Fix Sundials make config (#152)

* test: Add a test that uses sundials * ci: Disable fail-fast flag in CI * fix: Use SUNDIALS_TARGET in Makefile * Delete unnecessary old model --------- Co-authored-by: Brian Ward <[email protected]>
roualdes · Jul 6, 2023 · 7bf32a4 · 7bf32a4
1 parent ad320eb
commit 7bf32a4
Show file tree

Hide file tree

Showing 5 changed files with 23 additions and 8 deletions.
diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -14,6 +14,7 @@ jobs:
   build:
     runs-on: ${{matrix.os}}
     strategy:
+      fail-fast: false
       matrix:
         os: [windows-latest, ubuntu-latest, macos-latest]
     env:

diff --git a/Makefile b/Makefile
@@ -16,6 +16,7 @@ INC_FIRST ?= -I $(STAN)src -I $(RAPIDJSON)
 
 ## Set -fPIC globally since we're always building a shared library
 CXXFLAGS += -fPIC
+CXXFLAGS_SUNDIALS += -fPIC
 
 ## set flags for stanc compiler (math calls MIGHT? set STAN_OPENCL)
 ifdef STAN_OPENCL
@@ -56,12 +57,12 @@ $(BRIDGE_O) : $(BRIDGE_DEPS)
 .PRECIOUS: %.hpp
 
 ## builds executable (suffix depends on platform)
-%_model.so : %.hpp $(BRIDGE_O) $(LIBSUNDIALS) $(MPI_TARGETS) $(TBB_TARGETS)
+%_model.so : %.hpp $(BRIDGE_O) $(SUNDIALS_TARGETS) $(MPI_TARGETS) $(TBB_TARGETS)
 	@echo ''
 	@echo '--- Compiling C++ code ---'
 	$(COMPILE.cpp) -x c++ -o $(subst  \,/,$*).o $(subst \,/,$<)
 	@echo '--- Linking C++ code ---'
-	$(LINK.cpp) -shared -lm -o $(patsubst %.hpp, %_model.so, $(subst \,/,$<)) $(subst \,/,$*.o) $(BRIDGE_O) $(LDLIBS) $(LIBSUNDIALS) $(MPI_TARGETS) $(TBB_TARGETS)
+	$(LINK.cpp) -shared -lm -o $(patsubst %.hpp, %_model.so, $(subst \,/,$<)) $(subst \,/,$*.o) $(BRIDGE_O) $(LDLIBS) $(SUNDIALS_TARGETS) $(MPI_TARGETS) $(TBB_TARGETS)
 	$(RM) $(subst  \,/,$*).o
 
 .PHONY: docs
@@ -94,7 +95,7 @@ stan-update-remote:
 # print compilation command line config
 .PHONY: compile_info
 compile_info:
-	@echo '$(LINK.cpp) $(BRIDGE_O) $(LDLIBS) $(LIBSUNDIALS) $(MPI_TARGETS) $(TBB_TARGETS)'
+	@echo '$(LINK.cpp) $(BRIDGE_O) $(LDLIBS) $(SUNDIALS_TARGETS) $(MPI_TARGETS) $(TBB_TARGETS)'
 
 ## print value of makefile variable (e.g., make print-TBB_TARGETS)
 .PHONY: print-%

diff --git a/python/test/test_stanmodel.py b/python/test/test_stanmodel.py
@@ -42,6 +42,12 @@ def test_constructor():
     with pytest.raises(RuntimeError, match="find this text: datafails"):
         b4 = bs.StanModel(throw_data_so)
 
+    load_sundials = str(STAN_FOLDER / "ode_sundials" / "ode_sundials_model.so")
+    ode_sundials_data = (
+        STAN_FOLDER / "ode_sundials" / "ode_sundials.data.json"
+    ).read_text()
+    bs.StanModel(load_sundials, ode_sundials_data)
+
 
 def test_name():
     std_so = str(STAN_FOLDER / "stdnormal" / "stdnormal_model.so")

diff --git a/test_models/ode_sundials/ode_sundials.data.json b/test_models/ode_sundials/ode_sundials.data.json
@@ -0,0 +1,7 @@
+{
+    "T": 5,
+    "y0":[5.0, 6.0],
+    "t0": 0.0,
+    "ts": [1.0, 2.0, 3.0, 4.0, 5.0],
+    "theta": 0.1
+}
diff --git a/test_models/ode/ode.stan → test_models/ode_sundials/ode_sundials.stan b/test_models/ode/ode.stan → test_models/ode_sundials/ode_sundials.stan
@@ -1,6 +1,7 @@
-// example model from https://mc-stan.org/docs/stan-users-guide/measurement-error-models.html
 functions {
-  vector sho(real t, vector y, real theta) {
+  vector sho(real t,
+             vector y,
+             real theta) {
     vector[2] dydt;
     dydt[1] = y[2];
     dydt[2] = -y[1] - theta * y[2];
@@ -15,12 +16,11 @@ data {
   real theta;
 }
 model {
-
 }
 generated quantities {
-  array[T] vector[2] y_sim = ode_rk45(sho, y0, t0, ts, theta);
+  array[T] vector[2] y_sim = ode_bdf(sho, y0, t0, ts, theta);
   // add measurement error
-  for (t in 1 : T) {
+  for (t in 1:T) {
     y_sim[t, 1] += normal_rng(0, 0.1);
     y_sim[t, 2] += normal_rng(0, 0.1);
   }