -march=native -ffast-math -funroll-loops -ftree-vectorize")
 endif ()
 
 set (STANDARD_CHECK "-std=f2018 -pedantic-errors" )

examples/config/phase/mechanical/plastic/phenopowerlaw_Al.yaml

@@ -4,6 +4,9 @@ references:
     Acta Metallurgica 8(3):187-199, 1960,
     https://doi.org/10.1016/0001-6160(60)90127-9,
     fitted from Fig. 5
+  - U.F. Kocks,
+    Metallurgical and Materials Transactions B 1:1121–1143, 1970,
+    https://doi.org/10.1007/BF02900224
 output: [xi_sl, gamma_sl]
 N_sl: [12]
 n_sl: 20
@@ -12,4 +15,4 @@ h_0_sl-sl: 1.7e+8
 xi_0_sl: [5.0e+6]
 xi_inf_sl: [37.5e+6]
 h_sl-sl: [1, 1, 1.4, 1.4, 1.4, 1.4, 1.4]
-dot_gamma_0_sl: 4.5e-3
+dot_gamma_0_sl: 7.5e-5

examples/config/phase/mechanical/plastic/phenopowerlaw_Au.yaml

@@ -6,6 +6,9 @@ references:
   - I. Kovács and G.Vörös,
     International Journal of Plasticity 12:35-43, 1996,
     https://doi.org/10.1016/S0749-6419(95)00043-7
+  - U.F. Kocks,
+    Metallurgical and Materials Transactions B 1:1121–1143, 1970,
+    https://doi.org/10.1007/BF02900224
 output: [xi_sl, gamma_sl]
 N_sl: [12]
 n_sl: 83.3

examples/config/phase/mechanical/plastic/phenopowerlaw_Cu.yaml

@@ -4,6 +4,9 @@ references:
     Transactions of the Japan Institute of Metals 16(10):629-640, 1975,
     https://doi.org/10.2320/matertrans1960.16.629,
     fitted from Fig. 3b
+  - U.F. Kocks,
+    Metallurgical and Materials Transactions B 1:1121–1143, 1970,
+    https://doi.org/10.1007/BF02900224
 output: [xi_sl, gamma_sl]
 N_sl: [12]
 n_sl: 20

examples/config/phase/mechanical/plastic/phenopowerlaw_DP-steel-ferrite.yaml

@@ -3,6 +3,9 @@ references:
   - C.C. Tasan et al.,
     Acta Materialia 81:386-400, 2014,
     https://doi.org/10.1016/j.actamat.2014.07.071
+  - U.F. Kocks,
+    Metallurgical and Materials Transactions B 1:1121–1143, 1970,
+    https://doi.org/10.1007/BF02900224
 output: [xi_sl, gamma_sl]
 N_sl: [12, 12]
 n_sl: 20

python/damask/VERSION

@@ -1 +1 @@
-v3.0.0-alpha4-298-g01d545861
+v3.0.0-alpha4-308-gb79fc5c09

python/damask/_result.py

@@ -1355,15 +1355,17 @@ class Result:
                         dataset[...] = result['data']
                         dataset.attrs['overwritten'] = True
                     else:
+                        shape = result['data'].shape
                         if result['data'].size >= chunk_size*2:
-                            shape  = result['data'].shape
                             chunks = (chunk_size//np.prod(shape[1:]),)+shape[1:]
-                            dataset = f[group].create_dataset(result['label'],data=result['data'],
+                            compression = ('gzip',6)
-                                                              maxshape=shape, chunks=chunks,
-                                                              compression='gzip', compression_opts=6,
-                                                              shuffle=True,fletcher32=True)
                         else:
-                            dataset = f[group].create_dataset(result['label'],data=result['data'])
+                            chunks = shape
+                            compression = (None,None)
+                        dataset = f[group].create_dataset(result['label'],data=result['data'],
+                                                          maxshape=shape, chunks=chunks,
+                                                          compression=compression[0], compression_opts=compression[1],
+                                                          shuffle=True,fletcher32=True)
 
                     now = datetime.datetime.now().astimezone()
                     dataset.attrs['created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \
@@ -1759,7 +1761,7 @@ class Result:
             if type(obj) == h5py.Dataset and  _match(output,[name]):
                 d = obj.attrs['description'] if h5py3 else obj.attrs['description'].decode()
                 if not Path(name).exists() or overwrite:
-                    with open(name,'w') as f_out: f_out.write(obj[()].decode())
+                    with open(name,'w') as f_out: f_out.write(obj[0].decode())
                     print(f"Exported {d} to '{name}'.")
                 else:
                     print(f"'{name}' exists, {d} not exported.")

src/DAMASK_interface.f90

@@ -189,10 +189,10 @@ subroutine DAMASK_interface_init
   if (len_trim(workingDirArg) > 0) &
     print'(a)',      ' Working dir argument:   '//trim(workingDirArg)
   print'(a)',        ' Geometry argument:      '//trim(geometryArg)
-  print'(a)',        ' Loadcase argument:      '//trim(loadcaseArg)
+  print'(a)',        ' Load case argument:     '//trim(loadcaseArg)
   print'(/,a)',      ' Working directory:      '//getCWD()
   print'(a)',        ' Geometry file:          '//interface_geomFile
-  print'(a)',        ' Loadcase file:          '//interface_loadFile
+  print'(a)',        ' Load case file:         '//interface_loadFile
   print'(a)',        ' Solver job name:        '//getSolverJobName()
   if (interface_restartInc > 0) &
     print'(a,i6.6)', ' Restart from increment: ', interface_restartInc

src/HDF5_utilities.f90

@@ -77,10 +77,12 @@ module HDF5_utilities
   end interface HDF5_addAttribute
 
 #ifdef PETSC
-  logical, parameter, private :: parallel_default = .true.
+  logical, parameter :: parallel_default = .true.
 #else
-  logical, parameter, private :: parallel_default = .false.
+  logical, parameter :: parallel_default = .false.
 #endif
+  logical :: compression_possible
+
   public :: &
     HDF5_utilities_init, &
     HDF5_read, &
@@ -103,31 +105,38 @@ contains
 !--------------------------------------------------------------------------------------------------
 subroutine HDF5_utilities_init
 
-  integer         :: hdferr
+  integer :: hdferr, HDF5_major, HDF5_minor, HDF5_release, deflate_info
   integer(SIZE_T) :: typeSize
 
+
   print'(/,a)', ' <<<+-  HDF5_Utilities init  -+>>>'
 
-!--------------------------------------------------------------------------------------------------
+
-!initialize HDF5 library and check if integer and float type size match
   call h5open_f(hdferr)
-  if(hdferr < 0) error stop 'HDF5 error'
+  if (hdferr < 0) error stop 'HDF5 error'
 
   call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr)
-  if(hdferr < 0) error stop 'HDF5 error'
+  if (hdferr < 0) error stop 'HDF5 error'
   if (int(bit_size(0),SIZE_T)/=typeSize*8) &
     error stop 'Default integer size does not match H5T_NATIVE_INTEGER'
 
   call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr)
-  if(hdferr < 0) error stop 'HDF5 error'
+  if (hdferr < 0) error stop 'HDF5 error'
   if (int(storage_size(0.0_pReal),SIZE_T)/=typeSize*8) &
     error stop 'pReal does not match H5T_NATIVE_DOUBLE'
 
+  call H5get_libversion_f(HDF5_major,HDF5_minor,HDF5_release,hdferr)
+  if (hdferr < 0) error stop 'HDF5 error'
+  call H5Zget_filter_info_f(H5Z_FILTER_DEFLATE_F,deflate_info,hdferr)
+  if (hdferr < 0) error stop 'HDF5 error'
+  compression_possible = (HDF5_major == 1 .and. HDF5_minor >= 12) .and. &                           ! https://forum.hdfgroup.org/t/6186
+                         ior(H5Z_FILTER_ENCODE_ENABLED_F,deflate_info) > 0
+
 end subroutine HDF5_utilities_init
 
 
 !--------------------------------------------------------------------------------------------------
-!> @brief open and initializes HDF5 output file
+!> @brief Open and initialize HDF5 file.
 !--------------------------------------------------------------------------------------------------
 integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
 
@@ -1476,32 +1485,50 @@ subroutine HDF5_write_str(dataset,loc_id,datasetName)
   integer(HID_T),   intent(in) :: loc_id
   character(len=*), intent(in) :: datasetName                                                      !< name of the dataset in the file
 
-  integer(HID_T)  :: filetype_id, space_id, dataset_id
+  integer(HID_T)  :: filetype_id, memtype_id, space_id, dataset_id, dcpl
   integer :: hdferr
-  character(len=len_trim(dataset)+1,kind=C_CHAR), dimension(1), target :: dataset_
+  character(len=len_trim(dataset),kind=C_CHAR), target :: dataset_
-  type(C_PTR), target, dimension(1) :: ptr
 
 
-  dataset_(1) = trim(dataset)//C_NULL_CHAR
+  dataset_ = trim(dataset)
-  ptr(1) = c_loc(dataset_(1))
 
-  call h5tcopy_f(H5T_STRING, filetype_id, hdferr)
+  call h5tcopy_f(H5T_C_S1, filetype_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5tset_size_f(filetype_id, int(len(dataset_),HSIZE_T), hdferr)
+  call h5tset_size_f(filetype_id, int(len(dataset_)+1,HSIZE_T), hdferr)                            ! +1 for NULL
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call h5screate_f(H5S_SCALAR_F, space_id, hdferr)
+  call H5Tcopy_f(H5T_FORTRAN_S1, memtype_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
-  call h5dcreate_f(loc_id, datasetName, H5T_STRING, space_id, dataset_id, hdferr)
+  call H5Tset_size_f(memtype_id, int(len(dataset_),HSIZE_T), hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
-  call h5dwrite_f(dataset_id, H5T_STRING, c_loc(ptr), hdferr)
+  call h5pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr)
+  if (hdferr < 0) error stop 'HDF5 error'
+  call h5pset_chunk_f(dcpl, 1, [1_HSIZE_T], hdferr)
+  if (hdferr < 0) error stop 'HDF5 error'
+  call h5pset_shuffle_f(dcpl, hdferr)
+  if (hdferr < 0) error stop 'HDF5 error'
+  call h5pset_Fletcher32_f(dcpl,hdferr)
+  if (hdferr < 0) error stop 'HDF5 error'
+  if (compression_possible .and. len(dataset) > 1024*256) call h5pset_deflate_f(dcpl, 6, hdferr)
+  if (hdferr < 0) error stop 'HDF5 error'
+
+  call h5screate_simple_f(1, [1_HSIZE_T], space_id, hdferr)
+  if(hdferr < 0) error stop 'HDF5 error'
+  CALL h5dcreate_f(loc_id, datasetName, filetype_id, space_id, dataset_id, hdferr, dcpl)
   if(hdferr < 0) error stop 'HDF5 error'
 
+  call h5dwrite_f(dataset_id, memtype_id, c_loc(dataset_(1:1)), hdferr)
+  if(hdferr < 0) error stop 'HDF5 error'
+
+  call h5pclose_f(dcpl, hdferr)
+  if(hdferr < 0) error stop 'HDF5 error'
   call h5dclose_f(dataset_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
   call h5sclose_f(space_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
+  call h5tclose_f(memtype_id, hdferr)
+  if(hdferr < 0) error stop 'HDF5 error'
   call h5tclose_f(filetype_id, hdferr)
   if(hdferr < 0) error stop 'HDF5 error'
 
@@ -1907,11 +1934,12 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
     totalShape                                                                                      !< shape of the dataset (all processes)
   integer(HID_T),    intent(out) :: dset_id, filespace_id, memspace_id, plist_id
 
-  integer,          dimension(worldsize)      :: writeSize                                          !< contribution of all processes
+  integer, dimension(worldsize) :: writeSize                                                        !< contribution of all processes
   integer(HID_T) ::  dcpl
-  integer :: ierr, hdferr, HDF5_major, HDF5_minor, HDF5_release
+  integer :: ierr, hdferr
   integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T
 
+
 !-------------------------------------------------------------------------------------------------
 ! creating a property list for transfer properties (is collective when writing in parallel)
   call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
@@ -1938,24 +1966,26 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
   totalShape = [myShape(1:ubound(myShape,1)-1),int(sum(writeSize),HSIZE_T)]
 
 !--------------------------------------------------------------------------------------------------
-! compress (and chunk) larger datasets
+! chunk dataset, enable compression for larger datasets
   call h5pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr)
-  if(hdferr < 0) error stop 'HDF5 error'
+  if (hdferr < 0) error stop 'HDF5 error'
-  if(product(totalShape) >= chunkSize*2_HSIZE_T) then
+
-    call H5get_libversion_f(HDF5_major,HDF5_minor,HDF5_release,hdferr)
+  if (product(totalShape) > 0) then
+    call h5pset_shuffle_f(dcpl, hdferr)
     if (hdferr < 0) error stop 'HDF5 error'
-    if (HDF5_major == 1 .and. HDF5_minor >= 12) then                                                ! https://forum.hdfgroup.org/t/6186
+    call h5pset_Fletcher32_f(dcpl,hdferr)
+    if (hdferr < 0) error stop 'HDF5 error'
+
+    if (product(totalShape) >= chunkSize*2_HSIZE_T) then
       call h5pset_chunk_f(dcpl, size(totalShape), getChunks(totalShape,chunkSize), hdferr)
       if (hdferr < 0) error stop 'HDF5 error'
-      call h5pset_shuffle_f(dcpl, hdferr)
+      if (compression_possible) call h5pset_deflate_f(dcpl, 6, hdferr)
-      if (hdferr < 0) error stop 'HDF5 error'
+    else
-      call h5pset_deflate_f(dcpl, 6, hdferr)
+      call h5pset_chunk_f(dcpl, size(totalShape), totalShape, hdferr)
-      if (hdferr < 0) error stop 'HDF5 error'
-      call h5pset_Fletcher32_f(dcpl,hdferr)
-      if (hdferr < 0) error stop 'HDF5 error'
     endif
+    if (hdferr < 0) error stop 'HDF5 error'
   endif
-
+ 
 !--------------------------------------------------------------------------------------------------
 ! create dataspace in memory (local shape) and in file (global shape)
   call h5screate_simple_f(size(myShape), myShape, memspace_id, hdferr, myShape)

src/config.f90

@@ -83,9 +83,11 @@ subroutine parse_numerics()
     if (worldrank == 0) then
       print*, 'reading numerics.yaml'; flush(IO_STDOUT)
       fileContent = IO_read('numerics.yaml')
-      call results_openJobFile(parallel=.false.)
+      if (len(fileContent) > 0) then
-      call results_writeDataset_str(fileContent,'setup','numerics.yaml','numerics configuration')
+        call results_openJobFile(parallel=.false.)
-      call results_closeJobFile
+        call results_writeDataset_str(fileContent,'setup','numerics.yaml','numerics configuration')
+        call results_closeJobFile
+      endif
     endif
     call parallelization_bcast_str(fileContent)
 
@@ -113,9 +115,11 @@ subroutine parse_debug()
     if (worldrank == 0) then
       print*, 'reading debug.yaml'; flush(IO_STDOUT)
       fileContent = IO_read('debug.yaml')
-      call results_openJobFile(parallel=.false.)
+      if (len(fileContent) > 0) then
-      call results_writeDataset_str(fileContent,'setup','debug.yaml','debug configuration')
+        call results_openJobFile(parallel=.false.)
-      call results_closeJobFile
+        call results_writeDataset_str(fileContent,'setup','debug.yaml','debug configuration')
+        call results_closeJobFile
+      endif
     endif
     call parallelization_bcast_str(fileContent)
 

src/grid/grid_mech_FEM.f90

@@ -446,22 +446,26 @@ subroutine grid_mechanical_FEM_restartWrite
 
   fileHandle  = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
   groupHandle = HDF5_addGroup(fileHandle,'solver')
-
-  call HDF5_write(P_aim,groupHandle,'P_aim',.false.)
-  call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
-  call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
-  call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
   call HDF5_write(F,groupHandle,'F')
   call HDF5_write(F_lastInc,groupHandle,'F_lastInc')
   call HDF5_write(u_current,groupHandle,'u')
   call HDF5_write(u_lastInc,groupHandle,'u_lastInc')
-
-  call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
-  call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
-
   call HDF5_closeGroup(groupHandle)
   call HDF5_closeFile(fileHandle)
 
+  if (worldrank == 0) then
+    fileHandle  = HDF5_openFile(getSolverJobName()//'_restart.hdf5','a',.false.)
+    groupHandle = HDF5_openGroup(fileHandle,'solver')
+    call HDF5_write(P_aim,groupHandle,'P_aim',.false.)
+    call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
+    call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
+    call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
+    call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
+    call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
+    call HDF5_closeGroup(groupHandle)
+    call HDF5_closeFile(fileHandle)
+  endif
+
   call DMDAVecRestoreArrayF90(mechanical_grid,solution_current,u_current,ierr)
   CHKERRQ(ierr)
   call DMDAVecRestoreArrayF90(mechanical_grid,solution_lastInc,u_lastInc,ierr)

src/grid/grid_mech_spectral_basic.f90

@@ -389,21 +389,25 @@ subroutine grid_mechanical_spectral_basic_restartWrite
 
   fileHandle  = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
   groupHandle = HDF5_addGroup(fileHandle,'solver')
-
-  call HDF5_write(P_aim,groupHandle,'P_aim',.false.)
-  call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
-  call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
-  call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
   call HDF5_write(F,groupHandle,'F')
   call HDF5_write(F_lastInc,groupHandle,'F_lastInc')
-
-  call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
-  call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
-  call HDF5_write(C_minMaxAvg,groupHandle,'C_minMaxAvg',.false.)
-
   call HDF5_closeGroup(groupHandle)
   call HDF5_closeFile(fileHandle)
 
+  if (worldrank == 0) then
+    fileHandle  = HDF5_openFile(getSolverJobName()//'_restart.hdf5','a',.false.)
+    groupHandle = HDF5_openGroup(fileHandle,'solver')
+    call HDF5_write(P_aim,groupHandle,'P_aim',.false.)
+    call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
+    call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
+    call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
+    call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
+    call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
+    call HDF5_write(C_minMaxAvg,groupHandle,'C_minMaxAvg',.false.)
+    call HDF5_closeGroup(groupHandle)
+    call HDF5_closeFile(fileHandle)
+  endif
+
   if (num%update_gamma) call utilities_saveReferenceStiffness
 
   call DMDAVecRestoreArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr)

src/grid/grid_mech_spectral_polarisation.f90

@@ -445,22 +445,26 @@ subroutine grid_mechanical_spectral_polarisation_restartWrite
 
   fileHandle  = HDF5_openFile(getSolverJobName()//'_restart.hdf5','w')
   groupHandle = HDF5_addGroup(fileHandle,'solver')
-
-  call HDF5_write(F_aim,groupHandle,'P_aim',.false.)
-  call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
-  call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
-  call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
   call HDF5_write(F,groupHandle,'F')
   call HDF5_write(F_lastInc,groupHandle,'F_lastInc')
   call HDF5_write(F_tau,groupHandle,'F_tau')
   call HDF5_write(F_tau_lastInc,groupHandle,'F_tau_lastInc')
-
-  call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
-  call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
-
   call HDF5_closeGroup(groupHandle)
   call HDF5_closeFile(fileHandle)
 
+  if (worldrank == 0) then
+    fileHandle  = HDF5_openFile(getSolverJobName()//'_restart.hdf5','a',.false.)
+    groupHandle = HDF5_openGroup(fileHandle,'solver')
+    call HDF5_write(F_aim,groupHandle,'P_aim',.false.)
+    call HDF5_write(F_aim,groupHandle,'F_aim',.false.)
+    call HDF5_write(F_aim_lastInc,groupHandle,'F_aim_lastInc',.false.)
+    call HDF5_write(F_aimDot,groupHandle,'F_aimDot',.false.)
+    call HDF5_write(C_volAvg,groupHandle,'C_volAvg',.false.)
+    call HDF5_write(C_volAvgLastInc,groupHandle,'C_volAvgLastInc',.false.)
+    call HDF5_closeGroup(groupHandle)
+    call HDF5_closeFile(fileHandle)
+  endif
+
   if(num%update_gamma) call utilities_saveReferenceStiffness
 
   call DMDAVecRestoreArrayF90(da,solution_vec,FandF_tau,ierr); CHKERRQ(ierr)