Merge pull request #643 from mjberger/bouss_periodic

Bouss periodic and matrix reentrant corner and wall fixes. Also using new version of PETSc so changes to options and Makefile for example.

Author: rjleveque

examples/bouss/README.txt

@@ -16,6 +16,8 @@ OpenMP along with MPI.  Some flags have to be set as environment variables
 or directly in the application Makefile, e.g. see the lines commented out in
 radial_flat/Makefile.
 
+**Update:** Clawpack 5.12.0 now requires PETSc Version 3.23 (or later).
+
 The file setenv.sh illustrates how you might set some environment
 variables for the bash shell.
 

examples/bouss/petscMPIoptions

@@ -10,34 +10,32 @@
 #    https://petsc.org/release/manualpages/PC/PCSetFromOptions/
 
 # set min numbers of matrix rows per MPI rank  (default is 10000)
--pc_mpi_minimum_count_per_rank 5000
+-mpi_linear_solver_server_minimum_count_per_rank 5000
+-mpi_linear_solver_server
+-mpi_linear_solver_server_view
+-mpi_linear_solver_server_use_shared_memory false
 
-# convergence criterion for linear solver (larger than PETSc default):
--mpi_ksp_rtol 1.e-9
+# Krylov linear solver:
+-ksp_type gmres
+-ksp_max_it 200
+-ksp_reuse_preconditioner
 
-# linear solver:
--mpi_linear_solver_server
--ksp_type preonly
--mpi_ksp_type gmres
--mpi_ksp_max_it 200
--mpi_ksp_reuse_preconditioner
+# convergence criterion for linear solver (larger than PETSc default):
+-ksp_rtol 1.e-9
 
 # preconditioner:
--pc_type mpi
--mpi_pc_type gamg
--mpi_pc_gamg_symmetrize_graph true
--mpi_pc_gamg_sym_graph true
--mpi_linear_solver_server_view
+-pc_type gamg
+#-pc_type hypre
+
 
 # debug options:
 #-fp_trap off
 #-log_view
 #-start_in_debugger -debugger_rank 0
-#-mpi_ksp_view_mat binary
-#-mpi_ksp_view_rhs binary
-#-mpi_ksp_monitor_true_residual
-#-mpi_ksp_monitor
+#-ksp_monitor
+#-ksp_view
 #-info
 
 # test if any options are not used:
 #-options_left
+-options_view

examples/bouss/radial_flat/Makefile

@@ -36,30 +36,36 @@ ifndef PETSC_DIR
   $(error PETSC_DIR not set)
 endif
 
-ifndef PETSC_ARCH
-  $(error PETSC_ARCH not set)
-endif
-
 ifndef PETSC_OPTIONS
   PETSC_OPTIONS=MISSING
   $(error PETSC_OPTIONS must be declared as environment variable)
 endif
 
+ifndef CLAW_MPIEXEC
+  CLAW_MPIEXEC=MISSING
+  $(error CLAW_MPIEXEC must be declared as environment variable)
+endif
+
+ifndef CLAW_MPIFC
+  CLAW_MPIFC=MISSING
+  $(error Fortran compiler CLAW_MPIFC must be declared as environment variable)
+endif
+
+# Environment variable FC should be set to fortran compiler, e.g. gfortran
+FC = ${CLAW_MPIFC}
+
 # How many MPI processes to use:
 BOUSS_MPI_PROCS ?= 6
 
 EXE = $(PWD)/xgeoclaw
-RUNEXE="${PETSC_DIR}/${PETSC_ARCH}/bin/mpiexec -n ${BOUSS_MPI_PROCS}"
+#RUNEXE="${PETSC_DIR}/${PETSC_ARCH}/bin/mpiexec -n ${BOUSS_MPI_PROCS}"
+RUNEXE="${CLAW_MPIEXEC} -n ${BOUSS_MPI_PROCS}"
 SETRUN_FILE = setrun.py           # File containing function to make data
 OUTDIR = _output                  # Directory for output
 SETPLOT_FILE = setplot.py         # File containing function to set plots
 PLOTDIR = _plots                  # Directory for plots
 
 
-# Environment variable FC should be set to fortran compiler, e.g. gfortran
-
-FC = gfortran
-
 # Some compiler flags below are needed for PETSc
 PETSC_INCLUDE = $(PETSC_DIR)/include $(PETSC_DIR)/$(PETSC_ARCH)/include         
 INCLUDE += $(PETSC_INCLUDE)
@@ -121,6 +127,13 @@ check:
 	@env | grep PETSC_OPTIONS
 	@echo PETSC_DIR = $(PETSC_DIR)
 	@echo PETSC_ARCH = $(PETSC_ARCH)
+	@echo CLAW_MPIEXEC = $(CLAW_MPIEXEC)
 	@echo RUNEXE = $(RUNEXE)
+	@echo EXE = $(EXE)
+	@echo CLAW_MPIFC = $(CLAW_MPIFC)
+	@echo FC = $(FC)
 	@echo FFLAGS = $(FFLAGS)
+	@echo LFLAGS = $(LFLAGS)
+	@echo OUTDIR = $(OUTDIR)
+	@echo PLOTDIR = $(PLOTDIR)
 	@echo ===================

src/2d/bouss/Makefile.bouss

@@ -162,6 +162,7 @@ COMMON_SOURCES += \
   $(BOUSSLIB)/buildSparseMatrixMScoo.f90 \
   $(BOUSSLIB)/compressOut.f \
   $(BOUSSLIB)/matvec.f90 \
+  $(BOUSSLIB)/testSoln.f90 \
   $(BOUSSLIB)/petsc_driver.f90 \
   $(BOUSSLIB)/lookAtGrid.f90 \
   $(BOUSSLIB)/resetBoussStuff.f \

src/2d/bouss/bouss_module.f90

@@ -166,7 +166,7 @@ subroutine set_bouss(rest,time,naux)
         crs = .true.
     endif
 
-    ! crs = .false.  ! uncomment this line to force CRS with SGN for testing
+    ! crs = .false.  ! uncomment this line to force COO with SGN for testing
 
     !------------------------------------------
     if (rest) then
@@ -264,8 +264,8 @@ subroutine set_bouss(rest,time,naux)
     ! Boundary conditions to impose in computing Boussinesq update:
     if ((mthbc(1)==2) .or. (mthbc(2)==2) &
         .or. (mthbc(3)==2) .or. (mthbc(4)==2)) then
-        write(6,*) '*** Periodic BCs not supported in bouss_module'
-        stop
+        write(6,*) '*** Periodic BCs newly added to bouss_module'
+        !!stop
     endif
 
     if ((mthbc(1)==4) .or. (mthbc(2)==4) &