Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

benchmark_full segfault in RMF #16

Closed
barakr opened this issue Dec 17, 2013 · 4 comments
Closed

benchmark_full segfault in RMF #16

barakr opened this issue Dec 17, 2013 · 4 comments
Labels
bug

Comments

@barakr
Copy link
Collaborator

barakr commented Dec 17, 2013

I am not sure if this is error in npctransport or in RMF so need your opinion - this is the backtrace info from gdb when running benchmark_full. What does it look like to you?

Program received signal SIGABRT, Aborted.
0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
Missing separate debuginfos, use: debuginfo-install boost-filesystem-1.41.0-18.el6.x86_64 boost-iostreams-1.41.0-18.el6.x86_64 boost-program-options-1.41.0-18.el6.x86_64 boost-regex-1.41.0-18.el6.x86_64 boost-system-1.41.0-18.el6.x86_64 boost-thread-1.41.0-18.el6.x86_64 bzip2-libs-1.0.5-7.el6_0.x86_64 glibc-2.12-1.132.el6.x86_64 gmp-4.3.1-7.el6_2.2.x86_64 libgcc-4.4.7-4.el6.x86_64 libicu-4.2.1-9.1.el6_2.x86_64 libstdc++-4.4.7-4.el6.x86_64 libunwind-1.1-2.el6.x86_64 mpfr-2.4.1-6.el6.x86_64 protobuf-2.3.0-7.el6.x86_64 zlib-1.2.3-29.el6.x86_64
(gdb) backtrace
#0 0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
#1 0x00007ffff1e41105 in abort () from /lib64/libc.so.6
#2 0x00007ffff26f9a5d in __gnu_cxx::__verbose_terminate_handler() () from /usr/lib64/libstdc++.so.6
#3 0x00007ffff26f7be6 in ?? () from /usr/lib64/libstdc++.so.6
#4 0x00007ffff26f7c13 in std::terminate() () from /usr/lib64/libstdc++.so.6
#5 0x00007ffff26f7d0e in __cxa_throw () from /usr/lib64/libstdc++.so.6
#6 0x00007ffff5646a32 in IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model*, IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::IndexIMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::VectorIMP::base::Index<IMP::kernel::ParticleIndexTag >, IMP::rmf::HierarchyLoadLink::Data&) () from /netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#7 0x00007ffff5646ee1 in IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model*, IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::IndexIMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::VectorIMP::base::Index<IMP::kernel::ParticleIndexTag >, IMP::rmf::HierarchyLoadLink::Data&) () from /netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#8 0x00007ffff565389d in IMP::rmf::HierarchyLoadLink::do_add_link(IMP::kernel::Particle*, RMF::NodeConstHandle) ()

from /netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#9 0x00007ffff7b6b4b6 in IMP::rmf::SimpleLoadLinkIMP::kernel::Particle::link(RMF::NodeConstHandle, IMP::base::VectorIMP::base::Pointer<IMP::kernel::Particle > const&) () from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#10 0x00007ffff7b940b5 in void IMP::rmf::internal::link_helper<IMP::npctransport::HierarchyWithSitesLoadLink, IMP::base::VectorIMP::atom::Hierarchy >(RMF::FileConstHandle, IMP::base::VectorIMP::atom::Hierarchy const&) () from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#11 0x00007ffff7b0cf6c in IMP::npctransport::link_hierarchies_with_sites(RMF::FileConstHandle, IMP::base::VectorIMP::atom::Hierarchy const&) ()

from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#12 0x00007ffff7b0d158 in IMP::npctransport::SimulationData::initialize_positions_from_rmf(RMF::FileConstHandle, int) ()

from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#13 0x00007ffff7b0e3c1 in IMP::npctransport::SimulationData::initialize(std::basic_string<char, std::char_traits, std::allocator >, bool) ()

from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#14 0x00007ffff7b0f153 in IMP::npctransport::SimulationData::SimulationData(std::basic_string<char, std::char_traits, std::allocator >, bool, std::basic_string<char, std::char_traits, std::allocator >) () from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#15 0x00000000004103b8 in main ()
@ghost ghost assigned drussel Dec 17, 2013
@drussel
Copy link
Contributor

drussel commented Dec 17, 2013

I'm guessing it is something with RMF loading. Let me try to get the rigid
bodies cleaned up rather than patching things more and then lets take a
look? Or is it blocking something?

On Mon, Dec 16, 2013 at 4:55 PM, barakr [email protected] wrote:

I am not sure if this is error in npctransport or in RMF so need your
opinion - this is the backtrace info from gdb when running benchmark_full.
What does it look like to you?

Program received signal SIGABRT, Aborted.
0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
Missing separate debuginfos, use: debuginfo-install
boost-filesystem-1.41.0-18.el6.x86_64 boost-iostreams-1.41.0-18.el6.x86_64
boost-program-options-1.41.0-18.el6.x86_64 boost-regex-1.41.0-18.el6.x86_64
boost-system-1.41.0-18.el6.x86_64 boost-thread-1.41.0-18.el6.x86_64
bzip2-libs-1.0.5-7.el6_0.x86_64 glibc-2.12-1.132.el6.x86_64
gmp-4.3.1-7.el6_2.2.x86_64 libgcc-4.4.7-4.el6.x86_64
libicu-4.2.1-9.1.el6_2.x86_64 libstdc++-4.4.7-4.el6.x86_64
libunwind-1.1-2.el6.x86_64 mpfr-2.4.1-6.el6.x86_64
protobuf-2.3.0-7.el6.x86_64 zlib-1.2.3-29.el6.x86_64
(gdb) backtrace
#0 0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
#1 #1 0x00007ffff1e41105
in abort () from /lib64/libc.so.6
#2 #2 0x00007ffff26f9a5d
in _gnu_cxx::_verbose_terminate_handler() () from
/usr/lib64/libstdc++.so.6
#3 #3 0x00007ffff26f7be6
in ?? () from /usr/lib64/libstdc++.so.6
#4 #4 0x00007ffff26f7c13
in std::terminate() () from /usr/lib64/libstdc++.so.6
#5 #5 0x00007ffff26f7d0e
in cxa_throw () from /usr/lib64/libstdc++.so.6
#6 #6 0x00007ffff5646a32
in IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model,
IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::Index
IMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::Vector
IMP::base::Index<IMP::kernel::ParticleIndexTag >,
IMP::rmf::HierarchyLoadLink::Data&) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#7 #7 0x00007ffff5646ee1
in IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model,
IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::Index
IMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::Vector
IMP::base::Index<IMP::kernel::ParticleIndexTag >,
IMP::rmf::HierarchyLoadLink::Data&) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#8 #8 0x00007ffff565389d
in IMP::rmf::HierarchyLoadLink::do_add_link(IMP::kernel::Particle*,
RMF::NodeConstHandle) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#9 #9 0x00007ffff7b6b4b6
in IMP::rmf::SimpleLoadLinkIMP::kernel::Particle::link(RMF::NodeConstHandle,
IMP::base::VectorIMP::base::Pointer<IMP::kernel::Particle > const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#10 https://github.com/salilab/npctransport/issues/100x00007ffff7b940b5 in void IMP::rmf::internal::link_helper

(RMF::FileConstHandle, IMP::base::VectorIMP::atom::Hierarchy const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#11 https://github.com/salilab/npctransport/issues/110x00007ffff7b0cf6c in
IMP::npctransport::link_hierarchies_with_sites(RMF::FileConstHandle,
IMP::base::VectorIMP::atom::Hierarchy const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#12 https://github.com/salilab/npctransport/issues/120x00007ffff7b0d158 in
IMP::npctransport::SimulationData::initialize_positions_from_rmf(RMF::FileConstHandle,
int) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#13 https://github.com/salilab/npctransport/issues/130x00007ffff7b0e3c1 in
IMP::npctransport::SimulationData::initialize(std::basic_string,
std::allocator >, bool) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#14 https://github.com/salilab/npctransport/issues/140x00007ffff7b0f153 in
IMP::npctransport::SimulationData::SimulationData(std::basic_string,
std::allocator >, bool, std::basic_string, std::allocator >) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#15 https://github.com/salilab/npctransport/issues/150x00000000004103b8 in main ()

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/16
.

@barakr
Copy link
Collaborator Author

barakr commented Dec 17, 2013

no it's ok let me know when ready to look (or it will just disappear from
tests :)

On Tue, Dec 17, 2013 at 10:08 AM, drussel [email protected] wrote:

I'm guessing it is something with RMF loading. Let me try to get the rigid
bodies cleaned up rather than patching things more and then lets take a
look? Or is it blocking something?

On Mon, Dec 16, 2013 at 4:55 PM, barakr [email protected] wrote:

I am not sure if this is error in npctransport or in RMF so need your
opinion - this is the backtrace info from gdb when running
benchmark_full.
What does it look like to you?

Program received signal SIGABRT, Aborted.
0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
Missing separate debuginfos, use: debuginfo-install
boost-filesystem-1.41.0-18.el6.x86_64
boost-iostreams-1.41.0-18.el6.x86_64
boost-program-options-1.41.0-18.el6.x86_64
boost-regex-1.41.0-18.el6.x86_64
boost-system-1.41.0-18.el6.x86_64 boost-thread-1.41.0-18.el6.x86_64
bzip2-libs-1.0.5-7.el6_0.x86_64 glibc-2.12-1.132.el6.x86_64
gmp-4.3.1-7.el6_2.2.x86_64 libgcc-4.4.7-4.el6.x86_64
libicu-4.2.1-9.1.el6_2.x86_64 libstdc++-4.4.7-4.el6.x86_64
libunwind-1.1-2.el6.x86_64 mpfr-2.4.1-6.el6.x86_64
protobuf-2.3.0-7.el6.x86_64 zlib-1.2.3-29.el6.x86_64
(gdb) backtrace
#0 0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
#1 #1
0x00007ffff1e41105
in abort () from /lib64/libc.so.6
#2 #2
0x00007ffff26f9a5d
in _gnu_cxx::_verbose_terminate_handler() () from
/usr/lib64/libstdc++.so.6
#3 #3
0x00007ffff26f7be6
in ?? () from /usr/lib64/libstdc++.so.6
#4 #4
0x00007ffff26f7c13
in std::terminate() () from /usr/lib64/libstdc++.so.6
#5 #5
0x00007ffff26f7d0e
in cxa_throw () from /usr/lib64/libstdc++.so.6
#6 #6
0x00007ffff5646a32
in IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model,
IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::Index
IMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::Vector
IMP::base::Index<IMP::kernel::ParticleIndexTag >,
IMP::rmf::HierarchyLoadLink::Data&) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#7 #7
0x00007ffff5646ee1
in IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model,
IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::Index
IMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::Vector
IMP::base::Index<IMP::kernel::ParticleIndexTag >,
IMP::rmf::HierarchyLoadLink::Data&) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#8 #8
0x00007ffff565389d
in IMP::rmf::HierarchyLoadLink::do_add_link(IMP::kernel::Particle*,
RMF::NodeConstHandle) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#9 #9
0x00007ffff7b6b4b6
in
IMP::rmf::SimpleLoadLinkIMP::kernel::Particle::link(RMF::NodeConstHandle,
IMP::base::VectorIMP::base::Pointer<IMP::kernel::Particle > const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#10 https://github.com/salilab/npctransport/issues/100x00007ffff7b940b5
in void IMP::rmf::internal::link_helper

(RMF::FileConstHandle, IMP::base::VectorIMP::atom::Hierarchy const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#11 https://github.com/salilab/npctransport/issues/110x00007ffff7b0cf6c
in
IMP::npctransport::link_hierarchies_with_sites(RMF::FileConstHandle,
IMP::base::VectorIMP::atom::Hierarchy const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#12 https://github.com/salilab/npctransport/issues/120x00007ffff7b0d158
in

IMP::npctransport::SimulationData::initialize_positions_from_rmf(RMF::FileConstHandle,

int) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#13 https://github.com/salilab/npctransport/issues/130x00007ffff7b0e3c1
in
IMP::npctransport::SimulationData::initialize(std::basic_string,
std::allocator >, bool) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#14 https://github.com/salilab/npctransport/issues/140x00007ffff7b0f153
in
IMP::npctransport::SimulationData::SimulationData(std::basic_string,
std::allocator >, bool, std::basic_string, std::allocator >) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#15 https://github.com/salilab/npctransport/issues/150x00000000004103b8
in main ()

—
Reply to this email directly or view it on GitHub<
https://github.com/salilab/npctransport/issues/16>
.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/16#issuecomment-30775185
.

Barak

@drussel
Copy link
Contributor

drussel commented Dec 18, 2013

I just committed various RMF and IMP.rmf patches. Let's see how the tests
look tonight.

On Tue, Dec 17, 2013 at 3:37 PM, barakr [email protected] wrote:

no it's ok let me know when ready to look (or it will just disappear from
tests :)

On Tue, Dec 17, 2013 at 10:08 AM, drussel [email protected]
wrote:

I'm guessing it is something with RMF loading. Let me try to get the
rigid
bodies cleaned up rather than patching things more and then lets take a
look? Or is it blocking something?

On Mon, Dec 16, 2013 at 4:55 PM, barakr [email protected]
wrote:

I am not sure if this is error in npctransport or in RMF so need your
opinion - this is the backtrace info from gdb when running
benchmark_full.
What does it look like to you?

Program received signal SIGABRT, Aborted.
0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
Missing separate debuginfos, use: debuginfo-install
boost-filesystem-1.41.0-18.el6.x86_64
boost-iostreams-1.41.0-18.el6.x86_64
boost-program-options-1.41.0-18.el6.x86_64
boost-regex-1.41.0-18.el6.x86_64
boost-system-1.41.0-18.el6.x86_64 boost-thread-1.41.0-18.el6.x86_64
bzip2-libs-1.0.5-7.el6_0.x86_64 glibc-2.12-1.132.el6.x86_64
gmp-4.3.1-7.el6_2.2.x86_64 libgcc-4.4.7-4.el6.x86_64
libicu-4.2.1-9.1.el6_2.x86_64 libstdc++-4.4.7-4.el6.x86_64
libunwind-1.1-2.el6.x86_64 mpfr-2.4.1-6.el6.x86_64
protobuf-2.3.0-7.el6.x86_64 zlib-1.2.3-29.el6.x86_64
(gdb) backtrace
#0 0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
#1 #1
0x00007ffff1e41105
in abort () from /lib64/libc.so.6
#2 #2
0x00007ffff26f9a5d
in _gnu_cxx::_verbose_terminate_handler() () from
/usr/lib64/libstdc++.so.6
#3 #3
0x00007ffff26f7be6
in ?? () from /usr/lib64/libstdc++.so.6
#4 #4
0x00007ffff26f7c13
in std::terminate() () from /usr/lib64/libstdc++.so.6
#5 #5
0x00007ffff26f7d0e
in cxa_throw () from /usr/lib64/libstdc++.so.6
#6 #6
0x00007ffff5646a32
in
IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model,
IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::Index
IMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::Vector
IMP::base::Index<IMP::kernel::ParticleIndexTag >,
IMP::rmf::HierarchyLoadLink::Data&) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#7 #7
0x00007ffff5646ee1
in
IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model,
IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::Index
IMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::Vector
IMP::base::Index<IMP::kernel::ParticleIndexTag >,
IMP::rmf::HierarchyLoadLink::Data&) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#8 #8
0x00007ffff565389d
in IMP::rmf::HierarchyLoadLink::do_add_link(IMP::kernel::Particle*,
RMF::NodeConstHandle) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#9 #9
0x00007ffff7b6b4b6
in

IMP::rmf::SimpleLoadLinkIMP::kernel::Particle::link(RMF::NodeConstHandle,

IMP::base::VectorIMP::base::Pointer<IMP::kernel::Particle > const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#10 https://github.com/salilab/npctransport/issues/100x00007ffff7b940b5

in void IMP::rmf::internal::link_helper

(RMF::FileConstHandle, IMP::base::VectorIMP::atom::Hierarchy const&)
()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#11 https://github.com/salilab/npctransport/issues/110x00007ffff7b0cf6c

in

IMP::npctransport::link_hierarchies_with_sites(RMF::FileConstHandle,
IMP::base::VectorIMP::atom::Hierarchy const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#12 https://github.com/salilab/npctransport/issues/120x00007ffff7b0d158

in

IMP::npctransport::SimulationData::initialize_positions_from_rmf(RMF::FileConstHandle,

int) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#13 https://github.com/salilab/npctransport/issues/130x00007ffff7b0e3c1

in

IMP::npctransport::SimulationData::initialize(std::basic_string,
std::allocator >, bool) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#14 https://github.com/salilab/npctransport/issues/140x00007ffff7b0f153

in

IMP::npctransport::SimulationData::SimulationData(std::basic_string,
std::allocator >, bool, std::basic_string, std::allocator >) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#15 https://github.com/salilab/npctransport/issues/150x00000000004103b8

in main ()

—
Reply to this email directly or view it on GitHub<
https://github.com/salilab/npctransport/issues/16>
.

—
Reply to this email directly or view it on GitHub<
https://github.com/salilab/npctransport/issues/16#issuecomment-30775185>
.

Barak

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/16#issuecomment-30802991
.

@barakr
Copy link
Collaborator Author

barakr commented Dec 18, 2013

Cool

On Dec 17, 2013, at 9:37 PM, drussel [email protected] wrote:

I just committed various RMF and IMP.rmf patches. Let's see how the tests
look tonight.

On Tue, Dec 17, 2013 at 3:37 PM, barakr [email protected] wrote:

no it's ok let me know when ready to look (or it will just disappear from
tests :)

On Tue, Dec 17, 2013 at 10:08 AM, drussel [email protected]
wrote:

I'm guessing it is something with RMF loading. Let me try to get the
rigid
bodies cleaned up rather than patching things more and then lets take a
look? Or is it blocking something?

On Mon, Dec 16, 2013 at 4:55 PM, barakr [email protected]
wrote:

I am not sure if this is error in npctransport or in RMF so need your
opinion - this is the backtrace info from gdb when running
benchmark_full.
What does it look like to you?

Program received signal SIGABRT, Aborted.
0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
Missing separate debuginfos, use: debuginfo-install
boost-filesystem-1.41.0-18.el6.x86_64
boost-iostreams-1.41.0-18.el6.x86_64
boost-program-options-1.41.0-18.el6.x86_64
boost-regex-1.41.0-18.el6.x86_64
boost-system-1.41.0-18.el6.x86_64 boost-thread-1.41.0-18.el6.x86_64
bzip2-libs-1.0.5-7.el6_0.x86_64 glibc-2.12-1.132.el6.x86_64
gmp-4.3.1-7.el6_2.2.x86_64 libgcc-4.4.7-4.el6.x86_64
libicu-4.2.1-9.1.el6_2.x86_64 libstdc++-4.4.7-4.el6.x86_64
libunwind-1.1-2.el6.x86_64 mpfr-2.4.1-6.el6.x86_64
protobuf-2.3.0-7.el6.x86_64 zlib-1.2.3-29.el6.x86_64
(gdb) backtrace
#0 0x00007ffff1e3f925 in raise () from /lib64/libc.so.6
#1 #1
0x00007ffff1e41105
in abort () from /lib64/libc.so.6
#2 #2
0x00007ffff26f9a5d
in _gnu_cxx::_verbose_terminate_handler() () from
/usr/lib64/libstdc++.so.6
#3 #3
0x00007ffff26f7be6
in ?? () from /usr/lib64/libstdc++.so.6
#4 #4
0x00007ffff26f7c13
in std::terminate() () from /usr/lib64/libstdc++.so.6
#5 #5
0x00007ffff26f7d0e
in cxa_throw () from /usr/lib64/libstdc++.so.6
#6 #6
0x00007ffff5646a32
in
IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model,
IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::Index
IMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::Vector
IMP::base::Index<IMP::kernel::ParticleIndexTag >,
IMP::rmf::HierarchyLoadLink::Data&) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#7 #7
0x00007ffff5646ee1
in
IMP::rmf::HierarchyLoadLink::add_link_recursive(IMP::kernel::Model,
IMP::base::IndexIMP::kernel::ParticleIndexTag, IMP::base::Index
IMP::kernel::ParticleIndexTag, RMF::NodeConstHandle, IMP::base::Vector
IMP::base::Index<IMP::kernel::ParticleIndexTag >,
IMP::rmf::HierarchyLoadLink::Data&) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#8 #8
0x00007ffff565389d
in IMP::rmf::HierarchyLoadLink::do_add_link(IMP::kernel::Particle*,
RMF::NodeConstHandle) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_rmf.so
#9 #9
0x00007ffff7b6b4b6
in

IMP::rmf::SimpleLoadLinkIMP::kernel::Particle::link(RMF::NodeConstHandle,

IMP::base::VectorIMP::base::Pointer<IMP::kernel::Particle > const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#10 https://github.com/salilab/npctransport/issues/100x00007ffff7b940b5

in void IMP::rmf::internal::link_helper

(RMF::FileConstHandle, IMP::base::VectorIMP::atom::Hierarchy const&)
()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#11 https://github.com/salilab/npctransport/issues/110x00007ffff7b0cf6c

in

IMP::npctransport::link_hierarchies_with_sites(RMF::FileConstHandle,
IMP::base::VectorIMP::atom::Hierarchy const&) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#12 https://github.com/salilab/npctransport/issues/120x00007ffff7b0d158

in

IMP::npctransport::SimulationData::initialize_positions_from_rmf(RMF::FileConstHandle,

int) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#13 https://github.com/salilab/npctransport/issues/130x00007ffff7b0e3c1

in

IMP::npctransport::SimulationData::initialize(std::basic_string,
std::allocator >, bool) ()
from /netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#14 https://github.com/salilab/npctransport/issues/140x00007ffff7b0f153

in

IMP::npctransport::SimulationData::SimulationData(std::basic_string,
std::allocator >, bool, std::basic_string, std::allocator >) () from
/netapp/sali/barak/imp_git/debug/lib/libimp_npctransport.so
#15 https://github.com/salilab/npctransport/issues/150x00000000004103b8

in main ()

—
Reply to this email directly or view it on GitHub<
https://github.com/salilab/npctransport/issues/16>
.

—
Reply to this email directly or view it on GitHub<
https://github.com/salilab/npctransport/issues/16#issuecomment-30775185>
.

Barak

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/16#issuecomment-30802991
.

—
Reply to this email directly or view it on GitHub.

@barakr barakr closed this as completed Dec 19, 2013
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@drussel @barakr