Compile speedup

.github/workflows/main.yml

@@ -16,11 +16,11 @@ on:
 
 jobs:
   ubuntu-multiple-pythons:
-    name: Ubuntu with Python ${{ matrix.python-version }}
+    name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [ '3.5', '3.6', '3.7', '3.8', '3.9' ]
+        python-version: [ '3.6', '3.7', '3.8', '3.9' ]
         os: ['ubuntu-18.04', 'ubuntu-20.04']
       fail-fast: false
     steps:
@@ -40,7 +40,7 @@ jobs:
     - name: Install Python dependencies
       run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas
     - name: Build Cantera
-      run: python3 `which scons` build -j2
+      run: python3 `which scons` build -j2 debug=n
     - name: Test Cantera
       run: python3 `which scons` test
 
@@ -77,7 +77,7 @@ jobs:
     - name: Install Python dependencies
       run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas
     - name: Build Cantera
-      run: python3 `which scons` build -j2
+      run: python3 `which scons` build -j2 debug=n
     - name: Test Cantera
       run: python3 `which scons` test
 
@@ -101,15 +101,15 @@ jobs:
         architecture: x64
     - name: Install Apt dependencies
       run: |
-        sudo apt-get install libboost-dev gfortran liblapack-dev libblas-dev
+        sudo apt-get install libboost-dev gfortran liblapack-dev libblas-dev libsundials-dev
     - name: Upgrade pip
       run: python3 -m pip install -U pip setuptools wheel
     - name: Install Python dependencies
       run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas
     - name: Build Cantera
       run: |
         python3 `which scons` build blas_lapack_libs=lapack,blas coverage=y \
-        optimize=n -j2
+        optimize=n no_optimize_flags=-DNDEBUG -j2
     - name: Test Cantera
       run: python3 `which scons` test
     - name: Upload Coverage to Codecov
@@ -141,7 +141,7 @@ jobs:
           python3 -m pip install ruamel.yaml scons numpy cython sphinx\<4.0 \
           sphinxcontrib-katex sphinxcontrib-matlabdomain sphinxcontrib-doxylink
       - name: Build Cantera with documentation
-        run: python3 `which scons` build -j2 doxygen_docs=y sphinx_docs=y
+        run: python3 `which scons` build -j2 doxygen_docs=y sphinx_docs=y debug=n optimize=n
       # The known_hosts key is generated with `ssh-keygen -F cantera.org` from a
       # machine that has previously logged in to cantera.org and trusts
       # that it logged in to the right machine
@@ -180,7 +180,7 @@ jobs:
           python3-ruamel.yaml python-numpy cython3 libsundials-dev liblapack-dev \
           libblas-dev
       - name: Build Cantera
-        run: scons build python_cmd=/usr/bin/python3 blas_lapack_libs=lapack,blas -j2
+        run: scons build python_cmd=/usr/bin/python3 blas_lapack_libs=lapack,blas -j2 debug=n
       - name: Test Cantera
         run: scons test
 
@@ -189,7 +189,7 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        python-version: ['3.5', '3.6', '3.7', '3.8', '3.9']
+        python-version: ['3.6', '3.7', '3.8', '3.9']
       fail-fast: false
     steps:
       - uses: actions/checkout@v2
@@ -208,7 +208,7 @@ jobs:
       - name: Install Python dependencies
         run: python3 -m pip install ruamel.yaml scons numpy cython h5py pandas matplotlib scipy
       - name: Build Cantera
-        run: python3 `which scons` build -j2
+        run: python3 `which scons` build -j2 debug=n
       - name: Run the examples
         # See https://unix.stackexchange.com/a/392973 for an explanation of the -exec part
         run: |
@@ -254,7 +254,7 @@ jobs:
         run: |
           scons build extra_inc_dirs=$CONDA_PREFIX/include:$CONDA_PREFIX/include/eigen3 \
           extra_lib_dirs=$CONDA_PREFIX/lib system_fmt=y system_eigen=y system_yamlcpp=y \
-          system_sundials=y -j2 VERBOSE=True
+          system_sundials=y -j2 VERBOSE=True debug=n
         shell: bash -l {0}
       - name: Test Cantera
         run: scons test
@@ -282,7 +282,7 @@ jobs:
         python3 -m pip install ruamel.yaml scons numpy h5py pandas;
         python3 -m pip install https://github.com/cython/cython/archive/master.zip --install-option='--no-cython-compile';
     - name: Build Cantera
-      run: python3 `which scons` build blas_lapack_libs=lapack,blas python_package='full' -j2
+      run: python3 `which scons` build blas_lapack_libs=lapack,blas python_package='full' -j2 debug=n
     - name: Test Cantera
       run: python3 `which scons` test
 
@@ -293,13 +293,10 @@ jobs:
       matrix:
         os: ['windows-2019']
         vs-toolset: ['14.0', '14.2']
-        python-version: [ '3.5', '3.6', '3.7', '3.8', '3.9' ]
+        python-version: [ '3.6', '3.7', '3.8', '3.9' ]
         # Must use windows-2016 image because it installs VS2017 (MSVC 14.1)
         # Scons cannot find MSVC 14.1 when VS2019 is installed
         include:
-          - os: 'windows-2016'
-            vs-toolset: '14.1'
-            python-version: '3.5'
           - os: 'windows-2016'
             vs-toolset: '14.1'
             python-version: '3.6'

SConstruct

@@ -444,7 +444,12 @@ config_options = [
         'system_fmt',
         """Select whether to use the fmt library from a system installation
            ('y'), from a Git submodule ('n'), or to decide automatically
-           ('default').""",
+           ('default').  If you do not want to use the Git submodule and fmt
+           is not installed directly into system include and library
+           directories, then you will need to add those directories to
+           'extra_inc_dirs' and 'extra_lib_dirs'. This installation of fmt
+           must include the shared version of the library, for example,
+           'libfmt.so'.""",
         'default', ('default', 'y', 'n')),
     EnumVariable(
         'system_yamlcpp',
@@ -866,8 +871,9 @@ if not conf.CheckCXXHeader('cmath', '<>'):
     config_error('The C++ compiler is not correctly configured.')
 
 
-def get_expression_value(includes, expression):
-    s = ['#include ' + i for i in includes]
+def get_expression_value(includes, expression, defines=()):
+    s = ['#define ' + d for d in defines]
+    s.extend('#include ' + i for i in includes)
     s.extend(('#define Q(x) #x',
               '#define QUOTE(x) Q(x)',
               '#include <iostream>',
@@ -909,7 +915,7 @@ if env['system_fmt'] in ('n', 'default'):
                          '    git submodule update --init --recursive ext/fmt\n')
 
 fmt_include = '<fmt/format.h>' if env['system_fmt'] else '"../ext/fmt/include/fmt/format.h"'
-fmt_version_source = get_expression_value([fmt_include], 'FMT_VERSION')
+fmt_version_source = get_expression_value([fmt_include], 'FMT_VERSION', ['FMT_HEADER_ONLY'])
 retcode, fmt_lib_version = conf.TryRun(fmt_version_source, '.cpp')
 try:
     fmt_lib_version = divmod(float(fmt_lib_version.strip()), 10000)
@@ -1665,6 +1671,10 @@ else:
 linkLibs.extend(env['sundials_libs'])
 linkSharedLibs.extend(env['sundials_libs'])
 
+if env['system_fmt']:
+    linkLibs.append('fmt')
+    linkSharedLibs.append('fmt')
+
 if env['system_yamlcpp']:
     linkLibs.append('yaml-cpp')
     linkSharedLibs.append('yaml-cpp')

ext/SConscript

@@ -44,6 +44,10 @@ for subdir, extensions, prepFunction in libs:
 
 if not env['system_fmt']:
     license_files.append(('fmtlib', 'fmt/LICENSE.rst'))
+    localenv = prep_default(env)
+    localenv.Prepend(CPPPATH=Dir('#ext/fmt/include'))
+    libraryTargets.extend(
+        localenv.SharedObject(mglob(localenv, 'fmt/src', 'cc')))
     for name in ('format.h', 'ostream.h', 'printf.h', 'core.h', 'format-inl.h'):
         build(copyenv.Command("#include/cantera/ext/fmt/" + name,
                               "#ext/fmt/include/fmt/" + name,

include/cantera/base/AnyMap.h

@@ -7,13 +7,9 @@
 #define CT_ANYMAP_H
 
 #include "cantera/base/ct_defs.h"
-#include "cantera/base/global.h"
-#include "cantera/base/Units.h"
 #include "cantera/base/ctexceptions.h"
+#include "cantera/base/Units.h"
 
-#include <string>
-#include <vector>
-#include <memory>
 #include <unordered_map>
 #include <functional>
 

include/cantera/base/Array.h

@@ -8,10 +8,8 @@
 #ifndef CT_ARRAY_H
 #define CT_ARRAY_H
 
-#include "utilities.h"
-
+#include "ct_defs.h"
 #include <iostream>
-#include <cstring>
 
 namespace Cantera
 {
@@ -48,11 +46,7 @@ class Array2D
     /**
      * Default constructor. Create an empty array.
      */
-    Array2D() :
-        m_data(0),
-        m_nrows(0),
-        m_ncols(0) {
-    }
+    Array2D();
 
     //! Constructor.
     /*!
@@ -62,10 +56,7 @@ class Array2D
      * @param n   Number of columns
      * @param v   Default fill value. The default is 0.0
      */
-    Array2D(const size_t m, const size_t n, const doublereal v = 0.0)
-        :  m_data(0), m_nrows(m), m_ncols(n) {
-        m_data.assign(n*m, v);
-    }
+    Array2D(const size_t m, const size_t n, const double v=0.0);
 
     //! Constructor.
     /*!
@@ -77,43 +68,21 @@ class Array2D
      * @param values Initial values of the array. Must be of length m*n, and
      *     stored in column-major order.
      */
-    Array2D(const size_t m, const size_t n, const doublereal* values)
-        :  m_data(0), m_nrows(m), m_ncols(n) {
-        m_data.assign(values, values + n*m);
-    }
+    Array2D(const size_t m, const size_t n, const double* values);
 
-    Array2D(const Array2D& y) :
-        m_data(0),
-        m_nrows(0),
-        m_ncols(0) {
-        m_nrows = y.m_nrows;
-        m_ncols = y.m_ncols;
-        m_data = y.m_data;
-    }
+    Array2D(const Array2D& y);
 
     virtual ~Array2D() {}
 
-    Array2D& operator=(const Array2D& y) {
-        if (&y == this) {
-            return *this;
-        }
-        m_nrows = y.m_nrows;
-        m_ncols = y.m_ncols;
-        m_data = y.m_data;
-        return *this;
-    }
+    Array2D& operator=(const Array2D& y);
 
     //! Resize the array, and fill the new entries with 'v'
     /*!
      * @param n  This is the number of rows
      * @param m  This is the number of columns in the new matrix
      * @param v  Default fill value -> defaults to zero.
      */
-    void resize(size_t n, size_t m, doublereal v = 0.0) {
-        m_nrows = n;
-        m_ncols = m;
-        m_data.resize(n*m, v);
-    }
+    void resize(size_t n, size_t m, double v=0.0);
 
     //! Append a column to the existing matrix using a std vector
     /*!
@@ -122,13 +91,7 @@ class Array2D
      * @param c  This vector is the entries in the column to be added. It must
      *           have a length equal to m_nrows or greater.
      */
-    void appendColumn(const vector_fp& c) {
-        m_ncols++;
-        m_data.resize(m_nrows*m_ncols);
-        for (size_t m = 0; m < m_nrows; m++) {
-            value(m_ncols, m) = c[m];
-        }
-    }
+    void appendColumn(const vector_fp& c);
 
     //! Append a column to the existing matrix
     /*!
@@ -137,36 +100,22 @@ class Array2D
      * @param c  This vector of doubles is the entries in the column to be
      *           added. It must have a length equal to m_nrows or greater.
      */
-    void appendColumn(const doublereal* const c) {
-        m_ncols++;
-        m_data.resize(m_nrows*m_ncols);
-        for (size_t m = 0; m < m_nrows; m++) {
-            value(m_ncols, m) = c[m];
-        }
-    }
+    void appendColumn(const double* const c);
 
     //! Set the nth row to array rw
     /*!
      * @param  n   Index of the row to be changed
      * @param  rw  Vector for the row. Must have a length of m_ncols.
      */
-    void setRow(size_t n, const doublereal* const rw) {
-        for (size_t j = 0; j < m_ncols; j++) {
-            m_data[m_nrows*j + n] = rw[j];
-        }
-    }
+    void setRow(size_t n, const double* const rw);
 
     //! Get the nth row and return it in a vector
     /*!
      * @param n    Index of the row to be returned.
      * @param rw   Return Vector for the operation. Must have a length of
      *             m_ncols.
      */
-    void getRow(size_t n, doublereal* const rw) {
-        for (size_t j = 0; j < m_ncols; j++) {
-            rw[j] = m_data[m_nrows*j + n];
-        }
-    }
+    void getRow(size_t n, double* const rw);
 
     //! Set the values in column m to those in array col
     /*!
@@ -175,11 +124,7 @@ class Array2D
      * @param m   Column to set
      * @param col pointer to a col vector. Vector must have a length of m_nrows.
      */
-    void setColumn(size_t m, doublereal* const col) {
-        for (size_t i = 0; i < m_nrows; i++) {
-            m_data[m_nrows*m + i] = col[i];
-        }
-    }
+    void setColumn(size_t m, double* const col);
 
     //! Get the values in column m
     /*!
@@ -188,11 +133,7 @@ class Array2D
      * @param m    Column to set
      * @param col  pointer to a col vector that will be returned
      */
-    void getColumn(size_t m, doublereal* const col) {
-        for (size_t i = 0; i < m_nrows; i++) {
-            col[i] = m_data[m_nrows*m + i];
-        }
-    }
+    void getColumn(size_t m, double* const col);
 
     //! Set all of the entries to zero
     void zero() {
@@ -323,19 +264,7 @@ class Array2D
  * @param m   Object of type Array2D that you are querying
  * @returns a reference to the ostream.
  */
-inline std::ostream& operator<<(std::ostream& s, const Array2D& m)
-{
-    size_t nr = m.nRows();
-    size_t nc = m.nColumns();
-    for (size_t i = 0; i < nr; i++) {
-        s << m(i,0);
-        for (size_t j = 1; j < nc; j++) {
-            s << ", " << m(i,j);
-        }
-        s << std::endl;
-    }
-    return s;
-}
+std::ostream& operator<<(std::ostream& s, const Array2D& m);
 
 //! Overload the times equals operator for multiplication of a matrix and a
 //! scalar.
@@ -345,10 +274,7 @@ inline std::ostream& operator<<(std::ostream& s, const Array2D& m)
  * @param m   Matrix
  * @param a   scalar
  */
-inline void operator*=(Array2D& m, doublereal a)
-{
-    scale(m.begin(), m.end(), m.begin(), a);
-}
+void operator*=(Array2D& m, double a);
 
 }
 

include/cantera/base/FactoryBase.h

@@ -9,7 +9,6 @@
 #ifndef CT_FACTORY_BASE
 #define CT_FACTORY_BASE
 
-#include <vector>
 #include <mutex>
 #include <unordered_map>
 #include <functional>