Hello to all,
unfortunately, I have no admin rights and can not re-compile the library
with -DDEAL_II_WITH_TBB=OFF.
But I did
export DEAL_II_NUM_THREADS=1
to make sure that nothing like a race condition is involved.
However, my program is not parallelized explicitedly by myself.
If there is multi-threading, then just because I call
dealii functions which are multi-threaded per default.
Anyway, with DEAL_II_NUM_THREADS=1, valgrind does not produce any error
messages anymore (see valgrind.txt), but
my issue is still there. To give you a better insight, I attached the
output of my program once
with the print statement in my assembly routine
(output_print_NOT_outcommented.txt) and
without the print statement ( output_print_outcommented.txt).
As you can see, the RHS of my linear system after convergence is different
at some load steps.
And as I said, these differences sum up in repeating calls to my program
and, clearly, should not be there -- regardless how small they are.
What I did is to run my program with the address and undefined behavior
sanitizer of clang by passing some flags to cmake:
cmake -DCAMKE_CXX_FLAGS="-fsanitize=undefined" -DCMAKE_EXE_LINKER_FLAGS
="-fsanitize=undefined" -DCAMKE_CXX_FLAGS="-fsanitize=address"
-DCMAKE_EXE_LINKER_FLAGS ="-fsanitize=address"
-DCAMKE_CXX_FLAGS="-fno-optimize-sibling-calls" .
At the very end of my program (probably when the destructor is called or
even later), the sanitizers reported some errors (see
address_sanitizer.txt),
but this may be some false positives. In particular, no error is reported
during the relevant part of my program.
These errors occur with and without the print statement, and also in debug
mode.
If there is a bug in my program, this bug seems to be a tough one (at least
for me).
If someone of you (Wolfgang, Bruno, Daniel,...) were willed to have a look
at my code,
I would reduce the issue to a minimal working example and upload all source
files here or sent it do you directly.
I would highly appreciate that since I do not want to extend my code
further with that bug in it.
Best
Simon
<https://mail.google.com/mail/u/0?ui=2&ik=4a4452916d&attid=0.2&permmsgid=msg-a:r8629661344512179658&view=att&disp=safe&realattid=f_lfwmt5ix1>
Am Fr., 31. März 2023 um 15:06 Uhr schrieb Bruno Turcksin <
bruno.turck...@gmail.com>:
> Simon,
>
> Le ven. 31 mars 2023 à 08:58, Simon Wiesheier <simon.wieshe...@gmail.com>
> a écrit :
>
>>
>>
>> Given that it works fine in debug mode, there are likely no out-of-bound
>> violations. I just use std::vector and Vector<double> as data structures
>> which would be detected in debug mode.
>>
>> That's optimistic :) It's not because you are in debug mode that
> std::vector checks the bounds. The bounds are only checked when using at()
>
>
>> How can I run my program without TBB enabled?
>>
>
> Reconfigure and recompile deal.II with -D DEAL_II_WITH_TBB=OFF
>
> Best,
>
> Bruno
>
>
> --
> The deal.II project is located at http://www.dealii.org/
> For mailing list/forum options, see
> https://groups.google.com/d/forum/dealii?hl=en
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> .
>
--
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==3313580== Memcheck, a memory error detector
==3313580== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==3313580== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info
==3313580== Command: ./NeoHooke
==3313580== Parent PID: 3063539
==3313580==
==3313580==
==3313580== HEAP SUMMARY:
==3313580== in use at exit: 206,618 bytes in 1,302 blocks
==3313580== total heap usage: 277,987 allocs, 276,685 frees, 17,751,468 bytes
allocated
==3313580==
==3313580== LEAK SUMMARY:
==3313580== definitely lost: 0 bytes in 0 blocks
==3313580== indirectly lost: 0 bytes in 0 blocks
==3313580== possibly lost: 0 bytes in 0 blocks
==3313580== still reachable: 206,618 bytes in 1,302 blocks
==3313580== suppressed: 0 bytes in 0 blocks
==3313580== Reachable blocks (those to which a pointer was found) are not shown.
==3313580== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==3313580==
==3313580== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
Step 1 out of 10 load steps with current strain: 0.1*0.5 = 0.05
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 94 3.117e-07 1.000e+00
1 CST Assemble System SLV | 106 1.639e-09 7.998e-03
2 CST Assemble System SLV | 88 8.825e-10 2.862e-03
3 CST Assemble System SLV | 55 1.063e-10 1.500e-03
4 CST Assemble System SLV | 49 2.614e-11 1.620e-04
5 CST Assemble System SLV | 47 1.482e-12 8.528e-06
6 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 8.514e-07
Step 2 out of 10 load steps with current strain: 2.000e-01*5.000e-01 = 1.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 47 7.570e-09 1.000e+00
1 CST Assemble System SLV | 48 1.903e-11 4.958e-03
2 CST Assemble System SLV | 47 1.557e-13 1.588e-05
3 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 3.845e-09
Step 3 out of 10 load steps with current strain: 3.000e-01*5.000e-01 = 1.500e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 47 8.877e-09 1.000e+00
1 CST Assemble System SLV | 46 4.508e-11 1.108e-02
2 CST Assemble System SLV | 45 2.651e-11 3.337e-03
3 CST Assemble System SLV | 47 1.457e-14 1.514e-06
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 1.072e-10
Step 4 out of 10 load steps with current strain: 4.000e-01*5.000e-01 = 2.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 47 7.301e-09 1.000e+00
1 CST Assemble System SLV | 45 9.118e-11 1.256e-02
2 CST Assemble System SLV | 45 9.937e-13 2.392e-04
3 CST Assemble System SLV | 45 2.209e-16 6.772e-08
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 1.197e-13
Step 5 out of 10 load steps with current strain: 5.000e-01*5.000e-01 = 2.500e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 45 8.062e-09 1.000e+00
1 CST Assemble System SLV | 42 1.700e-10 2.016e-02
2 CST Assemble System SLV | 42 1.503e-12 3.099e-04
3 CST Assemble System SLV | 42 2.674e-16 3.797e-08
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 4.070e-14
Step 6 out of 10 load steps with current strain: 6.000e-01*5.000e-01 = 3.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 42 4.447e-09 1.000e+00
1 CST Assemble System SLV | 41 1.542e-10 1.687e-02
2 CST Assemble System SLV | 41 2.336e-12 2.577e-04
3 CST Assemble System SLV | 41 3.422e-16 6.428e-08
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 6.266e-14
Step 7 out of 10 load steps with current strain: 7.000e-01*5.000e-01 = 3.500e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 41 4.724e-09 1.000e+00
1 CST Assemble System SLV | 41 1.992e-10 5.067e-02
2 CST Assemble System SLV | 40 1.822e-11 1.629e-03
3 CST Assemble System SLV | 40 2.862e-14 2.663e-06
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 1.076e-10
Step 8 out of 10 load steps with current strain: 8.000e-01*5.000e-01 = 4.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 41 4.576e-09 1.000e+00
1 CST Assemble System SLV | 41 8.941e-11 2.600e-02
2 CST Assemble System SLV | 41 4.956e-12 1.182e-03
3 CST Assemble System SLV | 40 8.339e-15 1.543e-06
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 3.259e-11
Step 9 out of 10 load steps with current strain: 9.000e-01*5.000e-01 = 4.500e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 41 5.086e-09 1.000e+00
1 CST Assemble System SLV | 40 3.146e-10 8.407e-02
2 CST Assemble System SLV | 44 2.057e-09 5.927e-01
3 CST Assemble System SLV | 44 2.247e-10 4.182e-02
4 CST Assemble System SLV | 45 7.281e-12 1.281e-03
5 CST Assemble System SLV | 45 1.375e-14 3.519e-06
6 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 1.762e-10
Step 10 out of 10 load steps with current strain: 1.000e+00*5.000e-01 =
5.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 45 1.195e-08 1.000e+00
1 CST Assemble System SLV | 46 1.584e-08 2.264e+00
2 CST Assemble System SLV | 45 2.853e-09 3.281e-01
3 CST Assemble System SLV | 46 9.998e-11 1.797e-02
4 CST Assemble System SLV | 46 1.287e-12 1.043e-04
5 CST Assemble System SLV | 46 3.305e-16 4.150e-08
6 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 2.039e-13
Step 1 out of 10 load steps with current strain: 0.1*0.5 = 0.05
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 94 3.117e-07 1.000e+00
1 CST Assemble System SLV | 106 1.639e-09 7.998e-03
2 CST Assemble System SLV | 88 8.825e-10 2.862e-03
3 CST Assemble System SLV | 55 1.063e-10 1.500e-03
4 CST Assemble System SLV | 49 2.614e-11 1.620e-04
5 CST Assemble System SLV | 47 1.482e-12 8.528e-06
6 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 8.514e-07
Step 2 out of 10 load steps with current strain: 2.000e-01*5.000e-01 = 1.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 47 7.570e-09 1.000e+00
1 CST Assemble System SLV | 48 1.903e-11 4.958e-03
2 CST Assemble System SLV | 47 1.557e-13 1.588e-05
3 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 3.845e-09
Step 3 out of 10 load steps with current strain: 3.000e-01*5.000e-01 = 1.500e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 47 8.877e-09 1.000e+00
1 CST Assemble System SLV | 46 4.508e-11 1.108e-02
2 CST Assemble System SLV | 45 2.651e-11 3.337e-03
3 CST Assemble System SLV | 47 1.457e-14 1.514e-06
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 1.072e-10
Step 4 out of 10 load steps with current strain: 4.000e-01*5.000e-01 = 2.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 47 7.301e-09 1.000e+00
1 CST Assemble System SLV | 45 9.118e-11 1.256e-02
2 CST Assemble System SLV | 45 9.937e-13 2.392e-04
3 CST Assemble System SLV | 45 2.209e-16 6.772e-08
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 1.236e-13
Step 5 out of 10 load steps with current strain: 5.000e-01*5.000e-01 = 2.500e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 45 8.062e-09 1.000e+00
1 CST Assemble System SLV | 42 1.700e-10 2.016e-02
2 CST Assemble System SLV | 42 1.503e-12 3.099e-04
3 CST Assemble System SLV | 42 2.674e-16 3.797e-08
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 6.136e-14
Step 6 out of 10 load steps with current strain: 6.000e-01*5.000e-01 = 3.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 42 4.447e-09 1.000e+00
1 CST Assemble System SLV | 41 1.542e-10 1.687e-02
2 CST Assemble System SLV | 41 2.336e-12 2.577e-04
3 CST Assemble System SLV | 41 3.422e-16 6.428e-08
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 8.567e-14
Step 7 out of 10 load steps with current strain: 7.000e-01*5.000e-01 = 3.500e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 41 4.724e-09 1.000e+00
1 CST Assemble System SLV | 41 1.992e-10 5.067e-02
2 CST Assemble System SLV | 40 1.822e-11 1.629e-03
3 CST Assemble System SLV | 40 2.862e-14 2.663e-06
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 1.076e-10
Step 8 out of 10 load steps with current strain: 8.000e-01*5.000e-01 = 4.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 41 4.576e-09 1.000e+00
1 CST Assemble System SLV | 41 8.941e-11 2.600e-02
2 CST Assemble System SLV | 41 4.956e-12 1.182e-03
3 CST Assemble System SLV | 40 8.339e-15 1.543e-06
4 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 3.259e-11
Step 9 out of 10 load steps with current strain: 9.000e-01*5.000e-01 = 4.500e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 41 5.086e-09 1.000e+00
1 CST Assemble System SLV | 40 3.146e-10 8.407e-02
2 CST Assemble System SLV | 44 2.057e-09 5.927e-01
3 CST Assemble System SLV | 44 2.247e-10 4.182e-02
4 CST Assemble System SLV | 45 7.281e-12 1.281e-03
5 CST Assemble System SLV | 45 1.375e-14 3.519e-06
6 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 1.762e-10
Step 10 out of 10 load steps with current strain: 1.000e+00*5.000e-01 =
5.000e-01
__________________________________________________________________________________________
SOLVER STEP | LIN_IT LIN_RES RES_NORM
__________________________________________________________________________________________
0 CST Assemble System SLV | 45 1.195e-08 1.000e+00
1 CST Assemble System SLV | 46 1.584e-08 2.264e+00
2 CST Assemble System SLV | 45 2.853e-09 3.281e-01
3 CST Assemble System SLV | 46 9.998e-11 1.797e-02
4 CST Assemble System SLV | 46 1.287e-12 1.043e-04
5 CST Assemble System SLV | 46 3.305e-16 4.150e-08
6 CST Assemble System CONVERGED!
__________________________________________________________________________________________
Errors:
Rhs: 1.702e-13
==4060635==ERROR: LeakSanitizer: detected memory leaks
Direct leak of 792 byte(s) in 3 object(s) allocated from:
#0 0x7f3cfb18d608 in operator new[](unsigned long)
../../../../src/libsanitizer/asan/asan_new_delete.cpp:98
#1 0x7f3cda8675e2 in tbb::internal::task_stream<3>::initialize(unsigned
int)
(/calculate/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/intel-tbb-2020.3-ulfjl2ollhdkou6aoriwp27nlydyzuvj/lib/libtbb_debug.so.2+0x415e2)
#2 0x7f3cda862af0 in tbb::internal::arena::arena(tbb::internal::market&,
unsigned int, unsigned int) ../../src/tbb/arena.cpp:270
#3 0x7f3cda862c64 in
tbb::internal::arena::allocate_arena(tbb::internal::market&, unsigned int,
unsigned int) ../../src/tbb/arena.cpp:293
#4 0x7f3cda85ea68 in tbb::internal::market::create_arena(int, int, unsigned
long) ../../src/tbb/market.cpp:314
#5 0x7f3cda85c980 in tbb::internal::governor::init_scheduler(int, unsigned
long, bool) ../../src/tbb/governor.cpp:197
#6 0x7f3cda85d45a in tbb::task_scheduler_init::initialize(int, unsigned
long) ../../src/tbb/governor.cpp:490
#7 0x7f3cda85d3a8 in tbb::task_scheduler_init::initialize(int)
../../src/tbb/governor.cpp:478
#8 0x7f3ceefb573f in dealii::MultithreadInfo::set_thread_limit(unsigned
int)
/calculate/temp/ltmadmin/spack-stage-dealii-9.3.2-fpaxcn6bqnnmqjyg5nnmil5csgbvxate/spack-src/source/base/multithread_info.cc:93
#9 0x7f3ceefb5ada in dealii::MultithreadInfo::initialize_multithreading()
/calculate/temp/ltmadmin/spack-stage-dealii-9.3.2-fpaxcn6bqnnmqjyg5nnmil5csgbvxate/spack-src/source/base/multithread_info.cc:132
#10 0x7f3ceefb5af8 in DoOnce
/calculate/temp/ltmadmin/spack-stage-dealii-9.3.2-fpaxcn6bqnnmqjyg5nnmil5csgbvxate/spack-src/source/base/multithread_info.cc:147
#11 0x7f3ceefb9297 in __static_initialization_and_destruction_0
/calculate/temp/ltmadmin/spack-stage-dealii-9.3.2-fpaxcn6bqnnmqjyg5nnmil5csgbvxate/spack-src/source/base/multithread_info.cc:149
#12 0x7f3ceefb92b1 in _GLOBAL__sub_I_multithread_info.cc
/calculate/temp/ltmadmin/spack-stage-dealii-9.3.2-fpaxcn6bqnnmqjyg5nnmil5csgbvxate/spack-src/source/base/multithread_info.cc:152
#13 0x7f3cfb7a247d in call_init elf/dl-init.c:70
#14 0x7f3cfb7a2567 in call_init elf/dl-init.c:33
#15 0x7f3cfb7a2567 in _dl_init elf/dl-init.c:117
#16 0x7f3cfb7bc2e9 (/lib64/ld-linux-x86-64.so.2+0x202e9)
Direct leak of 544 byte(s) in 1 object(s) allocated from:
#0 0x7f3cfb18d608 in operator new[](unsigned long)
../../../../src/libsanitizer/asan/asan_new_delete.cpp:98
#1 0x7f3cd163efb3
(/calculate/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/oce-0.18.3-ecsmaa46gxbflztayfsqannu7m66vwcb/lib/libTKernel.so.11+0xa3fb3)
#2 0x7f3cfb7a247d in call_init elf/dl-init.c:70
#3 0x7f3cfb7a2567 in call_init elf/dl-init.c:33
#4 0x7f3cfb7a2567 in _dl_init elf/dl-init.c:117
#5 0x7f3cfb7bc2e9 (/lib64/ld-linux-x86-64.so.2+0x202e9)
SUMMARY: AddressSanitizer: 1336 byte(s) leaked in 4 allocation(s).
make[3]: *** [CMakeFiles/run.dir/build.make:71: CMakeFiles/run] Error 1
make[2]: *** [CMakeFiles/Makefile2:116: CMakeFiles/run.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:123: CMakeFiles/run.dir/rule] Error 2
