integrating recent changes from fermi-test into fermi

(i'll use "fermi" for more disruptive changes to the pipeline model such
as updating the MSHRs and getting rid of the warp tracker, ripping out DWF, etc...)

[git-p4: depot-paths = "//depot/gpgpu_sim_research/fermi/distribution/": change = 7805]

1 files changed, 0 insertions, 202 deletions

diff --git a/benchmarks/CUDA/MUM/mummergpu_exp.py b/benchmarks/CUDA/MUM/mummergpu_exp.py
deleted file mode 100644
index 6461a65..0000000
--- a/benchmarks/CUDA/MUM/mummergpu_exp.py
+++ /dev/null
@@ -1,202 +0,0 @@
-#!/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())