Public bug reported:
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)]
0x7fffeae31ea3 in lm7_ini_full_xyz () from /usr/lib/libmopac7.so.1
(gdb) bt
#0 0x7fffeae31ea3 in lm7_ini_full_xyz () from /usr/lib/libmopac7.so.1
#1 0x736e8eb5 in eng1_qm_mopac::eng1_qm_mopac(setup*, unsigned int,
unsigned int) () from /usr/lib/libghemical.so.4
#2 0x736df2e5 in setup1_qm::CreateEngineByIndex(unsigned int) ()
from /usr/lib/libghemical.so.4
#3 0x736bf125 in setup::CreateCurrentEngine() ()
from /usr/lib/libghemical.so.4
#4 0x736ad014 in model::DoGeomOpt(geomopt_param&, bool) ()
from /usr/lib/libghemical.so.4
#5 0x0047381a in gtk_project::process_job_GeomOpt(void*) ()
#6 0x73de1b84 in ?? () from /lib/libglib-2.0.so.0
#7 0x7fffefc6b9ca in start_thread () from /lib/libpthread.so.0
#8 0x7fffe9e0070d in clone () from /lib/libc.so.6
#9 0x in ?? ()
With MPQC 3.21 method:
writing MPQC-input file /tmp/mpqc.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)]
0x7fffe9d4da75 in raise () from /lib/libc.so.6
#0 0x7fffe9d4da75 in raise () from /lib/libc.so.6
#1 0x7fffe9d515c0 in abort () from /lib/libc.so.6
#2 0x7fffea3ec8e5 in __gnu_cxx::__verbose_terminate_handler() ()
from /usr/lib/libstdc++.so.6
#3 0x7fffea3ead16 in ?? () from /usr/lib/libstdc++.so.6
#4 0x7fffea3ead43 in std::terminate() () from /usr/lib/libstdc++.so.6
#5 0x7fffea3eae3e in __cxa_throw () from /usr/lib/libstdc++.so.6
#6 0x71b8864f in sc::Molecule::throw_if_atom_duplicated(int, double)
() from /usr/lib/libSCmolecule.so.7
#7 0x71b907b8 in sc::Molecule::Molecule(sc::Ref const&) ()
from /usr/lib/libSCmolecule.so.7
#8 0x71b93429 in sc::DescribedClass*
sc::create(sc::Ref const&) () from
/usr/lib/libSCmolecule.so.7
#9 0x706c8f1f in sc::StringKeyVal::key_value(char const*,
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#10 0x706cc2b8 in sc::PrefixKeyVal::key_value(char const*,
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#11 0x706c057a in sc::KeyVal::key_describedclassvalue(char const*,
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#12 0x706bd53a in sc::KeyVal::describedclassvalue(char const*,
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#13 0x71ba6b13 in
sc::MolecularEnergy::MolecularEnergy(sc::Ref const&) () from
/usr/lib/libSCmolecule.so.7
#14 0x728363b9 in sc::Wavefunction::Wavefunction(sc::Ref
const&) () from /usr/lib/libSCwfn.so.7
#15 0x7283fa12 in
sc::OneBodyWavefunction::OneBodyWavefunction(sc::Ref const&) ()
from /usr/lib/libSCwfn.so.7
#16 0x72ab8967 in sc::SCF::SCF(sc::Ref const&) ()
from /usr/lib/libSCscf.so.7
#17 0x72ac7060 in sc::CLSCF::CLSCF(sc::Ref const&) ()
from /usr/lib/libSCscf.so.7
#18 0x72ac939e in sc::CLHF::CLHF(sc::Ref const&) ()
from /usr/lib/libSCscf.so.7
#19 0x72acbe89 in sc::DescribedClass*
sc::create(sc::Ref const&) () from /usr/lib/libSCscf.so.7
#20 0x706c8f1f in sc::StringKeyVal::key_value(char const*,
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#21 0x706cc2b8 in sc::PrefixKeyVal::key_value(char const*,
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#22 0x706c057a in sc::KeyVal::key_describedclassvalue(char const*,
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#23 0x706bd53a in sc::KeyVal::describedclassvalue(char const*,
sc::KeyValValue const&) () from /usr/lib/libSCkeyval.so.7
#24 0x736e22c8 in eng1_qm_mpqc::eng1_qm_mpqc(setup*, unsigned int,
unsigned int) () from /usr/lib/libghemical.so.4
#25 0x736df29b in setup1_qm::CreateEngineByIndex(unsigned int) ()
from /usr/lib/libghemical.so.4
#26 0x736bf125 in setup::CreateCurrentEngine() ()
from /usr/lib/libghemical.so.4
#27 0x736ad014 in model::DoGeomOpt(geomopt_param&, bool) ()
from /usr/lib/libghemical.so.4
#28 0x0047381a in gtk_project::process_job_GeomOpt(void*) ()
#29 0x73de1b84 in ?? () from /lib/libglib-2.0.so.0
#30 0x7fffefc6b9ca in start_thread () from /lib/libpthread.so.0
#31 0x7fffe9e0070d in clone () from /lib/libc.so.6
#32 0x in ?? ()
** Affects: ghemical (Ubuntu)
Importance:
