Hi,
I have been working at trying to get a NeXus
(www.nexusformat.org<http://www.nexusformat.org>) file read into ParaView. The
NeXus format is HDF5 based and this seems to be the source of the current
problem that I'm encountering. When I try to open a NeXus file via this call:
NeXus::File *fh = new NeXus::File(filename, NXACC_READ);
I get the backtrace that's attached to this email. The lowest level frame is
given here:
Program received signal SIGSEGV, Segmentation fault.
0x00007fffd7a3da8b in H5FL_reg_malloc () from /usr/lib/libhdf5.so.6
(gdb) bt
#0 0x00007fffd7a3da8b in H5FL_reg_malloc () from /usr/lib/libhdf5.so.6
...
At first, this looked like an issue with the system HDF5 libraries, but I can
put the above line into a standalone program, link it against the same
libraries and I can open a file without any errors. I have searched the list
archive for any enlightenment, but I didn't find this particular problem. Is
there anything special about using HDF5 libraries in ParaView plugins that I
missed in the documentation? I am running on Ubuntu 10.04 using the provided
HDF5 libraries and I have compiled and linked the NeXus libraries against the
same HDF5 libraries.
I know about Xdmf and have tried that with success, but I do not want to go
down the two file route, so I'd really like to get this reader working. I can
provide more detailed information (like plugin source code, sample file etc.)
to anyone who can help, but I don't want to spam the entire list with it right
off the bat.
Thanks,
Michael
-------------------------------------------
Michael Reuter
Scientific Data Analysis Group
Neutron Scattering Science Division
Oak Ridge National Laboratory
***************************************************
Attempting to load /home/2zr/workspace/InElSxtalNeXus/libInElSxtalNeXus.so
Loaded shared library successfully. Now trying to validate that it's a ParaView
plugin.
Plugin's signature: paraviewplugin|GNU|3.8
Plugin signature verification successful. This is definitely a ParaView plugin
compiled with correct compiler for correct ParaView version.
Updating Shared Library Paths:
/home/2zr/build/ParaView/bin:/home/2zr/build/ParaView/bin:/home/2zr/build/ParaView/bin:/home/2zr/workspace/InElSxtalNeXus
Plugin instance located successfully. Now loading components from the plugin
instance based on the interfaces it implements.
----------------------------------------------------------------
Plugin Information:
Name : InElSxtalNeXus
Version : 1.0
ReqOnServer : 1
ReqOnClient : 1
ReqPlugins : ServerManager Plugin : Yes
Python Plugin : No
Opening
Program received signal SIGSEGV, Segmentation fault.
0x00007fffd7a3da8b in H5FL_reg_malloc () from /usr/lib/libhdf5.so.6
(gdb) bt
#0 0x00007fffd7a3da8b in H5FL_reg_malloc () from /usr/lib/libhdf5.so.6
#1 0x00007fffd7a3dc18 in H5FL_reg_calloc () from /usr/lib/libhdf5.so.6
#2 0x00007fffd7b7de3a in H5T_alloc () from /usr/lib/libhdf5.so.6
#3 0x00007fffd7c67ed7 in H5TN_init_interface () from /usr/lib/libhdf5.so.6
#4 0x00007fffd7b6e390 in ?? () from /usr/lib/libhdf5.so.6
#5 0x00007fffd7b6d9aa in H5T_init () from /usr/lib/libhdf5.so.6
#6 0x00007fffd797ea5d in H5_init_library () from /usr/lib/libhdf5.so.6
#7 0x00007fffd7a0f070 in H5Eset_auto1 () from /usr/lib/libhdf5.so.6
#8 0x00007fffd8115775 in NX5open (
filename=0x19c3850 "/home/2zr/data/CNCS_800_rebin0000.nxs", am=1,
pHandle=0x1) at napi5.c:144
#9 0x00007fffd81111a0 in NXinternalopen (
userfilename=0x1a47798 "/home/2zr/data/CNCS_800_rebin0000.nxs", am=1,
fileStack=<value optimized out>) at napi.c:405
#10 0x00007fffd8111565 in nxiopen_ (
userfilename=0x1a47798 "/home/2zr/data/CNCS_800_rebin0000.nxs", am=1,
gHandle=0x7fffffffc130) at napi.c:291
#11 0x00007fffd832e865 in File (this=<value optimized out>, filename=...,
access=1) at NeXusFile.cpp:143
#12 0x00007fffd8573b73 in vtkInElSxtalNeXus::Canreadfile(char const*) ()
from /home/2zr/workspace/InElSxtalNeXus/libInElSxtalNeXus.so
#13 0x00007fffd857399b in vtkInElSxtalNeXus::CanReadFile(char const*) ()
from /home/2zr/workspace/InElSxtalNeXus/libInElSxtalNeXus.so
#14 0x00007fffd857608f in vtkInElSxtalNeXusCommand(vtkClientServerInterpreter*,
vtkObjectBase*, char const*, vtkClientServerStream const&,
vtkClientServerStream&) () from
/home/2zr/workspace/InElSxtalNeXus/libInElSxtalNeXus.so
#15 0x00007fffe93352e2 in
vtkClientServerInterpreter::ProcessCommandInvoke(vtkClientServerStream const&,
int) ()
from /home/2zr/build/ParaView/bin/libvtkClientServer.so
#16 0x00007fffe93349ab in
vtkClientServerInterpreter::ProcessOneMessage(vtkClientServerStream const&,
int) ()
from /home/2zr/build/ParaView/bin/libvtkClientServer.so
#17 0x00007fffe9334843 in
vtkClientServerInterpreter::ProcessStream(vtkClientServerStream const&) () from
/home/2zr/build/ParaView/bin/libvtkClientServer.so
#18 0x00007fffeee5bc57 in
vtkSelfConnection::ProcessStreamLocally(vtkClientServerStream&) () from
/home/2zr/build/ParaView/bin/libvtkPVServerCommon.so
#19 0x00007fffeee5bc13 in
vtkSelfConnection::SendStreamToClient(vtkClientServerStream&) () from
/home/2zr/build/ParaView/bin/libvtkPVServerCommon.so
#20 0x00007fffeede399f in vtkProcessModuleConnection::SendStream(unsigned int,
vtkClientServerStream&) ()
from /home/2zr/build/ParaView/bin/libvtkPVServerCommon.so
#21 0x00007fffeede71dc in vtkProcessModuleConnectionManager::SendStream(long
long, unsigned int, vtkClientServerStream&, int) ()
from /home/2zr/build/ParaView/bin/libvtkPVServerCommon.so
#22 0x00007fffeedf10fc in vtkProcessModule::SendStream(long long, unsigned int,
vtkClientServerStream&, int) ()
from /home/2zr/build/ParaView/bin/libvtkPVServerCommon.so
#23 0x00007ffff458ecd2 in vtkSMReaderFactory::CanReadFile(char const*,
vtkSMProxy*) () from /home/2zr/build/ParaView/bin/libvtkPVServerManager.so
#24 0x00007ffff458ce61 in
vtkSMReaderFactory::vtkInternals::vtkValue::CanReadFile(char const*,
std::vector<std::string, std::allocator<std::string> > const&, long long, bool)
() from /home/2zr/build/ParaView/bin/libvtkPVServerManager.so
#25 0x00007ffff458e09f in vtkSMReaderFactory::CanReadFile(char const*, long
long) () from /home/2zr/build/ParaView/bin/libvtkPVServerManager.so
#26 0x00007ffff7b7d4b4 in pqLoadDataReaction::loadData(QStringList const&) ()
from /home/2zr/build/ParaView/bin/libpqApplicationComponents.so
#27 0x00007ffff7b7d1aa in pqLoadDataReaction::loadData() ()
from /home/2zr/build/ParaView/bin/libpqApplicationComponents.so
#28 0x00007ffff7ba46f5 in pqLoadDataReaction::onTriggered() ()
---Type <return> to continue, or q <return> to quit---
from /home/2zr/build/ParaView/bin/libpqApplicationComponents.so
#29 0x00007ffff7ba5eed in pqReaction::qt_metacall(QMetaObject::Call, int,
void**) () from /home/2zr/build/ParaView/bin/libpqApplicationComponents.so
#30 0x00007ffff7ba4637 in pqLoadDataReaction::qt_metacall(QMetaObject::Call,
int, void**) () from /home/2zr/build/ParaView/bin/libpqApplicationComponents.so
#31 0x00007ffff0dc4e3f in QMetaObject::activate(QObject*, QMetaObject const*,
int, void**) () from /usr/lib/libQtCore.so.4
#32 0x00007ffff1dac032 in QAction::triggered(bool) ()
from /usr/lib/libQtGui.so.4
#33 0x00007ffff1dae0ab in QAction::activate(QAction::ActionEvent) ()
from /usr/lib/libQtGui.so.4
#34 0x00007ffff21686ca in ?? () from /usr/lib/libQtGui.so.4
#35 0x00007ffff216897c in QAbstractButton::mouseReleaseEvent(QMouseEvent*) ()
from /usr/lib/libQtGui.so.4
#36 0x00007ffff22348ca in QToolButton::mouseReleaseEvent(QMouseEvent*) ()
from /usr/lib/libQtGui.so.4
#37 0x00007ffff1e08582 in QWidget::event(QEvent*) ()
from /usr/lib/libQtGui.so.4
#38 0x00007ffff1db222c in QApplicationPrivate::notify_helper(QObject*, QEvent*)
() from /usr/lib/libQtGui.so.4
#39 0x00007ffff1db8ecb in QApplication::notify(QObject*, QEvent*) ()
from /usr/lib/libQtGui.so.4
#40 0x00007ffff0db206c in QCoreApplication::notifyInternal(QObject*, QEvent*)
() from /usr/lib/libQtCore.so.4
#41 0x00007ffff1db80ae in QApplicationPrivate::sendMouseEvent(QWidget*,
QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool) ()
from /usr/lib/libQtGui.so.4
#42 0x00007ffff1e37f65 in ?? () from /usr/lib/libQtGui.so.4
#43 0x00007ffff1e368ac in QApplication::x11ProcessEvent(_XEvent*) ()
from /usr/lib/libQtGui.so.4
#44 0x00007ffff1e62882 in ?? () from /usr/lib/libQtGui.so.4
#45 0x00007fffe1eef8c2 in g_main_context_dispatch () from /lib/libglib-2.0.so.0
#46 0x00007fffe1ef3748 in ?? () from /lib/libglib-2.0.so.0
#47 0x00007fffe1ef38fc in g_main_context_iteration ()
from /lib/libglib-2.0.so.0
#48 0x00007ffff0ddb513 in
QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) ()
from /usr/lib/libQtCore.so.4
#49 0x00007ffff1e6246e in ?? () from /usr/lib/libQtGui.so.4
#50 0x00007ffff0db0992 in
QEventLoop::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () from
/usr/lib/libQtCore.so.4
#51 0x00007ffff0db0d6c in
QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () from
/usr/lib/libQtCore.so.4
#52 0x00007ffff0db4aab in QCoreApplication::exec() ()
from /usr/lib/libQtCore.so.4
#53 0x000000000040809c in main ()
(gdb)_______________________________________________
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