Create librom header file (#80)

* add get first columns to matrix header * add rom to dg_advection partial * add get first n columns and get truncated spatial basis * fix test typos * fix another test typo * fix more build bugs * test print * more test prints * Remove test prints * fix bug * remove member variables from basisreader * remove matrix interpolater * update qdeim to use vector * make style * typo * update gnat,deim,qdeim tests * remove test orig * pass vector by reference * fix typo * add check to deim,gnat,qdeim * add dg_advection rom example serial * precompute a_inv * remove num_rows from ROM_FE_Evolution * matrix interpolation * remove prints * add basis interpolater * make interpolater constructor protected * separate out dg_advection and create dg_advection global rom * put examples in different directories * update path * fix warnings * make style * update documentation * remove old doc files * update path * add spack documentation * add quotes to project brief * rename files * update cmake * fix stylize * add paper to doc * move matlab and baseline directories * update util imports * rename greedy * update gnat include * fix deim include * update svd path * add api file * add librom.h * update svd include * rename test * move src to lib * fix build * rename baselines * Update README.md * remove debug tip * update path * add librom include test
LLNL · Nov 11, 2021 · 13dee16 · 13dee16
1 parent d459d9f
commit 13dee16
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -16,6 +16,7 @@ jobs:
       - uses: ./.github/workflows/checkout_repo
       - name: Build libROM
         run: |
+            mkdir ${GITHUB_WORKSPACE}/build
             cd ${GITHUB_WORKSPACE}/build
             export CC=mpicc
             export CXX=mpicxx
@@ -40,6 +41,7 @@ jobs:
       - name: Build libROM
         run: |
             export FC=/usr/local/bin/gfortran-10
+            mkdir ${GITHUB_WORKSPACE}/build
             cd ${GITHUB_WORKSPACE}/build
             cmake -DCMAKE_BUILD_TYPE=Debug ..
             make

diff --git a/.github/workflows/run_tests/action.yml b/.github/workflows/run_tests/action.yml
@@ -15,7 +15,7 @@ runs:
           mpirun -n 3 --oversubscribe tests/test_RandomizedSVD
           ./tests/test_DMD
           mpirun -n 3 --oversubscribe tests/test_DMD
-          ./tests/test_GreedyParameterPointPreDefinedSampler
-          mpirun -n 3 --oversubscribe tests/test_GreedyParameterPointPreDefinedSampler
+          ./tests/test_GreedyCustomSampler
+          mpirun -n 3 --oversubscribe tests/test_GreedyCustomSampler
 
       shell: bash
diff --git a/AUTHORS b/AUTHORS
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,16 +8,6 @@
 #
 ###############################################################################
 
-# Debugging tip: If using the GNU Make generator (the default), build
-# with `make VERBOSE=1` to see flags being used by GNU Make. This
-# output helps in trying to diagnose configuration errors. The
-# equivalent for the Ninja generator is `ninja -v`. Also note that
-# because this project "uses Fortran" -- a Fortran compiler is
-# required to infer Fortran name-mangling conventions -- KitWare's
-# "ninja-fortran" is needed to run the resulting Ninja files. This
-# software can be installed, e.g., via Spack (`spack install
-# ninja-fortran`).
-
 # Require CMake version 3.12 or later to expose modern features of
 # CMake for maintainability. With additional work, it is possible to
 # rewrite the build system generator for CMake 3.10+, 3.8+, 3.1+,
@@ -46,9 +36,6 @@ list(APPEND CMAKE_MODULE_PATH ${libROM_CMAKE_MODULE_PATH})
 option(USE_MFEM "Build libROM with MFEM" OFF)
 option(BUILD_STATIC "Build libROM as a static library" OFF)
 
-include(FortranCInterface)
-FortranCInterface_HEADER(${CMAKE_SOURCE_DIR}/FCMangle.h
-  MACRO_NAMESPACE "CAROM_FC_")
 ## Set a bunch of variables to generate a configure header
 # Enable assertion checking if debug symbols generated
 if((CMAKE_BUILD_TYPE STREQUAL "Debug") OR
@@ -106,87 +93,13 @@ if(HDF5_FOUND)
   set(CAROM_HAVE_HDF5 1)
 endif(HDF5_FOUND)
 
-configure_file(${CMAKE_SOURCE_DIR}/CAROM_config.h.in
-  ${CMAKE_SOURCE_DIR}/CAROM_config.h @ONLY)
-
-# While it is tempting to use file globbing here, file globbing is
-# considered a "modern CMake anti-pattern" because "CMake is not a
-# build system -- it is a build system _generator_". Instead, use
-# some file name "stems" for generating file names. This construction
-# is useful when files may be moved to different directories.
-set(module_list
-  Matrix
-  Vector
-  BasisGenerator
-  BasisReader
-  BasisWriter
-  SVD
-  IncrementalSVD
-  IncrementalSVDFastUpdate
-  IncrementalSVDStandard
-  StaticSVD
-  RandomizedSVD
-  GreedyParameterPointSampler
-  GreedyParameterPointRandomSampler
-  GreedyParameterPointPreDefinedSampler
-  Interpolator
-  MatrixInterpolator
-  VectorInterpolator
-  Database
-  HDFDatabase
-  Utilities
-  ParallelBuffer
-  DMD
-  DEIM
-  QDEIM
-  GNAT
-  STSampling)
-set(source_files)
-foreach(module IN LISTS module_list)
-  list(APPEND source_files ${module}.C)
-endforeach(module) # IN LISTS module_list
-
-list(APPEND source_files
-  Options.h)
-
-if (USE_MFEM)
-    list(APPEND source_files
-      SampleMesh.hpp)
-endif()
-
-list(APPEND source_files
-  scalapack_c_wrapper.c
-  scalapack_f_wrapper.f90)
-if (BUILD_STATIC)
-  add_library(ROM ${source_files})
-else()
-  add_library(ROM SHARED ${source_files})
-endif()
-
 # List minimum version requirements for dependencies where possible to make
 # packaging easier later.
 find_package(HDF5 1.8.0 REQUIRED)
 
 find_package(BLAS 3.4.0 REQUIRED)
 find_package(LAPACK 3.4.0 REQUIRED)
 
-# If MKL libraries not found, search for reference ScaLAPACK. If MKL
-# libraries found, search for MKL ScaLAPACK; if MKL ScaLAPACK not
-# found, search for reference ScaLAPACK. It seems that only
-if (BLAS_LIBRARIES MATCHES ".*mkl.*")
-  find_package(MKL COMPONENTS BLACS ScaLAPACK)
-  if (NOT MKL_ScaLAPACK_FOUND)
-    find_package(ScaLAPACK REQUIRED)
-    target_link_libraries(ROM PUBLIC ${ScaLAPACK_LIBRARIES})
-  else()
-    target_link_libraries(ROM PUBLIC ${MKL_ScaLAPACK_LIBRARY} ${MKL_BLACS_LIBRARY} ${MKL_LIBRARIES})
-    target_include_directories(ROM PUBLIC ${MKL_INCLUDE_DIRS})
-  endif()
-else() # BLAS or LAPACK isn't MKL
-  find_package(ScaLAPACK REQUIRED)
-  target_link_libraries(ROM PUBLIC ${ScaLAPACK_LIBRARIES})
-endif()
-
 # In FindMPI.cmake, "CXX" refers to "the MPI C API [being] usable from C++"
 find_package(MPI 1.2 REQUIRED)
 
@@ -206,34 +119,7 @@ if (USE_MFEM)
     find_path(PARMETIS_INCLUDES metis.h "${CMAKE_SOURCE_DIR}/dependencies/parmetis-4.0.3/metis/include")
 endif()
 
-# PUBLIC dependencies are transitive; these dependencies are used in
-# the API headers *and* in their implementations
-#
-# INTERFACE dependencies are used in the API headers, but not in the
-# API implementation (e.g., API forwards objects to another library
-# without dereferencing those objects -- only pointers are used)
-#
-# PRIVATE dependencies are used in the API implementation, but not in
-# the headers
-#
-# Using both the MPI::MPI_C target and the two MPI_C "flag variables
-# (i.e., "MPI_C_LINK_FLAGS, MPI_C_LIBRARIES) is probably redundant,
-# but is done here to ease a potential rollback to CMake 2.8 or CMake
-# 3.0.
-target_link_libraries(ROM
-  PUBLIC ${MPI_C_LINK_FLAGS} ${MPI_C_LIBRARIES} MPI::MPI_C ${MPI_FORTRAN_LINK_FLAGS} ${MPI_FORTRAN_LIBRARIES} MPI::MPI_Fortran ${HDF5_LIBRARIES}
-  ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} ${MFEM} ${HYPRE} ${PARMETIS} ${METIS}
-  PRIVATE ${ZLIB_LIBRARIES} ZLIB::ZLIB)
-
-target_include_directories(ROM PUBLIC
-  ${CMAKE_CURRENT_SOURCE_DIR}
-  ${MFEM_INCLUDES}
-  ${HYPRE_INCLUDES}
-  ${PARMETIS_INCLUDES}
-  ${HDF5_C_INCLUDE_DIRS}
-  ${MPI_C_INCLUDE_DIRS}
-  ${MFEM_C_INCLUDE_DIRS}
-  PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+add_subdirectory(lib)
 
 # Use the C++11 standard as an entire feature instead of
 # enumerating individual compiler features for simplicity
@@ -281,6 +167,7 @@ endif()
 
 set(regression_test_names
   smoke_test
+  test_include
   uneven_dist
   weak_scaling
   random_test
@@ -312,7 +199,7 @@ if(GTEST_FOUND)
     StaticSVD
     RandomizedSVD
     IncrementalSVD
-    GreedyParameterPointPreDefinedSampler)
+    GreedyCustomSampler)
   foreach(stem IN LISTS unit_test_stems)
     add_executable(test_${stem} tests/test_${stem}.C)
     target_link_libraries(test_${stem} PRIVATE ROM

diff --git a/README.md b/README.md
@@ -16,40 +16,6 @@ non-intrusive black-box approaches.
 
 - Sparse identification of nonlinear dynamics (SINDy)
 
-# Authors
-Robert W. Anderson (LLNL),
-William Arrighi (LLNL),
-Siu Wun Cheung (LLNL),
-Youngsoo Choi (LLNL),
-Dylan Copeland (LLNL),
-Kevin Huynh (LLNL),
-Jessica Lauzon (Stanford),
-Sean McBane (UT Austin),
-Geoffrey Oxberry (LLNL).
-
-# License
-
-libROM is distributed under the terms of both the MIT license and the
-Apache License (Version 2.0). Users may choose either license at their
-option.
-
-All new contributions must be made under both the MIT and Apache-2.0 licenses.
-
-See
-[LICENSE-MIT](https://github.com/LLNL/libROM/blob/master/LICENSE-MIT),
-[LICENSE-APACHE](https://github.com/LLNL/libROM/blob/master/LICENSE-APACHE),
-[COPYRIGHT](https://github.com/LLNL/libROM/blob/master/COPYRIGHT), and
-[NOTICE](https://github.com/LLNL/libROM/blob/master/NOTICE) for
-details.
-
-Up to commit 299876e0a0304f25db56f1f9e2eb2c61ef199048, libROM was
-previously released under the terms of the BSD-3 license.
-
-SPDX_License-Identifier: (Apache-2.0 OR MIT)
-
-LLNL-CODE-686965 (up to commit 299876e0a0304f25db56f1f9e2eb2c61ef199048)
-LLNL-CODE-766763
-
 # Installation
 
 To compile libROM with default build settings (Mac and LLNL LC Machines):
@@ -83,3 +49,40 @@ To install libROM with MFEM using spack.
 ```sh
  spack install librom +mfem
 ```
+
+# License
+
+libROM is distributed under the terms of both the MIT license and the
+Apache License (Version 2.0). Users may choose either license at their
+option.
+
+All new contributions must be made under both the MIT and Apache-2.0 licenses.
+
+See
+[LICENSE-MIT](https://github.com/LLNL/libROM/blob/master/LICENSE-MIT),
+[LICENSE-APACHE](https://github.com/LLNL/libROM/blob/master/LICENSE-APACHE),
+[COPYRIGHT](https://github.com/LLNL/libROM/blob/master/COPYRIGHT), and
+[NOTICE](https://github.com/LLNL/libROM/blob/master/NOTICE) for
+details.
+
+Up to commit 299876e0a0304f25db56f1f9e2eb2c61ef199048, libROM was
+previously released under the terms of the BSD-3 license.
+
+SPDX_License-Identifier: (Apache-2.0 OR MIT)
+
+LLNL-CODE-686965 (up to commit 299876e0a0304f25db56f1f9e2eb2c61ef199048)
+LLNL-CODE-766763
+
+
+# Authors
+- Robert W. Anderson (LLNL)
+- William Arrighi (LLNL)
+- Kyle Chand (LLNL)
+- Siu Wun Cheung (LLNL)
+- Youngsoo Choi (LLNL)
+- Dylan Copeland (LLNL)
+- Kevin Huynh (LLNL)
+- Tanya Kostova-Vassilevska (LLNL)
+- Jessica Lauzon (Stanford)
+- Sean McBane (UT Austin)
+- Geoffrey Oxberry (LLNL)
diff --git a/build/.gitkeep b/build/.gitkeep
diff --git a/libROM_Design_and_Theory.pdf → docs/libROM_Design_and_Theory.pdf b/libROM_Design_and_Theory.pdf → docs/libROM_Design_and_Theory.pdf
diff --git a/examples/dmd/dg_advection.cpp b/examples/dmd/dg_advection.cpp
@@ -35,8 +35,8 @@
 //               are also illustrated.
 
 #include "mfem.hpp"
-#include "DMD.h"
-#include "Vector.h"
+#include "algo/DMD.h"
+#include "linalg/Vector.h"
 #include <cmath>
 #include <fstream>
 #include <iostream>

diff --git a/examples/dmd/dg_euler.cpp b/examples/dmd/dg_euler.cpp
@@ -43,8 +43,8 @@
 //               example.
 
 #include "mfem.hpp"
-#include "DMD.h"
-#include "Vector.h"
+#include "algo/DMD.h"
+#include "linalg/Vector.h"
 #include <cmath>
 #include <fstream>
 #include <sstream>

diff --git a/examples/dmd/heat_conduction.cpp b/examples/dmd/heat_conduction.cpp
@@ -28,8 +28,8 @@
 //               with ADIOS2 (adios2.readthedocs.io) is also illustrated.
 
 #include "mfem.hpp"
-#include "DMD.h"
-#include "Vector.h"
+#include "algo/DMD.h"
+#include "linalg/Vector.h"
 #include <cmath>
 #include <fstream>
 #include <iostream>

diff --git a/examples/dmd/nonlinear_elasticity.cpp b/examples/dmd/nonlinear_elasticity.cpp
@@ -36,8 +36,8 @@
 //               requirement for high-order implicit (SDIRK) time integration.
 
 #include "mfem.hpp"
-#include "DMD.h"
-#include "Vector.h"
+#include "algo/DMD.h"
+#include "linalg/Vector.h"
 #include <memory>
 #include <cmath>
 #include <iostream>

diff --git a/matlab/deim.m → examples/matlab/deim.m b/matlab/deim.m → examples/matlab/deim.m
diff --git a/matlab/dmd.m → examples/matlab/dmd.m b/matlab/dmd.m → examples/matlab/dmd.m
diff --git a/matlab/gnat.m → examples/matlab/gnat.m b/matlab/gnat.m → examples/matlab/gnat.m
diff --git a/matlab/qdeim.m → examples/matlab/qdeim.m b/matlab/qdeim.m → examples/matlab/qdeim.m
diff --git a/matlab/randomized_svd.m → examples/matlab/randomized_svd.m b/matlab/randomized_svd.m → examples/matlab/randomized_svd.m
diff --git a/matlab/second_diff.m → examples/matlab/second_diff.m b/matlab/second_diff.m → examples/matlab/second_diff.m
diff --git a/examples/prom/dg_advection_global_rom.cpp b/examples/prom/dg_advection_global_rom.cpp
@@ -44,9 +44,9 @@
 //               are also illustrated.
 
 #include "mfem.hpp"
-#include "Vector.h"
-#include "BasisGenerator.h"
-#include "BasisReader.h"
+#include "linalg/Vector.h"
+#include "linalg/BasisGenerator.h"
+#include "linalg/BasisReader.h"
 #include <cmath>
 #include <set>
 #include <fstream>

diff --git a/examples/prom/dg_advection_local_rom_matrix_interp.cpp b/examples/prom/dg_advection_local_rom_matrix_interp.cpp
@@ -51,11 +51,11 @@
 //               are also illustrated.
 
 #include "mfem.hpp"
-#include "Vector.h"
-#include "MatrixInterpolator.h"
-#include "VectorInterpolator.h"
-#include "BasisGenerator.h"
-#include "BasisReader.h"
+#include "linalg/Vector.h"
+#include "algo/manifold_interp/MatrixInterpolator.h"
+#include "algo/manifold_interp/VectorInterpolator.h"
+#include "linalg/BasisGenerator.h"
+#include "linalg/BasisReader.h"
 #include <cmath>
 #include <set>
 #include <fstream>
@@ -383,12 +383,12 @@ int main(int argc, char *argv[])
                    "Enable or disable matrix interpolation during the online phase.");
     args.AddOption(&interp_prep, "-interp_prep", "--interp_prep", "-no-interp_prep", "--no-interp_prep",
                    "Enable or disable matrix interpolation preparation during the online phase.");
-    args.AddOption(&ef, "-ef", "--energy_fraction",
-                   "Energy fraction.");
     args.AddOption(&rbf_type, "-rt", "--rbf_type",
                    "RBF type ('G' == gaussian, 'MQ'== multiquadric, 'IQ' == inverse quadratic, 'IMQ' == inverse multiquadric).");
     args.AddOption(&rbf_width, "-rw", "--rbf_width",
                    "RBF inverse width.");
+    args.AddOption(&ef, "-ef", "--energy_fraction",
+                   "Energy fraction.");
     args.AddOption(&rdim, "-rdim", "--rdim",
                    "Reduced dimension.");
     args.Parse();

diff --git a/examples/prom/mixed_nonlinear_diffusion.cpp b/examples/prom/mixed_nonlinear_diffusion.cpp
@@ -42,10 +42,10 @@
 #include <iostream>
 #include <algorithm>
 
-#include "BasisGenerator.h"
-#include "BasisReader.h"
-#include "DEIM.h"
-#include "SampleMesh.hpp"
+#include "linalg/BasisGenerator.h"
+#include "linalg/BasisReader.h"
+#include "hyperreduction/DEIM.h"
+#include "mfem/SampleMesh.hpp"
 
 
 typedef enum {ANALYTIC, INIT_STEP} PROBLEM;