opm-simulators
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OPM
Python tests fail when using shared libraries
On Ubuntu 23.10 I tested Python bindings using shared libraries like this:
#! /bin/bash
NPROC=5 # Number of build threads when running "make"
# export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
for repo in opm-common opm-grid opm-models opm-simulators
do
git clone [email protected]:OPM/"${repo}".git
done
global_cmake_flags="-DBUILD_SHARED_LIBS=ON"
build_opm_common() {
local flags="-DOPM_ENABLE_PYTHON=ON $global_cmake_flags"
cd opm-common
mkdir build
cd build
cmake $flags ..
make -j$NPROC
cd ../..
}
build_opm_grid() {
local flags="$global_cmake_flags"
cd opm-grid
mkdir build
cd build
cmake $flags ..
make -j$NPROC
cd ../..
}
build_opm_models() {
local flags="$global_cmake_flags"
cd opm-models
mkdir build
cd build
cmake $flags ..
make -j$NPROC
cd ../..
}
build_opm_simulators() {
local flags="-DOPM_ENABLE_PYTHON=ON $global_cmake_flags"
cd opm-simulators
mkdir build
cd build
cmake $flags ..
make -j$NPROC
cd ../..
}
build_opm_common
build_opm_grid
build_opm_models
build_opm_simulators
Then, after the build completed:
$ cd opm-simulators/build
$ ctest -R python_basic --output-on-failure
Test project /home/hakon/test/opm15/opm-simulators/build
Start 54: python_basic
1/1 Test #54: python_basic .....................***Failed 3.80 sec
**********************************************************************
* *
* This is flow 2024.10-pre *
* *
* Flow is a simulator for fully implicit three-phase black-oil flow, *
* including solvent and polymer capabilities. *
* For more information, see https://opm-project.org *
* *
**********************************************************************
Using 1 MPI processes with 2 OMP threads on each
Reading deck file 'SPE1CASE1.DATA'
0 Reading RUNSPEC in SPE1CASE1.DATA line 20
1 Reading TITLE in SPE1CASE1.DATA line 23
2 Reading DIMENS in SPE1CASE1.DATA line 26
3 Reading EQLDIMS in SPE1CASE1.DATA line 31
4 Reading TABDIMS in SPE1CASE1.DATA line 36
5 Reading OIL in SPE1CASE1.DATA line 39
6 Reading GAS in SPE1CASE1.DATA line 40
7 Reading WATER in SPE1CASE1.DATA line 41
8 Reading DISGAS in SPE1CASE1.DATA line 42
9 Reading FIELD in SPE1CASE1.DATA line 46
10 Reading START in SPE1CASE1.DATA line 48
11 Reading WELLDIMS in SPE1CASE1.DATA line 51
12 Reading UNIFOUT in SPE1CASE1.DATA line 62
13 Reading GRID in SPE1CASE1.DATA line 64
14 Reading INIT in SPE1CASE1.DATA line 71
15 Reading NOECHO in SPE1CASE1.DATA line 75
16 Reading DX in SPE1CASE1.DATA line 77
17 Reading DY in SPE1CASE1.DATA line 80
18 Reading DZ in SPE1CASE1.DATA line 83
19 Reading TOPS in SPE1CASE1.DATA line 87
20 Reading PORO in SPE1CASE1.DATA line 91
21 Reading PERMX in SPE1CASE1.DATA line 95
22 Reading PERMY in SPE1CASE1.DATA line 99
23 Reading PERMZ in SPE1CASE1.DATA line 103
24 Reading ECHO in SPE1CASE1.DATA line 107
25 Reading PROPS in SPE1CASE1.DATA line 109
26 Reading PVTW in SPE1CASE1.DATA line 112
27 Reading ROCK in SPE1CASE1.DATA line 125
28 Reading SWOF in SPE1CASE1.DATA line 132
29 Reading SGOF in SPE1CASE1.DATA line 161
30 Reading DENSITY in SPE1CASE1.DATA line 191
31 Reading PVDG in SPE1CASE1.DATA line 201
32 Reading PVTO in SPE1CASE1.DATA line 222
33 Reading SOLUTION in SPE1CASE1.DATA line 252
34 Reading EQUIL in SPE1CASE1.DATA line 255
35 Reading RSVD in SPE1CASE1.DATA line 275
36 Reading SUMMARY in SPE1CASE1.DATA line 283
37 Reading FOPR in SPE1CASE1.DATA line 287
38 Reading WGOR in SPE1CASE1.DATA line 291
39 Reading FGOR in SPE1CASE1.DATA line 296
40 Reading BPR in SPE1CASE1.DATA line 299
41 Reading BGSAT in SPE1CASE1.DATA line 305
42 Reading WBHP in SPE1CASE1.DATA line 318
43 Reading WGIR in SPE1CASE1.DATA line 322
44 Reading WGIT in SPE1CASE1.DATA line 326
45 Reading WGPR in SPE1CASE1.DATA line 330
46 Reading WGPT in SPE1CASE1.DATA line 334
47 Reading WOIR in SPE1CASE1.DATA line 338
48 Reading WOIT in SPE1CASE1.DATA line 342
49 Reading WOPR in SPE1CASE1.DATA line 346
50 Reading WOPT in SPE1CASE1.DATA line 350
51 Reading WWIR in SPE1CASE1.DATA line 354
52 Reading WWIT in SPE1CASE1.DATA line 358
53 Reading WWPR in SPE1CASE1.DATA line 362
54 Reading WWPT in SPE1CASE1.DATA line 366
55 Reading SCHEDULE in SPE1CASE1.DATA line 370
56 Reading RPTSCHED in SPE1CASE1.DATA line 372
57 Reading RPTRST in SPE1CASE1.DATA line 375
58 Reading DRSDT in SPE1CASE1.DATA line 380
59 Reading WELSPECS in SPE1CASE1.DATA line 385
60 Reading COMPDAT in SPE1CASE1.DATA line 394
61 Reading WCONPROD in SPE1CASE1.DATA line 404
62 Reading WCONINJE in SPE1CASE1.DATA line 414
63 Reading TSTEP in SPE1CASE1.DATA line 423
Warning: Unsupported keywords or keyword items:
NOECHO: keyword not supported
In file: SPE1CASE1.DATA, line 75
ECHO: keyword not supported
In file: SPE1CASE1.DATA, line 107
Creating grid from keywords DX, DY, DZ and TOPS
3 fluid phases are active
Processing dynamic information from
SPE1CASE1.DATA line 370
Initializing report step 0/12 at 2015-01-01 0 DAYS line 370
Processing keyword RPTSCHED at line 372
Processing keyword RPTRST at line 375
Processing keyword DRSDT at line 380
Processing keyword WELSPECS at line 385
Processing keyword COMPDAT at line 394
Processing keyword WCONPROD at line 404
Processing keyword WCONINJE at line 414
Complete report step 1 (31 DAYS) at 2015-02-01 (0 DAYS)
Initializing report step 2/12 at 2015-02-01 (0 DAYS) line 423
Complete report step 2 (28 DAYS) at 2015-03-01 (31 DAYS)
Initializing report step 3/12 at 2015-03-01 (31 DAYS) line 423
Complete report step 3 (31 DAYS) at 2015-04-01 (59 DAYS)
Initializing report step 4/12 at 2015-04-01 (59 DAYS) line 423
Complete report step 4 (30 DAYS) at 2015-05-01 (90 DAYS)
Initializing report step 5/12 at 2015-05-01 (90 DAYS) line 423
Complete report step 5 (31 DAYS) at 2015-06-01 (120 DAYS)
Processing grid
Total number of active cells: 300 / total pore volume: 534322820 RB
===============Saturation Functions Diagnostics===============
System: Black-oil system.
Relative permeability input format: Saturation Family I.
Number of saturation regions: 1
python3: /home/hakon/test/opm15/opm-models/opm/models/blackoil/blackoilprimaryvariables.hh:437: void Opm::BlackOilPrimaryVariables<TypeTag>::assignNaive(const FluidState&) [with FluidState = Opm::BlackOilFluidState<double, Opm::BlackOilFluidSystem<double, Opm::BlackOilDefaultIndexTraits>, true, false, true, false, false, false, false, 3>; TypeTag = Opm::Properties::TTag::FlowProblemTPFA]: Assertion `FluidSystem::phaseIsActive(waterPhaseIdx)' failed.
[hakon-Precision-3570:539868] *** Process received signal ***
[hakon-Precision-3570:539868] Signal: Aborted (6)
[hakon-Precision-3570:539868] Signal code: (-6)
[hakon-Precision-3570:539868] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42990)[0x7d35cfc42990]
[hakon-Precision-3570:539868] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x11b)[0x7d35cfc99a1b]
[hakon-Precision-3570:539868] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7d35cfc428e6]
[hakon-Precision-3570:539868] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd7)[0x7d35cfc268b7]
[hakon-Precision-3570:539868] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x267db)[0x7d35cfc267db]
[hakon-Precision-3570:539868] [ 5] /lib/x86_64-linux-gnu/libc.so.6(+0x39206)[0x7d35cfc39206]
[hakon-Precision-3570:539868] [ 6] /home/hakon/test/opm15/opm-simulators/build/python/opm/simulators/simulators.cpython-311-x86_64-linux-gnu.so(+0x13dfab)[0x7d35ceb3dfab]
[hakon-Precision-3570:539868] [ 7] /home/hakon/test/opm15/opm-simulators/build/python/opm/simulators/simulators.cpython-311-x86_64-linux-gnu.so(+0x2a85c9)[0x7d35ceca85c9]
[hakon-Precision-3570:539868] [ 8] /home/hakon/test/opm15/opm-simulators/build/python/opm/simulators/simulators.cpython-311-x86_64-linux-gnu.so(+0xfeef6)[0x7d35ceafeef6]
[hakon-Precision-3570:539868] [ 9] /home/hakon/test/opm15/opm-simulators/build/python/opm/simulators/simulators.cpython-311-x86_64-linux-gnu.so(+0x122ecf)[0x7d35ceb22ecf]
[hakon-Precision-3570:539868] [10] /home/hakon/test/opm15/opm-simulators/build/python/opm/simulators/simulators.cpython-311-x86_64-linux-gnu.so(+0xe9cad)[0x7d35ceae9cad]
[hakon-Precision-3570:539868] [11] /usr/bin/python3[0x512776]
[hakon-Precision-3570:539868] [12] /usr/bin/python3(_PyObject_MakeTpCall+0x22b)[0x4e0bab]
[hakon-Precision-3570:539868] [13] /usr/bin/python3(_PyEval_EvalFrameDefault+0x88a)[0x4f627a]
[hakon-Precision-3570:539868] [14] /usr/bin/python3[0x54e402]
[hakon-Precision-3570:539868] [15] /usr/bin/python3[0x54db12]
[hakon-Precision-3570:539868] [16] /usr/bin/python3(_PyEval_EvalFrameDefault+0x4794)[0x4fa184]
[hakon-Precision-3570:539868] [17] /usr/bin/python3(_PyObject_FastCallDictTstate+0x217)[0x4e8ef7]
[hakon-Precision-3570:539868] [18] /usr/bin/python3(_PyObject_Call_Prepend+0x61)[0x52f3b1]
[hakon-Precision-3570:539868] [19] /usr/bin/python3[0x632f36]
[hakon-Precision-3570:539868] [20] /usr/bin/python3(_PyObject_MakeTpCall+0x22b)[0x4e0bab]
[hakon-Precision-3570:539868] [21] /usr/bin/python3(_PyEval_EvalFrameDefault+0x88a)[0x4f627a]
[hakon-Precision-3570:539868] [22] /usr/bin/python3[0x54e402]
[hakon-Precision-3570:539868] [23] /usr/bin/python3[0x54db12]
[hakon-Precision-3570:539868] [24] /usr/bin/python3(_PyEval_EvalFrameDefault+0x4794)[0x4fa184]
[hakon-Precision-3570:539868] [25] /usr/bin/python3(_PyObject_FastCallDictTstate+0x217)[0x4e8ef7]
[hakon-Precision-3570:539868] [26] /usr/bin/python3(_PyObject_Call_Prepend+0x61)[0x52f3b1]
[hakon-Precision-3570:539868] [27] /usr/bin/python3[0x632f36]
[hakon-Precision-3570:539868] [28] /usr/bin/python3(_PyObject_MakeTpCall+0x22b)[0x4e0bab]
[hakon-Precision-3570:539868] [29] /usr/bin/python3(_PyEval_EvalFrameDefault+0x88a)[0x4f627a]
[hakon-Precision-3570:539868] *** End of error message ***
Subprocess aborted
0% tests passed, 1 tests failed out of 1
Total Test time (real) = 3.81 sec
The following tests FAILED:
54 - python_basic (Failed)
Errors while running CTest
These tests works of course fine when not building shared libraries. Since the Jenkin build is not using shared libraries when testing the Python bindings, this issue could have been present for a long time.
Assertion `FluidSystem::phaseIsActive(waterPhaseIdx)' failed.
I suspect this is an issue with static variables in shared libraries (opmsimulators.so, opmcommon.so). More specifically the static variable phaseIsActive_ in class BlackOilFluidSystem , see line 38 in BlackOilFluidSystem.hpp in opm-common, seems to suddenly change address in GDB.
the static variable phaseIsActive_ in class BlackOilFluidSystem seems to suddenly change address in GDB.
It appears that static variable is undefined in libopmcommon.so:
$ nm -D lib/libopmcommon.so | grep phaseIsActive_ | c++filt
0000000002cd8681 u Opm::BlackOilFluidSystem<double, Opm::BlackOilDefaultIndexTraits>::phaseIsActive_
0000000002cd8685 u Opm::BlackOilFluidSystem<float, Opm::BlackOilDefaultIndexTraits>::phaseIsActive_
which might be the problem.
@blattms Could this issue be related to #5358 ?
I am not expert, but it seems to look different to me.
@blattms I think issue should be solved by https://github.com/OPM/opm-common/pull/4087