def test_EcoliCore_cplex(self):
solved_fluxes = minspan(self.model,
cores=4,
timelimit=30,
verbose=False,
solver_name="cplex")
test_ecoli_core_model(self, solved_fluxes)
def test_EcoliCore_gurobi_ipcluster(self):
client, view = setup_cluster.start_engines()
hotstart = null(self.S.todense())
solved_fluxes = minspan(self.model, starting_fluxes=hotstart,
mapper=view.map_sync, verbose=False, solver_name="cplex")
test_ecoli_core_model(self, solved_fluxes)
setup_cluster.stop_engines()
def test_EcoliCore_cplex_multiprocessing(self):
pool = Pool()
solved_fluxes = minspan(self.model,
cores=2,
timelimit=45,
verbose=False,
solver_name="cplex",
mapper=pool.map)
test_ecoli_core_model(self, solved_fluxes)
def test_EcoliCore_gurobi_multiprocessing(self):
pool = Pool()
solved_fluxes = minspan(self.model,
cores=1,
timelimit=30,
verbose=False,
solver_name="gurobi",
mapper=pool.map)
test_ecoli_core_model(self, solved_fluxes)
def test_EcoliCore_gurobi_ipcluster(self):
client, view = setup_cluster.start_engines()
hotstart = null(self.S.todense())
solved_fluxes = minspan(self.model,
starting_fluxes=hotstart,
mapper=view.map_sync,
verbose=False,
solver_name="cplex")
test_ecoli_core_model(self, solved_fluxes)
setup_cluster.stop_engines()
v = c.direct_view()
except Exception, e:
print e
sleep(5)
return c, v
def stop_engines(mpi=False, verbose=False):
profile = profile_minspan_mpi_dir if mpi else profile_minspan_dir
silence = "" if verbose else "2>/dev/null"
os.system('ipcluster stop --profile-dir="%s" %s' % (profile, silence))
if __name__ == "__main__":
stop_engines()
c, v = start_engines()
print "%d engines connected" % (len(c.ids))
from minspan import *
from cobra.io import load_matlab_model
from time import time
model = load_matlab_model("testing_models.mat", "inj661")
S = model.to_array_based_model().S
start = time()
solved_fluxes = minspan(model, cores=1, verbose=True, mapper=v.map_sync, starting_fluxes="auto")
print "solved in %.2f seconds" % (time() - start)
print "nnz", nnz(solved_fluxes)
print "rank", matrix_rank(solved_fluxes)
print "max(S * v) =", abs(S * solved_fluxes).max()
#from IPython import embed; embed()
stop_engines()
def test_EcoliCore_cplex_multiprocessing(self):
pool = Pool()
solved_fluxes = minspan(self.model, cores=2, timelimit=45,
verbose=False, solver_name="cplex", mapper=pool.map)
test_ecoli_core_model(self, solved_fluxes)
def test_EcoliCore_gurobi_multiprocessing(self):
pool = Pool()
solved_fluxes = minspan(self.model, cores=1, timelimit=30,
verbose=False, solver_name="gurobi", mapper=pool.map)
test_ecoli_core_model(self, solved_fluxes)
def test_EcoliCore_cplex(self):
solved_fluxes = minspan(self.model, cores=4, timelimit=30,
verbose=False, solver_name="cplex")
test_ecoli_core_model(self, solved_fluxes)
def stop_engines(mpi=False, verbose=False):
profile = profile_minspan_mpi_dir if mpi else profile_minspan_dir
silence = "" if verbose else "2>/dev/null"
os.system('ipcluster stop --profile-dir="%s" %s' % (profile, silence))
if __name__ == "__main__":
stop_engines()
c, v = start_engines()
print "%d engines connected" % (len(c.ids))
from minspan import *
from cobra.io import load_matlab_model
from time import time
model = load_matlab_model("testing_models.mat", "inj661")
S = model.to_array_based_model().S
start = time()
solved_fluxes = minspan(model,
cores=1,
verbose=True,
mapper=v.map_sync,
starting_fluxes="auto")
print "solved in %.2f seconds" % (time() - start)
print "nnz", nnz(solved_fluxes)
print "rank", matrix_rank(solved_fluxes)
print "max(S * v) =", abs(S * solved_fluxes).max()
#from IPython import embed; embed()
stop_engines()