Merge pull request #8 from purdue-onchip/layerFdtd

Integrate layeredFD with VoVh and para-extraction in linux

Author: ShuzhanSun

layeredFD_setup.md

@@ -0,0 +1,44 @@
+# How to Setup Layered Finite-Difference Solver
+Please follow these instructions for running layered FD solver in Linux system or Windows system. Please direct all questions, bug reports, and issues to the primary maintainer:
+* [Shuzhan Sun](mailto:sun630@purdue.edu?subject=Inquiry%20for%20gds2Para), Graduate Research Assistant, School of ECE, Purdue University
+
+## Linux System
+The macro `SKIP_LAYERED_FD` in head file `fdtd.hpp` switches between layeredFD solver and V0Vh solver. Setup for each is:
+* Case 1: run V0Vh solver in Linux
+```C++
+#define SKIP_LAYERED_FD
+```
+
+* Case 2: run layeredFD solver in Linux
+```C++
+// #define SKIP_LAYERED_FD
+```
+
+Everything else is the same as [V0Vh solver](https://github.com/purdue-onchip/gds2Para/blob/master/purdue_install.md), including commands, final parameters, and storage styles.
+
+## Windows System
+Currently, only layeredFD solver is supported in Win32 system, and above macro `SKIP_LAYERED_FD` no longer changes anything in Win32 system.
+### How to Setup in Visual Studio (tested in Visual Studio 2017):
+1. Create a visual studio project inside the parent directory of folder `gds2Para`, and only include these files in project:
+```bash
+fdtd.hpp
+generateStiff.cpp
+layeredFdtd.hpp
+mapIndex.hpp
+matrixTypeDef.hpp
+mesh.cpp
+pardisoSolver.hpp
+sysInfoIO.hpp
+```
+2. Edit the `configuration` of the visual studio project to include Intel MKL. A simple way is to install [Intel Parallel Studio XE](https://software.intel.com/en-us/parallel-studio-xe/choose-download), which is free for student.
+3. Write a main function to call the layeredFD solver and put it next to the VS project solution (.sln). Example main function is `layeredFD.cpp`:
+```C++
+#include "gds2Para/src/layeredFdtd.hpp"
+int main(void) {
+    layeredFdtd();
+    return 0;
+}
+```
+### How to Run in Visual Studio
+1. Run the layeredFD solver in Linux (could stop ealier with `Ctrl+Z`) to generate a folder `temp_sysInfoIO` inside the parent directory of folder `gds2Para`. This step exports the structure information to a few txt files. This step is necessary because many codes for loading gds files cannot be compiled in Windows system.
+2. Back to Visual Studio, under mode `Debug x64`, run `Local Windows Debugger` in VS to get the parameters.

src/TestMain.cpp

@@ -351,13 +351,21 @@ int main(int argc, char** argv)
 #endif
 
             // Write object sys to files
-#ifndef SKIP_WRITE_SYS_TO_FILE
+#ifndef SKIP_LAYERED_FD
             WriteSysToFile(sys);
 #endif
 
             // Parameter generation
             clock_t t6 = clock();
+#ifndef SKIP_LAYERED_FD     // Run layered Finite-Difference solver
+            cout << endl << endl << "Results from Layered Finite-Difference Solver: " << endl;
+            status = solveE_Zpara_layered(&sys);
+            //cout << endl << endl << "Results from Reference (direct backslash with PARDISO): " << endl;
+            //solveE_Zpara_reference(&sys);
+#else                       // Run VoVh solver
+            cout << endl << endl << "Results from V0Vh Solver: " << endl;
             status = paraGenerator(&sys, xi, yi, zi);
+#endif
             if (status == 0)
             {
                 cout << "paraGenerator Success!" << endl;

src/fdtd.hpp

@@ -24,10 +24,12 @@
 #include <algorithm>
 #include <utility>
 
+//#define SKIP_LAYERED_FD   // Comment out if you want to run layered FD code in Linux, doesn't matter for Windows system
+
 // HYPRE and MKL data type control
-#define LARGE_SYSTEM (1) // Must leave defined with the current makefile. Comment out in windows system
-#ifdef LARGE_SYSTEM
-#define MKL_ILP64 (1) // Must define before including mkl.h if using long long int 
+#define LARGE_SYSTEM (1) // Must leave defined with the current makefile
+#if defined(LARGE_SYSTEM) && defined(__linux__)
+#define MKL_ILP64 (1) // Must define before including mkl.h if using long long int, MKL_ILP64 only works for Linux not for Windows
 typedef long long int myint;
 #else
 typedef int myint;
@@ -74,10 +76,6 @@ using namespace std;
 //#define SKIP_GENERATE_STIFF
 #define SKIP_STIFF_REFERENCE 
 
-// Disable layered FDTD code (comment out if you want to test layered FDTD)
-#define SKIP_WRITE_SYS_TO_FILE        // Skip writing sys obj to txt files
-#define SKIP_LAYERED_FDTD             // Skip the main function's calling layeredFdtd code
-
 // Function-like macros
 #define NELEMENT(x) ((sizeof x) / (sizeof x[0]))
 

src/pardisoSolver.hpp

@@ -111,7 +111,7 @@ int eliminateVolumE(const vector<BlockType> &layerS, myint N_surfE, myint N_volE
     /*denseB21B23.writeToFile("blockB21B23.txt");
     denseD0sD1s.writeToFile("blockD.txt");*/
 
-    denseB21B23.~denseFormatOfMatrix();                         // free combined dense [B21, B23]
+    //denseB21B23.~denseFormatOfMatrix();                         // free combined dense [B21, B23]
 
     // Convert B12, B32 to mkl internal CSR matrix handles
     sparse_matrix_t csrB12_mklHandle, csrB32_mklHandle;
@@ -148,7 +148,7 @@ int eliminateVolumE(const vector<BlockType> &layerS, myint N_surfE, myint N_volE
     (preducedS + 2)->writeToFile("block_C2.txt");
     (preducedS + 3)->writeToFile("block_C3.txt");*/
 
-    denseD0sD1s.~denseFormatOfMatrix();                         // free combined dense [D0s, D1s]
+    //denseD0sD1s.~denseFormatOfMatrix();                         // free combined dense [D0s, D1s]
     return 0;
 }
 
@@ -634,7 +634,7 @@ denseFormatOfMatrix reconstruct_e(fdtdMesh *psys, const mapIndex &indexMap, cons
 }
 
 // Solve E field and Z-parameters in Pardiso, solve layer by layer. (under developing)
-void solveE_Zpara_layered(fdtdMesh *psys) {
+int solveE_Zpara_layered(fdtdMesh *psys) {
 
     // Initilize Z-parameters for all frequencies
     psys->x.assign(psys->numPorts * psys->numPorts * psys->nfreq, complex<double>(0., 0.));
@@ -666,6 +666,7 @@ void solveE_Zpara_layered(fdtdMesh *psys) {
     // Print Z-parameters
     psys->print_z_V0_Vh();
 
+    return 0;
 }
 
 // Solve E field and Z-parameters in Pardiso, solve the whole structure as reference

src/sysInfoIO.hpp

@@ -3,6 +3,9 @@
 
 #include "fdtd.hpp"
 
+#include <sys/types.h>
+#include <sys/stat.h>   // "mkdir" in linux
+
 using namespace std;
 
 inline void WriteVectorIn1Line(ofstream &file_obj, const vector<double> &vec_x) {
@@ -23,12 +26,23 @@ void Write2DVectorIn1Line(ofstream &file_obj, const vector<vector<myint>> &vec_2
 	file_obj << endl;
 }
 
-// Write object sys to files
+// Write object sys to files (only works for Linux system due to paths)
 void WriteSysToFile(const fdtdMesh &sys) {
 	ofstream file_obj;
+	
+    // Create folder (if not exists) to store txt files, only in linux system
+#ifdef __linux__
+    struct stat st = { 0 };
+    if (stat("../temp_sysInfoIO", &st) == -1) {
+        if (mkdir("../temp_sysInfoIO", 0777) == -1) {
+            cerr << "Error in creating folder /temp_sysInfoIO!" << endl;
+            exit(2);
+        }
+    }
+#endif
 
 	// Write primitive types like a bool, int, or float in one txt file
-	file_obj.open("sys_PrimitiveType.txt", ios::out);
+	file_obj.open("../temp_sysInfoIO/sys_PrimitiveType.txt", ios::out);
 	file_obj << sys.numCdtRow << endl;
 	file_obj << sys.lengthUnit << endl;
 	file_obj << sys.freqUnit << endl;
@@ -48,34 +62,34 @@ void WriteSysToFile(const fdtdMesh &sys) {
 	file_obj.close();
 
 	// Write each vector in independent file
-	file_obj.open("sys_vec_stackEps.txt", ios::out);
+	file_obj.open("../temp_sysInfoIO/sys_vec_stackEps.txt", ios::out);
 	for (const auto& i : sys.stackEps)
 		file_obj << i << endl;
 	file_obj.close();
 
-	file_obj.open("sys_vec_stackSig.txt", ios::out);
+	file_obj.open("../temp_sysInfoIO/sys_vec_stackSig.txt", ios::out);
 	for (const auto& i : sys.stackSig)
 		file_obj << i << endl;
 	file_obj.close();
 
-	file_obj.open("sys_vec_stackBegCoor.txt", ios::out);
+	file_obj.open("../temp_sysInfoIO/sys_vec_stackBegCoor.txt", ios::out);
 	for (const auto& i : sys.stackBegCoor)
 		file_obj << i << endl;
 	file_obj.close();
 
-	file_obj.open("sys_vec_stackEndCoor.txt", ios::out);
+	file_obj.open("../temp_sysInfoIO/sys_vec_stackEndCoor.txt", ios::out);
 	for (const auto& i : sys.stackEndCoor)
 		file_obj << i << endl;
 	file_obj.close();
 
-	file_obj.open("sys_vec_stackName.txt", ios::out);
+	file_obj.open("../temp_sysInfoIO/sys_vec_stackName.txt", ios::out);
 	for (const auto& i : sys.stackName)
 		file_obj << i << endl;
 	file_obj.close();
 
 	// Write sys.portCoor. Every object of class fdtdPort takes n lines, being one element of vector portCoor
 	// output format: multiplicity ~ 1st line; x1 ~ 2nd line; ... someattri ~ n-th line.
-	file_obj.open("sys_vec_portCoor.txt", ios::out);
+	file_obj.open("../temp_sysInfoIO/sys_vec_portCoor.txt", ios::out);
 	for (int i = 0; i < sys.portCoor.size(); i++) {
 		const fdtdPort &ofdtdPort = sys.portCoor[i];
 
@@ -94,7 +108,7 @@ void WriteSysToFile(const fdtdMesh &sys) {
 	file_obj.close();
 
 	// Write sys.conductorIn, only export what is used by function meshAndMark
-	file_obj.open("sys_vec_conductorIn.txt", ios::out);
+	file_obj.open("../temp_sysInfoIO/sys_vec_conductorIn.txt", ios::out);
 	for (int i = 0; i < sys.conductorIn.size(); i++) {
 		const fdtdOneCondct &ofdtdOneCondct = sys.conductorIn[i];
 
@@ -114,7 +128,7 @@ void WriteSysToFile(const fdtdMesh &sys) {
 
 
 	// Write *pointer to file 
-	file_obj.open("sys_ptr_stackCdtMark.txt", ios::out);
+	file_obj.open("../temp_sysInfoIO/sys_ptr_stackCdtMark.txt", ios::out);
 	for (int i = 0; i < sys.numStack; i++)
 		file_obj << sys.stackCdtMark[i] << endl;
 	file_obj.close();
@@ -186,7 +200,7 @@ void ReadSysFromFile(fdtdMesh *psys) {
 	ifstream file_obj;
 
 	// Read primitive types like a bool, int, or float
-	file_obj.open("sys_PrimitiveType.txt", ios::in);
+	file_obj.open("temp_sysInfoIO/sys_PrimitiveType.txt", ios::in);
 	if (!file_obj.is_open()) {
 		perror("Error open");
 		exit(EXIT_FAILURE);
@@ -210,39 +224,39 @@ void ReadSysFromFile(fdtdMesh *psys) {
 	file_obj.close();
 
 	// Read each vector from independent file
-	file_obj.open("sys_vec_stackEps.txt", ios::in);
+	file_obj.open("temp_sysInfoIO/sys_vec_stackEps.txt", ios::in);
 	while (file_obj >> doubVecValue) {
 		psys->stackEps.push_back(doubVecValue);
 	}
 	file_obj.close();
 
-	file_obj.open("sys_vec_stackSig.txt", ios::in);
+	file_obj.open("temp_sysInfoIO/sys_vec_stackSig.txt", ios::in);
 	while (file_obj >> doubVecValue) {
 		psys->stackSig.push_back(doubVecValue);
 	}
 	file_obj.close();
 
-	file_obj.open("sys_vec_stackBegCoor.txt", ios::in);
+	file_obj.open("temp_sysInfoIO/sys_vec_stackBegCoor.txt", ios::in);
 	while (file_obj >> doubVecValue) {
 		psys->stackBegCoor.push_back(doubVecValue);
 	}
 	file_obj.close();
 
-	file_obj.open("sys_vec_stackEndCoor.txt", ios::in);
+	file_obj.open("temp_sysInfoIO/sys_vec_stackEndCoor.txt", ios::in);
 	while (file_obj >> doubVecValue) {
 		psys->stackEndCoor.push_back(doubVecValue);
 	}
 	file_obj.close();
 
-	file_obj.open("sys_vec_stackName.txt", ios::in);
+	file_obj.open("temp_sysInfoIO/sys_vec_stackName.txt", ios::in);
 	while (file_obj >> strVecValue) {
 		psys->stackName.push_back(strVecValue);
 	}
 	file_obj.close();
 
 	// Read sys.portCoor. Every object of class fdtdPort takes n lines, being one element of vector portCoor
 	// Input format: multiplicity ~ 1st line; x1 ~ 2nd line; ... someattri ~ n-th line.
-	file_obj.open("sys_vec_portCoor.txt", ios::in);
+	file_obj.open("temp_sysInfoIO/sys_vec_portCoor.txt", ios::in);
 
 	num_line = 0;
 	while (getline(file_obj, line)) {
@@ -275,7 +289,7 @@ void ReadSysFromFile(fdtdMesh *psys) {
 	file_obj.close();
 
 	// Read sys.conductorIn, only input what is used by function meshAndMark
-	file_obj.open("sys_vec_conductorIn.txt", ios::in);
+	file_obj.open("temp_sysInfoIO/sys_vec_conductorIn.txt", ios::in);
 
 	num_line = 0;
 	while (getline(file_obj, line)) {
@@ -300,7 +314,7 @@ void ReadSysFromFile(fdtdMesh *psys) {
 
 
 	// Read *pointer from file 
-	file_obj.open("sys_ptr_stackCdtMark.txt", ios::in);
+	file_obj.open("temp_sysInfoIO/sys_ptr_stackCdtMark.txt", ios::in);
 	psys->stackCdtMark = (double *)malloc(psys->numStack * sizeof(double));
 	for (int i = 0; i < psys->numStack; i++) {
 		file_obj >> psys->stackCdtMark[i];