creating branch for adding support for CUDA 3.x and Fermi

[git-p4: depot-paths = "//depot/gpgpu_sim_research/fermi/distribution/": change = 6829]

1 files changed, 202 insertions, 0 deletions

diff --git a/benchmarks/CUDA/MUM/mummergpu_exp.py b/benchmarks/CUDA/MUM/mummergpu_exp.py
new file mode 100644
index 0000000..6461a65
--- /dev/null
+++ b/benchmarks/CUDA/MUM/mummergpu_exp.py
@@ -0,0 +1,202 @@
+#!/usr/bin/env python
+# encoding: utf-8
+"""
+untitled.py
+
+Created by Cole Trapnell on 2007-05-01.
+Copyright (c) 2007 __MyCompanyName__. All rights reserved.
+"""
+
+import sys
+import getopt
+import os
+import time
+import timeit
+import csv
+
+help_message = '''
+This script runs the full cmatch experimental suite.
+'''
+
+
+class Usage(Exception):
+	def __init__(self, msg):
+		self.msg = msg
+
+#refs = ["NC_005810", "2","NC_003997"]
+#qry_lengths = [25, 50, 200, 800]
+
+refs = ["NC_003997"]
+qry_lengths = [25]
+
+def get_stats(filename):
+	stats = {}
+	statfile = open(filename)
+	stats = dict([(key, float(value)) for (key, value) in csv.reader(statfile)])
+	return stats
+
+def cmatch_query_string(ref, length):
+	return ref + "_q" + str(length) + "bp.fna"
+
+def mummer_query_string(ref, length):
+	return ref + "_q" + str(length) + "bp.fna"
+
+def runCmatch(ref, query, matchlen, onCPU, outfile):
+
+	if onCPU:
+		cpuFlag = "-C"
+		statfile = "%s-%ld.cpustats" % ( query, matchlen )
+	else:
+		cpuFlag = ""
+		statfile = "%s-%ld.gpustats" % ( query, matchlen )
+
+	
+	match_flags = " -l %d " % (matchlen)
+	
+	cmd = "mummergpu %s -s %s -M -b %s  %s %s > %s" % (cpuFlag,
+													statfile,
+													match_flags,
+													ref,
+													query,
+													outfile)
+ 	print >> sys.stderr, cmd
+ 	t = timeit.Timer("os.system('" + cmd + "')", "import os")
+ 	app_times = t.repeat(1, 1)
+ 	app_time_avg = sum(app_times)/len(app_times)
+ 	stats = get_stats(statfile)
+	return (app_time_avg, stats)
+
+def runMUMmer(ref, query, matchlen, outfile):
+	query_file = query
+	#for i in range(0,5):
+	#	query_files += query + " "
+		
+	cmd = "mummer -maxmatch -b -l %d %s %s 2>/dev/null  > %s" % (matchlen,
+															  ref,
+															  query_file,
+															  outfile)
+														
+ 	print >> sys.stderr , cmd
+ 	t = timeit.Timer("os.system('" + cmd + "')", "import os")
+ 	app_times = t.repeat(1, 1)
+ 	app_time_avg = sum(app_times)/len(app_times)
+ 
+	return app_time_avg
+
+def get_gpu_time(stats):
+	return stats["Kernel"] + stats["Copy queries to GPU"] + stats["Copy output from GPU"] + stats["Copy suffix tree to GPU"]
+
+def execute_synth_trial(fout, directory, ref, querylen, matchlen):
+	#cmatch_query_file = directory + "/" + ref + query
+
+	query_file = "%s/%s_q%dbp.fna" % (directory, ref, querylen)
+	ref_file = "%s/%s.fna" % (directory, ref)
+	cpu_outfile = query_file + "-cpu.out"
+	gpu_outfile = query_file + "-gpu.out"
+	mummer_outfile = query_file + "-mummer.out"
+	
+	(gpu_app_time_avg, gpu_stats) = runCmatch(ref_file,
+											  query_file,
+											  matchlen,
+											  False,
+											  gpu_outfile)
+	
+	(cpu_app_time_avg, cpu_stats) = runCmatch(ref_file,
+											  query_file,
+											  matchlen,
+											  True,
+											  cpu_outfile)
+
+	mummer_app_time_avg = runMUMmer(ref_file, query_file, matchlen == 0 and querylen or matchlen, mummer_outfile)
+	
+
+ 	kernel_speedup = cpu_stats["Kernel"] / get_gpu_time(gpu_stats)
+
+	print >>fout, querylen, matchlen, cpu_app_time_avg,gpu_app_time_avg, mummer_app_time_avg, cpu_app_time_avg / gpu_app_time_avg, mummer_app_time_avg / gpu_app_time_avg, kernel_speedup
+	#print cmd
+
+
+
+def execute_real_trial(fout, directory, ref, query, matchlen):
+	
+	ref_file = "%s/%s.fna" % (directory, ref)
+	query_file = "%s/%s.fna" % (directory, query)
+	cpu_outfile = query_file + "-cpu.out"
+	gpu_outfile = query_file + "-gpu.out"
+	mummer_outfile = query_file + "-mummer.out"
+	
+	(gpu_app_time_avg, gpu_stats) = runCmatch(ref_file,
+											  query_file,
+											  matchlen,
+											  False,
+											  gpu_outfile)
+	
+ 	(cpu_app_time_avg, cpu_stats) = runCmatch(ref_file,
+ 											  query_file,
+ 											  matchlen,
+ 											  True,
+											  cpu_outfile)
+
+	mummer_app_time_avg = runMUMmer(ref_file, query_file, matchlen, mummer_outfile)
+	
+
+
+ 	kernel_speedup = cpu_stats["Kernel"] /  get_gpu_time(gpu_stats)
+
+   	print >> fout, "-", matchlen,cpu_app_time_avg,gpu_app_time_avg, mummer_app_time_avg, cpu_app_time_avg / gpu_app_time_avg, mummer_app_time_avg / gpu_app_time_avg, kernel_speedup
+
+
+def run_different_query_lengths():
+	f = open("anthrax/speedup.out", "w")
+ 	print >> f, "QUERY,MATCH_LENGTH,CPU,GPU,MUMMER,CPU_SPEEDUP,MUMMER_SPEEDUP,KERNEL_SPEEDUP"	
+ 	execute_synth_trial(f,"anthrax", "NC_003997", 25, 25)
+ 	execute_synth_trial(f,"anthrax", "NC_003997", 50, 50)
+ 	execute_synth_trial(f,"anthrax", "NC_003997", 100,100)
+ 	execute_synth_trial(f,"anthrax", "NC_003997", 200,200) 
+ 	execute_synth_trial(f,"anthrax", "NC_003997", 400,400)
+ 	execute_synth_trial(f,"anthrax", "NC_003997", 800,800)
+	
+def run_ssuis_solexa():
+	f = open("s_suis/speedup.out", "w")
+ 	print >> f, "QUERY,MATCH_LENGTH,CPU,GPU,MUMMER,CPU_SPEEDUP,MUMMER_SPEEDUP,KERNEL_SPEEDUP"	
+	execute_real_trial(f,"s_suis", "cleanref", "cleanreads", 20)
+	
+def run_cereus_454():
+	f = open("cereus/speedup.out", "w")
+ 	print >> f, "QUERY,MATCH_LENGTH,CPU,GPU,MUMMER,CPU_SPEEDUP,MUMMER_SPEEDUP,KERNEL_SPEEDUP"	
+	execute_real_trial(f,"cereus", "cleanref", "cleanreads", 20)
+
+def run_briggsae_sanger():
+	f = open("cbriggsae/speedup.out", "w")
+ 	print >> f, "QUERY,MATCH_LENGTH,CPU,GPU,MUMMER,CPU_SPEEDUP,MUMMER_SPEEDUP,KERNEL_SPEEDUP"	
+	execute_real_trial(f,"cbriggsae", "cleanref", "cleanreads", 100)
+
+def main(argv=None):
+	if argv is None:
+		argv = sys.argv
+	try:
+		try:
+			opts, args = getopt.getopt(argv[1:], "hv", ["help"])
+		except getopt.error, msg:
+			raise Usage(msg)
+	
+		for option, value in opts:
+			if option == "-v":
+				verbose = True
+			if option in ("-h", "--help"):
+				raise Usage(help_message)
+
+		run_ssuis_solexa()
+		run_cereus_454()
+		run_briggsae_sanger()
+
+		run_different_query_lengths()
+		
+	except Usage, err:
+		print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+		print >> sys.stderr, "\t for help use --help"
+		return 2
+
+
+if __name__ == "__main__":
+	sys.exit(main())