smoke tests on all platforms

.github/workflows/cd.yml

@@ -64,6 +64,7 @@ jobs:
           brew install llvm
           echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
           source /Users/runner/.bash_profile
+          ln -s $(which gfortran-14) /usr/local/bin/gfortran
 
           gcc --version
           gfortran --version
@@ -218,7 +219,7 @@ jobs:
           mkdir build
           cd build
 
-          PATH="/c/Program\ Files/LLVM/bin:$PATH"
+          export PATH="/c/Program\ Files/LLVM/bin:$PATH"
 
           cmake \
           -G Ninja \
@@ -248,6 +249,9 @@ jobs:
           echo "working dir is $PWD"
 
           cd build
+
+          export PATH="/d/a/_temp/msys64/clang64/bin:$PATH"
+          pacman -Sy --noconfirm diffutils
 
           ctest -VV
 

.gitignore

@@ -19,3 +19,8 @@
 /all_solvers/*
 
 .DS_Store
+
+NFsim_v1.11/tests/smoke/SimID_273069657_0_.gdat
+NFsim_v1.11/tests/smoke/SimID_273069657_0_.species
+
+IDAWin/tests/smoke/SimID_1489333437_0_.ida

CMakeLists.txt

@@ -127,7 +127,13 @@ if (${OPTION_TARGET_DOCS})
 endif()
 
 if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
+	if (APPLE)
+		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
+	elseif (MINGW)
+		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
+	else ()
+		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libstdc++")
+	endif()
     set(CMAKE_OSX_DEPLOYMENT_TARGET "10.7" CACHE STRING "Choose minimum deploy target for Macos machines")
 endif()
 

Dockerfile

@@ -1,28 +1,11 @@
-FROM ubuntu:20.04 as build
+FROM python:3.9.7-slim AS build
 
 RUN apt-get -y update && apt-get install -y apt-utils && \
     apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran zlib1g-dev \
-    libhdf5-dev libcurl4-openssl-dev libboost-dev cmake wget python
-
-#
-# build PETSc with mpich for static linking
-#
-RUN mkdir /usr/local/petsc && \
-    cd /usr/local/petsc && \
-    wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.7.7.tar.gz && \
-    tar xzf petsc-3.7.7.tar.gz && \
-    cd petsc-3.7.7 && \
-    ./configure --with-shared-libraries=0 --download-fblaslapack=1 --with-debugging=1 --download-mpich && \
-    make PETSC_DIR=/usr/local/petsc/petsc-3.7.7 PETSC_ARCH=arch-linux2-c-debug all
-
-ENV PETSC_DIR=/usr/local/petsc/petsc-3.7.7 \
-    PETSC_ARCH=arch-linux2-c-debug
+    libhdf5-dev libcurl4-openssl-dev libboost-dev cmake wget python3 python3-pip
 
 COPY . /vcellroot
 
-#
-# build most solvers, and FiniteVolume without PETSc (FiniteVolume_x64)
-#
 RUN mkdir -p /vcellroot/build/bin
 WORKDIR /vcellroot/build
 
@@ -41,33 +24,9 @@ RUN /usr/bin/cmake \
     -DOPTION_TARGET_HY3S_SOLVERS=OFF \
     .. && \
     make && \
-    ctest
-
-#
-# build FiniteVolume with PETSc (FiniteVolume_PETSc_x64)
-#
-RUN mkdir -p /vcellroot/build_PETSc/bin
-WORKDIR /vcellroot/build_PETSc
-
-RUN /usr/bin/cmake \
-    -DOPTION_TARGET_MESSAGING=ON \
-    -DOPTION_TARGET_PARALLEL=OFF \
-    -DOPTION_TARGET_PETSC=ON \
-    -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-    -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-    -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
-    -DOPTION_TARGET_FV_SOLVER=ON \
-    -DOPTION_TARGET_STOCHASTIC_SOLVER=OFF \
-    -DOPTION_TARGET_NFSIM_SOLVER=OFF \
-    -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
-    -DOPTION_TARGET_SUNDIALS_SOLVER=OFF \
-    -DOPTION_TARGET_HY3S_SOLVERS=OFF \
-    .. && \
-    make && \
-    ctest
-
+    ctest -VV
 
-FROM eclipse-temurin:17 as jre-build
+FROM eclipse-temurin:17 AS jre-build
 
 # Create a custom Java runtime
 RUN $JAVA_HOME/bin/jlink \
@@ -81,22 +40,21 @@ RUN $JAVA_HOME/bin/jlink \
 # Define base image and copy in jlink created minimal Java 17 environment
 FROM python:3.9.7-slim
 ENV JAVA_HOME=/opt/java/openjdk
-ENV PATH "${JAVA_HOME}/bin:${PATH}"
+ENV PATH="${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17 and Python 3.9
-ENV DEBIAN_FRONTEND noninteractive
+ENV DEBIAN_FRONTEND=noninteractive
 ENV LANG=en_US.UTF-8
 
-RUN apt-get update && \
+RUN apt-get -y update && \
     apt-get install -y apt-utils && \
     apt-get install -q -y --no-install-recommends curl dnsutils
 
-RUN apt-get install -qq -y -o=Dpkg::Use-Pty=0 gcc gfortran zlib1g \
+RUN apt-get install -y -qq -o=Dpkg::Use-Pty=0 gcc gfortran zlib1g \
     libhdf5-103 libhdf5-cpp-103 libcurl4-openssl-dev zip
 
 COPY --from=build /vcellroot/build/bin /vcellbin
-COPY --from=build /vcellroot/build_PETSc/bin/FiniteVolume_PETSc_x64 /vcellbin/
+
 WORKDIR /vcellbin
 ENV PATH=/vcellbin:$PATH
-

IDAWin/CMakeLists.txt

@@ -35,6 +35,19 @@ install(TARGETS IDAWin ARCHIVE DESTINATION bin)
 
 enable_testing()
 
+if (MINGW)
+	set(test_sundials_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE}.exe)
+	set(python_cmd py)
+else (MINGW)
+	set(test_sundials_exe ${CMAKE_BINARY_DIR}/bin/${EXE_FILE})
+	set(python_cmd python3)
+endif (MINGW)
+set(test_dir ${CMAKE_CURRENT_SOURCE_DIR}/tests/smoke)
+
+# smoke test as a python script, for bash test example, see NFsim/tests/smoke
+add_test(NAME ${EXE_FILE}_smoke COMMAND ${python_cmd} ${test_dir}/smoke.py ${test_sundials_exe} WORKING_DIRECTORY ${test_dir})
+
+
 add_executable(
 		hello_test
 		hello_test.cpp

IDAWin/SundialsSolverStandalone.cpp

@@ -194,6 +194,12 @@ int main(int argc, char *argv[]) {
 				break;
 			}
 		}
+#ifdef USE_MESSAGING
+		// should only happen during testing for solver compiled with messaging but run locally.
+		if (SimulationMessaging::getInstVar() == nullptr) {
+			SimulationMessaging::create();
+		}
+#endif
 
 		if (solver.empty()) {
 			throw "Solver not defined ";

IDAWin/tests/smoke/SimID_1489333437_0_.cvodeInput

@@ -0,0 +1,14 @@
+SOLVER CVODE
+STARTING_TIME 0.0
+ENDING_TIME 1.0
+RELATIVE_TOLERANCE 1.0E-9
+ABSOLUTE_TOLERANCE 1.0E-9
+MAX_TIME_STEP 1.0
+OUTPUT_TIMES 8
+0.0 1.0E-5 1.0E-4 0.001 0.01 0.1 0.5 1.0
+NUM_EQUATIONS 2
+ODE s2 INIT 4.0;
+	 RATE  - ((2.0 * (-1.0 + (0.5 * s2)) * s2) - (4.0 * (3.5 - (0.5 * s2))));
+ODE s4 INIT 0.0;
+	 RATE 0.0;
+

IDAWin/tests/smoke/SimID_1489333437_0_.functions

@@ -0,0 +1,10 @@
+##---------------------------------------------
+##  /Users/jimschaff/.vcell/simdata/temp/SimID_1489333437_0_.functions
+##---------------------------------------------
+
+Compartment::J_r0; ((2.0 * (-1.0 + (0.5 * s2)) * s2) - (4.0 * (3.5 - (0.5 * s2)))); ; Nonspatial_VariableType; false
+Compartment::J_r1; 0.0; ; Nonspatial_VariableType; false
+Compartment::s0; (2.0 * (-1.0 + (0.5 * s2))); ; Nonspatial_VariableType; false
+Compartment::s1; (2.0 * (3.5 - (0.5 * s2))); ; Nonspatial_VariableType; false
+Compartment::s3;  - s4; ; Nonspatial_VariableType; false
+

IDAWin/tests/smoke/SimID_1489333437_0_.ida.expected

@@ -0,0 +1,9 @@
+t:s2:s4:
+0.00000000000000000E+00	4.00000000000000000E+00	0.00000000000000000E+00
+1.00000000000000008E-05	3.99998000095349759E+00	0.00000000000000000E+00
+1.00000000000000005E-04	3.99980008070643711E+00	0.00000000000000000E+00
+1.00000000000000002E-03	3.99800797408532871E+00	0.00000000000000000E+00
+1.00000000000000002E-02	3.98077784306128457E+00	0.00000000000000000E+00
+1.00000000000000006E-01	3.86170998966032331E+00	0.00000000000000000E+00
+5.00000000000000000E-01	3.74758417187014503E+00	0.00000000000000000E+00
+1.00000000000000000E+00	3.74179783773998942E+00	0.00000000000000000E+00

IDAWin/tests/smoke/SimID_1489333437_0_.log

@@ -0,0 +1,3 @@
+IDAData logfile
+IDAData text format version 1
+SimID_1489333437_0_.ida

IDAWin/tests/smoke/SimID_1489333437_0__0.simtask.xml

@@ -0,0 +1,76 @@
+<SimulationTask xmlns="http://sourceforge.net/projects/vcell/vcml" TaskId="0" JobIndex="0" isPowerUser="false">
+  <MathDescription Name="Application0_generated">
+    <Constant Name="_F_">96485.3321</Constant>
+    <Constant Name="_F_nmol_">9.64853321E-5</Constant>
+    <Constant Name="_K_GHK_">1.0E-9</Constant>
+    <Constant Name="_N_pmol_">6.02214179E11</Constant>
+    <Constant Name="_PI_">3.141592653589793</Constant>
+    <Constant Name="_R_">8314.46261815</Constant>
+    <Constant Name="_T_">300.0</Constant>
+    <Constant Name="K_millivolts_per_volt">1000.0</Constant>
+    <Constant Name="Kf_r0">1.0</Constant>
+    <Constant Name="Kf_r1">0.0</Constant>
+    <Constant Name="KMOLE">0.001660538783162726</Constant>
+    <Constant Name="Kr_r0">2.0</Constant>
+    <Constant Name="Kr_r1">0.0</Constant>
+    <Constant Name="s0_init_uM">2.0</Constant>
+    <Constant Name="s1_init_uM">3.0</Constant>
+    <Constant Name="s2_init_uM">4.0</Constant>
+    <Constant Name="s3_init_uM">0.0</Constant>
+    <Constant Name="s4_init_uM">0.0</Constant>
+    <Constant Name="Size_c0">0.5</Constant>
+    <VolumeVariable Name="s2" Domain="Compartment" />
+    <VolumeVariable Name="s4" Domain="Compartment" />
+    <Function Name="J_r0" Domain="Compartment">(((Kf_r0 * s0) * s2) - (Kr_r0 * s1))</Function>
+    <Function Name="J_r1" Domain="Compartment">((Kf_r1 * s3) - (Kr_r1 * s4))</Function>
+    <Function Name="K_s0_total" Domain="Compartment">((Size_c0 * s0_init_uM) - (Size_c0 * s2_init_uM))</Function>
+    <Function Name="K_s1_total" Domain="Compartment">((Size_c0 * s1_init_uM) + (Size_c0 * s2_init_uM))</Function>
+    <Function Name="K_s3_total" Domain="Compartment">((Size_c0 * s3_init_uM) + (Size_c0 * s4_init_uM))</Function>
+    <Function Name="s0" Domain="Compartment">((K_s0_total + (Size_c0 * s2)) / Size_c0)</Function>
+    <Function Name="s1" Domain="Compartment">((K_s1_total - (Size_c0 * s2)) / Size_c0)</Function>
+    <Function Name="s3" Domain="Compartment">((K_s3_total - (Size_c0 * s4)) / Size_c0)</Function>
+    <CompartmentSubDomain Name="Compartment">
+      <BoundaryType Boundary="Xm" Type="Value" />
+      <BoundaryType Boundary="Xp" Type="Value" />
+      <BoundaryType Boundary="Ym" Type="Value" />
+      <BoundaryType Boundary="Yp" Type="Value" />
+      <BoundaryType Boundary="Zm" Type="Value" />
+      <BoundaryType Boundary="Zp" Type="Value" />
+      <OdeEquation Name="s2" SolutionType="Unknown">
+        <Rate>- J_r0</Rate>
+        <Initial>s2_init_uM</Initial>
+      </OdeEquation>
+      <OdeEquation Name="s4" SolutionType="Unknown">
+        <Rate>J_r1</Rate>
+        <Initial>s4_init_uM</Initial>
+      </OdeEquation>
+    </CompartmentSubDomain>
+    <Version Name="Application0_generated" KeyValue="95705054" BranchId="95705055" Archived="0" Date="06-Aug-2015 13:27:28" FromVersionable="false">
+      <Owner Name="schaff" Identifier="17" />
+      <GroupAccess Type="1" />
+    </Version>
+  </MathDescription>
+  <Simulation Name="Simulation0">
+    <SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false" Solver="Combined Stiff Solver (IDA/CVODE)">
+      <TimeBound StartTime="0.0" EndTime="1.0" />
+      <TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0" />
+      <ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9" />
+      <OutputOptions OutputTimes="0.0,1.0E-5,1.0E-4,0.001,0.01,0.1,0.5,1.0" />
+      <NumberProcessors>1</NumberProcessors>
+    </SolverTaskDescription>
+    <MathOverrides />
+    <Version Name="temp simulation" KeyValue="1489333437" BranchId="1" Archived="1" Date="28-Jul-2024 18:28:21" FromVersionable="false">
+      <Owner Name="temp" Identifier="123" />
+      <GroupAccess Type="1" />
+    </Version>
+  </Simulation>
+  <Geometry Name="non-spatial420951543" Dimension="0">
+    <Extent X="10.0" Y="10.0" Z="10.0" />
+    <Origin X="0.0" Y="0.0" Z="0.0" />
+    <SubVolume Name="Compartment" Handle="0" Type="Compartmental" KeyValue="95705043" />
+    <Version Name="non-spatial420951543" KeyValue="95705039" BranchId="95705040" Archived="0" Date="06-Aug-2015 13:27:28" FromVersionable="false">
+      <Owner Name="schaff" Identifier="17" />
+      <GroupAccess Type="1" />
+    </Version>
+  </Geometry>
+</SimulationTask>