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lammps/regress/benchmark.py
3b9563910ef8lammm-master-deprecated

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benchmark.py
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#!/usr/bin/env python
"""
function: numerical comparisions of logs and corresponding benchmarks
usage: benchmark.py <nprocs> <njobs> <dirs>
"""
import sys
import os
import math
import re
from operator import itemgetter
from glob import glob
import time
import multiprocessing as mp
try:
import Queue as queue # 2.6
except ImportError:
import queue # 3.0
#====================================================
### constants
#====================================================
thermo_pattern = re.compile("^Step "); # fragile
data_pattern = re.compile("\s*\d"); # fragile
fail_pattern = re.compile("FAIL");
tol = 1.e-6 # 1.e-10
arch = "openmpi"
src_path = "../src/" #relative to home
exe_path = "../"+src_path
#====================================================
### date
#====================================================
def date():
return time.asctime()
#====================================================
### timer
#====================================================
## NOTE these don't seem to work how I expect them to
def start():
global dt
dt = -(time.clock())
def stop():
global dt
dt += (time.clock())
return dt
#====================================================
### run a benchmark
#====================================================
def run_test(test):
input = "in."+test;
log = "log."+test
stdout = "stdout."+test
ref = (glob(log+"*."+str(np)))[0];
msg = "==== comparing "+log+" with "+ref+" ====\n"
if (os.path.isfile(log)): os.remove(log)
if (os.path.isfile(stdout)): os.remove(stdout)
os.system(lmps+input+" >& "+stdout);
if (not os.path.isfile(log)) :
msg += "!!! no "+log+"\n";
msg += "!!! test "+test+" FAILED\n"
return msg
[cdict,cdata] = extract_data(log);
[bdict,bdata] = extract_data(ref);
cols = range(len(bdict))
if (len(cdata) != len(bdata)):
msg += "!!! data size "+str(len(cdata))+" does not match data "+str(len(bdata))+" in "+ref+"\n";
msg += "!!! test "+test+" FAILED\n"
return msg
fail = False
i = 0
for name in bdict:
[passing,cmsg] = compare(name,cdata[cols[i]],bdata[cols[i]]);
i += 1
msg += cmsg
if (not passing) : fail = True
if (fail) :
msg += "!!! test "+test+" FAILED\n"
else :
msg += "*** test "+test+" passed\n"
return msg
#====================================================
### extract data from log file
#====================================================
def extract_data(file):
dictionary = [];
data = []
read = False
for line in open(file):
if (read and data_pattern.match(line)) :
cols = line.split();
data.append(cols)
else :
read = False
if (thermo_pattern.match(line)):
dictionary = line.split();
read = True
return [dictionary,data]
#====================================================
### compare columns of current and benchmark
#====================================================
def compare(name,col1,col2):
err = 0.
norm1 = 0.
norm2 = 0.
n = len(col2)
for i in range(n):
v1 = float(col1[i])
v2 = float(col2[i])
norm1 += v1*v1
norm2 += v2*v2
dv = v1-v2
err += dv*dv
norm1 /= n
norm2 /= n
err /= n
if (norm2 > tol) :
msg = "{0:7s} relative error {1:4} wrt norm {2:7}\n".format(name,err,norm2)
else :
msg = "{0:7s} error {1:4}\n" .format(name,err)
return [(err < tol),msg];
#################################################################
class Worker(mp.Process):
def __init__(self, work_queue, result_queue):
mp.Process.__init__(self)
self.work_queue = work_queue
self.result_queue = result_queue
def run(self):
while True:
try:
job = self.work_queue.get_nowait()
except queue.Empty:
break
#print(">>> starting " + str(job[1]) + " ...")
os.chdir(job[0])
start()
msg = run_test(job[1])
elapsed_time = stop()
msg += "elapsed time "+str(elapsed_time)+"\n"
os.chdir(home)
self.result_queue.put([job[1],msg])
#====================================================
### parse
#====================================================
def init() :
global np, njobs, ntests, lmps, arch, home
home = os.getcwd()
if (len(sys.argv) < 4) :
print "usage: benchmark.py <nprocs> <njobs> <test_dirs>"
sys.exit(1)
np = int(sys.argv[1])
njobs = int(sys.argv[2])
lmps = "../"+src_path+"lmp_"+arch+" -in "
if (np > 1):
lmps = "mpirun -np "+str(np)+" "+lmps
else:
arch = "serial"
lmps = exe_path+"lmp_"+arch+" -in "
pool = mp.Pool(njobs)
dirs = sys.argv[3:]
tests = []
for dir in dirs:
os.chdir(dir);
for path in glob("./in.*"):
test = path[5:];
tests.append([dir,test])
os.chdir(home)
ntests = len(tests)
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
print "start: ",date()
print "arch:",arch,
print "nprocs:",np
print "ntests:",ntests,
print "njobs:",njobs
print "relative tolerance:",tol
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
print
return tests
#====================================================
### build executable
#====================================================
def build(arch):
os.system("cd ..; svn update >& svn_update.log")
os.system("cd ../src; make no-atc >& /dev/null")
os.system("cd ../src; make clean-all >& /dev/null")
#os.system("cd ../src; make yes-all >& /dev/null")
os.system("cd ../src; make yes-dipole >& /dev/null")
sys.stdout.flush()
print "** building ",arch,"...",
os.system("cd "+src_path+"; make -j "+str(np)+" "+arch+" >& build_"+arch+".log")
if (not os.path.isfile(src_path+"lmp_"+arch)) :
print "!!! build ",arch," FAILED"
sys.exit()
else:
print "done"
print
#====================================================
### main
#====================================================
if __name__ == '__main__':
tests = init()
build(arch)
work_queue = mp.Queue()
for test in tests:
work_queue.put(test)
result_queue = mp.Queue()
nfails = 0
fail_list = []
for i in range(njobs):
w = Worker(work_queue, result_queue)
w.start()
for i in range(ntests):
[test,msg] = result_queue.get()
if (fail_pattern.search(msg)) :
nfails += 1
fail_list.append(test)
#print msg # can print only if failed
print msg # can print only if failed
#print test, " passed"
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
print "end:",date()
if (nfails == 0):
print "*** no failures ***"
else :
print "!!!",nfails,"of",ntests,"tests failed"
for test in fail_list:
print test
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
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