def test_GLM_gamma_rand2(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname)
paramDict = define_params()
for trial in range(20):
# params is mutable. This is default.
params = {
'y': 54,
'n_folds': 3,
'family': "gamma",
'alpha': 0.5,
'lambda': 1e-4,
'max_iter': 24
}
colX = h2o_glm.pickRandGlmParams(paramDict, params)
kwargs = params.copy()
start = time.time()
glm = h2o_cmd.runGLMOnly(timeoutSecs=120,
parseKey=parseKey,
**kwargs)
print "glm end on ", csvPathname, 'took', time.time(
) - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
print "Trial #", trial, "completed\n"
def test_1mx10_hastie_10_2_cat_and_shuffle(self):
# gunzip it and cat it to create 2x and 4x replications in SYNDATASETS_DIR
# FIX! eventually we'll compare the 1x, 2x and 4x results like we do
# in other tests. (catdata?)
# This test also adds file shuffling, to see that row order doesn't matter
csvFilename = "1mx10_hastie_10_2.data.gz"
csvPathname = h2o.find_dataset('logreg' + '/' + csvFilename)
kmeans_doit(self, csvFilename, csvPathname, num_rows=1000000, timeoutSecs=60)
filename1x = "hastie_1x.data"
pathname1x = SYNDATASETS_DIR + '/' + filename1x
h2o_util.file_gunzip(csvPathname, pathname1x)
filename1xShuf = "hastie_1x.data_shuf"
pathname1xShuf = SYNDATASETS_DIR + '/' + filename1xShuf
h2o_util.file_shuffle(pathname1x, pathname1xShuf)
filename2x = "hastie_2x.data"
pathname2x = SYNDATASETS_DIR + '/' + filename2x
h2o_util.file_cat(pathname1xShuf, pathname1xShuf, pathname2x)
filename2xShuf = "hastie_2x.data_shuf"
pathname2xShuf = SYNDATASETS_DIR + '/' + filename2xShuf
h2o_util.file_shuffle(pathname2x, pathname2xShuf)
kmeans_doit(self, filename2xShuf, pathname2xShuf, num_rows=2000000, timeoutSecs=90)
# too big to shuffle?
filename4x = "hastie_4x.data"
pathname4x = SYNDATASETS_DIR + '/' + filename4x
h2o_util.file_cat(pathname2xShuf, pathname2xShuf, pathname4x)
kmeans_doit(self, filename4x, pathname4x, num_rows=4000000, timeoutSecs=120)
def test_rf_covtype_train_full(self):
csvFilename = 'train.csv'
csvPathname = h2o.find_dataset('bench/covtype/h2o/' + csvFilename)
print "\nUsing header=1 even though I shouldn't have to. Otherwise I get NA in first row and RF bad\n"
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname,
key2=csvFilename + ".hex",
header=1,
timeoutSecs=180)
for trial in range(1):
# params is mutable. This is default.
kwargs = paramDict
# adjust timeoutSecs with the number of trees
# seems ec2 can be really slow
timeoutSecs = 30 + kwargs['ntree'] * 20
start = time.time()
rfView = h2o_cmd.runRF(csvPathname=csvPathname,
timeoutSecs=timeoutSecs,
**kwargs)
elapsed = time.time() - start
print "RF end on ", csvPathname, 'took', elapsed, 'seconds.', \
"%d pct. of timeout" % ((elapsed/timeoutSecs) * 100)
classification_error = rfView['confusion_matrix'][
'classification_error']
self.assertLess(
classification_error, 0.02,
"train.csv should have full classification error <0.02")
print "Trial #", trial, "completed"
def test_putfile_a5m(self):
timeoutSecs = 500
csvFilenameList = [
# use different names for each parse
# doesn't fail if gzipped?
("a5m.csv", 'A', None),
("a5m.csv", 'B', None),
("a5m.csv", 'C', None),
]
# pop open a browser on the cloud
h2b.browseTheCloud()
for (csvFilename, key, trees) in csvFilenameList:
csvPathname = h2o.find_dataset(csvFilename)
# creates csvFilename and csvFilename.hex keys
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, key=key, timeoutSecs=500)
print csvFilename, 'parse time:', parseKey['response']['time']
print "Parse result['destination_key']:", parseKey['destination_key']
inspect = h2o_cmd.runInspect(key=parseKey['destination_key'])
print "\n" + csvFilename
start = time.time()
# constrain depth to 25
if trees is not None:
RFview = h2o_cmd.runRFOnly(trees=trees,depth=25,parseKey=parseKey,
timeoutSecs=timeoutSecs)
h2b.browseJsonHistoryAsUrlLastMatch("RFView")
# wait in case it recomputes it
time.sleep(10)
sys.stdout.write('.')
sys.stdout.flush()
def test_rf_params_rand2(self):
# for determinism, I guess we should spit out the seed?
# random.seed(SEED)
SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
# SEED =
random.seed(SEED)
print "\nUsing random seed:", SEED
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
for trial in range(10):
# params is mutable. This is default.
params = {'ntree': 13, 'parallel': 1, 'features': 7}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + (
(kwargs['ntree'] * 20) * max(1, kwargs['features'] / 15) *
(kwargs['parallel'] and 1 or 3))
start = time.time()
h2o_cmd.runRF(timeoutSecs=timeoutSecs,
retryDelaySecs=1,
csvPathname=csvPathname,
**kwargs)
elapsed = time.time() - start
print "Trial #", trial, "completed in", elapsed, "seconds.", "%d pct. of timeout" % (
(elapsed * 100) / timeoutSecs)
def test_GLM_gaussian_rand2(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname)
# for determinism, I guess we should spit out the seed?
# random.seed(SEED)
SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
# SEED =
random.seed(SEED)
print "\nUsing random seed:", SEED
paramDict = define_params()
for trial in range(20):
# params is mutable. This is default.
params = {
'y': 54,
'n_folds': 3,
'family': "gamma",
'alpha': 0.5,
'lambda': 1e-4,
'max_iter': 10
}
colX = h2o_glm.pickRandGlmParams(paramDict, params)
kwargs = params.copy()
start = time.time()
glm = h2o_cmd.runGLMOnly(timeoutSecs=120,
parseKey=parseKey,
**kwargs)
print "glm end on ", csvPathname, 'took', time.time(
) - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
print "Trial #", trial, "completed\n"
def test_GLM_gaussian_rand2(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname)
# for determinism, I guess we should spit out the seed?
# random.seed(SEED)
SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
# SEED =
random.seed(SEED)
print "\nUsing random seed:", SEED
paramDict = define_params()
for trial in range(20):
# params is mutable. This is default.
params = {'y': 54, 'num_cross_validation_folds': 3, 'family': "gaussian", 'alpha': 0.5, 'lambda': 1e-4, 'max_iter': 30}
colX = h2o_glm.pickRandGlmParams(paramDict, params)
kwargs = params.copy()
start = time.time()
glm = h2o_cmd.runGLMOnly(timeoutSecs=120, parseKey=parseKey, **kwargs)
print "glm end on ", csvPathname, 'took', time.time() - start, 'seconds'
start = time.time()
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
print "simpleCheckGLM end on ", csvPathname, 'took', time.time() - start, 'seconds'
print "Trial #", trial, "completed\n"
def test_loop_random_param_covtype(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, key='covtype')
# for determinism, I guess we should spit out the seed?
# random.seed(SEED)
SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
# SEED =
random.seed(SEED)
print "\nUsing random seed:", SEED
paramDict = define_params()
for trial in range(40):
# params is mutable. This is default.
params = {
'y': 54,
'num_cross_validation_folds' : 3,
'family' : 'binomial',
'max_iter' : 5,
'case': 1,
'alpha': 0,
'lambda': 0
}
colX = h2o_glm.pickRandGlmParams(paramDict, params)
kwargs = params.copy()
start = time.time()
glm = h2o_cmd.runGLMOnly(timeoutSecs=150, parseKey=parseKey, **kwargs)
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
# FIX! I suppose we have the problem of stdout/stderr not having flushed?
# should hook in some way of flushing the remote node stdout/stderr
h2o.check_sandbox_for_errors()
print "glm end on ", csvPathname, 'took', time.time() - start, 'seconds'
print "Trial #", trial, "completed\n"
def test_GLM_params_rand2_4082088627997819015(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, key='covtype')
paramDict = define_params()
for trial in range(40):
# params is mutable. This is default.
params = {
'y': 54,
'n_folds' : 3,
'family' : 'binomial',
'max_iter' : 5,
'case': 1,
'alpha': 0,
'lambda': 0
}
colX = h2o_glm.pickRandGlmParams(paramDict, params)
kwargs = params.copy()
start = time.time()
timeoutSecs = max(150, params['n_folds']*10 + params['max_iter']*10)
glm = h2o_cmd.runGLMOnly(timeoutSecs=timeoutSecs, parseKey=parseKey, **kwargs)
elapsed = time.time() - start
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
# FIX! I suppose we have the problem of stdout/stderr not having flushed?
# should hook in some way of flushing the remote node stdout/stderr
h2o.check_sandbox_for_errors()
print "glm end on ", csvPathname, 'took', elapsed, 'seconds.',\
"%d pct. of timeout" % ((elapsed*100)/timeoutSecs)
print "Trial #", trial, "completed\n"
def test_rf_strata_fail(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
timeoutSecs = 60
kwargs = {
'response_variable': 54,
'ntree': 50,
'features': '',
'depth': 2147483647,
'stat_type': 'ENTROPY',
'ignore': '',
'class_weights': '1=1.0,2=1.0,3=1.0,4=1.0,5=1.0,6=1.0,7=1.0',
'sampling_strategy': 'RANDOM',
'strata_samples':
'undefined=undefined,undefined=undefined,undefined=undefined,undefined=undefined,undefined=undefined,undefined=undefined,undefined=undefined',
'sample': '67',
'out_of_bag_error_estimate': 1,
'model_key': '',
'bin_limit': 1024,
'seed': 784834182943470027,
'parallel': 1,
'exclusive_split_limit': '',
'iterative_cm': 1,
'use_non_local_data': 0,
}
h2o_cmd.runRF(timeoutSecs=timeoutSecs,
csvPathname=csvPathname,
**kwargs)
def test_A_1mx10_hastie_10_2(self):
# gunzip it and cat it to create 2x and 4x replications in SYNDATASETS_DIR
csvFilename = "1mx10_hastie_10_2.data.gz"
csvPathname = h2o.find_dataset('logreg' + '/' + csvFilename)
y = "10"
x = ""
kwargs = {'x': x, 'y': y, 'case': -1, 'thresholds': 0.5}
(modelKey, validations1) = glm_doit(self, csvFilename, csvPathname,
timeoutSecs=60, pollTimeoutSecs=60, **kwargs)
print "Use", modelKey, "model on 2x and 4x replications and compare results to 1x"
filename1x = "hastie_1x.data"
pathname1x = SYNDATASETS_DIR + '/' + filename1x
h2o_util.file_gunzip(csvPathname, pathname1x)
filename2x = "hastie_2x.data"
pathname2x = SYNDATASETS_DIR + '/' + filename2x
h2o_util.file_cat(pathname1x,pathname1x,pathname2x)
glm_score(self,filename2x, pathname2x, modelKey, thresholds="0.5",
timeoutSecs=60, pollTimeoutSecs=60)
filename4x = "hastie_4x.data"
pathname4x = SYNDATASETS_DIR + '/' + filename4x
h2o_util.file_cat(pathname2x,pathname2x,pathname4x)
print "Iterating 3 times on this last one"
for i in range(3):
print "\nTrial #", i, "of", filename4x
glm_score(self,filename4x, pathname4x, modelKey, thresholds="0.5",
timeoutSecs=60, pollTimeoutSecs=60)
def test_GLM_poisson_1(self):
csvFilename = 'covtype.data'
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/' + csvFilename)
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, timeoutSecs=10)
inspect = h2o_cmd.runInspect(None, parseKey['destination_key'])
print "\n" + csvPathname, \
" num_rows:", "{:,}".format(inspect['num_rows']), \
" num_cols:", "{:,}".format(inspect['num_cols'])
if (1 == 0):
print "WARNING: just doing the first 33 features, for comparison to ??? numbers"
# pythonic!
x = ",".join(map(str, range(33)))
else:
x = ""
print "WARNING: max_iter set to 8 for benchmark comparisons"
max_iter = 8
y = "54"
kwargs = {
'x': x,
'y': y,
'family': 'poisson',
'link': 'log',
'n_folds': 0,
'max_iter': max_iter,
'beta_epsilon': 1e-3
}
timeoutSecs = 120
# L2
start = time.time()
kwargs.update({'alpha': 0, 'lambda': 0})
glm = h2o_cmd.runGLMOnly(parseKey=parseKey,
timeoutSecs=timeoutSecs,
**kwargs)
print "glm (L2) end on ", csvPathname, 'took', time.time(
) - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, 13, **kwargs)
# Elastic
kwargs.update({'alpha': 0.5, 'lambda': 1e-4})
start = time.time()
glm = h2o_cmd.runGLMOnly(parseKey=parseKey,
timeoutSecs=timeoutSecs,
**kwargs)
print "glm (Elastic) end on ", csvPathname, 'took', time.time(
) - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, 13, **kwargs)
# L1
kwargs.update({'alpha': 1, 'lambda': 1e-4})
start = time.time()
glm = h2o_cmd.runGLMOnly(parseKey=parseKey,
timeoutSecs=timeoutSecs,
**kwargs)
print "glm (L1) end on ", csvPathname, 'took', time.time(
) - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, 13, **kwargs)
def test_GLM_params_rand2_4082088627997819015(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, key='covtype')
paramDict = define_params()
for trial in range(40):
# params is mutable. This is default.
params = {
'y': 54,
'n_folds': 3,
'family': 'binomial',
'max_iter': 5,
'case': 1,
'alpha': 0,
'lambda': 0
}
colX = h2o_glm.pickRandGlmParams(paramDict, params)
kwargs = params.copy()
start = time.time()
timeoutSecs = max(150,
params['n_folds'] * 10 + params['max_iter'] * 10)
glm = h2o_cmd.runGLMOnly(timeoutSecs=timeoutSecs,
parseKey=parseKey,
**kwargs)
elapsed = time.time() - start
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
# FIX! I suppose we have the problem of stdout/stderr not having flushed?
# should hook in some way of flushing the remote node stdout/stderr
h2o.check_sandbox_for_errors()
print "glm end on ", csvPathname, 'took', elapsed, 'seconds.',\
"%d pct. of timeout" % ((elapsed*100)/timeoutSecs)
print "Trial #", trial, "completed\n"
def test_loop_random_param_covtype(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname)
paramDict = define_params()
for trial in range(20):
# params is mutable. This is default.
# FIX! does it never end if we don't have alpha specified?
params = {
'y': 54,
'n_folds': 3,
'family': "poisson",
'alpha': 0.5,
'lambda': 1e-4,
'beta_epsilon': 0.001,
'max_iter': 15,
}
colX = h2o_glm.pickRandGlmParams(paramDict, params)
kwargs = params.copy()
# make timeout bigger with xvals
timeoutSecs = 60 + (kwargs['n_folds']*20)
# or double the 4 seconds per iteration (max_iter+1 worst case?)
timeoutSecs = max(timeoutSecs, (8 * (kwargs['max_iter']+1)))
start = time.time()
glm = h2o_cmd.runGLMOnly(timeoutSecs=timeoutSecs, parseKey=parseKey, **kwargs)
print "glm end on ", csvPathname, 'took', time.time() - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
print "Trial #", trial, "completed\n"
def test_glm_covtype_single_cols(self):
timeoutSecs = 10
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
print "\n" + csvPathname
# columns start at 0
y = "54"
x = ""
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, timeoutSecs=15)
print "GLM binomial wth 1 X column at a time"
print "Result check: abs. value of coefficient and intercept returned are bigger than zero"
for colX in xrange(54):
if x == "":
x = str(colX)
else:
# x = x + "," + str(colX)
x = str(colX)
sys.stdout.write('.')
sys.stdout.flush()
print "\nx:", x
print "y:", y
start = time.time()
kwargs = {'x': x, 'y': y, 'n_folds': 6, 'case': 2}
glm = h2o_cmd.runGLMOnly(parseKey=parseKey,
timeoutSecs=timeoutSecs,
**kwargs)
h2o_glm.simpleCheckGLM(self, glm, colX, **kwargs)
print "glm end on ", csvPathname, 'took', time.time(
) - start, 'seconds'
def test_glm_covtype_single_cols(self):
timeoutSecs = 10
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
print "\n" + csvPathname
# columns start at 0
y = "54"
x = ""
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, timeoutSecs=15)
print "GLM binomial wth 1 X column at a time"
print "Result check: abs. value of coefficient and intercept returned are bigger than zero"
for colX in xrange(54):
if x == "":
x = str(colX)
else:
# x = x + "," + str(colX)
x = str(colX)
sys.stdout.write('.')
sys.stdout.flush()
print "\nx:", x
print "y:", y
start = time.time()
kwargs = {'x': x, 'y': y, 'n_folds': 6, 'case': 2}
glm = h2o_cmd.runGLMOnly(parseKey=parseKey, timeoutSecs=timeoutSecs, **kwargs)
h2o_glm.simpleCheckGLM(self, glm, colX, **kwargs)
print "glm end on ", csvPathname, 'took', time.time() - start, 'seconds'
def test_1mx10_hastie_10_2_cat_and_shuffle(self):
# gunzip it and cat it to create 2x and 4x replications in SYNDATASETS_DIR
# FIX! eventually we'll compare the 1x, 2x and 4x results like we do
# in other tests. (catdata?)
# This test also adds file shuffling, to see that row order doesn't matter
csvFilename = "1mx10_hastie_10_2.data.gz"
csvPathname = h2o.find_dataset('logreg' + '/' + csvFilename)
glm_doit(self, csvFilename, csvPathname, timeoutSecs=30)
filename1x = "hastie_1x.data"
pathname1x = SYNDATASETS_DIR + '/' + filename1x
h2o_util.file_gunzip(csvPathname, pathname1x)
filename1xShuf = "hastie_1x.data_shuf"
pathname1xShuf = SYNDATASETS_DIR + '/' + filename1xShuf
h2o_util.file_shuffle(pathname1x, pathname1xShuf)
filename2x = "hastie_2x.data"
pathname2x = SYNDATASETS_DIR + '/' + filename2x
h2o_util.file_cat(pathname1xShuf, pathname1xShuf, pathname2x)
filename2xShuf = "hastie_2x.data_shuf"
pathname2xShuf = SYNDATASETS_DIR + '/' + filename2xShuf
h2o_util.file_shuffle(pathname2x, pathname2xShuf)
glm_doit(self, filename2xShuf, pathname2xShuf, timeoutSecs=45)
# too big to shuffle?
filename4x = "hastie_4x.data"
pathname4x = SYNDATASETS_DIR + '/' + filename4x
h2o_util.file_cat(pathname2xShuf, pathname2xShuf, pathname4x)
glm_doit(self, filename4x, pathname4x, timeoutSecs=120)
def test_A_1mx10_hastie_10_2(self):
# gunzip it and cat it to create 2x and 4x replications in SYNDATASETS_DIR
# FIX! eventually we'll compare the 1x, 2x and 4x results like we do
# in other tests. (catdata?)
csvFilename = "1mx10_hastie_10_2.data.gz"
csvPathname = h2o.find_dataset('logreg' + '/' + csvFilename)
glm_doit(self,csvFilename, csvPathname, timeoutSecs=30)
filename1x = "hastie_1x.data"
pathname1x = SYNDATASETS_DIR + '/' + filename1x
h2o_util.file_gunzip(csvPathname, pathname1x)
filename2x = "hastie_2x.data"
pathname2x = SYNDATASETS_DIR + '/' + filename2x
h2o_util.file_cat(pathname1x,pathname1x,pathname2x)
glm_doit(self,filename2x, pathname2x, timeoutSecs=45)
filename4x = "hastie_4x.data"
pathname4x = SYNDATASETS_DIR + '/' + filename4x
h2o_util.file_cat(pathname2x,pathname2x,pathname4x)
print "Iterating 3 times on this last one for perf compare"
for i in range(3):
print "\nTrial #", i, "of", filename4x
glm_doit(self,filename4x, pathname4x, timeoutSecs=60)
def test_exec_filter_slice2(self):
timeoutSecs = 10
csvFilename = "covtype.data"
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
key2 = "c"
parseKey = h2o_cmd.parseFile(None, csvPathname, 'covtype.data', 'c',
10)
print csvFilename, 'parse time:', parseKey['response']['time']
print "Parse result['desination_key']:", parseKey['destination_key']
inspect = h2o_cmd.runInspect(None, parseKey['destination_key'])
for trial in range(10):
print "Doing the execs in order, to feed filters into slices"
nodeX = 0
for exprTemplate in exprList:
execExpr = h2e.fill_in_expr_template(exprTemplate,
colX=0,
n=0,
row=1,
key2=key2,
m=2)
time.sleep(2)
h2o.check_sandbox_for_errors()
execResultInspect, min_value = h2e.exec_expr(
h2o.nodes[nodeX],
execExpr,
resultKey="Result.hex",
timeoutSecs=4)
print "min_value:", min_value, "execExpr:", execExpr
h2o.verboseprint("min: ", min_value, "trial:", trial)
def test_A_1mx10_hastie_10_2(self):
# gunzip it and cat it to create 2x and 4x replications in SYNDATASETS_DIR
# FIX! eventually we'll compare the 1x, 2x and 4x results like we do
# in other tests. (catdata?)
csvFilename = "1mx10_hastie_10_2.data.gz"
csvPathname = h2o.find_dataset('logreg' + '/' + csvFilename)
glm_doit(self,csvFilename, csvPathname, timeoutSecs=75)
filename1x = "hastie_1x.data"
pathname1x = SYNDATASETS_DIR + '/' + filename1x
h2o_util.file_gunzip(csvPathname, pathname1x)
filename2x = "hastie_2x.data"
pathname2x = SYNDATASETS_DIR + '/' + filename2x
h2o_util.file_cat(pathname1x,pathname1x,pathname2x)
glm_doit(self,filename2x, pathname2x, timeoutSecs=75)
filename4x = "hastie_4x.data"
pathname4x = SYNDATASETS_DIR + '/' + filename4x
h2o_util.file_cat(pathname2x,pathname2x,pathname4x)
print "Iterating 3 times on this last one for perf compare"
for i in range(3):
print "\nTrial #", i, "of", filename4x
glm_doit(self,filename4x, pathname4x, timeoutSecs=150)
def test_rf_params_rand2(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
kwargs = {
'response_variable': 54,
'features': 7,
'sampling_strategy': 'STRATIFIED_LOCAL',
'out_of_bag_error_estimate': 1,
'strata_samples': '1=10,2=99,3=99,4=99,5=99,6=99,7=99',
'bin_limit': None,
'seed': '11111',
'model_key': '012345',
'ntree': 13,
'parallel': 1
}
for trial in range(2):
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + ((kwargs['ntree']*20) * max(1,kwargs['features']/15) * (kwargs['parallel'] and 1 or 3))
start = time.time()
rfv = h2o_cmd.runRF(timeoutSecs=timeoutSecs, retryDelaySecs=1, csvPathname=csvPathname, **kwargs)
elapsed = time.time()-start
cm = rfv['confusion_matrix']
classification_error = cm['classification_error']
rows_skipped = cm['rows_skipped']
# just want to catch the nan case when all rows are skipped
self.assertLess(rows_skipped, 581012)
self.assertLess(classification_error, 100) # error if nan
print "Trial #", trial, "completed in", elapsed, "seconds.", \
"%d pct. of timeout" % ((elapsed*100)/timeoutSecs)
def test_rf_covtype_train_oobe(self):
if (1 == 0):
csvFilename = 'train.csv'
csvPathname = h2o.find_dataset('bench/covtype/h2o/' + csvFilename)
print "\nUsing header=1 even though I shouldn't have to. Otherwise I get NA in first row and RF bad\n"
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname,
key2=csvFilename + ".hex",
header=1,
timeoutSecs=180)
# FIX! maybe try specifying column header with column name
### kwargs['response_variable'] = A55
else:
csvFilename = 'covtype.data'
print "\nUsing header=0 on the normal covtype.data"
csvPathname = h2o.find_dataset(
'UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname,
key2=csvFilename + ".hex",
header=0,
timeoutSecs=180)
inspect = h2o_cmd.runInspect(None, parseKey['destination_key'])
h2o_cmd.infoFromInspect(inspect, csvPathname)
for trial in range(1):
# params is mutable. This is default.
kwargs = paramDict
# adjust timeoutSecs with the number of trees
# seems ec2 can be really slow
timeoutSecs = 30 + kwargs['ntree'] * 20
start = time.time()
rfView = h2o_cmd.runRFOnly(parseKey=parseKey,
timeoutSecs=timeoutSecs,
**kwargs)
elapsed = time.time() - start
print "RF end on ", csvPathname, 'took', elapsed, 'seconds.', \
"%d pct. of timeout" % ((elapsed/timeoutSecs) * 100)
classification_error = rfView['confusion_matrix'][
'classification_error']
self.assertGreater(
classification_error, 0.01,
"train.csv should have out of bag error estimate greater than 0.01"
)
print "Trial #", trial, "completed"
def test_rand_inspect(self):
### h2b.browseTheCloud()
csvFilename = 'covtype.data'
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/' + csvFilename)
print "\n" + csvPathname
parseKey = h2o_cmd.parseFile(None,
csvPathname,
key=csvFilename,
timeoutSecs=10)
destination_key = parseKey['destination_key']
print csvFilename, 'parse time:', parseKey['response']['time']
print "Parse result['destination_key']:", destination_key
def inspect_and_check(nodeX,
destination_key,
offset,
view,
inspect=None):
inspectNew = h2o_cmd.runInspect(h2o.nodes[nodeX],
destination_key,
offset=offset,
view=view)
# FIX! get min/max/mean/variance for a col too?
constantNames = [
'num_cols',
'num_rows',
]
if inspect is not None:
for i in constantNames:
self.assertEqual(inspect[i], inspectNew[i])
return inspectNew
# going to use this to compare against future. num_rows/num_cols should always
# be the same, regardless of the view. just a coarse sanity check
origInspect = inspect_and_check(0, destination_key, 0, 1)
h2o.verboseprint(h2o.dump_json(origInspect))
num_rows = origInspect['num_rows']
num_cols = origInspect['num_cols']
lenNodes = len(h2o.nodes)
for i in range(1000):
# we want to use the boundary conditions, so have two level of random choices
offset = good_choices(num_rows)
view = good_choices(num_cols)
# randomize the node used
nodeX = random.randint(0, lenNodes - 1)
print "nodeX:", nodeX, "offset:", offset, "view:", view
inspect_and_check(nodeX, destination_key, offset, view,
origInspect)
# do it again, once in a while
r = random.randint(0, 10)
if (r == 0):
inspect_and_check(nodeX, destination_key, offset, view,
origInspect)
def test_poker_xlsx(self):
# maybe can get stuck during polling for parse progress?
# break it out for pollTimeoutSecs
parseKey = h2o_cmd.parseFile(
None,
h2o.find_dataset('poker/poker-hand-testing.xlsx'),
timeoutSecs=120,
pollTimeoutSecs=60)
h2o_cmd.runRFOnly(None, parseKey=parseKey, timeoutSecs=120)
def test_rf_params_rand2_7066883810153380318(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
for trial in range(10):
# params is mutable. This is default.
params = {'ntree': 23, 'parallel': 1, 'features': 7}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + ((kwargs['ntree']*20) * max(1,kwargs['features']/15) * (kwargs['parallel'] and 1 or 3))
h2o_cmd.runRF(timeoutSecs=timeoutSecs, csvPathname=csvPathname, **kwargs)
print "Trial #", trial, "completed"
def test_loop_random_param_covtype(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
for trial in range(10):
# params is mutable. This is default.
params = {'ntree': 13, 'parallel': 1, 'features': 7}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + ((kwargs['ntree']*20) * max(1,kwargs['features']/15) * (kwargs['parallel'] and 1 or 3))
h2o_cmd.runRF(timeoutSecs=timeoutSecs, csvPathname=csvPathname, **kwargs)
print "Trial #", trial, "completed"
def test_GLM_covtype(self):
csvFilename = 'covtype.data'
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/' + csvFilename)
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname,timeoutSecs=10)
inspect = h2o_cmd.runInspect(None, parseKey['destination_key'])
print "\n" + csvPathname, \
" num_rows:", "{:,}".format(inspect['num_rows']), \
" num_cols:", "{:,}".format(inspect['num_cols'])
if (1==0):
print "WARNING: just doing the first 33 features, for comparison to allstate numbers"
# pythonic!
x = ",".join(map(str,range(33)))
else:
x = ""
print "WARNING: max_iter set to 8 for benchmark comparisons"
max_iter = 8
y = "54"
# L2
args = {
'x': x,
'y': y,
'family': 'binomial',
'link': 'logit',
'num_cross_validation_folds': 0,
'case_mode': '=',
'case': 1,
'max_iter': max_iter,
'beta_eps': 1e-3}
timeoutSecs = 120
start = time.time()
kwargs.update({'alpha': 0, 'lambda': 0})
glm = h2o_cmd.runGLMOnly(parseKey=parseKey, timeoutSecs=timeoutSecs, **kwargs)
print "glm (L2) end on ", csvPathname, 'took', time.time() - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, 13, **kwargs)
# Elastic
kwargs.update({'alpha': 0.5, 'lambda': 1e-4})
start = time.time()
glm = h2o_cmd.runGLMOnly(parseKey=parseKey, timeoutSecs=timeoutSecs, **kwargs)
print "glm (Elastic) end on ", csvPathname, 'took', time.time() - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, 13, **kwargs)
# L1
kwargs.update({'alpha': 1, 'lambda': 1e-4})
start = time.time()
glm = h2o_cmd.runGLMOnly(parseKey=parseKey, timeoutSecs=timeoutSecs, **kwargs)
print "glm (L1) end on ", csvPathname, 'took', time.time() - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, 13, **kwargs)
def test_loop_random_exec_covtype(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(None, csvPathname, 'covtype.data', 'c.hex', 15)
print "\nParse key is:", parseKey['destination_key']
h2b.browseTheCloud()
h2e.exec_zero_list(zeroList)
start = time.time()
h2e.exec_expr_list_rand(len(h2o.nodes), exprList, 'c.hex',
maxCol=54, maxRow=400000, maxTrials=200, timeoutSecs=5)
h2o.check_sandbox_for_errors()
print "exec end on ", "covtype.data" , 'took', time.time() - start, 'seconds'
def test_rf_params_rand2(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
for trial in range(10):
# params is mutable. This is default.
params = {'ntree': 13, 'parallel': 1, 'features': 7}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + ((kwargs['ntree']*20) * max(1,kwargs['features']/15) * (kwargs['parallel'] and 1 or 3))
start = time.time()
h2o_cmd.runRF(timeoutSecs=timeoutSecs, retryDelaySecs=1, csvPathname=csvPathname, **kwargs)
elapsed = time.time()-start
print "Trial #", trial, "completed in", elapsed, "seconds.", "%d pct. of timeout" % ((elapsed*100)/timeoutSecs)
def test_rf_covtype_train_oobe(self):
if (1==0):
csvFilename = 'train.csv'
csvPathname = h2o.find_dataset('bench/covtype/h2o/' + csvFilename)
print "\nUsing header=1 even though I shouldn't have to. Otherwise I get NA in first row and RF bad\n"
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, key2=csvFilename + ".hex", header=1,
timeoutSecs=180)
# FIX! maybe try specifying column header with column name
### kwargs['response_variable'] = A55
else:
csvFilename = 'covtype.data'
print "\nUsing header=0 on the normal covtype.data"
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, key2=csvFilename + ".hex", header=0,
timeoutSecs=180)
inspect = h2o_cmd.runInspect(None, parseKey['destination_key'])
h2o_cmd.info_from_inspect(inspect, csvPathname)
for trial in range(1):
# params is mutable. This is default.
kwargs = paramDict
# adjust timeoutSecs with the number of trees
# seems ec2 can be really slow
timeoutSecs = 30 + kwargs['ntree'] * 20
start = time.time()
rfView = h2o_cmd.runRFOnly(parseKey=parseKey, timeoutSecs=timeoutSecs, **kwargs)
elapsed = time.time() - start
print "RF end on ", csvPathname, 'took', elapsed, 'seconds.', \
"%d pct. of timeout" % ((elapsed/timeoutSecs) * 100)
classification_error = rfView['confusion_matrix']['classification_error']
self.assertGreater(classification_error, 0.01,
"train.csv should have out of bag error estimate greater than 0.01")
print "Trial #", trial, "completed"
def test_A_1mx10_hastie_10_2(self):
# gunzip it and cat it to create 2x and 4x replications in SYNDATASETS_DIR
# FIX! eventually we'll compare the 1x, 2x and 4x results like we do
# in other tests. (catdata?)
csvFilename = "1mx10_hastie_10_2.data.gz"
csvPathname = h2o.find_dataset('logreg' + '/' + csvFilename)
glm_doit(self, csvFilename, csvPathname, timeoutSecs=300)
filename1x = "hastie_1x.data"
pathname1x = SYNDATASETS_DIR + '/' + filename1x
h2o_util.file_gunzip(csvPathname, pathname1x)
filename2x = "hastie_2x.data"
pathname2x = SYNDATASETS_DIR + '/' + filename2x
h2o_util.file_cat(pathname1x, pathname1x, pathname2x)
glm_doit(self, filename2x, pathname2x, timeoutSecs=300)
def test_GLM_gaussian_rand2(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname)
paramDict = define_params()
for trial in range(20):
# params is mutable. This is default.
params = {'y': 54, 'n_folds': 3, 'family': "gaussian", 'alpha': 0.5, 'lambda': 1e-4, 'max_iter': 30}
colX = h2o_glm.pickRandGlmParams(paramDict, params)
kwargs = params.copy()
start = time.time()
glm = h2o_cmd.runGLMOnly(timeoutSecs=120, parseKey=parseKey, **kwargs)
print "glm end on ", csvPathname, 'took', time.time() - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
print "Trial #", trial, "completed\n"
def test_A_1mx10_hastie_10_2(self):
# gunzip it and cat it to create 2x and 4x replications in SYNDATASETS_DIR
# FIX! eventually we'll compare the 1x, 2x and 4x results like we do
# in other tests. (catdata?)
csvFilename = "1mx10_hastie_10_2.data.gz"
csvPathname = h2o.find_dataset('logreg' + '/' + csvFilename)
glm_doit(self,csvFilename, csvPathname, timeoutSecs=300)
filename1x = "hastie_1x.data"
pathname1x = SYNDATASETS_DIR + '/' + filename1x
h2o_util.file_gunzip(csvPathname, pathname1x)
filename2x = "hastie_2x.data"
pathname2x = SYNDATASETS_DIR + '/' + filename2x
h2o_util.file_cat(pathname1x,pathname1x,pathname2x)
glm_doit(self,filename2x, pathname2x, timeoutSecs=300)
def test_rand_inspect(self):
### h2b.browseTheCloud()
csvFilename = 'covtype.data'
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/'+ csvFilename)
print "\n" + csvPathname
parseKey = h2o_cmd.parseFile(None, csvPathname, key=csvFilename, timeoutSecs=10)
destination_key = parseKey['destination_key']
print csvFilename, 'parse time:', parseKey['response']['time']
print "Parse result['destination_key']:", destination_key
def inspect_and_check(nodeX,destination_key,offset,view,inspect=None):
inspectNew = h2o_cmd.runInspect(h2o.nodes[nodeX], destination_key, offset=offset, view=view)
# FIX! get min/max/mean/variance for a col too?
constantNames = [
'num_cols',
'num_rows',
]
if inspect is not None:
for i in constantNames:
self.assertEqual(inspect[i], inspectNew[i])
return inspectNew
# going to use this to compare against future. num_rows/num_cols should always
# be the same, regardless of the view. just a coarse sanity check
origInspect = inspect_and_check(0,destination_key,0,1)
h2o.verboseprint(h2o.dump_json(origInspect))
num_rows = origInspect['num_rows']
num_cols = origInspect['num_cols']
lenNodes = len(h2o.nodes)
for i in range (1000):
# we want to use the boundary conditions, so have two level of random choices
offset = good_choices(num_rows)
view = good_choices(num_cols)
# randomize the node used
nodeX = random.randint(0,lenNodes-1)
print "nodeX:", nodeX, "offset:", offset, "view:", view
inspect_and_check(nodeX,destination_key,offset,view,origInspect)
# do it again, once in a while
r = random.randint(0,10)
if (r==0):
inspect_and_check(nodeX,destination_key,offset,view,origInspect)
def test_sum(self):
print "Replicating covtype.data by 2x for results comparison to 1x"
filename1x = 'covtype.data'
pathname1x = h2o.find_dataset('UCI/UCI-large/covtype' + '/' +
filename1x)
filename2x = "covtype_2x.data"
pathname2x = SYNDATASETS_DIR + '/' + filename2x
h2o_util.file_cat(pathname1x, pathname1x, pathname2x)
csvAll = [
(pathname1x, "cA", 5, 1),
(pathname2x, "cB", 5, 2),
(pathname2x, "cC", 5, 2),
]
h2b.browseTheCloud()
lenNodes = len(h2o.nodes)
firstDone = False
for (csvPathname, key2, timeoutSecs, resultMult) in csvAll:
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname,
key2=key2,
timeoutSecs=2000)
print "Parse result['Key']:", parseKey['destination_key']
# We should be able to see the parse result?
inspect = h2o_cmd.runInspect(None, parseKey['destination_key'])
print "\n" + csvPathname
h2o_exec.exec_zero_list(zeroList)
colResultList = h2o_exec.exec_expr_list_across_cols(
lenNodes, exprList, key2, maxCol=54, timeoutSecs=timeoutSecs)
print "\ncolResultList", colResultList
if not firstDone:
colResultList0 = list(colResultList)
good = [float(x) for x in colResultList0]
firstDone = True
else:
print "\n", colResultList0, "\n", colResultList
# create the expected answer...i.e. N * first
compare = [float(x) / resultMult for x in colResultList]
print "\n", good, "\n", compare
self.assertEqual(
good, compare,
'compare is not equal to good (first try * resultMult)')
def test_loop_random_param_covtype(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
# for determinism, I guess we should spit out the seed?
##### SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
SEED = 4201285065147091758
random.seed(SEED)
print "\nUsing random seed:", SEED
for trial in range(10):
# params is mutable. This is default.
params = {'ntree': 13, 'parallel': 1, 'features': 7}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + ((kwargs['ntree']*20) * max(1,kwargs['features']/15) * (kwargs['parallel'] and 1 or 3))
h2o_cmd.runRF(timeoutSecs=timeoutSecs, csvPathname=csvPathname, **kwargs)
print "Trial #", trial, "completed"
def test_B_putfile_files(self):
timeoutSecs = 500
# "covtype169x.data",
# "covtype.13x.shuffle.data",
# "3G_poker_shuffle"
# "covtype20x.data",
# "billion_rows.csv.gz",
csvFilenameList = [
("covtype.data", 'UCI/UCI-large/covtype/covtype.data', 1),
]
# pop open a browser on the cloud
h2b.browseTheCloud()
for (csvFilename, datasetPath, trees) in csvFilenameList:
csvPathname = h2o.find_dataset(datasetPath)
# creates csvFilename and csvFilename.hex keys
node = h2o.nodes[0]
key = node.put_file(csvPathname,
key=csvFilename,
timeoutSecs=timeoutSecs)
# not using parseFile...used to be a bug if we inspect the file we just put
# so we test that
inspect1 = h2o_cmd.runInspect(key=csvFilename)
parseKey = node.parse(key, timeoutSecs=500)
print csvFilename, 'parse time:', parseKey['response']['time']
print "Parse result['destination_key']:", parseKey[
'destination_key']
# We should be able to see the parse result?
inspect2 = h2o_cmd.runInspect(key=parseKey['destination_key'])
print "\n" + csvFilename
start = time.time()
# constrain depth to 25
if trees is not None:
RFview = h2o_cmd.runRFOnly(trees=trees,
depth=25,
parseKey=parseKey,
timeoutSecs=timeoutSecs)
sys.stdout.write('.')
sys.stdout.flush()
def test_rf_params_rand2_7066883810153380318(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
# for determinism, I guess we should spit out the seed?
# random.seed(SEED)
# SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
SEED = 7066883810153380318
random.seed(SEED)
print "\nUsing random seed:", SEED
for trial in range(10):
# params is mutable. This is default.
params = {'ntree': 23, 'parallel': 1, 'features': 7}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + ((kwargs['ntree']*20) * max(1,kwargs['features']/15) * (kwargs['parallel'] and 1 or 3))
h2o_cmd.runRF(timeoutSecs=timeoutSecs, csvPathname=csvPathname, **kwargs)
print "Trial #", trial, "completed"
def test_rf_params_rand2_7066883810153380318(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
# for determinism, I guess we should spit out the seed?
# random.seed(SEED)
# SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
SEED = 7066883810153380318
random.seed(SEED)
print "\nUsing random seed:", SEED
for trial in range(20):
# params is mutable. This is default.
params = {'ntree': 23, 'parallel': 1}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + kwargs['ntree'] * 10 * (kwargs['parallel'] and 1 or 3)
h2o_cmd.runRF(timeoutSecs=timeoutSecs, csvPathname=csvPathname, **kwargs)
print "Trial #", trial, "completed"
def test_loop_random_exec_covtype(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(None, csvPathname, 'covtype.data',
'c.hex', 15)
print "\nParse key is:", parseKey['destination_key']
h2b.browseTheCloud()
h2e.exec_zero_list(zeroList)
start = time.time()
h2e.exec_expr_list_rand(len(h2o.nodes),
exprList,
'c.hex',
maxCol=54,
maxRow=400000,
maxTrials=200,
timeoutSecs=15)
h2o.check_sandbox_for_errors()
print "exec end on ", "covtype.data", 'took', time.time(
) - start, 'seconds'
def test_loop_random_param_covtype(self):
start = time.time()
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname)
print "upload/parse end on ", csvPathname, 'took', time.time() - start, 'seconds'
kwargs = define_params()
for trial in range(3):
# make timeout bigger with xvals
timeoutSecs = 60 + (kwargs['n_folds']*20)
# or double the 4 seconds per iteration (max_iter+1 worst case?)
timeoutSecs = max(timeoutSecs, (8 * (kwargs['max_iter']+1)))
start = time.time()
glm = h2o_cmd.runGLMOnly(timeoutSecs=timeoutSecs, parseKey=parseKey, **kwargs)
print "glm end on ", csvPathname, 'took', time.time() - start, 'seconds'
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
print "Trial #", trial, "completed\n"
def test_rf_params_rand2(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
for trial in range(10):
# params is mutable. This is default.
params = {'ntree': 13, 'parallel': 1, 'features': 7}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + (
(kwargs['ntree'] * 20) * max(1, kwargs['features'] / 15) *
(kwargs['parallel'] and 1 or 3))
start = time.time()
h2o_cmd.runRF(timeoutSecs=timeoutSecs,
retryDelaySecs=1,
csvPathname=csvPathname,
**kwargs)
elapsed = time.time() - start
print "Trial #", trial, "completed in", elapsed, "seconds.", "%d pct. of timeout" % (
(elapsed * 100) / timeoutSecs)
def test_rf_params_rand2(self):
# for determinism, I guess we should spit out the seed?
# random.seed(SEED)
SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
# SEED =
random.seed(SEED)
print "\nUsing random seed:", SEED
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
for trial in range(20):
# params is mutable. This is default.
params = {'ntree': 13, 'parallel': 1}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
# seems ec2 can be really slow
timeoutSecs = 30 + 15 * (kwargs['parallel'] and 5 or 10)
h2o_cmd.runRF(timeoutSecs=timeoutSecs, retryDelaySecs=1, csvPathname=csvPathname, **kwargs)
print "Trial #", trial, "completed"
def test_rf_params_rand2(self):
# for determinism, I guess we should spit out the seed?
# random.seed(SEED)
SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
# SEED =
random.seed(SEED)
print "\nUsing random seed:", SEED
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
for trial in range(10):
# params is mutable. This is default.
params = {'ntree': 13, 'parallel': 1, 'features': 7}
colX = h2o_rf.pickRandRfParams(paramDict, params)
kwargs = params.copy()
# adjust timeoutSecs with the number of trees
timeoutSecs = 30 + ((kwargs['ntree']*20) * max(1,kwargs['features']/15) * (kwargs['parallel'] and 1 or 3))
start = time.time()
h2o_cmd.runRF(timeoutSecs=timeoutSecs, retryDelaySecs=1, csvPathname=csvPathname, **kwargs)
elapsed = time.time()-start
print "Trial #", trial, "completed in", elapsed, "seconds.", "%d pct. of timeout" % ((elapsed*100)/timeoutSecs)
def test_exec_covtype_cols(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(None, csvPathname, 'covtype.data', 'c.hex', 10)
print "\nParse key is:", parseKey['destination_key']
### h2b.browseTheCloud()
start = time.time()
# passes with suffix, fails without?
# suffix = ""
suffix = ".hex"
print "Using .hex suffix everywhere until we get type checking in H2O.." + \
"Fails with first size=1 otherwise"
for i in range(54):
execExpr = "Result" + str(i) + suffix + " = c.hex[" + str(i) + "]"
print "execExpr:", execExpr
h2e.exec_expr(h2o.nodes[0], execExpr, resultKey="Result" + str(i) + suffix,
timeoutSecs=4)
h2o.check_sandbox_for_errors()
print "exec end on ", "covtype.data" , 'took', time.time() - start, 'seconds'
def test_sum(self):
print "Replicating covtype.data by 2x for results comparison to 1x"
filename1x = 'covtype.data'
pathname1x = h2o.find_dataset('UCI/UCI-large/covtype' + '/' + filename1x)
filename2x = "covtype_2x.data"
pathname2x = SYNDATASETS_DIR + '/' + filename2x
h2o_util.file_cat(pathname1x,pathname1x,pathname2x)
csvAll = [
(pathname1x, "cA", 5, 1),
(pathname2x, "cB", 5, 2),
(pathname2x, "cC", 5, 2),
]
h2b.browseTheCloud()
lenNodes = len(h2o.nodes)
firstDone = False
for (csvPathname, key2, timeoutSecs, resultMult) in csvAll:
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, key2=key2, timeoutSecs=2000)
print "Parse result['Key']:", parseKey['destination_key']
# We should be able to see the parse result?
inspect = h2o_cmd.runInspect(None, parseKey['destination_key'])
print "\n" + csvPathname
h2o_exec.exec_zero_list(zeroList)
colResultList = h2o_exec.exec_expr_list_across_cols(lenNodes, exprList, key2, maxCol=54,
timeoutSecs=timeoutSecs)
print "\ncolResultList", colResultList
if not firstDone:
colResultList0 = list(colResultList)
good = [float(x) for x in colResultList0]
firstDone = True
else:
print "\n", colResultList0, "\n", colResultList
# create the expected answer...i.e. N * first
compare = [float(x)/resultMult for x in colResultList]
print "\n", good, "\n", compare
self.assertEqual(good, compare, 'compare is not equal to good (first try * resultMult)')
def test_loop_random_param_covtype(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname)
# for determinism, I guess we should spit out the seed?
# random.seed(SEED)
SEED = random.randint(0, sys.maxint)
# if you have to force to redo a test
# SEED =
random.seed(SEED)
paramDict = define_params()
print "\nUsing random seed:", SEED
for trial in range(20):
# params is mutable. This is default.
# FIX! does it never end if we don't have alpha specified?
params = {
'y': 54,
'num_cross_validation_folds': 3,
'family': "poisson",
'alpha': 0.5,
'lambda': 1e-4,
'beta_epsilon': 0.001,
'max_iter': 30
}
colX = h2o_glm.pickRandGlmParams(paramDict, params)
kwargs = params.copy()
# make timeout bigger with xvals
timeoutSecs = 60 + (kwargs['num_cross_validation_folds']*20)
# or double the 4 seconds per iteration (max_iter+1 worst case?)
timeoutSecs = max(timeoutSecs, (8 * (kwargs['max_iter']+1)))
start = time.time()
glm = h2o_cmd.runGLMOnly(timeoutSecs=timeoutSecs, parseKey=parseKey, **kwargs)
print "glm end on ", csvPathname, 'took', time.time() - start, 'seconds'
start = time.time()
h2o_glm.simpleCheckGLM(self, glm, None, **kwargs)
print "simpleCheckGLM end on ", csvPathname, 'took', time.time() - start, 'seconds'
print "Trial #", trial, "completed\n"
def test_exec_filter_slice(self):
timeoutSecs = 10
csvFilename = "covtype.data"
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
key2 = "c"
parseKey = h2o_cmd.parseFile(None, csvPathname, 'covtype.data', 'c', 10)
print csvFilename, 'parse time:', parseKey['response']['time']
print "Parse result['desination_key']:", parseKey['destination_key']
inspect = h2o_cmd.runInspect(None, parseKey['destination_key'])
for trial in range(10):
print "Doing the execs in order, to feed filters into slices"
nodeX = 0
for exprTemplate in exprList:
execExpr = h2e.fill_in_expr_template(exprTemplate, colX=0, n=0, row=1, key2=key2, m=2)
execResultInspect, min_value = h2e.exec_expr(h2o.nodes[nodeX], execExpr,
resultKey="Result.hex", timeoutSecs=4)
print "min_value:", min_value, "execExpr:", execExpr
h2o.verboseprint("min: ", min_value, "trial:", trial)
def test_putfile_a5m(self):
timeoutSecs = 500
csvFilenameList = [
# use different names for each parse
# doesn't fail if gzipped?
("a5m.csv", 'A', None),
("a5m.csv", 'B', None),
("a5m.csv", 'C', None),
]
# pop open a browser on the cloud
h2b.browseTheCloud()
for (csvFilename, key, trees) in csvFilenameList:
csvPathname = h2o.find_dataset(csvFilename)
# creates csvFilename and csvFilename.hex keys
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname,
key=key,
timeoutSecs=500)
print csvFilename, 'parse time:', parseKey['response']['time']
print "Parse result['destination_key']:", parseKey[
'destination_key']
inspect = h2o_cmd.runInspect(key=parseKey['destination_key'])
print "\n" + csvFilename
start = time.time()
# constrain depth to 25
if trees is not None:
RFview = h2o_cmd.runRFOnly(trees=trees,
depth=25,
parseKey=parseKey,
timeoutSecs=timeoutSecs)
h2b.browseJsonHistoryAsUrlLastMatch("RFView")
# wait in case it recomputes it
time.sleep(10)
sys.stdout.write('.')
sys.stdout.flush()
def test_GLM_gamma_fail1(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname)
for trial in range(5):
kwargs = {
'standardize': 1,
'family': 'gamma',
'link': 'familyDefault',
'y': 54,
'lambda': 0.0001,
'alpha': 0.5,
'max_iter': 25,
'n_folds': 1,
}
start = time.time()
glm = h2o_cmd.runGLMOnly(timeoutSecs=120, parseKey=parseKey, **kwargs)
print "glm end on ", csvPathname, 'took', time.time() - start, 'seconds'
# if we hit the max_iter, that means it probably didn't converge. should be 1-maxExpectedIter
# h2o_glm.simpleCheckGLM(self, glm, None, maxExpectedIterations=kwargs['max_iter']-2, **kwargs)
h2o_glm.simpleCheckGLM(self, glm, None, None, **kwargs)
print "Trial #", trial, "completed\n"
def test_B_putfile_files(self):
timeoutSecs = 500
# "covtype169x.data",
# "covtype.13x.shuffle.data",
# "3G_poker_shuffle"
# "covtype20x.data",
# "billion_rows.csv.gz",
csvFilenameList = [
("covtype.data", 'UCI/UCI-large/covtype/covtype.data', 1),
]
# pop open a browser on the cloud
h2b.browseTheCloud()
for (csvFilename, datasetPath, trees) in csvFilenameList:
csvPathname = h2o.find_dataset(datasetPath)
# creates csvFilename and csvFilename.hex keys
node = h2o.nodes[0]
key = node.put_file(csvPathname, key=csvFilename, timeoutSecs=timeoutSecs)
# not using parseFile...used to be a bug if we inspect the file we just put
# so we test that
inspect1 = h2o_cmd.runInspect(key=csvFilename)
parseKey = node.parse(key, timeoutSecs=500)
print csvFilename, 'parse time:', parseKey['response']['time']
print "Parse result['destination_key']:", parseKey['destination_key']
# We should be able to see the parse result?
inspect2 = h2o_cmd.runInspect(key=parseKey['destination_key'])
print "\n" + csvFilename
start = time.time()
# constrain depth to 25
if trees is not None:
RFview = h2o_cmd.runRFOnly(trees=trees,depth=25,parseKey=parseKey,
timeoutSecs=timeoutSecs)
sys.stdout.write('.')
sys.stdout.flush()
def test_exec_covtype_cols(self):
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
parseKey = h2o_cmd.parseFile(None, csvPathname, 'covtype.data',
'c.hex', 10)
print "\nParse key is:", parseKey['destination_key']
### h2b.browseTheCloud()
start = time.time()
# passes with suffix, fails without?
# suffix = ""
suffix = ".hex"
print "Using .hex suffix everywhere until we get type checking in H2O.." + \
"Fails with first size=1 otherwise"
for i in range(54):
execExpr = "Result" + str(i) + suffix + " = c.hex[" + str(i) + "]"
print "execExpr:", execExpr
h2e.exec_expr(h2o.nodes[0],
execExpr,
resultKey="Result" + str(i) + suffix,
timeoutSecs=4)
h2o.check_sandbox_for_errors()
print "exec end on ", "covtype.data", 'took', time.time(
) - start, 'seconds'
def test_rf_covtype_train_full(self):
csvFilename = 'train.csv'
csvPathname = h2o.find_dataset('bench/covtype/h2o/' + csvFilename)
print "\nUsing header=1 even though I shouldn't have to. Otherwise I get NA in first row and RF bad\n"
parseKey = h2o_cmd.parseFile(csvPathname=csvPathname, key2=csvFilename + ".hex", header=1,
timeoutSecs=180)
for trial in range(1):
# params is mutable. This is default.
kwargs = paramDict
# adjust timeoutSecs with the number of trees
# seems ec2 can be really slow
timeoutSecs = 30 + kwargs['ntree'] * 20
start = time.time()
rfView = h2o_cmd.runRF(csvPathname=csvPathname, timeoutSecs=timeoutSecs, **kwargs)
elapsed = time.time() - start
print "RF end on ", csvPathname, 'took', elapsed, 'seconds.', \
"%d pct. of timeout" % ((elapsed/timeoutSecs) * 100)
classification_error = rfView['confusion_matrix']['classification_error']
self.assertLess(classification_error, 0.02,
"train.csv should have full classification error <0.02")
print "Trial #", trial, "completed"
def test_G_RF_covtype(self):
h2o_cmd.runRF(
trees=6,
timeoutSecs=35,
retryDelaySecs=0.5,
csvPathname=h2o.find_dataset('UCI/UCI-large/covtype/covtype.data'))
def test_loop_random_exec_covtype(self):
lenNodes = len(h2o.nodes)
csvPathname = h2o.find_dataset('UCI/UCI-large/covtype/covtype.data')
key2 = 'c.hex'
parseKey = h2o_cmd.parseFile(None, csvPathname, 'covtype.data', key2,
10)
print "\nParse key is:", parseKey['destination_key']
h2b.browseTheCloud()
# for trial in range(53):
trial = 0
while (trial < 100):
for exprTemplate in exprList:
trial = trial + 1
n = trial
colX = random.randint(1, 54)
row = random.randint(1, 400000)
execExpr = exprTemplate
execExpr = re.sub('<col1>', str(colX), execExpr)
execExpr = re.sub('<col2>', str(colX + 1), execExpr)
execExpr = re.sub('<n>', str(n), execExpr)
execExpr = re.sub('<row>', str(row), execExpr)
execExpr = re.sub('<keyX>', str(key2), execExpr)
# pick a random node to execute it on
randNode = random.randint(0, lenNodes - 1)
print "\nexecExpr:", execExpr, "on node", randNode
start = time.time()
resultExec = h2o_cmd.runExecOnly(node=h2o.nodes[randNode],
expression=execExpr,
timeoutSecs=15)
h2o.verboseprint(h2o.dump_json(resultExec))
# print(h2o.dump_json(resultExec))
# FIX! race conditions. If json is done, does that mean you can inspect it??
# wait until the 2nd iteration, which will guarantee both Result1 and Result2 exist
if trial > 1:
inspectMe = random.choice(inspectList)
resultInspect = h2o.nodes[0].inspect(inspectMe)
h2o.verboseprint(h2o.dump_json(resultInspect))
resultInspect = h2o.nodes[1].inspect(inspectMe)
h2o.verboseprint(h2o.dump_json(resultInspect))
resultInspect = h2o.nodes[2].inspect(inspectMe)
h2o.verboseprint(h2o.dump_json(resultInspect))
# FIX! if we race the browser doing the exec too..it shouldn't be a problem?
# might be a bug?
# WARNING! we can't browse the Exec url history, since that will
# cause the Exec to execute again thru the browser..i.e. it has side effects
# just look at the last inspect, which should be the resultInspect!
# h2b.browseJsonHistoryAsUrlLastMatch("Inspect")
h2b.browseJsonHistoryAsUrlLastMatch("Exec")
# url = "http://192.168.0.37:54321/Exec?Expr=Result3+%3D+c.hex%5B26%5D+%2B+Result1&Key=Result"
# webbrowser.open_new_tab(url)
# FIX! I suppose we have the problem of stdout/stderr not having flushed?
# should hook in some way of flushing the remote node stdout/stderr
h2o.check_sandbox_for_errors()
print "exec end on ", "covtype.data", 'took', time.time(
) - start, 'seconds'
print "Trial #", trial, "completed\n"