On 25 August 2015 at 15:23, Alvaro Diez Gonzalez-Pardo <
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]
> Sent: 25 August 2015 14:22
> To: Alvaro Diez Gonzalez-Pardo
> Cc: 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>> 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>
> ***
> *** 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.
> _______________________________________________
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>
>
>
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