#165 Segfault of loading Acc4 SBML model from DOQCS

[dilawars]

Attached SBML model fails to load. It causes a segfault.

~~~~~

0 0x00007ffff782dcc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56

1 0x00007ffff78310d8 in __GI_abort () at abort.c:89

2 0x00007ffff7826b86 in __assert_fail_base (fmt=0x7ffff7977830 "%s%s%s:%u: %s%sAssertion `%s' failed.\n%n",

assertion=assertion@entry=0x7ffff4f2371e "base_ != Id()", 
file=file@entry=0x7ffff4f236f0 "/data/dilawars/moose3.0.1/sbml/SbmlReader.cpp", line=line@entry=111, 
function=function@entry=0x7ffff4f23f40 <SbmlReader::read(std::string, std::string, std::string)::__PRETTY_FUNCTION__> "Id SbmlReader::read(std::string, std::string, std::string)") at assert.c:92

3 0x00007ffff7826c32 in GIassert_fail (assertion=0x7ffff4f2371e "base != Id()",

file=0x7ffff4f236f0 "/data/dilawars/moose3.0.1/sbml/SbmlReader.cpp", line=111, 
function=0x7ffff4f23f40 <SbmlReader::read(std::string, std::string, std::string)::__PRETTY_FUNCTION__> "Id SbmlReader::read(std::string, std::string, std::string)") at assert.c:101

4 0x00007ffff4e59c88 in SbmlReader::read (this=0x7fffffffd500, filename=..., location=..., solverClass=...)

at /data/dilawars/moose3.0.1/sbml/SbmlReader.cpp:111

5 0x00007ffff4aaebe3 in Shell::doReadSBML (this=0xbcf118, fname=..., modelpath=..., solverclass=...)

at /data/dilawars/moose3.0.1/shell/Shell.cpp:457

6 0x00007ffff48a7a10 in moose_readSBML (dummy=0x0, args=0x7fffee720a70)

at /data/dilawars/moose3.0.1/pymoose/moosemodule.cpp:1516

7 0x000000000052c6d5 in PyEval_EvalFrameEx ()

8 0x000000000052cf32 in PyEval_EvalFrameEx ()

9 0x000000000055c594 in PyEval_EvalCodeEx ()

10 0x00000000005b7392 in PyEval_EvalCode ()

11 0x0000000000469663 in ?? ()

12 0x00000000004699e3 in PyRun_FileExFlags ()

13 0x0000000000469f1c in PyRun_SimpleFileExFlags ()

14 0x000000000046ab81 in Py_Main ()

15 0x00007ffff7818ec5 in __libc_start_main (main=0x46ac3f <main>, argc=3, argv=0x7fffffffdc68, init=<optimized out="">,

fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffdc58) at libc-start.c:287

16 0x000000000057497e in _start ()

~~~~~~

Checkin: 6779

[dilawars]

Equivalent annotated genesis model is working fine; except for

~~~~
Warning: ZombieEnz:setSolver: Dangling Enz, missing a substrate or product
~~~~~

problem.

[Anonymous]

[dilawars]

I installed libSBML-5.11.0. Still running into seg faults. Do I need to install a specific version of SBML. If yes, it needs to be reflected in dependencies else SBMLReader will break.

[dilawars]

Also acc4.xml does not seem to be in trunk branch. There is no way I can compare the this file. Online SBML validator http://sbml.org/Facilities/Validator/index.jsp) does not like the acc4.xml file on doqcs.

[rani]

Moose supports libSBML 5.9.0 (compiled with libxml2)
This is mentioned in the README.md file, at least since kheer kadam release.

Also, the SBML file you obtained from DOQCS corresponds to L2V1 sbml version. In moose we support SBML L3V1 only.

"Online SBML validator http://sbml.org/Facilities/Validator/index.jsp) does not like the acc4.xml file on doqcs" - because it validates for l2v4.

From now onwards use sbml files corresponding to L3V1 and use L3V1 validator only.

To convert models to SBML L3V1 version, load the corresponding genesis file in moose and use moose.writeSBML to export to SBML L3V1 format. Then you can read it back in moose using moose.readSBML