`segfault` when ksolve it used

[dilawar]

`segfault` when ksolve it used

[dilawar]

Code in the snippet above can be download from its first commit : https://raw.githubusercontent.com/dilawar/chemical_models/7dbefa57b6fe2b37ce54f5757104a79e3ead004e/Synapse/Miller_Zhabotinsky/bugs/bug_rate_term_assert.py

The latest version is here: https://github.com/dilawar/chemical_models/blob/master/Synapse/Miller_Zhabotinsky/bugs/bug_rate_term_assert.py

[dilawar]

valgrind output

==573== Process terminating with default action of signal 6 (SIGABRT)
==573==    at 0x4E7BCC9: raise (raise.c:56)
==573==    by 0x4E7F0D7: abort (abort.c:89)
==573==    by 0x4E74B85: __assert_fail_base (assert.c:92)
==573==    by 0x4E74C31: __assert_fail (assert.c:101)
==573==    by 0x6D3D158: Stoich::getRateTerms() const (Stoich.cpp:562)
==573==    by 0x6D5825D: Ksolve::updateRateTerms(unsigned int) (Ksolve.cpp:583)
==573==    by 0x6D46EDB: Stoich::setReacKf(Eref const&, double) const (Stoich.cpp:1701)
==573==    by 0x6D2E408: ZombieReac::vSetConcKf(Eref const&, double) (ZombieReac.cpp:124)
==573==    by 0x6BDC4DE: ReacBase::setConcKf(Eref const&, double) (ReacBase.cpp:260)
==573==    by 0x6BDC95E: ReacBase::zombify(Element*, Cinfo const*, Id) (ReacBase.cpp:321)
==573==    by 0x6D42A38: Stoich::zombifyModel(Eref const&, std::vector<Id, std::allocator<Id> > const&) (Stoich.cpp:1239)
==573==    by 0x6D3C1E8: Stoich::setElist(Eref const&, std::vector<ObjId, std::allocator<ObjId> > const&) (Stoich.cpp:390)

[dilawar]

Caused by previous two commits. Commit be02f46 is free from this bug.

[dilawar]

This file is also in repository tests/issues/issue_34.py .

[dilawar]

In following, I have converted ca to BufPool since its concentration is updated by a function. Also renamed the function to have func as name under BufPool. Now slightly different segfault.

# Issue 34 on github.
import moose
import moose.utils as mu

compt = moose.CubeMesh('/compt')
compt.volume = 1e-20

molecules = [ "ca", "S", "S1", "Sp" ]
pools = {}
tables = {}
for m in molecules:
    if m == "ca":
        # If a function is added to update the concentraction, we need to
        # create a BuffPool.
        pools[m] = moose.BufPool('/compt/%s' % m)
    else:
        pools[m] = moose.Pool('/compt/%s' % m)
    print("Created: %s" % pools[m])
    t = moose.Table2("/table%s" % m)
    print("Created: %s" % t)
    tables[m] = t
    moose.connect(t, 'requestOut', pools[m], 'getConc')

pools['ca'].nInit = 20

r_p0_p1 = moose.Reac('/compt/reacA')
funA = moose.Function('/compt/ca/func')
funA.expr = "{0}*(y0/{1})^6/(1+(y0/{1})^3)^2".format("1.5", "0.7e-3")
moose.connect(funA, 'requestOut',  pools['ca'], 'getConc')
moose.connect(funA, 'valueOut', pools['S1'], 'setConc')
moose.connect(r_p0_p1, 'sub', pools['S'], 'reac')
moose.connect(r_p0_p1, 'prd', pools['S1'], 'reac')

r_p1_up = moose.Reac('/compt/reacB')
moose.connect(r_p1_up, 'sub', pools['S1'], 'reac')
moose.connect(r_p1_up, 'prd', pools['Sp'], 'reac')

# Change GSolve to Ksolve and bugs go away.
k = moose.Gsolve('/compt/ksolve')
s = moose.Stoich('/compt/stoich')
s.compartment = compt
s.ksolve = k
s.path = '/compt/##'

moose.reinit()
print("Running for 10 seconds")
moose.start(10)

(gdb) bt
#0  0x00007ffff48ba95a in Gsolve::fillMathDep() () at /home1/dilawars/Work/GITHUB/BhallaLab/moose-core/python/moose/_moose.so
#1  0x00007ffff48bb3cb in Gsolve::rebuildGssaSystem() () at /home1/dilawars/Work/GITHUB/BhallaLab/moose-core/python/moose/_moose.so
#2  0x00007ffff48bb9b8 in Gsolve::reinit(Eref const&, ProcInfo const*) () at /home1/dilawars/Work/GITHUB/BhallaLab/moose-core/python/moose/_moose.so
#3  0x00007ffff466e2a8 in Clock::handleReinit(Eref const&) () at /home1/dilawars/Work/GITHUB/BhallaLab/moose-core/python/moose/_moose.so
#4  0x00007ffff461d7b1 in SetGet0::set(ObjId const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) ()
    at /home1/dilawars/Work/GITHUB/BhallaLab/moose-core/python/moose/_moose.so
#5  0x00007ffff46154bb in Shell::doReinit() () at /home1/dilawars/Work/GITHUB/BhallaLab/moose-core/python/moose/_moose.so
#6  0x00007ffff4352dc5 in moose_reinit () at /home1/dilawars/Work/GITHUB/BhallaLab/moose-core/python/moose/_moose.so
#7  0x00007ffff7b010d7 in PyEval_EvalFrameEx () at /usr/lib64/libpython2.7.so.1.0
#8  0x00007ffff7aff952 in PyEval_EvalCodeEx () at /usr/lib64/libpython2.7.so.1.0
#9  0x00007ffff7b23226 in PyEval_EvalCode () at /usr/lib64/libpython2.7.so.1.0
#10 0x00007ffff7b2d2fd in  () at /usr/lib64/libpython2.7.so.1.0
#11 0x00007ffff7b2d1e2 in PyRun_FileExFlags () at /usr/lib64/libpython2.7.so.1.0
#12 0x00007ffff7b2d0f6 in PyRun_SimpleFileExFlags () at /usr/lib64/libpython2.7.so.1.0
#13 0x00007ffff7b321f8 in Py_Main () at /usr/lib64/libpython2.7.so.1.0
#14 0x00007ffff747a610 in __libc_start_main () at /lib64/libc.so.6
#15 0x0000000000400799 in _start ()
(gdb) 

[dilawar]

Related to issue #48 .

[dilawar]

Fixed by @upibhalla . We need to use x0, x1, ... etc instead of y0,y1... etc. Working with CaMKII model with both deterministic and stochastic solvers.