enabled commandline with number of indices as argument

include/parpeamici/optimizationApplication.h

@@ -148,14 +148,15 @@ class OptimizationApplication {
 
 protected:
     // command line option parsing
-    const char *shortOptions = "dhvmt:o:s:";
-    struct option const longOptions[9] = {
+    const char *shortOptions = "dhvmt:o:s:g:";
+    struct option const longOptions[10] = {
         {"debug", no_argument, nullptr, 'd'},
         {"print-worklist", no_argument, nullptr, 'p'},
         {"help", no_argument, nullptr, 'h'},
         {"version", no_argument, nullptr, 'v'},
         {"mpi", no_argument, nullptr, 'm'},
         {"task", required_argument, nullptr, 't'},
+        {"gradient-check", required_argument, nullptr, 'g'},
         {"outfile-prefix", required_argument, nullptr, 'o'},
         {"first-start-idx", required_argument, nullptr, 's'},
         {nullptr, 0, nullptr, 0}};
@@ -165,6 +166,8 @@ class OptimizationApplication {
         gradientCheck
     };
 
+    std::vector<int> para_ind {};
+
     std::string dataFileName;
     std::string resultFileName;
 
@@ -175,6 +178,7 @@ class OptimizationApplication {
     std::unique_ptr<OptimizationProblem> problem;
     H5::H5File h5File = 0;
     OperationType operationType = OperationType::parameterEstimation;
+    int num_parameter_checks = 1;
     LoadBalancerMaster loadBalancer;
     bool withMPI = false;
 };

src/parpeamici/optimizationApplication.cpp

@@ -19,6 +19,8 @@
 #include <random>
 #include <csignal>
 #include <cstdlib>
+#include <sstream>
+#include <iostream>
 
 namespace parpe {
 
@@ -110,6 +112,21 @@ int OptimizationApplication::parseCliOptionsPostMpiInit(int argc, char **argv) {
             if (strcmp(optarg, "gradient_check") == 0)
                 operationType = OperationType::gradientCheck;
             break;
+        case 'g': {
+            operationType = OperationType::gradientCheck;
+            /*
+                Assuming the next argument is of the type n1,n2,...,nX.
+                This will be a string of comma separated ints, that need
+                to be converted to std::vector<int>.
+             */
+            std::stringstream ss(optarg);
+
+            for (int i; ss >> i;) {
+                para_ind.push_back(i);
+                if (ss.peek() == ',')
+                    ss.ignore();
+            }
+        } break;
         case 'o':
             resultFileName = processResultFilenameCommandLineArgument(optarg);
             break;
@@ -230,9 +247,10 @@ int OptimizationApplication::run(int argc, char **argv) {
 void OptimizationApplication::runMaster() {
     switch (operationType) {
     case OperationType::gradientCheck: {
-        const int numParameterIndicesToCheck = 10000;
-        optimizationProblemGradientCheckMultiEps(
-                    problem.get(), numParameterIndicesToCheck);
+        std::vector<double> multi_eps {1e-1, 1e-3, 1e-4, 1e-5, 1e-7};
+        optimizationProblemGradientCheckMultiEps(problem.get(),
+                                                 para_ind,
+                                                 multi_eps);
         break;
     }
     case OperationType::parameterEstimation:
@@ -266,8 +284,10 @@ void OptimizationApplication::runSingleProcess() {
     switch (operationType) {
     case OperationType::gradientCheck: {
         const int numParameterIndicesToCheck = 10000;
-        optimizationProblemGradientCheckMultiEps(
-                    problem.get(), numParameterIndicesToCheck);
+        const double epsilon = 1e-5;
+        optimizationProblemGradientCheck(problem.get(),
+                                         numParameterIndicesToCheck,
+                                         epsilon);
         break;
     }
     case OperationType::parameterEstimation:

src/parpeoptimization/optimizationProblem.cpp

@@ -58,7 +58,7 @@ void optimizationProblemGradientCheckMultiEps(OptimizationProblem *problem,
                                       int numParameterIndicesToCheck
                                       ) {
     // set eps
-    std::vector<double> multi_eps {1e-1, 1e-3, 1e-5, 1e-7, 1e-9};
+    std::vector<double> multi_eps {1e-1, 1e-3, 1e-4, 1e-5, 1e-7};
 
     // setting the number of parameters to the minimum of
     // numParamaterIndicesToCheck and dimension of the problem