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Scripts to reproduce experiments for reaction mining

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This commit is contained in:
Artur Meski
2023-11-06 21:07:01 +00:00
parent e9589cd0d9
commit 47e03694e4
16 changed files with 774 additions and 142 deletions
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2
examples/bdd/generators/gen_drs.py
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@@ -1,4 +1,4 @@
#!/usr/bin/env python
#!/usr/bin/env python3
import sys
import itertools

4
examples/smt/chain_reaction.py Normal file → Executable file
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@@ -28,7 +28,6 @@ import resource
def chain_reaction(print_system=False):
if len(sys.argv) < 1 + 3:
print("{source} <N> <M> <type>".format(source=sys.argv[0]))
print()
@@ -39,7 +38,7 @@ def chain_reaction(print_system=False):
print()
exit(1)
chainLen = int(sys.argv[1])
chainLen = int(sys.argv[1])
maxConc = int(sys.argv[2]) # depth (max concentration)
verify_rsc = bool(int(sys.argv[3]))
@@ -115,7 +114,6 @@ def chain_reaction(print_system=False):
def main():
chain_reaction()

117
examples/smt/heat_shock_response.py Normal file → Executable file
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@@ -28,8 +28,7 @@ import resource
def heat_shock_response(print_system=True, verify_rsc=True):
if len(sys.argv) < 1+1:
if len(sys.argv) < 1 + 1:
print("{source} <type>".format(source=sys.argv[0]))
print("type:")
print(" - 1 -- RSC")
@@ -37,72 +36,80 @@ def heat_shock_response(print_system=True, verify_rsc=True):
print()
exit(1)
verify_rsc=bool(int(sys.argv[1]))
verify_rsc = bool(int(sys.argv[1]))
stress_temp = 42
max_temp = 50
r = ReactionSystemWithConcentrations()
r.add_bg_set_entity(("hsp",1))
r.add_bg_set_entity(("hsf",1))
r.add_bg_set_entity(("hsf2",1))
r.add_bg_set_entity(("hsf3",1))
r.add_bg_set_entity(("hse",1))
r.add_bg_set_entity(("mfp",1))
r.add_bg_set_entity(("prot",1))
r.add_bg_set_entity(("hsf3:hse",1))
r.add_bg_set_entity(("hsp:mfp",1))
r.add_bg_set_entity(("hsp:hsf",1))
r.add_bg_set_entity(("temp",max_temp))
r.add_bg_set_entity(("heat",1))
r.add_bg_set_entity(("cool",1))
r.add_reaction([("hsf",1)], [("hsp",1)], [("hsf3",1)])
r.add_reaction([("hsf",1),("hsp",1),("mfp",1)], [], [("hsf3",1)])
r.add_reaction([("hsf3",1)], [("hse",1),("hsp",1)],[("hsf",1)])
r.add_reaction([("hsf3",1),("hsp",1),("mfp",1)], [("hse",1)], [("hsf",1)])
r.add_reaction([("hsf3",1),("hse",1)], [("hsp",1)], [("hsf3:hse",1)])
r.add_reaction([("hsp",1),("hsf3",1),("mfp",1),("hse",1)],[], [("hsf3:hse",1)])
r.add_reaction([("hse",1)], [("hsf3",1)], [("hse",1)])
r.add_reaction([("hsp",1),("hsf3",1),("hse",1)], [("mfp",1)], [("hse",1)])
r.add_reaction([("hsf3:hse",1)], [("hsp",1)], [("hsp",1),("hsf3:hse",1)])
r.add_reaction([("hsp",1),("mfp",1),("hsf3:hse",1)],[], [("hsp",1),("hsf3:hse",1)])
r.add_reaction([("hsf",1),("hsp",1)], [("mfp",1)], [("hsp:hsf",1)])
r.add_reaction([("hsp:hsf",1),("temp",stress_temp)],[], [("hsf",1),("hsp",1)])
r.add_reaction([("hsp:hsf",1)], [("temp",stress_temp)],[("hsp:hsf",1)])
r.add_reaction([("hsp",1),("hsf3:hse",1)], [("mfp",1)], [("hse",1),("hsp:hsf",1)])
r.add_reaction([("temp",stress_temp),("prot",1)], [], [("mfp",1),("prot",1)])
r.add_reaction([("prot",1)], [("temp",stress_temp)], [("prot",1)])
r.add_reaction([("hsp",1),("mfp",1)], [], [("hsp:mfp",1)])
r.add_reaction([("mfp",1)], [("hsp",1)], [("mfp",1)])
r.add_reaction([("hsp:mfp",1)], [], [("hsp",1),("prot",1)])
r.add_reaction_inc("temp", "heat", [("temp",1)],[("temp",max_temp)])
r.add_reaction_dec("temp", "cool", [("temp",1)],[])
r = ReactionSystemWithConcentrations()
r.add_bg_set_entity(("hsp", 1))
r.add_bg_set_entity(("hsf", 1))
r.add_bg_set_entity(("hsf2", 1))
r.add_bg_set_entity(("hsf3", 1))
r.add_bg_set_entity(("hse", 1))
r.add_bg_set_entity(("mfp", 1))
r.add_bg_set_entity(("prot", 1))
r.add_bg_set_entity(("hsf3:hse", 1))
r.add_bg_set_entity(("hsp:mfp", 1))
r.add_bg_set_entity(("hsp:hsf", 1))
r.add_bg_set_entity(("temp", max_temp))
r.add_bg_set_entity(("heat", 1))
r.add_bg_set_entity(("cool", 1))
r.add_permanency("temp",[("heat",1),("cool",1)])
r.add_reaction([("hsf", 1)], [("hsp", 1)], [("hsf3", 1)])
r.add_reaction([("hsf", 1), ("hsp", 1), ("mfp", 1)], [], [("hsf3", 1)])
r.add_reaction([("hsf3", 1)], [("hse", 1), ("hsp", 1)], [("hsf", 1)])
r.add_reaction([("hsf3", 1), ("hsp", 1), ("mfp", 1)], [("hse", 1)], [("hsf", 1)])
r.add_reaction([("hsf3", 1), ("hse", 1)], [("hsp", 1)], [("hsf3:hse", 1)])
r.add_reaction(
[("hsp", 1), ("hsf3", 1), ("mfp", 1), ("hse", 1)], [], [("hsf3:hse", 1)]
)
r.add_reaction([("hse", 1)], [("hsf3", 1)], [("hse", 1)])
r.add_reaction([("hsp", 1), ("hsf3", 1), ("hse", 1)], [("mfp", 1)], [("hse", 1)])
r.add_reaction([("hsf3:hse", 1)], [("hsp", 1)], [("hsp", 1), ("hsf3:hse", 1)])
r.add_reaction(
[("hsp", 1), ("mfp", 1), ("hsf3:hse", 1)], [], [("hsp", 1), ("hsf3:hse", 1)]
)
r.add_reaction([("hsf", 1), ("hsp", 1)], [("mfp", 1)], [("hsp:hsf", 1)])
r.add_reaction(
[("hsp:hsf", 1), ("temp", stress_temp)], [], [("hsf", 1), ("hsp", 1)]
)
r.add_reaction([("hsp:hsf", 1)], [("temp", stress_temp)], [("hsp:hsf", 1)])
r.add_reaction(
[("hsp", 1), ("hsf3:hse", 1)], [("mfp", 1)], [("hse", 1), ("hsp:hsf", 1)]
)
r.add_reaction([("temp", stress_temp), ("prot", 1)], [], [("mfp", 1), ("prot", 1)])
r.add_reaction([("prot", 1)], [("temp", stress_temp)], [("prot", 1)])
r.add_reaction([("hsp", 1), ("mfp", 1)], [], [("hsp:mfp", 1)])
r.add_reaction([("mfp", 1)], [("hsp", 1)], [("mfp", 1)])
r.add_reaction([("hsp:mfp", 1)], [], [("hsp", 1), ("prot", 1)])
r.add_reaction_inc("temp", "heat", [("temp", 1)], [("temp", max_temp)])
r.add_reaction_dec("temp", "cool", [("temp", 1)], [])
r.add_permanency("temp", [("heat", 1), ("cool", 1)])
c = ContextAutomatonWithConcentrations(r)
c.add_init_state("0")
c.add_state("1")
c.add_transition("0", [("hsf",1),("prot",1),("hse",1),("temp",35)], "1")
c.add_transition("1", [("cool",1)], "1")
c.add_transition("1", [("heat",1)], "1")
c.add_transition("0", [("hsf", 1), ("prot", 1), ("hse", 1), ("temp", 35)], "1")
c.add_transition("1", [("cool", 1)], "1")
c.add_transition("1", [("heat", 1)], "1")
c.add_transition("1", [], "1")
rc = ReactionSystemWithAutomaton(r,c)
rc = ReactionSystemWithAutomaton(r, c)
if print_system:
rc.show()
prop_req = [ ("mfp",1) ]
prop_block = [ ]
prop = (prop_req,prop_block)
rs_prop = (state_translate_rsc2rs(prop_req),state_translate_rsc2rs(prop_block))
prop_req = [("mfp", 1)]
prop_block = []
prop = (prop_req, prop_block)
rs_prop = (state_translate_rsc2rs(prop_req), state_translate_rsc2rs(prop_block))
if verify_rsc:
smt_rsc = SmtCheckerRSC(rc)
smt_rsc.check_reachability(prop,max_level=40)
smt_rsc.check_reachability(prop, max_level=40)
else:
orc = rc.get_ordinary_reaction_system_with_automaton()
if print_system:
@@ -117,10 +124,10 @@ def state_translate_rsc2rs(p):
def main():
heat_shock_response()
if __name__ == "__main__":
main()
# EOF

17
examples/smt/mutex_param.py Normal file → Executable file
View File

@@ -42,7 +42,7 @@ def powerset(iterable, N=None):
def mutex_param_bench(cmd_args):
"""
Mutex Benchmark
Parametric
"""
@@ -77,7 +77,6 @@ def mutex_param_bench(cmd_args):
Inhib = [("s", 1)]
for i in range(n_proc):
r.add_reaction([E("out", i), E("act", i)], Inhib, [E("req", i)])
r.add_reaction([E("out", i)], [E("act", i)], [E("out", i)])
@@ -189,7 +188,7 @@ def mutex_param_bench(cmd_args):
def mutex_nonparam_bench(cmd_args):
"""
Mutex Benchmark
Parametric
"""
@@ -217,7 +216,6 @@ def mutex_nonparam_bench(cmd_args):
Inhib = [("s", 1)]
for i in range(n_proc):
r.add_reaction([E("out", i), E("act", i)], Inhib, [E("req", i)])
r.add_reaction([E("out", i)], [E("act", i)], [E("out", i)])
@@ -297,7 +295,7 @@ def mutex_nonparam_bench(cmd_args):
def mutex_nonparam_bench_oldimpl(cmd_args):
"""
Mutex Benchmark
Parametric
"""
@@ -325,7 +323,6 @@ def mutex_nonparam_bench_oldimpl(cmd_args):
Inhib = [("s", 1)]
for i in range(n_proc):
r.add_reaction([E("out", i), E("act", i)], Inhib, [E("req", i)])
r.add_reaction([E("out", i)], [E("act", i)], [E("out", i)])
@@ -407,7 +404,6 @@ def state_translate_rsc2rs(p):
def mutex_bench_main(cmd_args):
mode = cmd_args.mode
if mode == "p":
@@ -422,17 +418,16 @@ def mutex_bench_main(cmd_args):
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
"scaling",
help="scaling parameter value",
)
parser.add_argument(
"mode",
choices=['p', 'np-p', 'np-np'],
choices=["p", "np-p", "np-np"],
help="Selects the mode: p - parameter synthesis (parametric implementation), np-p - non-parametric with parametric implementation (with the parameters substituted), np-np - non-parametric with non-parametric implementation (parameters substituted)",
)
@@ -447,7 +442,7 @@ def main():
)
args = parser.parse_args()
mutex_bench_main(args)

150
examples/smt/scalable_chain.py Normal file → Executable file
View File

@@ -31,76 +31,102 @@ from itertools import chain, combinations
import sys
import resource
def generate_system(chainLen, maxConc):
"""
This function generates the reaction system with concentrations
for the scalable chain benchmark
chainLen is the length of the chain
maxConc is the maximal concentration
"""
r = ReactionSystemWithConcentrations()
r.add_bg_set_entity(("inc",1))
r.add_bg_set_entity(("dec",1))
for i in range(1,chainLen+1):
r.add_bg_set_entity(("e_" + str(i),maxConc))
for i in range(1,chainLen+1):
ent = "e_" + str(i)
r.add_reaction_inc(ent, "inc", [(ent, 1)],[(ent,maxConc)])
r.add_reaction_dec(ent, "dec", [(ent, 1)],[])
if i < chainLen:
r.add_reaction([(ent,maxConc)],[],[("e_"+str(i+1),1)])
r.add_reaction([("e_" + str(chainLen),maxConc)],[("dec",1)],[("e_" + str(chainLen),maxConc)])
r = ReactionSystemWithConcentrations()
r.add_bg_set_entity(("inc", 1))
r.add_bg_set_entity(("dec", 1))
for i in range(1, chainLen + 1):
r.add_bg_set_entity(("e_" + str(i), maxConc))
for i in range(1, chainLen + 1):
ent = "e_" + str(i)
r.add_reaction_inc(ent, "inc", [(ent, 1)], [(ent, maxConc)])
r.add_reaction_dec(ent, "dec", [(ent, 1)], [])
if i < chainLen:
r.add_reaction([(ent, maxConc)], [], [("e_" + str(i + 1), 1)])
r.add_reaction(
[("e_" + str(chainLen), maxConc)],
[("dec", 1)],
[("e_" + str(chainLen), maxConc)],
)
c = ContextAutomatonWithConcentrations(r)
c.add_init_state("init")
c.add_state("working")
c.add_transition("init", [("e_1",1),("inc",1)], "working")
c.add_transition("working", [("inc",1)], "working")
rc = ReactionSystemWithAutomaton(r,c)
c.add_transition("init", [("e_1", 1), ("inc", 1)], "working")
c.add_transition("working", [("inc", 1)], "working")
rc = ReactionSystemWithAutomaton(r, c)
return rc
def generate_formula(formula_number, chainLen, maxConc):
"""
This function generates the rsLTL formula
This function generates the rsLTL formula
corresponding to the formula_number parameter
"""
if formula_number == 1:
ret = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0, (BagDescription.f_entity('e_'+str(chainLen)) >= maxConc) )
ret = Formula_rsLTL.f_F(
BagDescription.f_entity("inc") > 0,
(BagDescription.f_entity("e_" + str(chainLen)) >= maxConc),
)
elif formula_number == 2:
f_tmp = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0, (BagDescription.f_entity('e_'+str(chainLen)) == maxConc) )
for i in range(chainLen-1,0,-1):
f_tmp = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0, f_tmp & (BagDescription.f_entity('e_'+str(i)) == maxConc) )
f_tmp = Formula_rsLTL.f_F(
BagDescription.f_entity("inc") > 0,
(BagDescription.f_entity("e_" + str(chainLen)) == maxConc),
)
for i in range(chainLen - 1, 0, -1):
f_tmp = Formula_rsLTL.f_F(
BagDescription.f_entity("inc") > 0,
f_tmp & (BagDescription.f_entity("e_" + str(i)) == maxConc),
)
ret = f_tmp
elif formula_number == 3:
ret = Formula_rsLTL.f_G( BagDescription.f_TRUE(),
ret = Formula_rsLTL.f_G(
BagDescription.f_TRUE(),
Formula_rsLTL.f_Implies(
(BagDescription.f_entity('e_1') == 1),
(BagDescription.f_entity("e_1") == 1),
Formula_rsLTL.f_F(
BagDescription.f_entity("inc") > 0,
(BagDescription.f_entity('e_'+str(chainLen)) == maxConc)
)
)
(BagDescription.f_entity("e_" + str(chainLen)) == maxConc),
),
),
)
elif formula_number == 4:
ret = Formula_rsLTL.f_F( BagDescription.f_entity("inc") > 0 , BagDescription.f_entity('e_1') == maxConc )
ret = Formula_rsLTL.f_F(
BagDescription.f_entity("inc") > 0,
BagDescription.f_entity("e_1") == maxConc,
)
elif formula_number == 5:
ret = Formula_rsLTL.f_X(BagDescription.f_TRUE(), Formula_rsLTL.f_U( BagDescription.f_entity("inc") > 0 , BagDescription.f_entity('e_1') > 0, BagDescription.f_entity('e_2') > 0 ) )
ret = Formula_rsLTL.f_X(
BagDescription.f_TRUE(),
Formula_rsLTL.f_U(
BagDescription.f_entity("inc") > 0,
BagDescription.f_entity("e_1") > 0,
BagDescription.f_entity("e_2") > 0,
),
)
else:
ret = None
assert ret is not None, "Unknown formula"
return ret
@@ -110,64 +136,64 @@ def save_statistics(smt_rsc, formula_number, chainLen, maxConc):
"""
Saves the statistics fetched from smt_rsc into files
"""
time=0
mem_usage=resource.getrusage(resource.RUSAGE_SELF).ru_maxrss/(1024*1024)
filename_t="bench_rsc_F" + str(formula_number) + "_time.log"
filename_m="bench_rsc_F" + str(formula_number) + "_mem.log"
time=smt_rsc.get_verification_time()
time = 0
mem_usage = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss / (1024 * 1024)
filename_t = "bench_rsc_F" + str(formula_number) + "_time.log"
filename_m = "bench_rsc_F" + str(formula_number) + "_mem.log"
time = smt_rsc.get_verification_time()
f=open(filename_t, 'a')
log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(time) + ")\n"
f = open(filename_t, "a")
log_str = "(" + str(chainLen) + "," + str(maxConc) + "," + str(time) + ")\n"
f.write(log_str)
f.close()
f=open(filename_m, 'a')
log_str="(" + str(chainLen) + "," + str(maxConc) + "," + str(mem_usage) + ")\n"
f = open(filename_m, "a")
log_str = "(" + str(chainLen) + "," + str(maxConc) + "," + str(mem_usage) + ")\n"
f.write(log_str)
f.close()
def scalable_chain(print_system=False):
"""
This is the entry point for the benchmark
"""
if len(sys.argv) < 1+3:
if len(sys.argv) < 1 + 3:
print("arguments: <chainLen> <maxConc> <formulaNumber>")
exit(1)
chainLen=int(sys.argv[1]) # chain length
maxConc=int(sys.argv[2]) # depth (max concentration)
formula_number=int(sys.argv[3])
chainLen = int(sys.argv[1]) # chain length
maxConc = int(sys.argv[2]) # depth (max concentration)
formula_number = int(sys.argv[3])
if chainLen < 1 or maxConc < 1:
print("be reasonable")
exit(1)
if not formula_number in range(1,5+1):
if not formula_number in range(1, 5 + 1):
print("formulaNumber must be in 1..5")
exit(1)
# Generate the reaction systems with concentrations
rc = generate_system(chainLen, maxConc)
# Generate the formula
form = generate_formula(formula_number, chainLen, maxConc)
# Optional dump/print of the system
if print_system:
rc.show()
# Create an instance of the SMT checker for RS with concentrations
smt_rsc = SmtCheckerRSC(rc)
# Start the verification process
smt_rsc.check_rsltl(formula=form)
save_statistics(smt_rsc, formula_number, chainLen, maxConc)
def main():
scalable_chain(print_system=True)
if __name__ == "__main__":
main()