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
***
*** 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.Hello,
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
***
*** 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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