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incorporating changes in PETSc and DAMASK

This commit is contained in:
Martin Diehl 2017-11-20 12:57:30 +01:00
parent c81a438546
commit 90c617e055
2 changed files with 152 additions and 302 deletions
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447
installation/patch/PETSc3.8
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@ -1,38 +1,36 @@
From 2355d41203f829e5a24154184ab1a1a05e40b5e2 Mon Sep 17 00:00:00 2001
From 1cc8e60d02323c3c9448df73bfc8f36f697e939a Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Sun, 5 Nov 2017 12:48:31 +0100
Subject: [PATCH 1/3] adjusted calling of PETSc routines. Compiles but crashes
conditional prints for worldrank not needed (redirected to /dev/null) failing
during compilation is faster than during runtime
Date: Mon, 20 Nov 2017 12:53:47 +0100
Subject: [PATCH] existing patch + further fixes
---
src/DAMASK_spectral.f90 | 27 ++++++------------
src/constitutive.f90 | 6 ++--
src/damage_local.f90 | 8 ++----
src/damage_none.f90 | 8 ++----
src/damage_nonlocal.f90 | 8 ++----
src/homogenization_RGC.f90 | 8 ++----
src/homogenization_isostrain.f90 | 8 ++----
src/homogenization_none.f90 | 10 ++-----
src/hydrogenflux_cahnhilliard.f90 | 8 ++----
src/hydrogenflux_isoconc.f90 | 10 ++-----
src/kinematics_cleavage_opening.f90 | 8 ++----
src/kinematics_slipplane_opening.f90 | 8 ++----
src/kinematics_thermal_expansion.f90 | 8 ++----
src/kinematics_vacancy_strain.f90 | 8 ++----
src/mesh.f90 | 10 +++----
src/numerics.f90 | 13 ++++-----
src/spectral_damage.f90 | 37 +++++++-----------------
src/spectral_interface.f90 | 31 ++++++++++----------
src/spectral_mech_AL.f90 | 43 +++++++++-------------------
src/spectral_mech_Basic.f90 | 48 +++++++++++--------------------
src/spectral_mech_Polarisation.f90 | 49 +++++++++++---------------------
src/spectral_thermal.f90 | 55 ++++++++++++++++--------------------
src/spectral_utilities.f90 | 34 ++++++++--------------
23 files changed, 156 insertions(+), 297 deletions(-)
src/DAMASK_spectral.f90 | 27 +++++--------
src/constitutive.f90 | 6 +--
src/damage_local.f90 | 8 +---
src/damage_none.f90 | 8 +---
src/damage_nonlocal.f90 | 8 +---
src/homogenization_RGC.f90 | 8 +---
src/homogenization_isostrain.f90 | 8 +---
src/homogenization_none.f90 | 10 ++---
src/hydrogenflux_cahnhilliard.f90 | 8 +---
src/hydrogenflux_isoconc.f90 | 10 ++---
src/kinematics_cleavage_opening.f90 | 8 +---
src/kinematics_slipplane_opening.f90 | 8 +---
src/kinematics_thermal_expansion.f90 | 8 +---
src/kinematics_vacancy_strain.f90 | 8 +---
src/mesh.f90 | 12 +++---
src/numerics.f90 | 13 +++----
src/spectral_damage.f90 | 39 ++++++-------------
src/spectral_interface.f90 | 31 ++++++++-------
src/spectral_mech_AL.f90 | 46 ++++++++--------------
src/spectral_mech_Basic.f90 | 52 +++++++++----------------
src/spectral_mech_Polarisation.f90 | 52 +++++++++----------------
src/spectral_thermal.f90 | 75 +++++++++++++++++-------------------
src/spectral_utilities.f90 | 34 ++++++----------
23 files changed, 175 insertions(+), 312 deletions(-)
diff --git a/src/DAMASK_spectral.f90 b/src/DAMASK_spectral.f90
index dc529b2e..ee6b20fc 100644
index f32bfb7b..c315b1b8 100644
--- a/src/DAMASK_spectral.f90
+++ b/src/DAMASK_spectral.f90
@@ -12,6 +12,8 @@ program DAMASK_spectral
@ -82,9 +80,9 @@ index dc529b2e..ee6b20fc 100644
@@ -448,7 +440,7 @@ program DAMASK_spectral
call MPI_file_write(resUnit, &
reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)), &
[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), &
- (outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults, &
+ int((outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults), &
[(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)]), &
- (outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt), &
+ int(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults, &
MPI_DOUBLE, MPI_STATUS_IGNORE, ierr)
if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_write')
enddo
@ -101,9 +99,9 @@ index dc529b2e..ee6b20fc 100644
@@ -646,7 +637,7 @@ program DAMASK_spectral
min(i*((maxRealOut)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt)
call MPI_file_write(resUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)),&
[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), &
- (outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults,&
+ int((outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults), &
[(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)]), &
- (outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt),&
+ int(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults,&
MPI_DOUBLE, MPI_STATUS_IGNORE, ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_write')
enddo
@ -454,7 +452,7 @@ index 791c0e3c..9558f506 100644
maxNinstance = int(count(phase_kinematics == KINEMATICS_vacancy_strain_ID),pInt)
if (maxNinstance == 0_pInt) return
diff --git a/src/mesh.f90 b/src/mesh.f90
index 87160f2c..6e3b4823 100644
index 666fe1e3..a314c22c 100644
--- a/src/mesh.f90
+++ b/src/mesh.f90
@@ -115,11 +115,6 @@ module mesh
@ -488,8 +486,17 @@ index 87160f2c..6e3b4823 100644
integer(C_INTPTR_T) :: devNull, local_K, local_K_offset
integer :: ierr, worldsize
#endif
@@ -518,8 +518,6 @@ subroutine mesh_init(ip,el)
integer(pInt), intent(in) :: el, ip
integer(pInt) :: j
logical :: myDebug
-
- external :: MPI_comm_size
write(6,'(/,a)') ' <<<+- mesh init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
diff --git a/src/numerics.f90 b/src/numerics.f90
index 2085e221..d2d00f3e 100644
index 70c7f3c3..e7d54893 100644
--- a/src/numerics.f90
+++ b/src/numerics.f90
@@ -10,9 +10,6 @@ module numerics
@ -527,7 +534,7 @@ index 2085e221..d2d00f3e 100644
call MPI_Comm_rank(PETSC_COMM_WORLD,worldrank,ierr);CHKERRQ(ierr)
call MPI_Comm_size(PETSC_COMM_WORLD,worldsize,ierr);CHKERRQ(ierr)
diff --git a/src/spectral_damage.f90 b/src/spectral_damage.f90
index 72765987..cea6f69c 100644
index 72765987..11da3b96 100644
--- a/src/spectral_damage.f90
+++ b/src/spectral_damage.f90
@@ -4,8 +4,10 @@
@ -597,8 +604,12 @@ index 72765987..cea6f69c 100644
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, & !< cut off stencil at boundary
DMDA_STENCIL_BOX, & !< Moore (26) neighborhood around central point
grid(1),grid(2),grid(3), & !< global grid
@@ -126,7 +116,7 @@ subroutine spectral_damage_init()
@@ -124,9 +114,11 @@ subroutine spectral_damage_init()
damage_grid,ierr) !< handle, error
CHKERRQ(ierr)
call SNESSetDM(damage_snes,damage_grid,ierr); CHKERRQ(ierr) !< connect snes to da
+ call DMsetFromOptions(damage_grid,ierr); CHKERRQ(ierr)
+ call DMsetUp(damage_grid,ierr); CHKERRQ(ierr)
call DMCreateGlobalVector(damage_grid,solution,ierr); CHKERRQ(ierr) !< global solution vector (grid x 1, i.e. every def grad tensor)
call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,spectral_damage_formResidual,&
- PETSC_NULL_OBJECT,ierr) !< residual vector of same shape as solution vector
@ -606,16 +617,16 @@ index 72765987..cea6f69c 100644
CHKERRQ(ierr)
call SNESSetFromOptions(damage_snes,ierr); CHKERRQ(ierr) !< pull it all together with additional cli arguments
call SNESGetType(damage_snes,snes_type,ierr); CHKERRQ(ierr)
@@ -214,7 +204,7 @@ type(tSolutionState) function spectral_damage_solution(timeinc,timeinc_old,loadC
@@ -214,7 +206,7 @@ type(tSolutionState) function spectral_damage_solution(timeinc,timeinc_old,loadC
params%timeinc = timeinc
params%timeincOld = timeinc_old
- call SNESSolve(damage_snes,PETSC_NULL_OBJECT,solution,ierr); CHKERRQ(ierr)
+ call SNESSolve(damage_snes,PETSC_NULL_SNES,solution,ierr); CHKERRQ(ierr)
+ call SNESSolve(damage_snes,PETSC_NULL_VEC,solution,ierr); CHKERRQ(ierr)
call SNESGetConvergedReason(damage_snes,reason,ierr); CHKERRQ(ierr)
if (reason < 1) then
@@ -360,9 +350,6 @@ subroutine spectral_damage_forward()
@@ -360,9 +352,6 @@ subroutine spectral_damage_forward()
PetscScalar, dimension(:,:,:), pointer :: x_scal
PetscErrorCode :: ierr
@ -625,7 +636,7 @@ index 72765987..cea6f69c 100644
if (cutBack) then
damage_current = damage_lastInc
damage_stagInc = damage_lastInc
@@ -405,10 +392,6 @@ subroutine spectral_damage_destroy()
@@ -405,10 +394,6 @@ subroutine spectral_damage_destroy()
implicit none
PetscErrorCode :: ierr
@ -716,7 +727,7 @@ index 3c8489d0..51360ac1 100644
getGeometryFile = geometryParameter
posExt = scan(getGeometryFile,'.',back=.true.)
diff --git a/src/spectral_mech_AL.f90 b/src/spectral_mech_AL.f90
index 6d0fff28..e7ff0fbe 100644
index 6d0fff28..dc221f6c 100644
--- a/src/spectral_mech_AL.f90
+++ b/src/spectral_mech_AL.f90
@@ -5,6 +5,8 @@
@ -778,9 +789,12 @@ index 6d0fff28..e7ff0fbe 100644
write(6,'(/,a)') ' <<<+- DAMASK_spectral_solverAL init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
@@ -166,9 +161,9 @@ subroutine AL_init
@@ -165,10 +160,12 @@ subroutine AL_init
da,ierr) ! handle, error
CHKERRQ(ierr)
call SNESSetDM(snes,da,ierr); CHKERRQ(ierr)
+ call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
+ call DMsetUp(da,ierr); CHKERRQ(ierr)
call DMCreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr)
- call DMDASNESSetFunctionLocal(da,INSERT_VALUES,AL_formResidual,PETSC_NULL_OBJECT,ierr)
+ call DMDASNESSetFunctionLocal(da,INSERT_VALUES,AL_formResidual,PETSC_NULL_SNES,ierr)
@ -790,7 +804,7 @@ index 6d0fff28..e7ff0fbe 100644
CHKERRQ(ierr)
call SNESSetFromOptions(snes,ierr); CHKERRQ(ierr)
@@ -280,8 +275,7 @@ type(tSolutionState) function &
@@ -280,8 +277,7 @@ type(tSolutionState) function &
SNESConvergedReason :: reason
external :: &
@ -800,16 +814,17 @@ index 6d0fff28..e7ff0fbe 100644
incInfo = incInfoIn
@@ -304,7 +298,7 @@ type(tSolutionState) function &
@@ -304,8 +300,7 @@ type(tSolutionState) function &
!--------------------------------------------------------------------------------------------------
! solve BVP
- call SNESSolve(snes,PETSC_NULL_OBJECT,solution_vec,ierr)
+ call SNESSolve(snes,PETSC_NULL_SNES,solution_vec,ierr)
CHKERRQ(ierr)
- CHKERRQ(ierr)
+ call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
@@ -383,10 +377,6 @@ subroutine AL_formResidual(in,x_scal,f_scal,dummy,ierr)
! check convergence
@@ -383,10 +378,6 @@ subroutine AL_formResidual(in,x_scal,f_scal,dummy,ierr)
integer(pInt) :: &
i, j, k, e
@ -820,7 +835,7 @@ index 6d0fff28..e7ff0fbe 100644
F => x_scal(1:3,1:3,1,&
XG_RANGE,YG_RANGE,ZG_RANGE)
F_lambda => x_scal(1:3,1:3,2,&
@@ -697,11 +687,6 @@ subroutine AL_destroy()
@@ -697,11 +688,6 @@ subroutine AL_destroy()
implicit none
PetscErrorCode :: ierr
@ -833,7 +848,7 @@ index 6d0fff28..e7ff0fbe 100644
call SNESDestroy(snes,ierr); CHKERRQ(ierr)
call DMDestroy(da,ierr); CHKERRQ(ierr)
diff --git a/src/spectral_mech_Basic.f90 b/src/spectral_mech_Basic.f90
index cfb72712..b02cfd8c 100644
index 55403ee7..fe9eb493 100644
--- a/src/spectral_mech_Basic.f90
+++ b/src/spectral_mech_Basic.f90
@@ -5,6 +5,8 @@
@ -888,7 +903,7 @@ index cfb72712..b02cfd8c 100644
write(6,'(/,a)') ' <<<+- DAMASK_spectral_solverBasicPETSc init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
@@ -152,14 +146,14 @@ subroutine basicPETSc_init
@@ -152,19 +146,20 @@ subroutine basicPETSc_init
grid(1),grid(2),localK, & ! local grid
da,ierr) ! handle, error
CHKERRQ(ierr)
@ -896,6 +911,8 @@ index cfb72712..b02cfd8c 100644
- call DMCreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr) ! global solution vector (grid x 9, i.e. every def grad tensor)
- call DMDASNESSetFunctionLocal(da,INSERT_VALUES,BasicPETSC_formResidual,PETSC_NULL_OBJECT,ierr) ! residual vector of same shape as solution vector
+ call SNESsetDM(snes,da,ierr); CHKERRQ(ierr)
+ call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
+ call DMsetUp(da,ierr); CHKERRQ(ierr)
+ call DMcreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr) ! global solution vector (grid x 9, i.e. every def grad tensor)
+ call DMDASNESsetFunctionLocal(da,INSERT_VALUES,BasicPETSC_formResidual,PETSC_NULL_SNES,ierr) ! residual vector of same shape as solution vector
CHKERRQ(ierr)
@ -909,7 +926,12 @@ index cfb72712..b02cfd8c 100644
!--------------------------------------------------------------------------------------------------
! init fields
@@ -253,8 +247,7 @@ type(tSolutionState) function &
call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr) ! get the data out of PETSc to work with
-
restart: if (restartInc > 1_pInt) then
if (iand(debug_level(debug_spectral),debug_spectralRestart)/= 0) &
write(6,'(/,a,'//IO_intOut(restartInc-1_pInt)//',a)') &
@@ -253,8 +248,7 @@ type(tSolutionState) function &
SNESConvergedReason :: reason
external :: &
@ -919,16 +941,17 @@ index cfb72712..b02cfd8c 100644
incInfo = incInfoIn
@@ -274,7 +267,7 @@ type(tSolutionState) function &
@@ -274,8 +268,7 @@ type(tSolutionState) function &
!--------------------------------------------------------------------------------------------------
! solve BVP
- call SNESSolve(snes,PETSC_NULL_OBJECT,solution_vec,ierr)
+ call SNESSolve(snes,PETSC_NULL_SNES,solution_vec,ierr)
CHKERRQ(ierr)
- CHKERRQ(ierr)
+ call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
@@ -337,10 +330,6 @@ subroutine BasicPETSC_formResidual(in,x_scal,f_scal,dummy,ierr)
! check convergence
@@ -336,10 +329,6 @@ subroutine BasicPETSC_formResidual(in,x_scal,f_scal,dummy,ierr)
PetscObject :: dummy
PetscErrorCode :: ierr
@ -939,7 +962,7 @@ index cfb72712..b02cfd8c 100644
call SNESGetNumberFunctionEvals(snes,nfuncs,ierr); CHKERRQ(ierr)
call SNESGetIterationNumber(snes,PETScIter,ierr); CHKERRQ(ierr)
@@ -556,11 +545,6 @@ subroutine BasicPETSc_destroy()
@@ -555,11 +544,6 @@ subroutine BasicPETSc_destroy()
implicit none
PetscErrorCode :: ierr
@ -952,7 +975,7 @@ index cfb72712..b02cfd8c 100644
call SNESDestroy(snes,ierr); CHKERRQ(ierr)
call DMDestroy(da,ierr); CHKERRQ(ierr)
diff --git a/src/spectral_mech_Polarisation.f90 b/src/spectral_mech_Polarisation.f90
index ecf707d4..2b9dddc0 100644
index ecf707d4..3b024f56 100644
--- a/src/spectral_mech_Polarisation.f90
+++ b/src/spectral_mech_Polarisation.f90
@@ -5,6 +5,8 @@
@ -1014,7 +1037,7 @@ index ecf707d4..2b9dddc0 100644
write(6,'(/,a)') ' <<<+- DAMASK_spectral_solverPolarisation init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
@@ -164,13 +159,13 @@ subroutine Polarisation_init
@@ -164,13 +159,15 @@ subroutine Polarisation_init
grid(1),grid(2),localK, & ! local grid
da,ierr) ! handle, error
CHKERRQ(ierr)
@ -1022,6 +1045,8 @@ index ecf707d4..2b9dddc0 100644
- call DMCreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr)
- call DMDASNESSetFunctionLocal(da,INSERT_VALUES,Polarisation_formResidual,PETSC_NULL_OBJECT,ierr)
+ call SNESsetDM(snes,da,ierr); CHKERRQ(ierr)
+ call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
+ call DMsetUp(da,ierr); CHKERRQ(ierr)
+ call DMcreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr)
+ call DMDASNESsetFunctionLocal(da,INSERT_VALUES,Polarisation_formResidual,PETSC_NULL_SNES,ierr)
CHKERRQ(ierr)
@ -1033,7 +1058,7 @@ index ecf707d4..2b9dddc0 100644
!--------------------------------------------------------------------------------------------------
! init fields
@@ -280,8 +275,7 @@ type(tSolutionState) function &
@@ -280,8 +277,7 @@ type(tSolutionState) function &
SNESConvergedReason :: reason
external :: &
@ -1043,16 +1068,17 @@ index ecf707d4..2b9dddc0 100644
incInfo = incInfoIn
@@ -304,7 +298,7 @@ type(tSolutionState) function &
@@ -304,8 +300,7 @@ type(tSolutionState) function &
!--------------------------------------------------------------------------------------------------
! solve BVP
- call SNESSolve(snes,PETSC_NULL_OBJECT,solution_vec,ierr)
+ call SNESSolve(snes,PETSC_NULL_SNES,solution_vec,ierr)
CHKERRQ(ierr)
- CHKERRQ(ierr)
+ call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
@@ -383,10 +377,6 @@ subroutine Polarisation_formResidual(in,x_scal,f_scal,dummy,ierr)
! check convergence
@@ -383,10 +378,6 @@ subroutine Polarisation_formResidual(in,x_scal,f_scal,dummy,ierr)
integer(pInt) :: &
i, j, k, e
@ -1063,7 +1089,7 @@ index ecf707d4..2b9dddc0 100644
F => x_scal(1:3,1:3,1,&
XG_RANGE,YG_RANGE,ZG_RANGE)
F_tau => x_scal(1:3,1:3,2,&
@@ -698,11 +688,6 @@ subroutine Polarisation_destroy()
@@ -698,11 +689,6 @@ subroutine Polarisation_destroy()
implicit none
PetscErrorCode :: ierr
@ -1076,7 +1102,7 @@ index ecf707d4..2b9dddc0 100644
call SNESDestroy(snes,ierr); CHKERRQ(ierr)
call DMDestroy(da,ierr); CHKERRQ(ierr)
diff --git a/src/spectral_thermal.f90 b/src/spectral_thermal.f90
index 322f1203..cc0f7678 100644
index 322f1203..2374d83b 100644
--- a/src/spectral_thermal.f90
+++ b/src/spectral_thermal.f90
@@ -4,6 +4,8 @@
@ -1151,25 +1177,64 @@ index 322f1203..cc0f7678 100644
!--------------------------------------------------------------------------------------------------
! initialize solver specific parts of PETSc
@@ -127,7 +122,7 @@ subroutine spectral_thermal_init
call SNESSetDM(thermal_snes,thermal_grid,ierr); CHKERRQ(ierr) ! connect snes to da
call DMCreateGlobalVector(thermal_grid,solution ,ierr); CHKERRQ(ierr) ! global solution vector (grid x 1, i.e. every def grad tensor)
call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,spectral_thermal_formResidual,&
@@ -124,16 +119,18 @@ subroutine spectral_thermal_init
grid (1),grid(2),localK, & ! local grid
thermal_grid,ierr) ! handle, error
CHKERRQ(ierr)
- call SNESSetDM(thermal_snes,thermal_grid,ierr); CHKERRQ(ierr) ! connect snes to da
- call DMCreateGlobalVector(thermal_grid,solution ,ierr); CHKERRQ(ierr) ! global solution vector (grid x 1, i.e. every def grad tensor)
- call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,spectral_thermal_formResidual,&
- PETSC_NULL_OBJECT,ierr) ! residual vector of same shape as solution vector
+ call SNESsetDM(thermal_snes,thermal_grid,ierr); CHKERRQ(ierr) ! connect snes to da
+ call DMsetFromOptions(thermal_grid,ierr); CHKERRQ(ierr)
+ call DMsetUp(thermal_grid,ierr); CHKERRQ(ierr)
+ call DMcreateGlobalVector(thermal_grid,solution,ierr); CHKERRQ(ierr) ! global solution vector (grid x 1, i.e. every def grad tensor)
+ call DMDASNESsetFunctionLocal(thermal_grid,INSERT_VALUES,spectral_thermal_formResidual,&
+ PETSC_NULL_SNES,ierr) ! residual vector of same shape as solution vector
CHKERRQ(ierr)
call SNESSetFromOptions(thermal_snes,ierr); CHKERRQ(ierr) ! pull it all together with additional cli arguments
- call SNESSetFromOptions(thermal_snes,ierr); CHKERRQ(ierr) ! pull it all together with additional cli arguments
+ call SNESsetFromOptions(thermal_snes,ierr); CHKERRQ(ierr) ! pull it all together with additional cli arguments
@@ -215,7 +210,7 @@ type(tSolutionState) function spectral_thermal_solution(timeinc,timeinc_old,load
!--------------------------------------------------------------------------------------------------
! init fields
- call DMDAGetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,ierr)
+ call DMDAgetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,ierr)
CHKERRQ(ierr)
xend = xstart + xend - 1
yend = ystart + yend - 1
@@ -149,9 +146,9 @@ subroutine spectral_thermal_init
temperature_lastInc(i,j,k) = temperature_current(i,j,k)
temperature_stagInc(i,j,k) = temperature_current(i,j,k)
enddo; enddo; enddo
- call DMDAVecGetArrayF90(thermal_grid,solution,x_scal,ierr); CHKERRQ(ierr) !< get the data out of PETSc to work with
+ call DMDAvecGetArrayF90(thermal_grid,solution,x_scal,ierr); CHKERRQ(ierr) !< get the data out of PETSc to work with
x_scal(xstart:xend,ystart:yend,zstart:zend) = temperature_current
- call DMDAVecRestoreArrayF90(thermal_grid,solution,x_scal,ierr); CHKERRQ(ierr)
+ call DMDAvecRestoreArrayF90(thermal_grid,solution,x_scal,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! thermal reference diffusion update
@@ -205,8 +202,8 @@ type(tSolutionState) function spectral_thermal_solution(timeinc,timeinc_old,load
external :: &
VecMin, &
VecMax, &
- SNESSolve, &
- SNESGetConvergedReason
+ SNESsolve, &
+ SNESgetConvergedReason
spectral_thermal_solution%converged =.false.
@@ -215,7 +212,7 @@ type(tSolutionState) function spectral_thermal_solution(timeinc,timeinc_old,load
params%timeinc = timeinc
params%timeincOld = timeinc_old
- call SNESSolve(thermal_snes,PETSC_NULL_OBJECT,solution,ierr); CHKERRQ(ierr)
+ call SNESSolve(thermal_snes,PETSC_NULL_SNES,solution,ierr); CHKERRQ(ierr)
+ call SNESsolve(thermal_snes,PETSC_NULL_VEC,solution,ierr); CHKERRQ(ierr)
call SNESGetConvergedReason(thermal_snes,reason,ierr); CHKERRQ(ierr)
if (reason < 1) then
@@ -245,14 +240,12 @@ type(tSolutionState) function spectral_thermal_solution(timeinc,timeinc_old,load
@@ -245,14 +242,12 @@ type(tSolutionState) function spectral_thermal_solution(timeinc,timeinc_old,load
call VecMin(solution,position,minTemperature,ierr); CHKERRQ(ierr)
call VecMax(solution,position,maxTemperature,ierr); CHKERRQ(ierr)
@ -1191,7 +1256,7 @@ index 322f1203..cc0f7678 100644
end function spectral_thermal_solution
diff --git a/src/spectral_utilities.f90 b/src/spectral_utilities.f90
index 1ad25174..bbef337f 100644
index 1bbf2e60..52bb07fd 100644
--- a/src/spectral_utilities.f90
+++ b/src/spectral_utilities.f90
@@ -5,15 +5,16 @@
@ -1282,7 +1347,7 @@ index 1ad25174..bbef337f 100644
write(6,'(/,a)') ' ... calculating curl ......................................................'
flush(6)
@@ -1096,9 +1089,6 @@ function utilities_forwardField(timeinc,field_lastInc,rate,aim)
@@ -1099,9 +1092,6 @@ function utilities_forwardField(timeinc,field_lastInc,rate,aim)
real(pReal), dimension(3,3) :: fieldDiff !< <a + adot*t> - aim
PetscErrorCode :: ierr
@ -1292,7 +1357,7 @@ index 1ad25174..bbef337f 100644
utilities_forwardField = field_lastInc + rate*timeinc
if (present(aim)) then !< correct to match average
fieldDiff = sum(sum(sum(utilities_forwardField,dim=5),dim=4),dim=3)*wgt
@@ -1190,8 +1180,6 @@ subroutine utilities_updateIPcoords(F)
@@ -1193,8 +1183,6 @@ subroutine utilities_updateIPcoords(F)
integer(pInt) :: i, j, k, m, ierr
real(pReal), dimension(3) :: step, offset_coords
real(pReal), dimension(3,3) :: Favg
@ -1304,225 +1369,3 @@ index 1ad25174..bbef337f 100644
--
2.15.0
From 237f199bbf574bb2509123ce8b037ac751abd15d Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Sun, 5 Nov 2017 13:45:52 +0100
Subject: [PATCH 2/3] extra function calls for da needed
(https://lists.mcs.anl.gov/pipermail/petsc-users/2017-February/031538.html)
SNESsolve requires PETSC_NULL_VEC not PETSC_NULL_SNES (indicating b=0)
---
src/spectral_damage.f90 | 4 +++-
src/spectral_mech_AL.f90 | 5 +++--
src/spectral_mech_Basic.f90 | 6 +++---
src/spectral_mech_Polarisation.f90 | 5 +++--
src/spectral_thermal.f90 | 22 ++++++++++++----------
5 files changed, 24 insertions(+), 18 deletions(-)
diff --git a/src/spectral_damage.f90 b/src/spectral_damage.f90
index cea6f69c..2c195c56 100644
--- a/src/spectral_damage.f90
+++ b/src/spectral_damage.f90
@@ -114,6 +114,8 @@ subroutine spectral_damage_init()
damage_grid,ierr) !< handle, error
CHKERRQ(ierr)
call SNESSetDM(damage_snes,damage_grid,ierr); CHKERRQ(ierr) !< connect snes to da
+ call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
+ call DMsetUp(da,ierr); CHKERRQ(ierr)
call DMCreateGlobalVector(damage_grid,solution,ierr); CHKERRQ(ierr) !< global solution vector (grid x 1, i.e. every def grad tensor)
call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,spectral_damage_formResidual,&
PETSC_NULL_SNES,ierr) !< residual vector of same shape as solution vector
@@ -204,7 +206,7 @@ type(tSolutionState) function spectral_damage_solution(timeinc,timeinc_old,loadC
params%timeinc = timeinc
params%timeincOld = timeinc_old
- call SNESSolve(damage_snes,PETSC_NULL_SNES,solution,ierr); CHKERRQ(ierr)
+ call SNESSolve(damage_snes,PETSC_NULL_VEC,solution,ierr); CHKERRQ(ierr)
call SNESGetConvergedReason(damage_snes,reason,ierr); CHKERRQ(ierr)
if (reason < 1) then
diff --git a/src/spectral_mech_AL.f90 b/src/spectral_mech_AL.f90
index e7ff0fbe..dc221f6c 100644
--- a/src/spectral_mech_AL.f90
+++ b/src/spectral_mech_AL.f90
@@ -160,6 +160,8 @@ subroutine AL_init
da,ierr) ! handle, error
CHKERRQ(ierr)
call SNESSetDM(snes,da,ierr); CHKERRQ(ierr)
+ call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
+ call DMsetUp(da,ierr); CHKERRQ(ierr)
call DMCreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr)
call DMDASNESSetFunctionLocal(da,INSERT_VALUES,AL_formResidual,PETSC_NULL_SNES,ierr)
CHKERRQ(ierr)
@@ -298,8 +300,7 @@ type(tSolutionState) function &
!--------------------------------------------------------------------------------------------------
! solve BVP
- call SNESSolve(snes,PETSC_NULL_SNES,solution_vec,ierr)
- CHKERRQ(ierr)
+ call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! check convergence
diff --git a/src/spectral_mech_Basic.f90 b/src/spectral_mech_Basic.f90
index b02cfd8c..c335f2d7 100644
--- a/src/spectral_mech_Basic.f90
+++ b/src/spectral_mech_Basic.f90
@@ -147,6 +147,8 @@ subroutine basicPETSc_init
da,ierr) ! handle, error
CHKERRQ(ierr)
call SNESsetDM(snes,da,ierr); CHKERRQ(ierr)
+ call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
+ call DMsetUp(da,ierr); CHKERRQ(ierr)
call DMcreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr) ! global solution vector (grid x 9, i.e. every def grad tensor)
call DMDASNESsetFunctionLocal(da,INSERT_VALUES,BasicPETSC_formResidual,PETSC_NULL_SNES,ierr) ! residual vector of same shape as solution vector
CHKERRQ(ierr)
@@ -158,7 +160,6 @@ subroutine basicPETSc_init
!--------------------------------------------------------------------------------------------------
! init fields
call DMDAVecGetArrayF90(da,solution_vec,F,ierr); CHKERRQ(ierr) ! get the data out of PETSc to work with
-
restart: if (restartInc > 1_pInt) then
if (iand(debug_level(debug_spectral),debug_spectralRestart)/= 0) &
write(6,'(/,a,'//IO_intOut(restartInc-1_pInt)//',a)') &
@@ -267,8 +268,7 @@ type(tSolutionState) function &
!--------------------------------------------------------------------------------------------------
! solve BVP
- call SNESSolve(snes,PETSC_NULL_SNES,solution_vec,ierr)
- CHKERRQ(ierr)
+ call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! check convergence
diff --git a/src/spectral_mech_Polarisation.f90 b/src/spectral_mech_Polarisation.f90
index 2b9dddc0..3b024f56 100644
--- a/src/spectral_mech_Polarisation.f90
+++ b/src/spectral_mech_Polarisation.f90
@@ -160,6 +160,8 @@ subroutine Polarisation_init
da,ierr) ! handle, error
CHKERRQ(ierr)
call SNESsetDM(snes,da,ierr); CHKERRQ(ierr)
+ call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
+ call DMsetUp(da,ierr); CHKERRQ(ierr)
call DMcreateGlobalVector(da,solution_vec,ierr); CHKERRQ(ierr)
call DMDASNESsetFunctionLocal(da,INSERT_VALUES,Polarisation_formResidual,PETSC_NULL_SNES,ierr)
CHKERRQ(ierr)
@@ -298,8 +300,7 @@ type(tSolutionState) function &
!--------------------------------------------------------------------------------------------------
! solve BVP
- call SNESSolve(snes,PETSC_NULL_SNES,solution_vec,ierr)
- CHKERRQ(ierr)
+ call SNESsolve(snes,PETSC_NULL_VEC,solution_vec,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! check convergence
diff --git a/src/spectral_thermal.f90 b/src/spectral_thermal.f90
index cc0f7678..7115538c 100644
--- a/src/spectral_thermal.f90
+++ b/src/spectral_thermal.f90
@@ -119,16 +119,18 @@ subroutine spectral_thermal_init
grid (1),grid(2),localK, & ! local grid
thermal_grid,ierr) ! handle, error
CHKERRQ(ierr)
- call SNESSetDM(thermal_snes,thermal_grid,ierr); CHKERRQ(ierr) ! connect snes to da
- call DMCreateGlobalVector(thermal_grid,solution ,ierr); CHKERRQ(ierr) ! global solution vector (grid x 1, i.e. every def grad tensor)
- call DMDASNESSetFunctionLocal(thermal_grid,INSERT_VALUES,spectral_thermal_formResidual,&
+ call SNESsetDM(thermal_snes,thermal_grid,ierr); CHKERRQ(ierr) ! connect snes to da
+ call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
+ call DMsetUp(da,ierr); CHKERRQ(ierr)
+ call DMcreateGlobalVector(thermal_grid,solution,ierr); CHKERRQ(ierr) ! global solution vector (grid x 1, i.e. every def grad tensor)
+ call DMDASNESsetFunctionLocal(thermal_grid,INSERT_VALUES,spectral_thermal_formResidual,&
PETSC_NULL_SNES,ierr) ! residual vector of same shape as solution vector
CHKERRQ(ierr)
- call SNESSetFromOptions(thermal_snes,ierr); CHKERRQ(ierr) ! pull it all together with additional cli arguments
+ call SNESsetFromOptions(thermal_snes,ierr); CHKERRQ(ierr) ! pull it all together with additional cli arguments
!--------------------------------------------------------------------------------------------------
! init fields
- call DMDAGetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,ierr)
+ call DMDAgetCorners(thermal_grid,xstart,ystart,zstart,xend,yend,zend,ierr)
CHKERRQ(ierr)
xend = xstart + xend - 1
yend = ystart + yend - 1
@@ -144,9 +146,9 @@ subroutine spectral_thermal_init
temperature_lastInc(i,j,k) = temperature_current(i,j,k)
temperature_stagInc(i,j,k) = temperature_current(i,j,k)
enddo; enddo; enddo
- call DMDAVecGetArrayF90(thermal_grid,solution,x_scal,ierr); CHKERRQ(ierr) !< get the data out of PETSc to work with
+ call DMDAvecGetArrayF90(thermal_grid,solution,x_scal,ierr); CHKERRQ(ierr) !< get the data out of PETSc to work with
x_scal(xstart:xend,ystart:yend,zstart:zend) = temperature_current
- call DMDAVecRestoreArrayF90(thermal_grid,solution,x_scal,ierr); CHKERRQ(ierr)
+ call DMDAvecRestoreArrayF90(thermal_grid,solution,x_scal,ierr); CHKERRQ(ierr)
!--------------------------------------------------------------------------------------------------
! thermal reference diffusion update
@@ -200,8 +202,8 @@ type(tSolutionState) function spectral_thermal_solution(timeinc,timeinc_old,load
external :: &
VecMin, &
VecMax, &
- SNESSolve, &
- SNESGetConvergedReason
+ SNESsolve, &
+ SNESgetConvergedReason
spectral_thermal_solution%converged =.false.
@@ -210,7 +212,7 @@ type(tSolutionState) function spectral_thermal_solution(timeinc,timeinc_old,load
params%timeinc = timeinc
params%timeincOld = timeinc_old
- call SNESSolve(thermal_snes,PETSC_NULL_SNES,solution,ierr); CHKERRQ(ierr)
+ call SNESsolve(thermal_snes,PETSC_NULL_VEC,solution,ierr); CHKERRQ(ierr)
call SNESGetConvergedReason(thermal_snes,reason,ierr); CHKERRQ(ierr)
if (reason < 1) then
--
2.15.0
From 1af2e332a1b86f388aa9e481255f4405874d7960 Mon Sep 17 00:00:00 2001
From: Martin Diehl <m.diehl@mpie.de>
Date: Sun, 5 Nov 2017 14:18:45 +0100
Subject: [PATCH 3/3] named better in thermal and damage
---
src/spectral_damage.f90 | 4 ++--
src/spectral_thermal.f90 | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/spectral_damage.f90 b/src/spectral_damage.f90
index 2c195c56..11da3b96 100644
--- a/src/spectral_damage.f90
+++ b/src/spectral_damage.f90
@@ -114,8 +114,8 @@ subroutine spectral_damage_init()
damage_grid,ierr) !< handle, error
CHKERRQ(ierr)
call SNESSetDM(damage_snes,damage_grid,ierr); CHKERRQ(ierr) !< connect snes to da
- call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
- call DMsetUp(da,ierr); CHKERRQ(ierr)
+ call DMsetFromOptions(damage_grid,ierr); CHKERRQ(ierr)
+ call DMsetUp(damage_grid,ierr); CHKERRQ(ierr)
call DMCreateGlobalVector(damage_grid,solution,ierr); CHKERRQ(ierr) !< global solution vector (grid x 1, i.e. every def grad tensor)
call DMDASNESSetFunctionLocal(damage_grid,INSERT_VALUES,spectral_damage_formResidual,&
PETSC_NULL_SNES,ierr) !< residual vector of same shape as solution vector
diff --git a/src/spectral_thermal.f90 b/src/spectral_thermal.f90
index 7115538c..2374d83b 100644
--- a/src/spectral_thermal.f90
+++ b/src/spectral_thermal.f90
@@ -120,8 +120,8 @@ subroutine spectral_thermal_init
thermal_grid,ierr) ! handle, error
CHKERRQ(ierr)
call SNESsetDM(thermal_snes,thermal_grid,ierr); CHKERRQ(ierr) ! connect snes to da
- call DMsetFromOptions(da,ierr); CHKERRQ(ierr)
- call DMsetUp(da,ierr); CHKERRQ(ierr)
+ call DMsetFromOptions(thermal_grid,ierr); CHKERRQ(ierr)
+ call DMsetUp(thermal_grid,ierr); CHKERRQ(ierr)
call DMcreateGlobalVector(thermal_grid,solution,ierr); CHKERRQ(ierr) ! global solution vector (grid x 1, i.e. every def grad tensor)
call DMDASNESsetFunctionLocal(thermal_grid,INSERT_VALUES,spectral_thermal_formResidual,&
PETSC_NULL_SNES,ierr) ! residual vector of same shape as solution vector
--
2.15.0

7
installation/patch/README.md
View File

@ -16,3 +16,10 @@ patch -p1 < installation/patch/nameOfPatch
* **PETSc-3.8** adjusts all includes nad calls to PETSc to the 3.8.x API
This allows to use the current version of PETSc
## Create patch
commit your changes
```bash
git format-patch PATH_TO_COMPARE --stdout >
```