Optimizations related to matrix conversion (#148)

* First work on in place. * Optimization of the code related to conversion. This also incldues some code reduction work. * Something wrong with the CI? * Noticed a linting error.
william-dawson · May 21, 2020 · 40b2433 · 40b2433
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commit 40b2433
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -82,6 +82,4 @@ jobs:
         TESTEXAMPLES:     ${{ matrix.testexamples }}
     - name:               lint
       run:                |
-        cd UnitTests
-        bash lint.sh
-        cd ../
+        bash UnitTests/lint.sh
diff --git a/Source/Fortran/MatrixConversionModule.F90 b/Source/Fortran/MatrixConversionModule.F90
@@ -3,11 +3,11 @@
 !> to data structures used in other programs.
 MODULE MatrixConversionModule
   USE DataTypesModule, ONLY : NTREAL
-  USE MatrixMapsModule, ONLY : MapMatrix_psr
   USE PSMatrixModule, ONLY : Matrix_ps, ConvertMatrixToReal, CopyMatrix, &
-       & DestructMatrix
+       & DestructMatrix, MergeMatrixLocalBlocks, SplitMatrixToLocalBlocks
   USE PSMatrixAlgebraModule, ONLY : PairwiseMultiplyMatrix, ScaleMatrix, &
        & IncrementMatrix
+  USE SMatrixModule, ONLY : Matrix_lsr, DestructMatrix
   IMPLICIT NONE
   PRIVATE
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@@ -27,16 +27,17 @@ SUBROUTINE SnapMatrixToSparsityPattern(mat, pattern)
     TYPE(Matrix_ps) :: filtered
     TYPE(Matrix_ps) :: pattern_1s
     TYPE(Matrix_ps) :: pattern_0s
-    TYPE(Matrix_ps) :: pattern_real
-    INTEGER :: II
+    TYPE(Matrix_lsr) :: local_mat
 
     !! First we need to make sure that the sparsity pattern is all 1s.
     IF (pattern%is_complex) THEN
-       CALL ConvertMatrixToReal(pattern, pattern_real)
+       CALL ConvertMatrixToReal(pattern, pattern_1s)
     ELSE
-       CALL CopyMatrix(pattern, pattern_real)
+       CALL CopyMatrix(pattern, pattern_1s)
     END IF
-    CALL MapMatrix_psr(pattern_real, pattern_1s, SetMatrixToOne)
+    CALL MergeMatrixLocalBlocks(pattern_1s, local_mat)
+    local_mat%values = 1.0_NTREAL
+    CALL SplitMatrixToLocalBlocks(pattern_1s, local_mat)
 
     !! Then all zeros
     CALL CopyMatrix(pattern_1s, pattern_0s)
@@ -54,19 +55,9 @@ SUBROUTINE SnapMatrixToSparsityPattern(mat, pattern)
     !! Cleanup
     CALL DestructMatrix(pattern_1s)
     CALL DestructMatrix(pattern_0s)
-    CALL DestructMatrix(pattern_real)
     CALL DestructMatrix(filtered)
+    CALL DestructMatrix(local_mat)
 
   END SUBROUTINE SnapMatrixToSparsityPattern
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-  FUNCTION SetMatrixToOne(row, column, val) RESULT(valid)
-    INTEGER, INTENT(INOUT), OPTIONAL :: row
-    INTEGER, INTENT(INOUT), OPTIONAL :: column
-    REAL(NTREAL), INTENT(INOUT), OPTIONAL :: val
-    LOGICAL :: valid
-
-    val = 1.0_NTREAL
-    valid = .TRUE.
-  END FUNCTION SetMatrixToOne
-!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
-END MODULE
+END MODULE
diff --git a/Source/Fortran/MatrixReduceModule.F90 b/Source/Fortran/MatrixReduceModule.F90
@@ -41,10 +41,12 @@ MODULE MatrixReduceModule
   PUBLIC :: ReduceAndComposeMatrixSizes
   PUBLIC :: ReduceAndComposeMatrixData
   PUBLIC :: ReduceAndComposeMatrixCleanup
+  PUBLIC :: ReduceAndComposeMatrix
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   PUBLIC :: ReduceAndSumMatrixSizes
   PUBLIC :: ReduceAndSumMatrixData
   PUBLIC :: ReduceAndSumMatrixCleanup
+  PUBLIC :: ReduceAndSumMatrix
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   PUBLIC :: TestReduceSizeRequest
   PUBLIC :: TestReduceInnerRequest
@@ -62,6 +64,10 @@ MODULE MatrixReduceModule
      MODULE PROCEDURE ReduceAndComposeMatrixCleanup_lsr
      MODULE PROCEDURE ReduceAndComposeMatrixCleanup_lsc
   END INTERFACE
+  INTERFACE ReduceAndComposeMatrix
+     MODULE PROCEDURE ReduceAndComposeMatrix_lsr
+     MODULE PROCEDURE ReduceAndComposeMatrix_lsc
+  END INTERFACE
   INTERFACE ReduceAndSumMatrixSizes
      MODULE PROCEDURE ReduceAndSumMatrixSizes_lsr
      MODULE PROCEDURE ReduceAndSumMatrixSizes_lsc
@@ -74,6 +80,10 @@ MODULE MatrixReduceModule
      MODULE PROCEDURE ReduceAndSumMatrixCleanup_lsr
      MODULE PROCEDURE ReduceAndSumMatrixCleanup_lsc
   END INTERFACE
+  INTERFACE ReduceAndSumMatrix
+     MODULE PROCEDURE ReduceAndSumMatrix_lsr
+     MODULE PROCEDURE ReduceAndSumMatrix_lsc
+  END INTERFACE
 CONTAINS!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   !> The first routine to call, gathers the sizes of the data to be sent.
   SUBROUTINE ReduceAndComposeMatrixSizes_lsr(matrix, communicator, &
@@ -249,6 +259,38 @@ PURE SUBROUTINE ReduceAndComposeMatrixCleanup_lsc(matrix, gathered_matrix, &
 #endif
 
   END SUBROUTINE ReduceAndComposeMatrixCleanup_lsc
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  !> Reduce and sum the matrices in one step. If you use this method, you
+  !> lose the opportunity for overlapping communication.
+  SUBROUTINE ReduceAndComposeMatrix_lsr(matrix, gathered_matrix, comm)
+    !> The matrix to send.
+    TYPE(Matrix_lsr), INTENT(IN)    :: matrix
+    !> The matrix we are gathering.
+    TYPE(Matrix_lsr), INTENT(INOUT) :: gathered_matrix
+    !> The communicator to send along.
+    INTEGER, INTENT(INOUT)              :: comm
+    !! Local Variables
+    TYPE(ReduceHelper_t) :: helper
+
+    INCLUDE "comm_includes/ReduceAndComposeMatrix.f90"
+
+  END SUBROUTINE ReduceAndComposeMatrix_lsr
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  !> Reduce and sum the matrices in one step. If you use this method, you
+  !> lose the opportunity for overlapping communication.
+  SUBROUTINE ReduceAndComposeMatrix_lsc(matrix, gathered_matrix, comm)
+    !> The matrix to send.
+    TYPE(Matrix_lsc), INTENT(IN)    :: matrix
+    !> The matrix we are gathering.
+    TYPE(Matrix_lsc), INTENT(INOUT) :: gathered_matrix
+    !> The communicator to send along.
+    INTEGER, INTENT(INOUT)              :: comm
+    !! Local Variables
+    TYPE(ReduceHelper_t) :: helper
+
+    INCLUDE "comm_includes/ReduceAndComposeMatrix.f90"
+
+  END SUBROUTINE ReduceAndComposeMatrix_lsc
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   !> The first routine to call, gathers the sizes of the data to be sent.
   SUBROUTINE ReduceAndSumMatrixSizes_lsr(matrix, communicator,  &
@@ -425,6 +467,40 @@ PURE SUBROUTINE ReduceAndSumMatrixCleanup_lsc(matrix, gathered_matrix, &
     END IF
 #endif
   END SUBROUTINE ReduceAndSumMatrixCleanup_lsc
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  !> Reduce and sum the matrices in one step. If you use this method, you
+  !> lose the opportunity for overlapping communication.
+  SUBROUTINE ReduceAndSumMatrix_lsr(matrix, gathered_matrix, threshold, comm)
+    !> The matrix to send.
+    TYPE(Matrix_lsr), INTENT(IN)        :: matrix
+    !> The gathered_matrix the matrix being gathered.
+    TYPE(Matrix_lsr), INTENT(INOUT)     :: gathered_matrix
+    !> The threshold the threshold for flushing values.
+    REAL(NTREAL), INTENT(IN)            :: threshold
+    !> The communicator to send along.
+    INTEGER, INTENT(INOUT)              :: comm
+    !! Local Data
+    TYPE(ReduceHelper_t) :: helper
+
+    INCLUDE "comm_includes/ReduceAndSumMatrix.f90"
+  END SUBROUTINE ReduceAndSumMatrix_lsr
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+  !> Reduce and sum the matrices in one step. If you use this method, you
+  !> lose the opportunity for overlapping communication.
+  SUBROUTINE ReduceAndSumMatrix_lsc(matrix, gathered_matrix, threshold, comm)
+    !> The matrix to send.
+    TYPE(Matrix_lsc), INTENT(IN)        :: matrix
+    !> The threshold the threshold for flushing values.
+    TYPE(Matrix_lsc), INTENT(INOUT)     :: gathered_matrix
+    !> The threshold the threshold for flushing values.
+    REAL(NTREAL), INTENT(IN)            :: threshold
+    !> The communicator to send along.
+    INTEGER, INTENT(INOUT)              :: comm
+    !! Local Data
+    TYPE(ReduceHelper_t) :: helper
+
+    INCLUDE "comm_includes/ReduceAndSumMatrix.f90"
+  END SUBROUTINE ReduceAndSumMatrix_lsc
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
   !> Test if a request for the size of the matrices is complete.
   FUNCTION TestReduceSizeRequest(helper) RESULT(request_completed)

diff --git a/Source/Fortran/PSMatrixModule.F90 b/Source/Fortran/PSMatrixModule.F90
@@ -9,11 +9,8 @@ MODULE PSMatrixModule
        & WriteListElement, WriteHeader
   USE MatrixMarketModule, ONLY : ParseMMHeader, MM_COMPLEX, WriteMMSize, &
        & WriteMMLine, MAX_LINE_LENGTH
-  USE MatrixReduceModule, ONLY : ReduceHelper_t, ReduceAndComposeMatrixSizes, &
-       & ReduceAndComposeMatrixData, ReduceAndComposeMatrixCleanup, &
-       & ReduceANdSumMatrixSizes, ReduceAndSumMatrixData, &
-       & ReduceAndSumMatrixCleanup, TestReduceSizeRequest, &
-       & TestReduceInnerRequest, TestReduceDataRequest
+  USE MatrixReduceModule, ONLY : ReduceHelper_t, ReduceAndComposeMatrix, &
+       & ReduceAndSumMatrix
   USE PermutationModule, ONLY : Permutation_t, ConstructDefaultPermutation
   USE ProcessGridModule, ONLY : ProcessGrid_t, global_grid, IsRoot, &
        & SplitProcessGrid
@@ -773,23 +770,29 @@ END SUBROUTINE WriteMatrixToMatrixMarket_psc
   !> This routine fills in a matrix based on local triplet lists. Each process
   !> should pass in triplet lists with global coordinates. It does not matter
   !> where each triplet is stored, as long as global coordinates are given.
-  SUBROUTINE FillMatrixFromTripletList_psr(this,triplet_list,preduplicated_in)
+  !> However, if you explicitly set prepartitioned_in to True, all data must be
+  !> on the correct process. In that case, there is no communication required.
+  SUBROUTINE FillMatrixFromTripletList_psr(this, triplet_list, &
+       & preduplicated_in, prepartitioned_in)
     !> The matrix to fill.
     TYPE(Matrix_ps) :: this
     !> The triplet list of values.
     TYPE(TripletList_r) :: triplet_list
     !> If lists are preduplicated across slices set this to true.
     LOGICAL, INTENT(IN), OPTIONAL :: preduplicated_in
+    !> If all lists only contain local matrix elements set this to true.
+    LOGICAL, INTENT(IN), OPTIONAL :: prepartitioned_in
     !! Local Data
     TYPE(Matrix_ps) :: temp_matrix
+    TYPE(TripletList_r) :: shifted
     TYPE(TripletList_r) :: sorted_triplet_list
     TYPE(Matrix_lsr) :: local_matrix
     TYPE(Matrix_lsr) :: gathered_matrix
     !! Local Data
     TYPE(Permutation_t) :: basic_permutation
-    TYPE(ReduceHelper_t) :: gather_helper
     REAL(NTREAL), PARAMETER :: threshold = 0.0_NTREAL
     LOGICAL :: preduplicated
+    LOGICAL :: prepartitioned
 
     IF (this%is_complex) THEN
        CALL ConvertMatrixToReal(this, temp_matrix)
@@ -803,23 +806,29 @@ END SUBROUTINE FillMatrixFromTripletList_psr
   !> This routine fills in a matrix based on local triplet lists. Each process
   !> should pass in triplet lists with global coordinates. It does not matter
   !> where each triplet is stored, as long as global coordinates are given.
-  SUBROUTINE FillMatrixFromTripletList_psc(this,triplet_list,preduplicated_in)
+  !> However, if you explicitly set prepartitioned_in to True, all data must be
+  !> on the correct process. In that case, there is no communication required.
+  SUBROUTINE FillMatrixFromTripletList_psc(this, triplet_list, &
+       & preduplicated_in, prepartitioned_in)
     !> The matrix to fill.
     TYPE(Matrix_ps) :: this
     !> The triplet list of values.
     TYPE(TripletList_c) :: triplet_list
     !> If lists are preduplicated across slices set this to true.
     LOGICAL, INTENT(IN), OPTIONAL :: preduplicated_in
+    !> If all lists only contain local matrix elements set this to true.
+    LOGICAL, INTENT(IN), OPTIONAL :: prepartitioned_in
     !! Local Data
+    TYPE(TripletList_c) :: shifted
     TYPE(TripletList_c) :: sorted_triplet_list
     TYPE(Matrix_lsc) :: local_matrix
     TYPE(Matrix_lsc) :: gathered_matrix
     !! Local Data
     TYPE(Matrix_ps) :: temp_matrix
     TYPE(Permutation_t) :: basic_permutation
-    TYPE(ReduceHelper_t) :: gather_helper
     REAL(NTREAL), PARAMETER :: threshold = 0.0_NTREAL
     LOGICAL :: preduplicated
+    LOGICAL :: prepartitioned
 
     IF (.NOT. this%is_complex) THEN
        CALL ConvertMatrixToComplex(this, temp_matrix)
@@ -849,9 +858,6 @@ SUBROUTINE FillMatrixIdentity_psr(this)
     TYPE(Matrix_ps), INTENT(INOUT) :: this
     !! Local Data
     TYPE(TripletList_r) :: triplet_list
-    TYPE(TripletList_r) :: unsorted_triplet_list
-    TYPE(TripletList_r) :: sorted_triplet_list
-    TYPE(Matrix_lsr) :: local_matrix
 
     INCLUDE "distributed_includes/FillMatrixIdentity.f90"
 
@@ -863,9 +869,6 @@ SUBROUTINE FillMatrixIdentity_psc(this)
     TYPE(Matrix_ps), INTENT(INOUT) :: this
     !! Local Data
     TYPE(TripletList_c) :: triplet_list
-    TYPE(TripletList_c) :: unsorted_triplet_list
-    TYPE(TripletList_c) :: sorted_triplet_list
-    TYPE(Matrix_lsc) :: local_matrix
 
     INCLUDE "distributed_includes/FillMatrixIdentity.f90"
 
@@ -908,9 +911,6 @@ SUBROUTINE FillMatrixPermutation_psr(this, permutation_vector, rows)
     LOGICAL, INTENT(IN) :: rows
     !! Local Data
     TYPE(TripletList_r) :: triplet_list
-    TYPE(TripletList_r) :: unsorted_triplet_list
-    TYPE(TripletList_r) :: sorted_triplet_list
-    TYPE(Matrix_lsr) :: local_matrix
 
     INCLUDE "distributed_includes/FillMatrixPermutation.f90"
 
@@ -926,9 +926,6 @@ SUBROUTINE FillMatrixPermutation_psc(this, permutation_vector, rows)
     LOGICAL, INTENT(IN) :: rows
     !! Local Data
     TYPE(TripletList_c) :: triplet_list
-    TYPE(TripletList_c) :: unsorted_triplet_list
-    TYPE(TripletList_c) :: sorted_triplet_list
-    TYPE(Matrix_lsc) :: local_matrix
 
     INCLUDE "distributed_includes/FillMatrixPermutation.f90"
 

diff --git a/Source/Fortran/comm_includes/ReduceAndComposeMatrix.f90 b/Source/Fortran/comm_includes/ReduceAndComposeMatrix.f90
@@ -0,0 +1,11 @@
+  CALL ReduceAndComposeMatrixSizes(matrix, comm, gathered_matrix, helper)
+  DO WHILE(.NOT. TestReduceSizeRequest(helper))
+  END DO
+
+  CALL ReduceAndComposeMatrixData(matrix, comm, gathered_matrix, helper)
+  DO WHILE(.NOT. TestReduceInnerRequest(helper))
+  END DO
+  DO WHILE(.NOT. TestReduceDataRequest(helper))
+  END DO
+
+  CALL ReduceAndComposeMatrixCleanup(matrix, gathered_matrix, helper)
diff --git a/Source/Fortran/comm_includes/ReduceAndSumMatrix.f90 b/Source/Fortran/comm_includes/ReduceAndSumMatrix.f90
@@ -0,0 +1,11 @@
+  CALL ReduceAndSumMatrixSizes(matrix, comm, gathered_matrix, helper)
+  DO WHILE(.NOT. TestReduceSizeRequest(helper))
+  END DO
+
+  CALL ReduceAndSumMatrixData(matrix, gathered_matrix, comm, helper)
+  DO WHILE(.NOT. TestReduceInnerRequest(helper))
+  END DO
+  DO WHILE(.NOT. TestReduceDataRequest(helper))
+  END DO
+
+  CALL ReduceAndSumMatrixCleanup(matrix, gathered_matrix, threshold, helper)