def test_one(self):
assert "A" == Local().run(A(1, 0))
assert "A" == Local().run(A(10, 0))
assert "A" == Local().run(A(3, 10))
assert "A" == LocalFromRanges([2, 4]).run(A(10, 0))
assert "A" == LocalFromRanges([2, 9, 10]).run(A(3, 0))
assert "A" == LocalFromRanges([2, 9, 10]).run(A(3, 10))
np.random.seed(0)
for i in xrange(1000):
end = int(np.random.uniform(low=1, high=15))
a_work_count = int(np.random.uniform(low=1, high=15))
b_work_count = int(np.random.uniform(low=0, high=3))
extra_steps = int(np.random.uniform(low=0, high=end - 1))
if end > 1:
list = sorted(
np.random.random_integers(low=1,
high=end - 1,
size=extra_steps))
else:
list = []
list.append(end)
if i % 100 == 0: logging.info("random test case # {0}".format(i))
assert "A" == LocalFromRanges(list).run(
A(a_work_count, b_work_count))
def execute_fs(test_snps, pheno, G0, covar):
"""
run feature selection
"""
result = {}
fs_result = {}
# fs unconditioned
########################
tmp_uuid = str(uuid.uuid4())[0:13]
out_fn = "tmp_pheno_%s.txt" % (tmp_uuid)
out_data = pd.DataFrame({
"id1": G0.iid[:, 0],
"id2": G0.iid[:, 1],
"y": pheno["vals"]
})
out_data.to_csv(out_fn, sep=" ", header=False, index=False)
# write out covariates
items = [
('id1', G0.iid[:, 0]),
('id2', G0.iid[:, 1]),
]
items += [("pc_%i" % i, covar["vals"][:, i])
for i in xrange(covar["vals"].shape[1])]
cov_df = pd.DataFrame.from_items(items)
cov_fn = "tmp_cov_%s.txt" % (tmp_uuid)
cov_df.to_csv(cov_fn, sep=" ", header=False, index=False)
#TODO: fix include_all!!
fsd = create_feature_selection_distributable(G0,
out_fn,
None,
0,
"fs_out",
include_all=False,
cov_fn=cov_fn)
fs_result["result_uncond_all"] = Local().run(fsd)
best_k, best_delta, best_obj, best_snps = fs_result["result_uncond_all"]
fs_idx = argintersect_left(G0.sid, best_snps)
G_fs = G0[:, fs_idx]
result["fs_all"] = single_snp(test_snps, pheno,
G0=G_fs).sort(["Chr", "ChrPos"
])["PValue"].as_matrix()
result["fs_all_cov"] = single_snp(
test_snps, pheno, G0=G_fs,
covar=covar).sort(["Chr", "ChrPos"])["PValue"].as_matrix()
return result, fs_result
def test_local_single(self):
"""
test leave one chromosome out iterator
"""
# run on 4 core locally
runner = Local(4)
result = d_map(dummy, self.args, runner, input_files=[self.fn])
expect = [
'', 'A', 'AA', 'AAA', 'AAAB', 'AAABB', 'AAABBB', 'AAABBBC',
'AAABBBCC', 'AAABBBCCC'
]
assert expect == result
def run(self,
methods,
num_causal,
num_repeats,
num_pcs,
description,
runner,
seed=None,
plot_fn=None):
self.precompute_pca()
input_files = [self.snp_fn + ext
for ext in [".bed", ".fam", ".bim"]] + [self.eigen_fn]
input_args = [(methods, self.snp_fn, self.eigen_fn, num_causal,
num_pcs, seed, sim_id) for sim_id in range(num_repeats)]
output_list = distributed_map.d_map(semisynth_simulations.compute_core,
input_args,
runner,
input_files=input_files)
############################################
results_fn = "%s_results.runs_%i.causals_%i.pickle.bzip" % (
description, num_repeats, num_causal)
reduced_results_fn = results_fn.replace("runs", "reduced.runs")
save(results_fn, output_list)
methods = output_list[0][0].keys()
arg_list = [(method, results_fn) for method in methods]
#reduce_runner = Hadoop(len(methods), mapmemory=90*1024, reducememory=90*1024, mkl_num_threads=1, queue="shared")
reduce_runner = Local()
combine_output = distributed_map.d_map(
semisynth_simulations.combine_results,
arg_list,
reduce_runner,
input_files=[results_fn])
save(reduced_results_fn, combine_output)
title = "%i causal, %i repeats" % (num_causal, num_repeats)
visualize_reduced_results(methods,
combine_output,
title=title,
plot_fn=plot_fn)
return combine_output
def run_sim_and_compare(self, name, method):
logging.info('in test_all')
import fastlmm.util.runner as runner
currentFolder = os.path.dirname(os.path.realpath(__file__))
snp_fn = os.path.realpath(currentFolder + "/../../data/mouse/alldata")
out_prefix = currentFolder + "/tempdir/mouse_"
description = "test_run_{0}".format(name)
runner = Local()
num_causals = 500
num_repeats = 1
num_pcs = 5
expected_prefix = currentFolder + "/expected/"
methods = [method]
combine_output = run_simulation(snp_fn, out_prefix, methods, num_causals, num_repeats, num_pcs, description, runner, plot_fn="out.png", seed=42)
from fastlmm.util.pickle_io import load
filename = "%s%s.bzip" % (expected_prefix, name)
co = load(filename)
compare_nested(combine_output, co)
def main():
logging.basicConfig(level=logging.INFO)
#snp_fn = "data/toydata.5chrom"
snp_fn = "data/mouse/alldata"
out_prefix = "results/mouse_"
description = "test_run"
queue = "shared"
#runner = Hadoop2(200, mapmemory=40*1024, reducememory=90*1024, mkl_num_threads=4, queue=queue)
print "using snps", snp_fn
#runner = LocalMultiProc(20)
runner = Local()
num_causals = 500
num_repeats = 3
num_pcs = 5
# make this a tuple of function and kwargs
from GWAS_benchmark.methods import execute_lmm, execute_linear_regression, execute_dual_fs, execute_fs
methods = [execute_fs, execute_linear_regression]
run_simulation(snp_fn, out_prefix, methods, num_causals, num_repeats,
num_pcs, description, runner)
if __name__ == '__main__':
from fastlmm.association.tests.testepistasis import TestEpistasis
suites = unittest.TestSuite([getTestSuite()])
if False: #Standard test run
r = unittest.TextTestRunner(failfast=False)
r.run(suites)
else: #Cluster test run
from fastlmm.util.distributabletest import DistributableTest
runner = HPC(
10,
'RR1-N13-09-H44',
r'\\msr-arrays\Scratch\msr-pool\Scratch_Storage4\Redmond',
remote_python_parent=
r"\\msr-arrays\Scratch\msr-pool\Scratch_Storage4\REDMOND\carlk\Source\carlk\july_7_14\tests\runs\2014-07-24_15_02_02_554725991686\pythonpath",
update_remote_python_parent=True,
priority="AboveNormal",
mkl_num_threads=1)
runner = Local()
#runner = LocalMultiProc(taskcount=20,mkl_num_threads=5)
#runner = LocalInParts(1,2,mkl_num_threads=1) # For debugging the cluster runs
#runner = Hadoop(100, mapmemory=8*1024, reducememory=8*1024, mkl_num_threads=1, queue="default")
distributable_test = DistributableTest(suites, "temp_test")
print runner.run(distributable_test)
logging.info("done with testing")
def mf_to_runner_function(mf):
excluded_nodes = [
] #'GCRCM07B20','GCRCM11B05','GCRCM10B06','GCRCM02B07']#'GCRCM02B11','GCRCM03B07'] #'GCRCM22B06','GCRCN0383','GCRCM02B07','GCRCN0179','GCRCM37B13','GCRCN0376','GCRCN0456']#'gcrcn0231']#"MSR-HDP-DN0316","MSR-HDP-DN0321","MSR-HDP-DN0336","MSR-HDP-DN0377","MSR-HDP-DN0378","MSR-HDP-DN0314","MSR-HDP-DN0335","MSRQC073","MSRQC002","MSRQC015"]
remote_python_parent = r"\\GCR\Scratch\RR1\escience\carlk\data\carlk\pythonpath10262016"
clean_up = False
if mf == "debug":
runner_function = lambda ignore: LocalInParts(
215,
215,
mkl_num_threads=20,
result_file="result.p",
run_dir=r"C:\deldir\test\outputx")
elif mf == "local":
runner_function = lambda ignore: Local()
elif mf == "local1":
runner_function = lambda ignore: Local(1)
elif mf == "lmp":
runner_function = lambda ignore: LocalMultiProc(22, 5)
elif mf == "lmp4":
runner_function = lambda ignore: LocalMultiProc(4, 5)
elif mf == "lmpl":
runner_function = lambda taskcount: LocalMultiProc(
taskcount, taskcount, just_one_process=True)
elif mf == "nodeP":
runner_function = lambda taskcount: HPC(
min(taskcount, 30100),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='node', #core, socket, node
update_remote_python_parent=True,
template="Preemptable",
priority="Lowest",
excluded_nodes=excluded_nodes,
#mkl_num_threads=20,
nodegroups="Preemptable",
runtime="0:11:0", # day:hour:min
#min = 10 #max(1,min(taskcount,110)//20)
#max = min(taskcount,500),
clean_up=clean_up,
)
elif mf == "nodeP99":
runner_function = lambda taskcount: HPC(
min(taskcount, 30100),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='node', #core, socket, node
update_remote_python_parent=True,
template="Preemptable",
priority="Lowest",
excluded_nodes=excluded_nodes,
#mkl_num_threads=20,
nodegroups="Preemptable,B99",
runtime="0:11:0", # day:hour:min
#min = 10 #max(1,min(taskcount,110)//20)
#max = min(taskcount,500),
clean_up=clean_up,
)
elif mf == "nodeL99":
runner_function = lambda taskcount: HPC(
min(taskcount, 30100),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='node', #core, socket, node
update_remote_python_parent=True,
template="LongRunQ",
priority="Lowest",
excluded_nodes=excluded_nodes,
#mkl_num_threads=20,
nodegroups="LongRunQ,B99",
runtime="11:0:0", # day:hour:min
#min = 10 #max(1,min(taskcount,110)//20)
#max = min(taskcount,500),
clean_up=clean_up,
)
elif mf == "socketP":
runner_function = lambda taskcount: HPC(
min(taskcount, 30100),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='socket', #core, socket, node
update_remote_python_parent=True,
template="Preemptable",
priority="Lowest",
excluded_nodes=excluded_nodes,
mkl_num_threads=10,
nodegroups="Preemptable",
runtime="0:11:0", # day:hour:min
#min = max(1,min(taskcount,110)//20),
clean_up=clean_up,
)
elif mf == "coreP":
runner_function = lambda taskcount: HPC(
min(taskcount, 1000),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='core', #core, socket, node
update_remote_python_parent=True,
template="Preemptable",
priority="Lowest",
excluded_nodes=excluded_nodes,
mkl_num_threads=1,
runtime="0:11:0", # day:hour:min
nodegroups="Preemptable",
#min = min(taskcount,1100)
min=1,
max=200 * 20,
clean_up=clean_up,
)
elif mf == "coreP99":
runner_function = lambda taskcount: HPC(
min(taskcount, 1000),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='core', #core, socket, node
update_remote_python_parent=True,
template="Preemptable",
priority="Lowest",
excluded_nodes=excluded_nodes,
mkl_num_threads=1,
runtime="0:11:0", # day:hour:min
nodegroups="Preemptable,B99",
#min = min(taskcount,1100)
min=1,
max=200 * 20,
clean_up=clean_up,
)
elif mf == "coreAz":
runner_function = lambda taskcount: HPC(
min(taskcount, 1000),
'GCR',
r"\\GCR\Scratch\AZ-USCentral\escience",
remote_python_parent=
r"\\GCR\Scratch\AZ-USCentral\escience\carlk\data\carlk\pythonpath",
unit='core', #core, socket, node
update_remote_python_parent=True,
template="Azure IaaS USCentral",
mkl_num_threads=1,
runtime="0:8:0", # day:hour:min,
clean_up=clean_up,
)
elif mf == "nodeE":
runner_function = lambda taskcount: HPC(
min(taskcount, 10100),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='node', #core, socket, node
update_remote_python_parent=True,
template="ExpressQ",
priority="Normal",
#node_local = False,
#mkl_num_threads=20,
runtime="0:4:0", # day:hour:min
#min = min(taskcount,100),
clean_up=clean_up,
)
elif mf == "50tasks":
runner_function = lambda taskcount: HPC(
50,
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='node', #core, socket, node
update_remote_python_parent=True,
template="ExpressQ",
priority="Normal",
#mkl_num_threads=20,
runtime="0:4:0", # day:hour:min
#min = min(taskcount,100),
clean_up=clean_up,
)
elif mf == "coreE":
runner_function = lambda taskcount: HPC(
min(taskcount, 10100),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='core', #core, socket, node
update_remote_python_parent=True,
template="ExpressQ",
priority="Normal",
mkl_num_threads=1,
runtime="0:4:0", # day:hour:min
#min = min(taskcount,100),
clean_up=clean_up,
)
elif mf == "nodeA":
runner_function = lambda taskcount: HPC(
min(taskcount, 30100),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='node', #core, socket, node
update_remote_python_parent=True,
template="Admin Template",
clean_up=clean_up,
)
elif mf == "socketA":
runner_function = lambda taskcount: HPC(
min(taskcount, 30100),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='socket', #core, socket, node
update_remote_python_parent=True,
template="Admin Template",
clean_up=clean_up,
)
elif mf == "coreA":
runner_function = lambda taskcount: HPC(
min(taskcount, 30100),
'GCR',
r"\\GCR\Scratch\RR1\escience",
remote_python_parent=remote_python_parent,
unit='core', #core, socket, node
update_remote_python_parent=True,
template="Admin Template",
clean_up=clean_up,
)
elif mf == "nodeH":
runner_function = lambda taskcount: Hadoop2(min(taskcount, 100000),
mapmemory=58 * 1024,
reducememory=8 * 1024,
min_alloc=2048,
xmx=3072,
mkl_num_threads=14,
queue="shared",
skipdatacheck=True,
skipsourcecheck=True)
elif mf == "coreH":
runner_function = lambda taskcount: Hadoop2(min(taskcount, 100000),
mapmemory=8 * 1024,
reducememory=8 * 1024,
min_alloc=2048,
xmx=3072,
mkl_num_threads=1,
queue="shared",
skipdatacheck=True,
skipsourcecheck=True)
else:
raise Exception("don't find mf=" + mf)
return runner_function
def simulate_ascertained(methods,
prevalence,
iid_count,
num_causal,
num_repeats,
description,
snp_args,
phenotype_args,
runner=Local(),
seed=None,
plot_fn=None):
"""
run a synthetic simulation using ascertained data
:param methods: A list of functions implementing methods to be compared.
:type methods: list<function>
:param prevalence: Prior probability of a case, e.g. .1
:type prevalence: a float between 0.0 and 1.0 (exclusive)
:param iid_count: The number of individuals to generate.
:type iid_count: int
:param num_causal: The number causal SNPs in the simulation.
:type num_causal: int
:param num_repeats: The number of repeats in the simulation.
:type num_repeats: int
:param description: Short description string of experiment (for output)
:type description: str
:param num_repeats: The number of repeats in the simulation.
:type num_repeats: int
:param snp_args: arguments for an internal call to :func:`GWAS_benchmark.snp_gen`. Do not include
'iid_count' or 'seed'
:type snp_args: dictionary
:param phenotype_args: arguments for an internal call to :func:`.generate_phenotype`. Do not include
'snp_count' or 'seed'
:type phenotype_args: dictionary
:param runner: a Runner object (e.g. Local, Hadoop, HPC)
:type runner: Runner
:param seed: a random seed to control random number generation
:type seed: int
:param plot_fn: filename under which to save the output figure
:type plot_fn: str
"""
input_args = [(methods, num_causal, prevalence, iid_count, snp_args,
phenotype_args, seed, sim_id)
for sim_id in range(num_repeats)]
output_list = distributed_map.d_map(
semisynth_simulations.compute_core_ascertained, input_args, runner)
############################################
results_fn = "%s_ascertained_results.runs_%i.causals_%i.pickle.bzip" % (
description, num_repeats, num_causal)
reduced_results_fn = results_fn.replace("runs", "reduced.runs")
save(results_fn, output_list)
methods = output_list[0][0].keys()
arg_list = [(method, results_fn) for method in methods]
combine_output = distributed_map.d_map(
semisynth_simulations.combine_results,
arg_list,
Local(),
input_files=[results_fn])
save(reduced_results_fn, combine_output)
title = "%i causal, %i repeats" % (num_causal, num_repeats)
visualize_reduced_results(methods,
combine_output,
title=title,
plot_fn=plot_fn)
return combine_output