Add Levenberg-Marquardt model calibration

.github/workflows/documentation.yml

@@ -12,7 +12,7 @@ jobs:
         run: mkdir docs/html
       - name: Build doxygen documentation
         continue-on-error: true
-        uses: mattnotmitt/[email protected].4
+        uses: mattnotmitt/[email protected].5
         with:
           working-directory: '.'
           doxyfile-path: 'docs/cpp/Doxyfile'

.github/workflows/test.yml

@@ -8,20 +8,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-18.04, ubuntu-20.04, ubuntu-22.04, macos-11, macos-12]
+        os: [ubuntu-20.04, ubuntu-22.04, macos-11, macos-12]
       fail-fast: false
     steps:
       - uses: actions/checkout@v2
       - name: Install ubuntu dependencies
         if: ${{ matrix.os == 'ubuntu-*' }}
         run: sudo apt update && sudo apt install build-essential cmake
-      - name: Build svZeroDSolver
-        run: |
-          mkdir Release
-          cd Release
-          cmake -DCMAKE_BUILD_TYPE=Release ..
-          cmake --build .
-      - name: Install test dependencies
+      - name: Install svZeroDPlus
         run: |
           conda create -n zerod python=3.9
           conda run -n zerod pip install pytest pytest-cov pytest-mock

.gitignore

@@ -28,3 +28,5 @@ docs/python/build
 Release*/
 Debug*/
 externals/
+*.so
+build

CMakeLists.txt

@@ -4,17 +4,6 @@ set(CMAKE_CXX_STANDARD_REQUIRED True)
 project(svZeroDSolver)
 include(FetchContent)
 
-# -----------------------------------------------------------------------------
-# Fetch simdjson
-# -----------------------------------------------------------------------------
-set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-FetchContent_Declare(
-  simdjson
-  GIT_REPOSITORY https://github.com/simdjson/simdjson.git
-  GIT_TAG  master
-  GIT_SHALLOW TRUE)
-FetchContent_MakeAvailable(simdjson)
-
 # -----------------------------------------------------------------------------
 # Fetch Eigen
 # -----------------------------------------------------------------------------
@@ -44,17 +33,41 @@ if(NOT pybind11_POPULATED)
     add_subdirectory(${pybind11_SOURCE_DIR} ${pybind11_BINARY_DIR})
 endif()
 
+# -----------------------------------------------------------------------------
+# Fetch nlohmann/json
+# -----------------------------------------------------------------------------
+FetchContent_Declare(
+    json
+    URL https://github.com/nlohmann/json/releases/download/v3.11.2/json.tar.xz
+)
+FetchContent_MakeAvailable(json)
+
+# -----------------------------------------------------------------------------
+# Fetch pybind11_json
+# -----------------------------------------------------------------------------
+FetchContent_Declare(
+    pybind11_json
+    GIT_REPOSITORY https://github.com/pybind/pybind11_json.git
+    GIT_TAG        master
+)
+FetchContent_MakeAvailable(pybind11_json)
+
 # -----------------------------------------------------------------------------
 # Set executable and python library
 # -----------------------------------------------------------------------------
-add_executable(svzerodsolver src/main.cpp)
-pybind11_add_module(libsvzerodsolver src/python.cpp)
+include_directories(src)
+add_executable(svzerodsolver applications/svzerodsolver.cpp)
+add_executable(svzerodcalibrator applications/svzerodcalibrator.cpp)
+pybind11_add_module(svzerodplus EXCLUDE_FROM_ALL applications/svzerodplus.cpp)
 add_subdirectory("src/interface")
 
 # -----------------------------------------------------------------------------
 # Link libraries
 # -----------------------------------------------------------------------------
 target_link_libraries(svzerodsolver PRIVATE Eigen3::Eigen)
-target_link_libraries(svzerodsolver PRIVATE simdjson)
-target_link_libraries(libsvzerodsolver PRIVATE Eigen3::Eigen)
-target_link_libraries(libsvzerodsolver PRIVATE simdjson)
+target_link_libraries(svzerodsolver PRIVATE nlohmann_json::nlohmann_json)
+target_link_libraries(svzerodcalibrator PRIVATE Eigen3::Eigen)
+target_link_libraries(svzerodcalibrator PRIVATE nlohmann_json::nlohmann_json)
+target_link_libraries(svzerodplus PRIVATE Eigen3::Eigen)
+target_link_libraries(svzerodplus PRIVATE nlohmann_json::nlohmann_json)
+target_link_libraries(svzerodplus PRIVATE pybind11_json)

applications/svzerodcalibrator.cpp

@@ -0,0 +1,64 @@
+// Copyright (c) Stanford University, The Regents of the University of
+//               California, and others.
+//
+// All Rights Reserved.
+//
+// See Copyright-SimVascular.txt for additional details.
+//
+// Permission is hereby granted, free of charge, to any person obtaining
+// a copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to
+// permit persons to whom the Software is furnished to do so, subject
+// to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+// IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+// TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+// PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+// OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+/**
+ * @file svzerodcalibrator.cpp
+ * @brief Main routine for svZeroDCalibrator
+ */
+#include "optimize/calibrate.hpp"
+
+// Setting scalar type to double
+typedef double T;
+
+int main(int argc, char* argv[]) {
+  DEBUG_MSG("Starting svZeroDCalibrator");
+
+  // Get input and output file name
+  if (argc != 3) {
+    std::cout
+        << "Usage: svzerodcalibrator path/to/config.json path/to/output.json"
+        << std::endl;
+    exit(1);
+  }
+
+  // Get input and output file names
+  std::string input_file = argv[1];
+  std::string output_file = argv[2];
+
+  // Parse the configuration
+  DEBUG_MSG("Parse configuration");
+  std::ifstream ifs(input_file);
+  const auto& config = nlohmann::json::parse(ifs);
+
+  auto output_config = OPT::calibrate<T>(config);
+
+  // Write optimized simulation config
+  std::ofstream o(output_file);
+  o << std::setw(4) << output_config << std::endl;
+}

applications/svzerodplus.cpp

@@ -0,0 +1,104 @@
+// Copyright (c) Stanford University, The Regents of the University of
+//               California, and others.
+//
+// All Rights Reserved.
+//
+// See Copyright-SimVascular.txt for additional details.
+//
+// Permission is hereby granted, free of charge, to any person obtaining
+// a copy of this software and associated documentation files (the
+// "Software"), to deal in the Software without restriction, including
+// without limitation the rights to use, copy, modify, merge, publish,
+// distribute, sublicense, and/or sell copies of the Software, and to
+// permit persons to whom the Software is furnished to do so, subject
+// to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included
+// in all copies or substantial portions of the Software.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+// IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+// TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+// PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+// OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+/**
+ * @file svzerodplus.cpp
+ * @brief Python interface for svZeroDSolver
+ */
+#include <pybind11/eigen.h>
+#include <pybind11/operators.h>
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include "optimize/calibrate.hpp"
+#include "pybind11_json/pybind11_json.hpp"
+#include "solve/solver.hpp"
+
+namespace py = pybind11;
+
+PYBIND11_MODULE(svzerodplus, m) {
+  using Solver = SOLVE::Solver<double>;
+  m.doc() = "svZeroDSolver";
+  py::class_<Solver>(m, "Solver")
+      .def(py::init([](py::dict& config) {
+        const nlohmann::json& config_json = config;
+        return Solver(config_json);
+      }))
+      .def(py::init([](std::string config_file) {
+        std::ifstream ifs(config_file);
+        const auto& config_json = nlohmann::json::parse(ifs);
+        return Solver(config_json);
+      }))
+      .def("copy", [](Solver& solver) { return Solver(solver); })
+      .def("run", &Solver::run)
+      .def("get_single_result", &Solver::get_single_result)
+      .def("get_single_result_avg", &Solver::get_single_result_avg)
+      .def("update_block_params", &Solver::update_block_params);
+
+  m.def("simulate", [](py::dict& config) {
+    const nlohmann::json& config_json = config;
+    auto solver = Solver(config_json);
+    solver.run();
+    return solver.get_full_result();
+  });
+  m.def("calibrate", [](py::dict& config) {
+    const nlohmann::json& config_json = config;
+    return OPT::calibrate<double>(config);
+  });
+  m.def("run_simulation_cli", []() {
+    py::module_ sys = py::module_::import("sys");
+    auto argv = sys.attr("argv").cast<std::vector<std::string>>();
+    if (argv.size() != 3) {
+      std::cout
+          << "Usage: svzerodsolver path/to/config.json path/to/output.json"
+          << std::endl;
+      exit(1);
+    }
+    std::ifstream ifs(argv[1]);
+    const auto& config = nlohmann::json::parse(ifs);
+    auto solver = SOLVE::Solver<double>(config);
+    solver.run();
+    solver.write_result_to_csv(argv[2]);
+  });
+  m.def("run_calibration_cli", []() {
+    py::module_ sys = py::module_::import("sys");
+    auto argv = sys.attr("argv").cast<std::vector<std::string>>();
+    if (argv.size() != 3) {
+      std::cout
+          << "Usage: svzerodcalibrator path/to/config.json path/to/output.json"
+          << std::endl;
+      exit(1);
+    }
+    std::ifstream ifs(argv[1]);
+    const auto& config = nlohmann::json::parse(ifs);
+    auto output_config = OPT::calibrate<double>(config);
+    std::ofstream o(argv[2]);
+    o << std::setw(4) << output_config << std::endl;
+  });
+}

src/main.cpp → applications/svzerodsolver.cpp

@@ -28,10 +28,10 @@
 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 /**
- * @file main.cpp
+ * @file svzerodsolver.cpp
  * @brief Main routine of svZeroDSolver
  */
-#include "main.hpp"
+#include "solve/solver.hpp"
 
 /**
  *
@@ -50,28 +50,37 @@
  * @param argv Command line arguments
  * @return Return code
  */
-int main(int argc, char *argv[]) {
+int main(int argc, char* argv[]) {
   DEBUG_MSG("Starting svZeroDSolver");
 
   // Get input and output file name
-  if (argc != 3) {
-    std::cout << "Usage: svzerodsolver path/to/config.json path/to/output.csv"
-              << std::endl;
-    exit(1);
+  if (argc < 2 && argc > 3) {
+    std::runtime_error(
+        "Usage: svzerodsolver path/to/config.json "
+        "(optional:path/to/output.csv)");
   }
   std::string input_file = argv[1];
-  std::string output_file = argv[2];
-
-  std::ifstream input_file_stream(input_file);
-  std::stringstream buffer;
-  buffer << input_file_stream.rdbuf();
-  std::string config = buffer.str();
+  std::string output_file;
+  if (argc == 3) {
+    output_file = argv[2];
+  } else {
+    // If output file is not provided, default is <path to .json>+"output.csv"
+    std::size_t end_of_path = input_file.rfind("/");
+    if (end_of_path == std::string::npos) {
+      end_of_path = input_file.rfind("\\");  // For Windows paths (?)
+      if (end_of_path == std::string::npos) {
+        std::runtime_error("Could not find path to .json file.");
+      }
+    }
+    output_file = input_file.substr(0, end_of_path) + "output.csv";
+  }
 
-  auto output = run(config);
+  std::ifstream ifs(input_file);
+  const auto& config = nlohmann::json::parse(ifs);
 
-  std::ofstream ofs(output_file);
-  ofs << output;
-  ofs.close();
+  auto solver = SOLVE::Solver<double>(config);
+  solver.run();
+  solver.write_result_to_csv(output_file);
 
   return 0;
 }

container/profiling/Dockerfile

@@ -0,0 +1,32 @@
+FROM ubuntu:22.04
+
+# Install dependencies
+RUN apt-get -q update && \
+    DEBIAN_FRONTEND=noninteractive \
+    TZ=Europe/Berlin \
+    apt-get -q -y --no-install-recommends install \
+    git \
+    gcc \
+    g++ \
+    make \
+    cmake \
+    python3 \
+    python3-dev \
+    ca-certificates \
+    google-perftools \
+    libgoogle-perftools-dev \
+    graphviz \
+    ghostscript \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY . /opt/svzerodplus
+
+RUN mkdir -p /opt/svzerodplus-build/relwithdebinfo && \
+    cd /opt/svzerodplus-build/relwithdebinfo && \
+    cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo /opt/svzerodplus && \
+    cmake --build . --target svzerodsolver
+
+WORKDIR /opt/data
+RUN chmod +x /opt/svzerodplus/container/profiling/entrypoint.sh
+ENTRYPOINT ["/opt/svzerodplus/container/profiling/entrypoint.sh"]

container/profiling/entrypoint.sh

@@ -0,0 +1,5 @@
+#! /bin/bash
+
+export LIBPROFILER=$(find /usr/lib -name "libprofiler.so")
+LD_PRELOAD=$LIBPROFILER CPUPROFILE=/opt/main.prof CPUPROFILE_FREQUENCY=100000 /opt/svzerodplus-build/relwithdebinfo/svzerodsolver $@ /opt/output.csv
+google-pprof --pdf /opt/svzerodplus-build/relwithdebinfo/svzerodsolver /opt/main.prof > profiling_report.pdf