From 69f2911e04ffb1b19eef1fafb8c040af271f656e Mon Sep 17 00:00:00 2001
From: Tor Aamodt <aamodt@ece.ubc.ca>
Date: Thu, 15 Jul 2010 18:09:46 -0800
Subject: creating branch for adding support for CUDA 3.x and Fermi

[git-p4: depot-paths = "//depot/gpgpu_sim_research/fermi/distribution/": change = 6829]
---
 benchmarks/CUDA/MUM/mummergpu_main.cpp | 152 +++++++++++++++++++++++++++++++++
 1 file changed, 152 insertions(+)
 create mode 100644 benchmarks/CUDA/MUM/mummergpu_main.cpp

(limited to 'benchmarks/CUDA/MUM/mummergpu_main.cpp')

diff --git a/benchmarks/CUDA/MUM/mummergpu_main.cpp b/benchmarks/CUDA/MUM/mummergpu_main.cpp
new file mode 100644
index 0000000..41d5fe3
--- /dev/null
+++ b/benchmarks/CUDA/MUM/mummergpu_main.cpp
@@ -0,0 +1,152 @@
+#include <stdio.h>
+#include <unistd.h>
+#include <fstream>
+
+#define ulong4 uint32_t
+#include "mummergpu.h"
+
+char * OPT_reffilename = NULL;
+char * OPT_qryfilename = NULL;
+char * OPT_dotfilename = NULL;
+char * OPT_texfilename = NULL;
+int    OPT_num_reference_pages = 1;
+char * OPT_stats_file = NULL;
+
+// MUMmer options
+int  OPT_match_length = 20;
+bool OPT_reverse = false;
+bool OPT_forwardreverse = false;
+bool OPT_forwardcoordinates = false;
+bool OPT_showQueryLength = false;
+bool OPT_maxmatch = false;
+
+MUMMERGPU_OPTIONS options = DEFAULT;
+
+void printHelp()
+{
+   fprintf(stderr, 
+		   "Align a set of query strings to a reference sequence using the GPU.\n"
+		   "\n"
+		   "Usage: mummergpu [options] reference.fa query.fa\n"
+		   "\n"
+		   "Options\n"
+		   "  -h Print this help\n"
+//		   "  -d file.dot Output suffix tree in dot format\n"
+//		   "  -t file.tex Output suffix tree texture\n"
+		   "  -C             Compute the matches using the CPU instead of the GPU\n"
+		   "  -s <file>      write timing and memory stats to <file> \n"
+           "\n"
+           "  -l <matchlen>  minimal match length to report [Default: 20]\n"
+           "  -b             compute forward and reverse complement matches\n"
+           "  -r             only compute reverse complement matches\n"
+           "  -c             report the query-position of a reverse complement match\n"
+           "                 relative to the original query sequence\n"
+           "  -L             show the length of the query sequences on the header line\n"
+	  );
+
+   exit(0);
+}
+
+void printUsage()
+{
+   fprintf(stderr, "Usage: mummergpu [options] reference.fa query.fa\n");
+   exit(0);
+}
+
+
+void ParseCommandLine(int argc, char ** argv)
+{
+   bool errflg = false;
+   int ch;
+   optarg = NULL;
+
+   while(!errflg && ((ch = getopt (argc, argv, "aCchql:d:t:s:brcLM")) != EOF))
+   {
+      switch  (ch)
+	  {
+		 case 'h': printHelp(); break;
+		 case '?': fprintf(stderr, "Unknown option %c\n", optopt); errflg = true; break;
+		 case 'd': OPT_dotfilename = optarg; break;
+		 case 't': OPT_texfilename = optarg; break;
+		 case 'C': options |= ON_CPU; break;
+		 case 'l': OPT_match_length = atoi(optarg); break;
+         case 'b': OPT_forwardreverse = true; break;
+         case 'r': OPT_reverse = true; break;
+		 case 's': OPT_stats_file = optarg; break;
+         case 'c': OPT_forwardcoordinates = true; break;
+         case 'L': OPT_showQueryLength = true; break;
+         case 'M': OPT_maxmatch = true; break;
+
+		 default: errflg = true; break;
+	  };
+   }
+
+   if ((optind != argc-2) || errflg) { printUsage(); }
+
+   if (!OPT_maxmatch)
+   {
+     OPT_maxmatch = true;
+   }
+
+   if (OPT_reverse && OPT_forwardreverse)
+   {
+     fprintf(stderr, "ERROR: Reverse (-r) and Forward & Reverse (-b) specified\n");
+     exit(1);
+   }
+
+   OPT_reffilename = argv[optind++];
+   OPT_qryfilename = argv[optind++];
+}
+
+int main(int argc, char* argv[])
+{
+
+   ParseCommandLine(argc, argv);
+
+   int err = 0;
+
+   Reference ref;
+   if ((err = createReference(OPT_reffilename, &ref)))
+   {
+	  printStringForError(err);
+	  exit(err);
+   }
+   
+   QuerySet queries;
+   if ((err = createQuerySet(OPT_qryfilename, &queries)))
+   {
+	  printStringForError(err);
+	  exit(err);
+   }
+
+   MatchContext ctx;
+   if ((err = createMatchContext(&ref, 
+								&queries, 
+								0, 
+								options, 
+								OPT_match_length, 
+								OPT_stats_file,
+								OPT_reverse,
+                                OPT_forwardreverse,
+                                OPT_forwardcoordinates,
+                                OPT_showQueryLength,
+								&ctx)))
+   {
+	  printStringForError(err);
+	  exit(err);
+   }   
+
+   if ((err = matchQueries(&ctx)))
+   {
+	  printStringForError(err);
+	  exit(err);
+   }   
+   
+   if ((err = destroyMatchContext(&ctx)))
+   {
+	  printStringForError(err);
+	  exit(err);
+   }   
+}
+
+
-- 
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