reHC*, implemented an internal time limit.

include/timelimit.hpp

@@ -0,0 +1,39 @@
+/**
+ *
+ *                              reHC-*
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
+ *
+ * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
+ *
+ * Distributed under the terms of the GNU General Public License (GPL)
+ *
+ *
+ * This file is part of reHC-* (reHCstar),
+ * previously known as ZRHC-* (ZRHCstar).
+ *
+ * reHC-* is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * reHC-* is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with reHC-*.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **/
+#ifndef __TIMELIMIT_HPP__
+#define __TIMELIMIT_HPP__
+
+// Minimum number of CPU seconds that the process can use
+#define MIN_TIME_LIMIT (0)
+
+
+void register_time_limit(unsigned long int secs);
+
+
+
+#endif //__TIMELIMIT_HPP__

src/application/main.cpp

@@ -33,6 +33,7 @@
 #include "log.hpp"
 #include "assertion.hpp"
 #include "utility.hpp"
+#include "timelimit.hpp"
 
 #include <iostream>
 #include <fstream>
@@ -200,9 +201,18 @@ class rehcstar_application_t: public application_t {
 		 "Windows overlap each other by half their length.")
 		;
 
+	 po::options_description exec_opt("Execution Management Options",
+												 po::options_description::m_default_line_length,
+												 po::options_description::m_default_line_length-16);
+	 exec_opt.add_options()
+		("time-limit", po::value< unsigned int >()->default_value(0),
+		 "Maximum (approximated) execution time in seconds (0=no limit).")
+		;
+
 	 modes.add(files);
 	 modes.add(errors);
 	 modes.add(recombs);
+	 modes.add(exec_opt);
 	 return modes;
   };
 
@@ -300,6 +310,11 @@ class rehcstar_application_t: public application_t {
 	 rehcstar_t rehcstar;
 	 rehcstar.prepare_program_options(vm);
 
+// Check if a time-limit is specified
+	 if (vm["time-limit"].as<unsigned int>()>0) {
+		register_time_limit(vm["time-limit"].as<unsigned int>());
+	 }
+
 // Dispatch the work depending on the program parameters
 #ifndef ONLY_INTERNAL_SAT_SOLVER
 	 if (vm["create"].as<bool>()) {

src/lib/timelimit.cpp

@@ -0,0 +1,63 @@
+/**
+ *
+ *                              reHC-*
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
+ *
+ * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
+ *
+ * Distributed under the terms of the GNU General Public License (GPL)
+ *
+ *
+ * This file is part of reHC-* (reHCstar),
+ * previously known as ZRHC-* (ZRHCstar).
+ *
+ * reHC-* is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * reHC-* is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with reHC-*.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ **/
+
+#include "timelimit.hpp"
+
+#include "log.hpp"
+
+#include <csignal>
+#include <cstdlib>
+#include <sys/resource.h>
+
+void exceeded_time_limit(int sig, siginfo_t * info, void * context) {
+  ROOT_FATAL("Time limit reached. Exiting now...");
+  exit(EXIT_FAILURE);
+};
+
+void register_time_limit(unsigned long int secs) {
+  if (secs>0){
+	 if (secs<=MIN_TIME_LIMIT) secs= MIN_TIME_LIMIT;
+	 ROOT_INFO("Setting time-limit to " << secs << " seconds.");
+// Setting time-limit
+	 struct sigaction act;
+	 act.sa_sigaction= exceeded_time_limit;
+	 sigemptyset(&act.sa_mask);
+	 act.sa_flags= SA_SIGINFO;
+	 sigaction(SIGXCPU, &act, NULL);
+	 struct rlimit cpu_limit;
+	 getrlimit(RLIMIT_CPU, &cpu_limit);
+	 cpu_limit.rlim_cur= secs;
+	 cpu_limit.rlim_max= secs+10;
+	 const int lim_res= setrlimit(RLIMIT_CPU, &cpu_limit);
+	 if (lim_res!=0) {
+		ROOT_ERROR("Failed to set the \"hard\" time-limit! "
+					  "Error: " << lim_res << ". Continuing anyway...");
+	 }
+
+  }
+};