Please reply to the mailing list. On 25 August 2015 at 15:42, Alvaro Diez Gonzalez-Pardo < alvaro.diez.gonzalez-pa...@cern.ch> wrote:
> No it is not, should it? > > Yes, initialise the bounding box tree outside of a threaded region. Garth > Alvaro > ________________________________________ > From: Garth N. Wells [gn...@cam.ac.uk] > Sent: 25 August 2015 16:25 > To: Alvaro Diez Gonzalez-Pardo > Subject: Re: [FEniCS] Multi-thread issue when using dolfin Function > > On 25 August 2015 at 15:23, Alvaro Diez Gonzalez-Pardo < > alvaro.diez.gonzalez-pa...@cern.ch<mailto: > alvaro.diez.gonzalez-pa...@cern.ch>> wrote: > Thanks for the advice > > Unfortunately the code is still not working after calling > Mesh::bounding_box_tree(). > > The conflincting part of the code now looks like this: > > safeRead.lock(); > _detector->get_mesh()->bounding_box_tree(); > _detector->get_d_f_grad()->eval(wrap_e_field, wrap_x); > _detector->get_w_f_grad()->eval(wrap_w_field, wrap_x); > safeRead.unlock(); > > > > I don't know the details of how your threading works, but is > > _detector->get_mesh()->bounding_box_tree(); > > outside of a threaded region? > > Garth > > thanks in advance for any help > > Alvaro Diez > ________________________________________ > From: Garth N. Wells [gn...@cam.ac.uk<mailto:gn...@cam.ac.uk>] > Sent: 25 August 2015 14:22 > To: Alvaro Diez Gonzalez-Pardo > Cc: fenics@fenicsproject.org<mailto:fenics@fenicsproject.org> > Subject: Re: [FEniCS] Multi-thread issue when using dolfin Function > > It looks like the 'auto' build and caching of the bounding box tree is not > thread-safe (we can add this to the reasons why I think the user should be > tasked with managing the bounding box tree initialisation). > > Try calling Mesh::bounding_box_tree() before any calls to Function::eval. > > Garth > > > On 25 August 2015 at 12:10, Alvaro Diez Gonzalez-Pardo < > alvaro.diez.gonzalez-pa...@cern.ch<mailto: > alvaro.diez.gonzalez-pa...@cern.ch><mailto: > alvaro.diez.gonzalez-pa...@cern.ch<mailto: > alvaro.diez.gonzalez-pa...@cern.ch>>> wrote: > Hello, > > I write to you to report a problem I've been having when trying to use > dolfin functions in parallel exectution. Note that this does not refer to > computation using dolfin libraries but rather using the results in parallel. > > you'll find the error report below this lines and as an attachment as well. > > thanks in advance for the help. > > Alvaro Diez > > =======================================ERROR > REPORT:===================================================================== > > > I'm trying to parallelize a program that uses dolfin libraries to solve > Poisson and Laplace equations. I am using C++11 built-in multithreading > class "thread.h". > My class Carrier contains: > > class Carrier > { > private: > [...] > SMSDetector * _detector; > [...] > } > > where SMSDetector is: > > class SMSDetector > { > private: > [...] > Function _w_f_grad; // function to > store the weighting field > (vectorial) > [...] > public: > Function * get_w_f_grad(); > > } > > When the number of threads used for the simulation is bigger than one > (i.e. parallel execution) the program crashes with segmentation fault. The > program needs to evaluate, for each Carrier I create a method like: > > _detector->get_w_f_grad()->eval(wrap_w_field, wrap_x); > > where the arguments for eval were defined as: > > Array<double> wrap_x(2, _x.data()); > Array<double> wrap_w_field(2, _w_field.data()); > > > The error persists even when mutexes are implemented to avoid race > conditions produced when several Carriers try to access the eval(). > The error message I get (only the first time I run it after rebooting the > machine) is: > > terminate called after throwing an instance of > 'std::runtime_error' what(): > > *** > > ------------------------------------------------------------------------- > *** DOLFIN encountered an error. If you are not able to > resolve this issue > *** using the information listed below, you can ask for > help at > *** > *** fenics@fenicsproject.org<mailto: > fenics@fenicsproject.org><mailto:fenics@fenicsproject.org<mailto: > fenics@fenicsproject.org>> > *** > *** Remember to include the error message listed below > and, if possible, > *** include a *minimal* running example to reproduce the > error. > *** > *** > > ------------------------------------------------------------------------- > *** Error: Unable to compute collisions with bounding > box tree. > *** Reason: Bounding box tree has not been built. You > need to call tree.build(). > *** Where: This error was encountered inside > BoundingBoxTree.cpp. > *** Process: unknown > *** > *** DOLFIN version: 1.5.0 > *** Git changeset: unknown > *** > > ------------------------------------------------------------------------- > > [pcssd30:03650] *** Process received signal *** > [pcssd30:03650] Signal: Aborted (6) > [pcssd30:03650] Signal code: (-6) > [pcssd30:03650] [ 0] [0xb7735410] > [pcssd30:03650] [ 1] [0xb7735428] > [pcssd30:03650] [ 2] > /lib/i386-linux-gnu/libc.so.6(gsignal+0x47) [0xb57bf607] > [pcssd30:03650] [ 3] > /lib/i386-linux-gnu/libc.so.6(abort+0x143) [0xb57c2a33] > [pcssd30:03650] [ 4] > /usr/lib/i386-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x155) > [0xb59cfd45] > [pcssd30:03650] [ 5] > /usr/lib/i386-linux-gnu/libstdc++.so.6(+0x70a33) [0xb59cda33] > [pcssd30:03650] [ 6] > /usr/lib/i386-linux-gnu/libstdc++.so.6(+0x70aad) [0xb59cdaad] > [pcssd30:03650] [ 7] > /usr/lib/i386-linux-gnu/libstdc++.so.6(+0x9cc6d) [0xb59f9c6d] > [pcssd30:03650] [ 8] > /lib/i386-linux-gnu/libpthread.so.0(+0x6f70) [0xb5570f70] > [pcssd30:03650] [ 9] > /lib/i386-linux-gnu/libc.so.6(clone+0x5e) [0xb587cbee] > [pcssd30:03650] *** End of error message *** > > Aborted (core dumped) > > When using a debugger (gdb), the error message reads: > > "Program received signal SIGSEGV, Segmentation fault. 0xb7d90bd4 > in dolfin::MeshTopology::dim() const () from > /usr/lib/i386-linux-gnu/libdolfin.so.1.5" > > For more details on how the code works, the full program > source-code is available on Github-> https://github.com/AlGepe/TRACS/ an > the problematic part seems to be from line 87 of Carrier.cpp to the end of > that method, most likely in lines 120 - 125 of that file. > _______________________________________________ > fenics mailing list > fenics@fenicsproject.org<mailto:fenics@fenicsproject.org><mailto: > fenics@fenicsproject.org<mailto:fenics@fenicsproject.org>> > http://fenicsproject.org/mailman/listinfo/fenics > > > >
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