1.0.2 (#67)

* Changed the control flow in main to allow a try/catch of a bad_alloc exception.

* Adjusted memory allocation behavior (larger models will use slightly less memory)

Author: DanielOlson

src/cli.cpp

@@ -634,9 +634,14 @@ void Settings::assign_settings() {
       this->window_size = 100 * this->max_period;
     }
 
+    // medium models use less than 1 GB per thread
+    else if (period_memory <= 4000000) {
+      this->window_size = 50 * this->max_period;
+    }
+
     // Large models use less than 4 GB per thread
     else {
-      this->window_size = 50 * this->max_period;
+      this->window_size = 25 * this->max_period;
     }
 
   }
@@ -670,7 +675,7 @@ void Settings::print_memory_usage() {
   dp_size *= (unsigned long long)(this->window_size + (2 * this->overlap));
   printf("----------------------------\n");
   printf("Maximum repeat period: %llu\n", this->max_period);
-  printf("Number of states: %i\n", num_states);
+  printf("Number of model states: %i\n", num_states);
   printf("Total sequence window size: %lli\n",
          (this->window_size + 2 * this->overlap));
   printf("DP matrix cells: %llu\n", dp_size);
@@ -689,6 +694,7 @@ void Settings::print_memory_usage() {
 
   printf("*Actual memory usage will be slightly greater due to "
          "output repeat queue and repeat split matrices\n");
+  printf("============================\n");
 }
 
 // This could be done in less code with templates. Yikcy wicky yucky wucky.

src/cli.hpp

@@ -5,7 +5,7 @@
 #ifndef ULTRA_CLI_HPP
 #define ULTRA_CLI_HPP
 
-#define ULTRA_VERSION_STRING "1.0.0"
+#define ULTRA_VERSION_STRING "1.0.2"
 
 
 #include "../lib/CLI11.hpp"

src/main.cpp

@@ -2,9 +2,10 @@
 #include "mask.hpp"
 #include "ultra.hpp"
 #include <string>
+#include <new>  // for std::bad_alloc
 
-int main(int argc, const char *argv[]) {
 
+int main_wrapper(int argc, const char * argv[]) {
   // Prepare settings
   Settings *settings = new Settings();
   settings->prepare_settings();
@@ -13,8 +14,8 @@ int main(int argc, const char *argv[]) {
   }
 
   settings->assign_settings();
+  settings->print_memory_usage();
   if (settings->show_memory) {
-    settings->print_memory_usage();
     exit(0);
   }
 
@@ -172,3 +173,30 @@ int main(int argc, const char *argv[]) {
 
   return 0;
 }
+
+
+int main(int argc, const char *argv[]) {
+
+  char *reserve_memory = (char *)malloc(65536);
+  try {
+    int r = main_wrapper(argc, argv);
+    return r;
+  }
+  catch (const std::bad_alloc& e) {
+    // This block is executed if memory allocation fails
+    free(reserve_memory); // May be necessary in order to print
+    std::cerr << "Memory allocation failed: " << e.what() << std::endl;
+    std::cerr << "Your model may be too large to fit in memory"  << std::endl;
+    std::cerr << "Try running: ultra --mem <your arguments> to see expected memory usage" << std::endl;
+  }
+  catch (const std::exception& e) {
+    // This block is executed for any other standard exceptions
+    std::cerr << "Standard exception caught: " << e.what() << std::endl;
+  }
+  catch (...) {
+    // This block catches any other non-standard exceptions
+    std::cerr << "Unknown exception caught!" << std::endl;
+  }
+
+  return -1;
+}