create pyvcell_fvsolver Python module using pybind11 and vcell library

virtualcell · Jun 2, 2024 · 66f5bd6 · 66f5bd6
1 parent 0dbfb49
commit 66f5bd6
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Showing 8 changed files with 163 additions and 70 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -46,7 +46,8 @@ endif()
 
 cmake_minimum_required(VERSION 3.13...3.27)
 project(fvsolver)
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
 enable_language(CXX)
 enable_language(C)
 enable_language(Fortran)
@@ -95,6 +96,8 @@ include (FindZLIB)
 option(OPTION_TARGET_MESSAGING "Messaging (requires libcurl)" off)
 option(OPTION_TARGET_DOCS "Generate Doxygen documentation" on)
 option(OPTION_TARGET_FV_SOLVER on)
+option(OPTION_TARGET_MESSAGING "Messaging (requires libcurl)" off)
+
 
 if (${OPTION_TARGET_DOCS})
 #	if (DOXYGEN_FOUND AND ${CMAKE_VERSION} GREATER_EQUAL 3.9)
@@ -213,47 +216,33 @@ endif()
 
 	add_subdirectory(VCellMessaging)
 
- 	if (${OPTION_TARGET_FV_SOLVER})
-		add_subdirectory(VCellZipUtils)
-		add_subdirectory(libzip-1.2.0)
-	endif()
-
-    if (${OPTION_TARGET_FV_SOLVER})
-    	message(STATUS "adding ExpressionParser")
-		add_subdirectory(ExpressionParser)
-	endif()
+	add_subdirectory(VCellZipUtils)
 
-	if (${OPTION_TARGET_FV_SOLVER}
-		)
-    	message(STATUS "adding sundials")
-		add_subdirectory(sundials)
-	endif ()
-
-	if (${OPTION_TARGET_FV_SOLVER})
-		if (NOT APPLE)
-			add_subdirectory(blas)
-		endif()
+	add_subdirectory(libzip-1.2.0)
+
+	add_subdirectory(ExpressionParser)
+
+	add_subdirectory(sundials)
+
+	if (NOT APPLE)
+		add_subdirectory(blas)
 	endif()
 
-	if (OPTION_TARGET_FV_SOLVER)
-		option(OPTION_VCELL "Compile Smoldyn for VCell" ON)
-		option(OPTION_NSV "Compile Smoldyn with NextSubvolume functionality" OFF)
-		option(OPTION_USE_OPENGL "Build with OpenGL support" OFF)
-		option(OPTION_USE_ZLIB "Build with Zlib support" ON)
-		option(OPTION_USE_LIBTIFF "Build with LibTiff support" OFF)
-		option(OPTION_USE_ICONV "Build with Libiconv support" OFF)
-		SET(HAVE_ZLIB TRUE)
-		set(OPTION_TARGET_LIBSMOLDYN ON)
-		set(OPTION_VCELL ON)
-		add_subdirectory(bridgeVCellSmoldyn)
-		add_subdirectory(smoldyn-2.38)
-	endif ()
-
-	if (${OPTION_TARGET_FV_SOLVER})
-		add_subdirectory(VCell)
-		add_subdirectory(PCGPack) 
-		add_subdirectory(qhull)
-	endif ()
+	option(OPTION_VCELL "Compile Smoldyn for VCell" ON)
+	option(OPTION_NSV "Compile Smoldyn with NextSubvolume functionality" OFF)
+	option(OPTION_USE_OPENGL "Build with OpenGL support" OFF)
+	option(OPTION_USE_ZLIB "Build with Zlib support" ON)
+	option(OPTION_USE_LIBTIFF "Build with LibTiff support" OFF)
+	option(OPTION_USE_ICONV "Build with Libiconv support" OFF)
+	SET(HAVE_ZLIB TRUE)
+	set(OPTION_TARGET_LIBSMOLDYN ON)
+	set(OPTION_VCELL ON)
+	add_subdirectory(bridgeVCellSmoldyn)
+	add_subdirectory(smoldyn-2.38)
+
+	add_subdirectory(VCell)
+	add_subdirectory(PCGPack)
+	add_subdirectory(qhull)
 
 	add_subdirectory(extern/pybind11)
 	add_subdirectory(pyvcell-fvsolver)

diff --git a/pyvcell-fvsolver/CMakeLists.txt b/pyvcell-fvsolver/CMakeLists.txt
@@ -1,14 +1,18 @@
-project(example)
+project(pyvcell_fvsolver)
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 set(HEADER_FILES
-    include/add.h
+        include/SolverMain.h
 )
 
 set(SOURCE_FILES
-    src/add.cpp
-    src/example.cpp
+        src/pyvcell_fvsolver.cpp
+        src/SolverMain.cpp
 )
 
 include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include)
 
-pybind11_add_module(example ${SOURCE_FILES} ${HEADER_FILES})
+pybind11_add_module(pyvcell_fvsolver ${SOURCE_FILES} ${HEADER_FILES})
+
+target_link_libraries(pyvcell_fvsolver PRIVATE vcell)
diff --git a/pyvcell-fvsolver/include/SolverMain.h b/pyvcell-fvsolver/include/SolverMain.h
@@ -0,0 +1,13 @@
+//
+// Created by Jim Schaff on 6/1/24.
+//
+
+#ifndef SOLVERMAIN_H
+#define SOLVERMAIN_H
+
+#include <string>
+
+std::string version();
+int solve(const std::string& inputFilename, const std::string& outputDir);
+
+#endif //SOLVERMAIN_H
diff --git a/pyvcell-fvsolver/include/add.h b/pyvcell-fvsolver/include/add.h
diff --git a/pyvcell-fvsolver/src/SolverMain.cpp b/pyvcell-fvsolver/src/SolverMain.cpp
@@ -0,0 +1,100 @@
+//
+// Created by Jim Schaff on 6/1/24.
+//
+#include "SolverMain.h"
+
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <filesystem>
+using namespace std;
+
+#undef USE_MESSAGING
+
+#include <VCELL/FVSolver.h>
+#include <sys/stat.h>
+#include <VCELL/SimTool.h>
+#include <VCELL/SimulationMessaging.h>
+#include <VCELL/GitDescribe.h>
+#include <Exception.h>
+#include <vcellhybrid.h>
+
+
+
+void vcellExit(int returnCode, string& errorMsg) {
+	if (SimulationMessaging::getInstVar() == 0) {
+		if (returnCode != 0) {
+			cerr << errorMsg << endl;
+		}
+	} else if (!SimulationMessaging::getInstVar()->isStopRequested()) {
+		if (returnCode != 0) {
+			SimulationMessaging::getInstVar()->setWorkerEvent(new WorkerEvent(JOB_FAILURE, errorMsg.c_str()));
+		}
+	}
+}
+
+std::string version()
+{
+	return "Finite Volume version " + std::string(g_GIT_DESCRIBE) + " with smoldyn version " + std::string(VERSION);
+}
+
+int solve(const std::string& inputFilename, const std::string& outputDir) {
+	// Check if output directory exists, if not create it
+	std::filesystem::path dirPath(outputDir);
+	if (!std::filesystem::exists(dirPath)) {
+		std::filesystem::create_directories(dirPath);
+	}
+
+	// Open the input file
+	std::ifstream inputFile(inputFilename);
+	if (!inputFile.is_open()) {
+		throw std::runtime_error("Could not open input file: " + inputFilename);
+	}
+
+	vcellhybrid::setHybrid(); //get smoldyn library in correct state
+  	int returnCode = 0;
+	string errorMsg = "Exception : ";
+
+	bool bSimZip = true;
+	int taskID = 0;
+
+	SimulationMessaging::create();
+
+	FVSolver* fvSolver = nullptr;
+
+	try {
+		fvSolver = new FVSolver(inputFile, taskID, outputDir.c_str(), bSimZip);
+
+		inputFile.close();
+
+		if(fvSolver->getNumVariables() == 0){
+			//sims with no reactions and no diffusing species cause exit logic to 'wait' forever
+			//never sending a job failed or job finished message and never cleaning up threads
+			throw invalid_argument("FiniteVolume error: Must have at least 1 variable or reaction to solve");
+		}
+		fvSolver->solve();
+
+	} catch (const char *exStr){
+		errorMsg += exStr;
+		returnCode = 1;
+	} catch (string& exStr){
+		errorMsg += exStr;
+		returnCode = 1;
+	} catch (VCell::Exception& ex){
+		errorMsg += ex.getMessage();
+		returnCode = 1;
+	} catch (std::exception & e) {
+		errorMsg += e.what();
+		returnCode = 1;
+	} catch (...){
+		errorMsg += "unknown error";
+		returnCode = 1;
+	}
+
+	if (inputFile.is_open()) {
+		inputFile.close();
+	}
+	vcellExit(returnCode, errorMsg);
+	delete fvSolver;
+	return returnCode;
+}
diff --git a/pyvcell-fvsolver/src/add.cpp b/pyvcell-fvsolver/src/add.cpp
diff --git a/pyvcell-fvsolver/src/example.cpp b/pyvcell-fvsolver/src/example.cpp
diff --git a/pyvcell-fvsolver/src/pyvcell_fvsolver.cpp b/pyvcell-fvsolver/src/pyvcell_fvsolver.cpp
@@ -0,0 +1,13 @@
+#include <../../extern/pybind11/include/pybind11/pybind11.h>
+
+#include "SolverMain.h"
+
+namespace py = pybind11;
+
+PYBIND11_MODULE(pyvcell_fvsolver, m) {
+    m.doc() = "VCell FiniteVolume plugin"; // optional module docstring
+
+    m.def("version", &version, "A function that returns the version of the FiniteVolume solver");
+
+    m.def("solve", &solve, "A function that invokes the FiniteVolume solver", py::arg("inputFilename"), py::arg("outputDir"));
+}