Application Crash when doing geometry optimisation

[Jerome Pansanel]

Binary package hint: ghemical

1. Ubuntu version
Description: Ubuntu 10.04.1 LTS
Release: 10.04

2. Ghemical version
ghemical:
  Installed : 2.98-2

Problem description
If I use an MM engine based on mopac (ie PM3) or mpqc (ie 3.21G) for geometry optimization, the program crash (segfault).
Running a gdb ghemical with PM3 gives:
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffdf1cb700 (LWP 7467)]
0x00007fffeae31ea3 in lm7_ini_full_xyz () from /usr/lib/libmopac7.so.1
(gdb) bt
#0 0x00007fffeae31ea3 in lm7_ini_full_xyz () from /usr/lib/libmopac7.so.1
#1 0x00007ffff36e8eb5 in eng1_qm_mopac::eng1_qm_mopac(setup*, unsigned int, unsigned int) () from /usr/lib/libghemical.so.4
#2 0x00007ffff36df2e5 in setup1_qm::CreateEngineByIndex(unsigned int) ()
   from /usr/lib/libghemical.so.4
#3 0x00007ffff36bf125 in setup::CreateCurrentEngine() ()
   from /usr/lib/libghemical.so.4
#4 0x00007ffff36ad014 in model::DoGeomOpt(geomopt_param&, bool) ()
   from /usr/lib/libghemical.so.4
#5 0x000000000047381a in gtk_project::process_job_GeomOpt(void*) ()
#6 0x00007ffff3de1b84 in ?? () from /lib/libglib-2.0.so.0
#7 0x00007fffefc6b9ca in start_thread () from /lib/libpthread.so.0
#8 0x00007fffe9e0070d in clone () from /lib/libc.so.6
#9 0x0000000000000000 in ?? ()

With MPQC 3.21 method:
writing MPQC-input file /tmp/mpqc0000.in
using ProcMessageGrp as MessageGroup...
using PthreadThreadGrp as ThreadGroup...
  Reading file /usr/share/mpqc/atominfo.kv.
terminate called after throwing an instance of 'sc::InputError'
  what():

Program received signal SIGABRT, Aborted.
[Switching to Thread 0x7fffdf1cb700 (LWP 7473)]
0x00007fffe9d4da75 in raise () from /lib/libc.so.6

#0 0x00007fffe9d4da75 in raise () from /lib/libc.so.6
#1 0x00007fffe9d515c0 in abort () from /lib/libc.so.6
#2 0x00007fffea3ec8e5 in __gnu_cxx::__verbose_terminate_handler() ()
   from /usr/lib/libstdc++.so.6
#3 0x00007fffea3ead16 in ?? () from /usr/lib/libstdc++.so.6
#4 0x00007fffea3ead43 in std::terminate() () from /usr/lib/libstdc++.so.6
#5 0x00007fffea3eae3e in __cxa_throw () from /usr/lib/libstdc++.so.6
#6 0x00007ffff1b8864f in sc::Molecule::throw_if_atom_duplicated(int, double)
    () from /usr/lib/libSCmolecule.so.7
#7 0x00007ffff1b907b8 in sc::Molecule::Molecule(sc::Ref<sc::KeyVal> const&) ()
   from /usr/lib/libSCmolecule.so.7
#8 0x00007ffff1b93429 in sc::DescribedClass* sc::create<sc::Molecule>(sc::Ref<sc::KeyVal> const&) () from /usr/lib/libSCmolecule.so.7
#9 0x00007ffff06c8f1f in sc::StringKeyVal::key_value(char const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#10 0x00007ffff06cc2b8 in sc::PrefixKeyVal::key_value(char const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#11 0x00007ffff06c057a in sc::KeyVal::key_describedclassvalue(char const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#12 0x00007ffff06bd53a in sc::KeyVal::describedclassvalue(char const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#13 0x00007ffff1ba6b13 in sc::MolecularEnergy::MolecularEnergy(sc::Ref<sc::KeyVal> const&) () from /usr/lib/libSCmolecule.so.7
#14 0x00007ffff28363b9 in sc::Wavefunction::Wavefunction(sc::Ref<sc::KeyVal> const&) () from /usr/lib/libSCwfn.so.7
#15 0x00007ffff283fa12 in sc::OneBodyWavefunction::OneBodyWavefunction(sc::Ref<sc::KeyVal> const&) () from /usr/lib/libSCwfn.so.7
#16 0x00007ffff2ab8967 in sc::SCF::SCF(sc::Ref<sc::KeyVal> const&) ()
   from /usr/lib/libSCscf.so.7
#17 0x00007ffff2ac7060 in sc::CLSCF::CLSCF(sc::Ref<sc::KeyVal> const&) ()
   from /usr/lib/libSCscf.so.7
#18 0x00007ffff2ac939e in sc::CLHF::CLHF(sc::Ref<sc::KeyVal> const&) ()
   from /usr/lib/libSCscf.so.7
#19 0x00007ffff2acbe89 in sc::DescribedClass* sc::create<sc::CLHF>(sc::Ref<sc::KeyVal> const&) () from /usr/lib/libSCscf.so.7
#20 0x00007ffff06c8f1f in sc::StringKeyVal::key_value(char const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#21 0x00007ffff06cc2b8 in sc::PrefixKeyVal::key_value(char const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#22 0x00007ffff06c057a in sc::KeyVal::key_describedclassvalue(char const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#23 0x00007ffff06bd53a in sc::KeyVal::describedclassvalue(char const*, sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#24 0x00007ffff36e22c8 in eng1_qm_mpqc::eng1_qm_mpqc(setup*, unsigned int, unsigned int) () from /usr/lib/libghemical.so.4
#25 0x00007ffff36df29b in setup1_qm::CreateEngineByIndex(unsigned int) ()
   from /usr/lib/libghemical.so.4
#26 0x00007ffff36bf125 in setup::CreateCurrentEngine() ()
   from /usr/lib/libghemical.so.4
#27 0x00007ffff36ad014 in model::DoGeomOpt(geomopt_param&, bool) ()
   from /usr/lib/libghemical.so.4
#28 0x000000000047381a in gtk_project::process_job_GeomOpt(void*) ()
#29 0x00007ffff3de1b84 in ?? () from /lib/libglib-2.0.so.0
#30 0x00007fffefc6b9ca in start_thread () from /lib/libpthread.so.0
#31 0x00007fffe9e0070d in clone () from /lib/libc.so.6
#32 0x0000000000000000 in ?? ()

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.