Merge remote-tracking branch 'origin/develop'

README.md

@@ -1,3 +1,6 @@
+<p align="center">
+  <img src="documentation/pestpplogo.png" alt="pestpplogo image">
+</p>
 # PEST++
 
 ## Tools for non-intrusive and scalable parameter estimation and uncertainty quantification

benchmarks/basic_tests.py

@@ -953,6 +953,51 @@ def mf6_v5_glm_test():
     assert oe.shape[0] == pst.pestpp_options["glm_num_reals"],"{0},{1}".\
         format(oe.shape[0],pst.pestpp_options["glm_num_reals"])
 
+
+def cmdline_test():
+    model_d = "mf6_freyberg"
+    local=True
+    if "linux" in platform.platform().lower() and "10par" in model_d:
+        #print("travis_prep")
+        #prep_for_travis(model_d)
+        local=False
+
+    t_d = os.path.join(model_d,"template")
+    pst_name = "freyberg6_run_glm.pst"
+    pst = pyemu.Pst(os.path.join(t_d,"freyberg6_run_glm.pst"))
+    pst.pestpp_options["debug_parse_only"] = True
+    pst_name = "CmdLine_test.pst" #camel case on purpose for linux testing
+    pst.write(os.path.join(t_d,pst_name))
+    pyemu.os_utils.run("{0} {1}".format(exe_path,pst_name),cwd=t_d)
+    pyemu.os_utils.run("{0} {1} /h :4004".format(exe_path,pst_name),cwd=t_d)
+    pyemu.os_utils.run("{0} {1} /r /h :4004".format(exe_path.replace("-ies","-glm"),pst_name),cwd=t_d) 
+    pyemu.os_utils.run("{0} {1} /r ".format(exe_path.replace("-ies","-glm"),pst_name),cwd=t_d) 
+
+    try:
+        pyemu.os_utils.run("{0} {1} \\h :4004".format(exe_path,pst_name),cwd=t_d) 
+
+    except:
+        pass
+    else:
+        raise Exception("should have failed")
+
+    try:
+        pyemu.os_utils.run("{0} {1} :4004".format(exe_path,pst_name),cwd=t_d) 
+
+    except:
+        pass
+    else:
+        raise Exception("should have failed")
+
+    try:
+        pyemu.os_utils.run("{0} {1} /h 4004".format(exe_path,pst_name),cwd=t_d) 
+
+    except:
+        pass
+    else:
+        raise Exception("should have failed")
+
+
 if __name__ == "__main__":
 
     #glm_long_name_test()
@@ -973,3 +1018,4 @@ def mf6_v5_glm_test():
     #mf6_v5_sen_test()
     #mf6_v5_opt_stack_test()
     #mf6_v5_glm_test()
+    #cmdline_test()

src/libs/common/config_os.h

@@ -2,7 +2,7 @@
 #define CONFIG_OS_H_
 
 
-#define PESTPP_VERSION "5.0.0";
+#define PESTPP_VERSION "5.0.3";
 
 #if defined(_WIN32) || defined(_WIN64)
 #define OS_WIN

src/libs/common/utilities.cpp

@@ -624,7 +624,7 @@ void  thread_exceptions::rethrow()
 		}
 		catch (const std::exception& e)
 		{
-			ss << e.what() << ", ";
+			ss << e.what() << " ";
 		}
 	}
 	throw runtime_error(ss.str());
@@ -1428,7 +1428,159 @@ string get_time_string_short()
 }
 
 
-} // end of namespace pest_utils
+CmdLine::CmdLine(int argc, char* argv[]) :
+	ctl_file_name(""), panther_host_name(""), panther_port(""), 
+	runmanagertype(RunManagerType::SERIAL),org_cmdline_str(""),
+	restart(false),jac_restart(false)
+{
+	for (int i = 0; i < argc; ++i)
+	{
+		org_cmdline_str.append(" ");
+		org_cmdline_str.append(argv[i]);
+	}
+	cout << "...processing command line: '" << org_cmdline_str << "'" << endl;
+	vector<string> org_cmdline_vec(argc);
+	copy(argv, argv + argc, org_cmdline_vec.begin());
+	vector<string> lower_cmdline_vec = org_cmdline_vec;
+	for (vector<string>::iterator it = lower_cmdline_vec.begin(); it != lower_cmdline_vec.end(); ++it)
+	{
+		transform(it->begin(), it->end(), it->begin(), ::tolower);
+	}
+
+	if (org_cmdline_vec.size() >= 2) 
+	{
+		ctl_file_name = org_cmdline_vec[1];
+	}
+	else 
+	{
+		throw_cmdline_error("too few args, no control file name found");
+	}
+
+	//check for shitty restar flags
+	vector<string> temp, temp_lower;
+	for (int i = 0; i < lower_cmdline_vec.size(); i++)
+	{
+		if (lower_cmdline_vec[i] == "/r")
+		{
+			restart = true;
+		}
+		else if (lower_cmdline_vec[i] == "/j")
+		{
+			if (restart)
+				throw_cmdline_error("both '/r' and '/j' supplied");
+			jac_restart = true;
+		}
+		else
+		{
+			temp.push_back(org_cmdline_vec[i]);
+			temp_lower.push_back(lower_cmdline_vec[i]);
+		}
+	}
+	org_cmdline_vec = temp;
+	lower_cmdline_vec = temp_lower;
+
+
+	if ((lower_cmdline_vec.size() == 3) || (lower_cmdline_vec.size() > 4))
+	{
+		throw_cmdline_error("wrong number of args, expecting 2 (serial run mgr) or 4 (parallel run mgr)");
+	}
+
+	//serial run mgr...done
+	if (lower_cmdline_vec.size() == 2)
+	{
+		cout << "...using serial run manager" << endl;
+		return;
+	}
+
+	//check for various run mgr options
+	string third_arg = lower_cmdline_vec[2];
+	if (third_arg == "/e")
+	{
+		cout << "...using external run manager" << endl;
+		runmanagertype = RunManagerType::EXTERNAL;
+	}
+	else if (third_arg == "/g")
+	{
+		cout << "...using genie run manager" << endl;
+		runmanagertype = RunManagerType::GENIE;
+	}
+	else if (third_arg == "/h")
+	{
+		//assume worker, but check for master later...
+		runmanagertype = RunManagerType::PANTHER_WORKER;
+	}
+	else
+	{
+		throw_cmdline_error("unrecognized commandline arg '" + third_arg + "', expecting '/h','/e','/g'");
+	}
+
+	if (runmanagertype == RunManagerType::PANTHER_WORKER)
+	{
+		string forth_arg = org_cmdline_vec[3];
+		if (forth_arg.find(":") == string::npos)
+		{
+			throw_cmdline_error("panther master/worker arg '" + forth_arg + "' doesn't have a ':' char");
+		}
+		if (forth_arg[0] == ':')
+		{
+			//panther master
+			runmanagertype = RunManagerType::PANTHER_MASTER;
+			panther_port = forth_arg.substr(1);
+			try
+			{
+				int test = stoi(panther_port);
+			}
+			catch (...)
+			{
+				throw_cmdline_error("error casting master port number '" + panther_port + "' to int");
+			}
+			cout << "...using panther run manager in master mode using port " << panther_port << endl;
+		}
+		else
+		{
+			//panther worker
+			vector<string> tokens;
+			tokenize(forth_arg, tokens, ":");
+			if (tokens.size() != 2)
+				throw_cmdline_error("wrong number of colon-delimited tokens in panther worker arg '" + forth_arg);
+			panther_host_name = tokens[0];
+			panther_port = tokens[1];
+			try
+			{
+				int test = stoi(panther_port);
+			}
+			catch (...)
+			{
+				throw_cmdline_error("error casting master port number '" + panther_port + "' to int");
+			}
+			cout << "...using panther run manager in worker mode using hostname '" << panther_host_name << "' and port " << panther_port << endl;
+		}
+	}
+	return;
+
+}
+
+
+void CmdLine::throw_cmdline_error(string message)
+{
+	cerr << "--------------------------------------------------------" << endl;
+	cerr << "COMMAND LINE ERROR: " << message << endl;
+	cerr << "usage:" << endl << endl;
+	cerr << "    serial run manager:" << endl;
+	cerr << "        pestpp-xxx control_file.pst" << endl << endl;
+	cerr << "    PANTHER master:" << endl;
+	cerr << "        pestpp-xxx control_file.pst /H :port" << endl << endl;
+	cerr << "    PANTHER worker:" << endl;
+	cerr << "        pestpp-xxx control_file.pst /H hostname:port " << endl << endl;
+
+	cerr << " additional options can be found in the PEST++ users manual" << endl;
+	cerr << "--------------------------------------------------------" << endl;
+	exit(1);
+}
+
+// end of namespace pest_utils
+}
+
 
 
 

src/libs/common/utilities.h

@@ -376,6 +376,22 @@ string get_time_string();
 string get_time_string_short();
 
 
+class CmdLine {
+
+public:
+	enum class RunManagerType { SERIAL, PANTHER_MASTER, PANTHER_WORKER, GENIE, EXTERNAL };
+	CmdLine(int argc, char* argv[]);
+	string ctl_file_name;
+	string panther_host_name;
+	string org_cmdline_str;
+	string panther_port;
+	bool jac_restart;
+	bool restart;
+	RunManagerType runmanagertype;
+private:
+	void throw_cmdline_error(string message);
+
+};
 
 }  // end namespace pest_utils
 #endif /* UTILITIES_H_ */

src/libs/pestpp_common/Ensemble.cpp

@@ -2207,12 +2207,12 @@ void ParameterEnsemble::save_fixed()
 		}
 	}
 	// add the "base" if its not in the real names already
-	if (find(real_names.begin(), real_names.end(), base_name) == real_names.end())
+	if (find(real_names.begin(), real_names.end(), BASE_REAL_NAME) == real_names.end())
 	{
 		Parameters pars = pest_scenario_ptr->get_ctl_parameters();
 		for (auto fname : fixed_names)
 		{
-			pair<string, string> key(base_name, fname);
+			pair<string, string> key(BASE_REAL_NAME, fname);
 			fixed_map[key] = pars[fname];
 		}
 	}

src/libs/pestpp_common/Ensemble.h

@@ -16,6 +16,7 @@
 #include "PerformanceLog.h"
 
 
+const string BASE_REAL_NAME = "BASE";
 
 class Ensemble
 {
@@ -102,7 +103,6 @@ class Ensemble
 	//ObjectiveFunc *obj_func_ptr;
 	//OutputFileWriter &output_file_writer;
 	//PerformanceLog *performance_log;
-	string base_name = "BASE";
 	Eigen::MatrixXd reals;
 	vector<string> var_names;
 	vector<string> real_names;	

src/libs/pestpp_common/EnsembleMethodUtils.cpp

@@ -1009,11 +1009,11 @@ void save_base_real_par_rei(Pest& pest_scenario, ParameterEnsemble& pe, Observat
 {
 	stringstream ss;
 	map<string, int> vmap = pe.get_real_map();
-	if (vmap.find("BASE") != vmap.end())
+	if (vmap.find(BASE_REAL_NAME) != vmap.end())
 	{
 		ParamTransformSeq pts = pest_scenario.get_base_par_tran_seq();
 		Parameters pars;
-		pars.update(pe.get_var_names(), eigenvec_2_stlvec(pe.get_real_vector("BASE")));
+		pars.update(pe.get_var_names(), eigenvec_2_stlvec(pe.get_real_vector(BASE_REAL_NAME)));
 		if (pe.get_trans_status() == ParameterEnsemble::transStatus::NUM)
 			pts.numeric2ctl_ip(pars);
 		// save parameters to .par file
@@ -1025,14 +1025,14 @@ void save_base_real_par_rei(Pest& pest_scenario, ParameterEnsemble& pe, Observat
 		file_manager.close_file("par");
 
 		vmap = oe.get_real_map();
-		if (vmap.find("BASE") == vmap.end())
+		if (vmap.find(BASE_REAL_NAME) == vmap.end())
 		{
 			//message(2, "unable to find 'BASE' realization in obs ensemble for saving .base.rei file, continuing...");
 		}
 		else
 		{
 			Observations obs;
-			obs.update(oe.get_var_names(), eigenvec_2_stlvec(oe.get_real_vector("BASE")));
+			obs.update(oe.get_var_names(), eigenvec_2_stlvec(oe.get_real_vector(BASE_REAL_NAME)));
 			ObjectiveFunc obj_func(&(pest_scenario.get_ctl_observations()), &(pest_scenario.get_ctl_observation_info()), &(pest_scenario.get_prior_info()));
 			// save new residuals to .rei file
 			ss.str("");