incorporate upstream geoclaw updates

examples/bouss/README.txt

@@ -28,9 +28,6 @@ variables properly, see:
 The file setenv.sh illustrates how you might set some environment
 variables for the bash shell.
 
-The file setenv.sh illustrates how you might set some environment
-variables for the bash shell.
-
 A file petscMPIoptions is also required to set some PETSc parameters for the
 iterative method used to solve the large sparse linear systems that arise at 
 each refinement level when the Boussinesq equations are solved. 

examples/storm-surge/isaac/test_isaac.py

@@ -4,16 +4,15 @@
 Primarily tests all of the input formats GeoClaw handles
 """
 
-from pathlib import Path
-import os
 import gzip
+import os
 import unittest
-import pytest
-
-import numpy as np
+from pathlib import Path
 
-import clawpack.geoclaw.test as test
 import clawpack.clawutil as clawutil
+import clawpack.geoclaw.test as test
+import numpy as np
+import pytest
 from clawpack.geoclaw.surge.storm import Storm
 
 days2seconds = lambda t: t * 60.0**2 * 24.0

src/2d/bouss/Makefile.bouss

@@ -159,6 +159,7 @@ COMMON_SOURCES += \
   $(BOUSSLIB)/buildSparseMatrixSGNcrs.f90 \
   $(BOUSSLIB)/prepBuildSparseMatrixSGNcoo.f90 \
   $(BOUSSLIB)/buildSparseMatrixSGNcoo.f90 \
+  $(BOUSSLIB)/buildSparseMatrixSGNcoo_blocks.f90 \
   $(BOUSSLIB)/buildSparseMatrixMScoo.f90 \
   $(BOUSSLIB)/compressOut.f \
   $(BOUSSLIB)/matvec.f90 \

src/2d/bouss/amr2.f90

@@ -860,7 +860,6 @@ program amr2
     write(*,format_string)
     write(*,*)
     write(timing_unit,*)
-    close(timing_unit)
 
     if (isolver.eq. 2) then
 !     if (countIterRef == 0) then
@@ -933,6 +932,7 @@ program amr2
     close(dbugunit)
 
 #ifdef HAVE_PETSC
+      call PetscViewerASCIIStdoutSetFileUnit(timing_unit,ierr)
       call PetscFinalize(ierr)
 #endif
 

src/2d/bouss/bouss_module.f90

@@ -19,7 +19,7 @@ module bouss_module
 
     logical :: startWithBouss
 
-    logical :: crs  
+    logical :: crs, origCooFormat   
 
     real(kind=8) :: startBoussTime
 
@@ -165,8 +165,17 @@ subroutine set_bouss(rest,time,naux)
         ! using compressed row storage (CRS, also known as CSR or Yale) format:
         crs = .true.
     endif
-
-    ! crs = .false.  ! uncomment this line to force COO with SGN for testing
+    ! if crs is false this will force SGN to use triplet COO form
+    ! crs = .false.  
+
+     ! origCoo format ordered unknowns by all u updates then all v updates 
+     ! block format is u and v together for a given cell. Better cache
+     ! performance, better for debugging and comparing with crs.
+     ! also reads into matlab for cond number testing, plotting,
+     ! so keeping around
+     !origCooFormat = .false.  ! set to false to use block format with coo
+     ! setting to avoid uninitialized var, but not used unless crs set to false
+     origCooFormat = .true. 
 
     !------------------------------------------
     if (rest) then

src/2d/bouss/buildSparseMatrixSGNcoo.f90

@@ -952,7 +952,7 @@ subroutine buildSparseMatrixSGNcoo(q,qold,aux,soln,rhs,                    &
                 ! Need to add comments on SGN RHS.
 
               if (debug) then
-                  write(67,*) '++b i,j,rhs = ',i,j,rhs(k_ij),rhs(k_ij + nD)
+                  write(67,*) '++before  i,j,rhs = ',i,j,rhs(k_ij),rhs(k_ij + nD)
               endif 
 
               !RHS for SGN 
@@ -976,20 +976,26 @@ subroutine buildSparseMatrixSGNcoo(q,qold,aux,soln,rhs,                    &
                     + 0.5d0*h_ij*wy + w(i,j)*etay)
 
 
+              if (debug) then
+                  write(67,*) '++after   i,j,rhs = ',i,j,rhs(k_ij),rhs(k_ij + nD)
+              endif 
+
               if (debug) then
                 write(44,998) nelt,nelt-neltSt
  998                format("                               ending with nelt ",i6,"   used ",i5)
               endif
 
-            enddo
-        enddo
 
-        if (debug .and. .false.) then ! dump matrix to look for singularity 
-           write(88,*)" level ",levelBouss
+        if (debug) then ! dump matrix to look for singularity 
+           write(88,*)" triplets for i,j ",i,j," level  ",levelBouss
            do k = neltBegin+1, nelt
-              write(88,103) minfo_matrix_ia(k),minfo_matrix_ja(k),minfo_matrix_sa(k)
- 103          format(2i8,e16.7)
+              !write(88,103) minfo_matrix_ia(k),minfo_matrix_ja(k),minfo_matrix_sa(k)
+              write(88,103) minfo_matrix_sa(k)
+ !103          format(2i8,e16.7)
+ 103          format(e16.7)
            end do
+           write(88,*)
+
            !close(88)
            !write(89,*)" level ",levelBouss
            !do k = 1,2*numBoussCells
@@ -1000,6 +1006,9 @@ subroutine buildSparseMatrixSGNcoo(q,qold,aux,soln,rhs,                    &
            !!stop
         endif
 
+            enddo
+        enddo
+
         if (debug) then
          if (mptr .eq. 1) then
            write(88,*)" grid ",mptr," level ",levelBouss,"x,y,ia,ja,sa"