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Sherman-Morrison/Makefile

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Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
## Compilers
New implementations for Sherman Morisson - SM2: Slagel splitting implementation (http://hdl.handle.net/10919/52966) - SM3: Keep close to zero denominators for later - Update tests to show the squared residual
2021-03-15 14:01:38 +01:00
ARCH =
CXX = clang++
FC = flang-7
Changed code to treat the dataset as replacement updates, instead of additive updates. Before the updates are used to compute the inverse they are transformed accordingly. However, this breaks the 4x4 example in update cycle 8169.
2021-03-12 12:38:50 +01:00
H5CXX = h5c++
Put more comments in Makefile.
2021-02-04 18:52:26 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
## Compiler flags
New implementations for Sherman Morisson - SM2: Slagel splitting implementation (http://hdl.handle.net/10919/52966) - SM3: Keep close to zero denominators for later - Update tests to show the squared residual
2021-03-15 14:01:38 +01:00
CXXFLAGS = -O0
Changed code to treat the dataset as replacement updates, instead of additive updates. Before the updates are used to compute the inverse they are transformed accordingly. However, this breaks the 4x4 example in update cycle 8169.
2021-03-12 12:38:50 +01:00
FFLAGS = $(CXXFLAGS)
H5CXXFLAGS = $(CXXFLAGS) -fPIC
FLIBS = -lstdc++
The algorithm now works for the following 4x4 example with 2 updates: S = [1,0,1,-1; 0,1,1,0; -1,0,-1,0; 1,1,1,1] S_inv = [1,-1,1,1; 1,0,2,1; -1,1,-2,-1; -1,0,-1,0] u1 = [0,-2,0,0] u2 = [0,-1,0,0] upd_idx = [2,4] To go from Maponi's examples where the number of updates is always equal to the the dimension of the matrix, and the decomposition is always diagonal, to cases with a non-diagonal decomposition and a number of updates unequal to its size, the following changed needed to be made: * in the calculation of the {y0k} an extra inner for-loop needs to be added to make it a full matrix-vector multiplication due to the fact that A0 is not a diagonal matrix * in some places the use of the update-order vector p needs the be replaced with that of upd_idx to make sure the correct component of the ylk is selected and the proper rank-1 matrices are constructed * when a matrix is passed from Fortran to C++ with 2D adressing, it is passed in colum-major order. The passed matrix needs to be transposed before passing to C++. Doing this inside the algorithm will break compatibility with called from C/C++.
2021-02-21 18:28:08 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
INCLUDE = -I $(INC_DIR)/
Add a standard Sherman-Morisson implementation - It can serve as a baseline reference - It can serve as a starting point for including the pivot and splitting techniques from Maponi and Slaggel without the full complexity of the MaponiA3 algorithm
2021-03-05 17:00:48 +01:00
DEPS_CXX = $(OBJ_DIR)/SM_MaponiA3.o $(OBJ_DIR)/SM_Standard.o
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
DEPS_F = $(DEPS_CXX) $(OBJ_DIR)/SM_MaponiA3_mod.o $(OBJ_DIR)/Helpers_mod.o
The algorithm now works for the following 4x4 example with 2 updates: S = [1,0,1,-1; 0,1,1,0; -1,0,-1,0; 1,1,1,1] S_inv = [1,-1,1,1; 1,0,2,1; -1,1,-2,-1; -1,0,-1,0] u1 = [0,-2,0,0] u2 = [0,-1,0,0] upd_idx = [2,4] To go from Maponi's examples where the number of updates is always equal to the the dimension of the matrix, and the decomposition is always diagonal, to cases with a non-diagonal decomposition and a number of updates unequal to its size, the following changed needed to be made: * in the calculation of the {y0k} an extra inner for-loop needs to be added to make it a full matrix-vector multiplication due to the fact that A0 is not a diagonal matrix * in some places the use of the update-order vector p needs the be replaced with that of upd_idx to make sure the correct component of the ylk is selected and the proper rank-1 matrices are constructed * when a matrix is passed from Fortran to C++ with 2D adressing, it is passed in colum-major order. The passed matrix needs to be transposed before passing to C++. Doing this inside the algorithm will break compatibility with called from C/C++.
2021-02-21 18:28:08 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
SRC_DIR := src
TST_DIR := tests
INC_DIR := include
OBJ_DIR := build
BIN_DIR := bin
The algorithm now works for the following 4x4 example with 2 updates: S = [1,0,1,-1; 0,1,1,0; -1,0,-1,0; 1,1,1,1] S_inv = [1,-1,1,1; 1,0,2,1; -1,1,-2,-1; -1,0,-1,0] u1 = [0,-2,0,0] u2 = [0,-1,0,0] upd_idx = [2,4] To go from Maponi's examples where the number of updates is always equal to the the dimension of the matrix, and the decomposition is always diagonal, to cases with a non-diagonal decomposition and a number of updates unequal to its size, the following changed needed to be made: * in the calculation of the {y0k} an extra inner for-loop needs to be added to make it a full matrix-vector multiplication due to the fact that A0 is not a diagonal matrix * in some places the use of the update-order vector p needs the be replaced with that of upd_idx to make sure the correct component of the ylk is selected and the proper rank-1 matrices are constructed * when a matrix is passed from Fortran to C++ with 2D adressing, it is passed in colum-major order. The passed matrix needs to be transposed before passing to C++. Doing this inside the algorithm will break compatibility with called from C/C++.
2021-02-21 18:28:08 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
EXEC := $(BIN_DIR)/cMaponiA3_test_3x3_3 \
Added environment variables source script. Added test script that loops over update cycles. Added test program that loops internally over test cycles.
2021-02-28 09:28:42 +01:00
$(BIN_DIR)/test_internal_h5 \
$(BIN_DIR)/test_external_h5 \
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
$(BIN_DIR)/fMaponiA3_test_3x3_3 \
$(BIN_DIR)/fMaponiA3_test_4x4_2 \
$(BIN_DIR)/QMCChem_dataset_test
The algorithm now works for the following 4x4 example with 2 updates: S = [1,0,1,-1; 0,1,1,0; -1,0,-1,0; 1,1,1,1] S_inv = [1,-1,1,1; 1,0,2,1; -1,1,-2,-1; -1,0,-1,0] u1 = [0,-2,0,0] u2 = [0,-1,0,0] upd_idx = [2,4] To go from Maponi's examples where the number of updates is always equal to the the dimension of the matrix, and the decomposition is always diagonal, to cases with a non-diagonal decomposition and a number of updates unequal to its size, the following changed needed to be made: * in the calculation of the {y0k} an extra inner for-loop needs to be added to make it a full matrix-vector multiplication due to the fact that A0 is not a diagonal matrix * in some places the use of the update-order vector p needs the be replaced with that of upd_idx to make sure the correct component of the ylk is selected and the proper rank-1 matrices are constructed * when a matrix is passed from Fortran to C++ with 2D adressing, it is passed in colum-major order. The passed matrix needs to be transposed before passing to C++. Doing this inside the algorithm will break compatibility with called from C/C++.
2021-02-21 18:28:08 +01:00
Put more comments in Makefile.
2021-02-04 18:52:26 +01:00
## Build tagets
Prepared the example matrix of Example 8 of the paper and its decomposition in the Fortran code and made a basic call to the subroutine MYSUBROUTINE, which is bound to the C++ void function 'Sherman-Morrison();. For now compilation fails with lots of undefined references.'
2021-02-04 13:12:34 +01:00
.PHONY: all clean distclean
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
all: $(EXEC)
Prepared the example matrix of Example 8 of the paper and its decomposition in the Fortran code and made a basic call to the subroutine MYSUBROUTINE, which is bound to the C++ void function 'Sherman-Morrison();. For now compilation fails with lots of undefined references.'
2021-02-04 13:12:34 +01:00
clean:
File tree restructured. Written build script build.sh. TODO: convert buld script into Makefile.
2021-02-26 17:28:52 +01:00
@rm -vrf $(OBJ_DIR)
C++ redesign of data-structures - Use flat arrays - Use real type for all matrices - Merge _f MaponiA3 files
2021-02-09 13:40:52 +01:00
Prepared the example matrix of Example 8 of the paper and its decomposition in the Fortran code and made a basic call to the subroutine MYSUBROUTINE, which is bound to the C++ void function 'Sherman-Morrison();. For now compilation fails with lots of undefined references.'
2021-02-04 13:12:34 +01:00
distclean: clean
File tree restructured. Written build script build.sh. TODO: convert buld script into Makefile.
2021-02-26 17:28:52 +01:00
@rm -vrf $(BIN_DIR) \
Slater* Updates.dat
The algorithm now works for the following 4x4 example with 2 updates: S = [1,0,1,-1; 0,1,1,0; -1,0,-1,0; 1,1,1,1] S_inv = [1,-1,1,1; 1,0,2,1; -1,1,-2,-1; -1,0,-1,0] u1 = [0,-2,0,0] u2 = [0,-1,0,0] upd_idx = [2,4] To go from Maponi's examples where the number of updates is always equal to the the dimension of the matrix, and the decomposition is always diagonal, to cases with a non-diagonal decomposition and a number of updates unequal to its size, the following changed needed to be made: * in the calculation of the {y0k} an extra inner for-loop needs to be added to make it a full matrix-vector multiplication due to the fact that A0 is not a diagonal matrix * in some places the use of the update-order vector p needs the be replaced with that of upd_idx to make sure the correct component of the ylk is selected and the proper rank-1 matrices are constructed * when a matrix is passed from Fortran to C++ with 2D adressing, it is passed in colum-major order. The passed matrix needs to be transposed before passing to C++. Doing this inside the algorithm will break compatibility with called from C/C++.
2021-02-21 18:28:08 +01:00
Prepared the example matrix of Example 8 of the paper and its decomposition in the Fortran code and made a basic call to the subroutine MYSUBROUTINE, which is bound to the C++ void function 'Sherman-Morrison();. For now compilation fails with lots of undefined references.'
2021-02-04 13:12:34 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
#### COMPILING
$(BIN_DIR) $(OBJ_DIR):
mkdir -p $@
Prepared the main Fortran infrastructure for the C++ calls. Updated the makefile.
2021-02-04 11:39:00 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
### IMPLICIT BUILD RULES
## C++ objects
$(OBJ_DIR)/%.o: $(TST_DIR)/%.cpp $(INC_DIR)/* | $(OBJ_DIR)
$(CXX) $(CXXFLAGS) $(ARCH) $(INCLUDE) -c -o $@ $<
Added QMCChem test dataset with 3 updates. Renamed files, added the Fortran program QMCChem_dataset_test.f90 to start testing the QMCChem dataset. Wrote and tested Fortran code to import the test dataset.
2021-02-12 12:04:21 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
## HDF5/C++ objects
$(OBJ_DIR)/%_h5.o: $(TST_DIR)/%_h5.cpp $(INC_DIR)/* | $(OBJ_DIR)
$(H5CXX) $(H5CXXFLAGS) $(INCLUDE) -c -o $@ $<
Add test infrastructure for datasets
2021-02-16 10:49:15 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
## Fortran modules
$(OBJ_DIR)/%_mod.o: $(SRC_DIR)/%_mod.f90 | $(OBJ_DIR)
Rewrote matMul function so it doesn't declare memory inside.
2021-03-01 16:08:14 +01:00
$(FC) $(FFLAGS) $(ARCH) -J$(OBJ_DIR)/ -c -o $@ $<
Test infrastructure for hdf5 datasets and python hdf5 datasert conversion tool. Made small corrections to compensate for changes made after branching-off from test_dataset. Everything compilers Everything works except for the HDF5 dataset test program that gives an I/O error.
2021-02-22 10:51:07 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
## Fortran objects
$(OBJ_DIR)/%.o: $(TST_DIR)/%.f90 | $(OBJ_DIR)
$(FC) $(FFLAGS) $(ARCH) -I $(OBJ_DIR)/ -c -o $@ $<
File tree restructured. Written build script build.sh. TODO: convert buld script into Makefile.
2021-02-26 17:28:52 +01:00
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
### EXPLICIT BUILD RULES
## special compiler flag -fPIC otherwise h5c++ builds fail
$(OBJ_DIR)/SM_MaponiA3.o: $(SRC_DIR)/SM_MaponiA3.cpp $(INC_DIR)/* | $(OBJ_DIR)
$(CXX) $(CXXFLAGS) -fPIC $(ARCH) $(INCLUDE) -c -o $@ $<
Add a standard Sherman-Morisson implementation - It can serve as a baseline reference - It can serve as a starting point for including the pivot and splitting techniques from Maponi and Slaggel without the full complexity of the MaponiA3 algorithm
2021-03-05 17:00:48 +01:00
$(OBJ_DIR)/SM_Standard.o: $(SRC_DIR)/SM_Standard.cpp $(INC_DIR)/* | $(OBJ_DIR)
$(CXX) $(CXXFLAGS) -fPIC $(ARCH) $(INCLUDE) -c -o $@ $<
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
#### LINKING
$(BIN_DIR)/cMaponiA3_test_3x3_3: $(OBJ_DIR)/cMaponiA3_test_3x3_3.o $(DEPS_CXX) | $(BIN_DIR)
$(CXX) -o $@ $^
Added environment variables source script. Added test script that loops over update cycles. Added test program that loops internally over test cycles.
2021-02-28 09:28:42 +01:00
$(BIN_DIR)/test_internal_h5: $(OBJ_DIR)/test_internal_h5.o $(DEPS_CXX) | $(BIN_DIR)
$(H5CXX) -o $@ $^
$(BIN_DIR)/test_external_h5: $(OBJ_DIR)/test_external_h5.o $(DEPS_CXX) | $(BIN_DIR)
Restructuring complete. Updated makefile.
2021-02-27 12:25:55 +01:00
$(H5CXX) -o $@ $^
$(BIN_DIR)/fMaponiA3_test_3x3_3: $(DEPS_F) $(OBJ_DIR)/fMaponiA3_test_3x3_3.o | $(BIN_DIR)
$(FC) $(FLIBS) -o $@ $^
$(BIN_DIR)/fMaponiA3_test_4x4_2: $(DEPS_F) $(OBJ_DIR)/fMaponiA3_test_4x4_2.o | $(BIN_DIR)
$(FC) $(FLIBS) -o $@ $^
$(BIN_DIR)/QMCChem_dataset_test: $(DEPS_F) $(OBJ_DIR)/QMCChem_dataset_test.o | $(BIN_DIR)
$(FC) $(FLIBS) -o $@ $^
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