arbor-sim · noraabiakar · Feb 24, 2022 · Feb 1, 2022 · Feb 1, 2022 · Feb 1, 2022
diff --git a/.github/workflows/test-everything.yml b/.github/workflows/test-everything.yml
@@ -83,6 +83,7 @@ jobs:
             mpi:   "ON",
             simd:  "OFF"
           }
+        variant: [shared, static]
     env:
         CC:         ${{ matrix.config.cc }}
         CXX:        ${{ matrix.config.cxx }}
@@ -149,13 +150,22 @@ jobs:
           mpic++ --show
           mpicc --show
           echo $PYTHONPATH
-      - name: Build arbor
+      - if:   ${{ matrix.variant == 'static' }}
+        name: Build arbor
         run: |
           mkdir build
           cd build
           cmake .. -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=${{ matrix.config.simd }} -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=${{ matrix.config.mpi }} -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_NEUROML=ON
           make -j4 tests examples pyarb html
           cd -
+      - if:   ${{ matrix.variant == 'shared' }}
+        name: Build arbor
+        run: |
+          mkdir build
+          cd build
+          cmake .. -DCMAKE_CXX_COMPILER=$CXX -DCMAKE_C_COMPILER=$CC -DARB_WITH_PYTHON=ON -DARB_VECTORIZE=${{ matrix.config.simd }} -DPython3_EXECUTABLE=`which python` -DARB_WITH_MPI=${{ matrix.config.mpi }} -DARB_USE_BUNDLED_LIBS=ON -DARB_WITH_NEUROML=ON -DBUILD_SHARED_LIBS=ON
+          make -j4 tests examples pyarb html
+          cd -
       - name: Install arbor
         run: |
           cd build

diff --git a/.gitignore b/.gitignore
@@ -24,6 +24,7 @@ __pycache__
 *.swq
 *.swm
 *.swl
+*~
 
 .cache
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -172,8 +172,11 @@ set(CMAKE_CXX_EXTENSIONS OFF)
 # Data and internal scripts go here
 set(ARB_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATAROOTDIR}/arbor)
 # Derived paths for arbor-build-catalogue
-file(RELATIVE_PATH ARB_REL_DATADIR ${CMAKE_INSTALL_FULL_BINDIR} ${CMAKE_INSTALL_FULL_DATAROOTDIR}/arbor)
-file(RELATIVE_PATH ARB_REL_PACKAGEDIR ${CMAKE_INSTALL_FULL_BINDIR} ${CMAKE_INSTALL_FULL_LIBDIR}/cmake/arbor)
+get_filename_component(absolute_full_bindir ${CMAKE_INSTALL_FULL_BINDIR} REALPATH)
+get_filename_component(absolute_full_datarootdir ${CMAKE_INSTALL_FULL_DATAROOTDIR} REALPATH)
+get_filename_component(absolute_full_libdir ${CMAKE_INSTALL_FULL_LIBDIR} REALPATH)
+file(RELATIVE_PATH ARB_REL_DATADIR ${absolute_full_bindir} ${absolute_full_datarootdir}/arbor)
+file(RELATIVE_PATH ARB_REL_PACKAGEDIR ${absolute_full_bindir} ${absolute_full_libdir}/cmake/arbor)
 
 # Interface library `arbor-config-defs` collects configure-time defines
 # for arbor, arborenv, arborio, of the form ARB_HAVE_XXX. These

diff --git a/arbor/CMakeLists.txt b/arbor/CMakeLists.txt
@@ -136,5 +136,10 @@ endif()
 
 set_target_properties(arbor PROPERTIES CUDA_RESOLVE_DEVICE_SYMBOLS ON)
 
+export_visibility(arbor)
+
+install(FILES ${CMAKE_CURRENT_BINARY_DIR}/include/arbor/export.hpp
+    DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/arbor)
+
 install(TARGETS arbor EXPORT arbor-targets ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
 
diff --git a/arbor/assert.cpp b/arbor/assert.cpp
@@ -6,7 +6,7 @@
 
 namespace arb {
 
-void abort_on_failed_assertion(
+void ARB_ARBOR_API abort_on_failed_assertion(
     const char* assertion,
     const char* file,
     int line,
@@ -22,7 +22,7 @@ void abort_on_failed_assertion(
     std::abort();
 }
 
-void ignore_failed_assertion(
+void ARB_ARBOR_API ignore_failed_assertion(
     const char* assertion,
     const char* file,
     int line,

diff --git a/arbor/backends/gpu/forest.hpp b/arbor/backends/gpu/forest.hpp
@@ -2,14 +2,15 @@
 
 #include <vector>
 
+#include <arbor/export.hpp>
 #include "tree.hpp"
 
 namespace arb {
 namespace gpu {
 
 using size_type = int;
 
-struct forest {
+struct ARB_ARBOR_API forest {
     forest(const std::vector<size_type>& p, const std::vector<size_type>& cell_cv_divs);
 
     void optimize();

diff --git a/arbor/backends/gpu/matrix_assemble.cu b/arbor/backends/gpu/matrix_assemble.cu
@@ -154,7 +154,7 @@ void assemble_matrix_interleaved(
 
 } // namespace kernels
 
-void assemble_matrix_flat(
+ARB_ARBOR_API void assemble_matrix_flat(
         fvm_value_type* d,
         fvm_value_type* rhs,
         const fvm_value_type* invariant_d,

diff --git a/arbor/backends/gpu/matrix_fine.cu b/arbor/backends/gpu/matrix_fine.cu
@@ -245,7 +245,7 @@ void solve_matrix_fine(
 
 } // namespace kernels
 
-void gather(
+ARB_ARBOR_API void gather(
     const fvm_value_type* from,
     fvm_value_type* to,
     const fvm_index_type* p,
@@ -257,7 +257,7 @@ void gather(
     kernels::gather<<<griddim, blockdim>>>(from, to, p, n);
 }
 
-void scatter(
+ARB_ARBOR_API void scatter(
     const fvm_value_type* from,
     fvm_value_type* to,
     const fvm_index_type* p,
@@ -269,7 +269,7 @@ void scatter(
     kernels::scatter<<<griddim, blockdim>>>(from, to, p, n);
 }
 
-void assemble_matrix_fine(
+ARB_ARBOR_API void assemble_matrix_fine(
     fvm_value_type* d,
     fvm_value_type* rhs,
     const fvm_value_type* invariant_d,
@@ -308,7 +308,7 @@ void assemble_matrix_fine(
 // num_levels   = [3, 2, 3, ...]
 // num_cells    = [2, 3, ...]
 // num_blocks   = level_start.size() - 1 = num_levels.size() = num_cells.size()
-void solve_matrix_fine(
+ARB_ARBOR_API void solve_matrix_fine(
     fvm_value_type* rhs,
     fvm_value_type* d,                     // diagonal values
     const fvm_value_type* u,               // upper diagonal (and lower diagonal as the matrix is SPD)

diff --git a/arbor/backends/gpu/matrix_fine.hpp b/arbor/backends/gpu/matrix_fine.hpp
@@ -1,5 +1,6 @@
 #include <arbor/fvm_types.hpp>
 
+#include <arbor/export.hpp>
 #include <ostream>
 
 namespace arb {
@@ -13,19 +14,19 @@ struct level_metadata {
 };
 
 // C wrappers around kernels
-void gather(
+ARB_ARBOR_API void gather(
     const fvm_value_type* from,
     fvm_value_type* to,
     const fvm_index_type* p,
     unsigned n);
 
-void scatter(
+ARB_ARBOR_API void scatter(
     const fvm_value_type* from,
     fvm_value_type* to,
     const fvm_index_type* p,
     unsigned n);
 
-void assemble_matrix_fine(
+ARB_ARBOR_API void assemble_matrix_fine(
     fvm_value_type* d,
     fvm_value_type* rhs,
     const fvm_value_type* invariant_d,
@@ -39,7 +40,7 @@ void assemble_matrix_fine(
     const fvm_index_type* perm,
     unsigned n);
 
-void solve_matrix_fine(
+ARB_ARBOR_API void solve_matrix_fine(
     fvm_value_type* rhs,
     fvm_value_type* d,                     // diagonal values
     const fvm_value_type* u,               // upper diagonal (and lower diagonal as the matrix is SPD)

diff --git a/arbor/backends/gpu/matrix_solve.cu b/arbor/backends/gpu/matrix_solve.cu
@@ -86,7 +86,7 @@ void solve_matrix_interleaved(
 
 } // namespace kernels
 
-void solve_matrix_flat(
+ARB_ARBOR_API void solve_matrix_flat(
     fvm_value_type* rhs,
     fvm_value_type* d,
     const fvm_value_type* u,

diff --git a/arbor/backends/gpu/matrix_state_flat.hpp b/arbor/backends/gpu/matrix_state_flat.hpp
@@ -1,5 +1,6 @@
 #pragma once
 
+#include <arbor/export.hpp>
 #include <arbor/fvm_types.hpp>
 
 #include "memory/memory.hpp"
@@ -13,15 +14,15 @@ namespace gpu {
 
 // CUDA implementation entry points:
 
-void solve_matrix_flat(
+ARB_ARBOR_API void solve_matrix_flat(
     fvm_value_type* rhs,
     fvm_value_type* d,
     const fvm_value_type* u,
     const fvm_index_type* p,
     const fvm_index_type* cell_cv_divs,
     int num_mtx);
 
-void assemble_matrix_flat(
+ARB_ARBOR_API void assemble_matrix_flat(
     fvm_value_type* d,
     fvm_value_type* rhs,
     const fvm_value_type* invariant_d,

diff --git a/arbor/backends/gpu/multi_event_stream.hpp b/arbor/backends/gpu/multi_event_stream.hpp
@@ -2,6 +2,7 @@
 
 // Indexed collection of pop-only event queues --- CUDA back-end implementation.
 
+#include <arbor/export.hpp>
 #include <arbor/arbexcept.hpp>
 #include <arbor/common_types.hpp>
 #include <arbor/fvm_types.hpp>
@@ -18,7 +19,7 @@ namespace arb {
 namespace gpu {
 
 // Base class provides common implementations across event types.
-class multi_event_stream_base {
+class ARB_ARBOR_API multi_event_stream_base {
 public:
     using size_type = cell_size_type;
     using value_type = fvm_value_type;

diff --git a/arbor/backends/gpu/shared_state.cpp b/arbor/backends/gpu/shared_state.cpp
@@ -459,7 +459,7 @@ void shared_state::take_samples(const sample_event_stream::state& s, array& samp
 }
 
 // Debug interface
-std::ostream& operator<<(std::ostream& o, shared_state& s) {
+ARB_ARBOR_API std::ostream& operator<<(std::ostream& o, shared_state& s) {
     o << " cv_to_intdom " << s.cv_to_intdom << "\n";
     o << " time         " << s.time << "\n";
     o << " time_to      " << s.time_to << "\n";

diff --git a/arbor/backends/gpu/shared_state.hpp b/arbor/backends/gpu/shared_state.hpp
@@ -28,7 +28,7 @@ namespace gpu {
  *     Xo_     cao              external calcium concentration
  */
 
-struct ion_state {
+struct ARB_ARBOR_API ion_state {
     iarray node_index_; // Instance to CV map.
     array iX_;          // (A/m²) current density
     array eX_;          // (mV) reversal potential
@@ -62,7 +62,7 @@ struct ion_state {
     void reset();
 };
 
-struct istim_state {
+struct ARB_ARBOR_API istim_state {
     // Immutable data (post construction/initialization):
     iarray accu_index_;     // Instance to accumulator index (accu_stim_ index) map.
     iarray accu_to_cv_;     // Accumulator index to CV map.
@@ -99,7 +99,7 @@ struct istim_state {
     istim_state() = default;
 };
 
-struct shared_state {
+struct ARB_ARBOR_API shared_state {
     struct mech_storage {
         array data_;
         iarray indices_;
@@ -202,7 +202,7 @@ struct shared_state {
 };
 
 // For debugging only
-std::ostream& operator<<(std::ostream& o, shared_state& s);
+ARB_ARBOR_API std::ostream& operator<<(std::ostream& o, shared_state& s);
 
 } // namespace gpu
 } // namespace arb
diff --git a/arbor/backends/gpu/stimulus.cu b/arbor/backends/gpu/stimulus.cu
@@ -52,7 +52,7 @@ void istim_add_current_impl(int n, istim_pp pp) {
 
 } // namespace kernel
 
-void istim_add_current_impl(int n, const istim_pp& pp) {
+ARB_ARBOR_API void istim_add_current_impl(int n, const istim_pp& pp) {
     constexpr unsigned block_dim = 128;
     const unsigned grid_dim = impl::block_count(n, block_dim);
     if (!grid_dim) return;

diff --git a/arbor/backends/gpu/stimulus.hpp b/arbor/backends/gpu/stimulus.hpp
@@ -1,5 +1,6 @@
 #pragma once
 
+#include <arbor/export.hpp>
 #include <arbor/fvm_types.hpp>
 
 namespace arb {
@@ -25,7 +26,7 @@ struct istim_pp {
     fvm_value_type* current_density;
 };
 
-void istim_add_current_impl(int n, const istim_pp& pp);
+ARB_ARBOR_API void istim_add_current_impl(int n, const istim_pp& pp);
 
 } // namespace gpu
 } // namespace arb
diff --git a/arbor/backends/multicore/shared_state.cpp b/arbor/backends/multicore/shared_state.cpp
@@ -347,7 +347,7 @@ void shared_state::take_samples(
 }
 
 // (Debug interface only.)
-std::ostream& operator<<(std::ostream& out, const shared_state& s) {
+ARB_ARBOR_API std::ostream& operator<<(std::ostream& out, const shared_state& s) {
     using io::csv;
 
     out << "n_intdom     " << s.n_intdom << "\n";

diff --git a/arbor/backends/multicore/shared_state.hpp b/arbor/backends/multicore/shared_state.hpp
@@ -7,6 +7,7 @@
 #include <utility>
 #include <vector>
 
+#include <arbor/export.hpp>
 #include <arbor/assert.hpp>
 #include <arbor/common_types.hpp>
 #include <arbor/fvm_types.hpp>
@@ -38,7 +39,7 @@ namespace multicore {
  *     Xo_     cao              external calcium concentration
  */
 
-struct ion_state {
+struct ARB_ARBOR_API ion_state {
     unsigned alignment = 1; // Alignment and padding multiple.
 
     iarray node_index_;     // Instance to CV map.
@@ -73,7 +74,7 @@ struct ion_state {
     void reset();
 };
 
-struct istim_state {
+struct ARB_ARBOR_API istim_state {
     unsigned alignment = 1; // Alignment and padding multiple.
 
     // Immutable data (post initialization):
@@ -105,7 +106,7 @@ struct istim_state {
     istim_state() = default;
 };
 
-struct shared_state {
+struct ARB_ARBOR_API shared_state {
     struct mech_storage {
         array data_;
         iarray indices_;
@@ -207,7 +208,7 @@ struct shared_state {
 };
 
 // For debugging only:
-std::ostream& operator<<(std::ostream& o, const shared_state& s);
+ARB_ARBOR_API std::ostream& operator<<(std::ostream& o, const shared_state& s);
 
 
 } // namespace multicore

diff --git a/arbor/cable_cell_param.cpp b/arbor/cable_cell_param.cpp
@@ -12,7 +12,7 @@
 
 namespace arb {
 
-void check_global_properties(const cable_cell_global_properties& G) {
+ARB_ARBOR_API void check_global_properties(const cable_cell_global_properties& G) {
     auto& param = G.default_parameters;
 
     if (!param.init_membrane_potential) {

diff --git a/arbor/common_types_io.cpp b/arbor/common_types_io.cpp
@@ -4,7 +4,7 @@
 
 namespace arb {
 
-std::ostream& operator<<(std::ostream& o, lid_selection_policy policy) {
+ARB_ARBOR_API std::ostream& operator<<(std::ostream& o, lid_selection_policy policy) {
     switch (policy) {
     case lid_selection_policy::round_robin:
         return o << "round_robin";
@@ -14,11 +14,11 @@ std::ostream& operator<<(std::ostream& o, lid_selection_policy policy) {
     return o;
 }
 
-std::ostream& operator<<(std::ostream& o, arb::cell_member_type m) {
+ARB_ARBOR_API std::ostream& operator<<(std::ostream& o, arb::cell_member_type m) {
     return o << m.gid << ':' << m.index;
 }
 
-std::ostream& operator<<(std::ostream& o, arb::cell_kind k) {
+ARB_ARBOR_API std::ostream& operator<<(std::ostream& o, arb::cell_kind k) {
     o << "cell_kind::";
     switch (k) {
     case arb::cell_kind::spike_source:
@@ -33,7 +33,7 @@ std::ostream& operator<<(std::ostream& o, arb::cell_kind k) {
     return o;
 }
 
-std::ostream& operator<<(std::ostream& o, arb::backend_kind k) {
+ARB_ARBOR_API std::ostream& operator<<(std::ostream& o, arb::backend_kind k) {
     o << "backend_kind::";
     switch (k) {
     case arb::backend_kind::multicore:
-Original file line number
+Diff line change
@@ Expand Up / @@ -24,6 +24,7 @@ __pycache__ @@
     *.swq
     *.swm
     *.swl
+    *~
     .cache
@@ Expand Down @@