Yade

[Solved] Compilation failed on vtk8.2.0

Asked by Kan Su

Update: This was solved at #9, and the answer is summerized at #10. Below are the original posts.

--------------------------------

Sorry for my English first, it's not my mother language.
I'm trying to build yade-2021.01a from source for Archlinux (linux 5.10.7). I'm trying to complie it with most feature enabled.
But I found several problems:
1. I'm using CMake 3.19.3. When I use
```
cmake ../trunk \
        -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_LIBDIR=lib -DNOSUFFIX=ON -DPYTHON_VERSION=-1 \
        -DENABLE_SPH=ON -DENABLE_PROFILING=ON -DCHOLMOD_GPU=ON -DENABLE_LIQMIGRATION=ON -DENABLE_MASK_ARBITRARY=ON -DENABLE_DEFORM=ON -DVECTORIZE=ON -DENABLE_OAR=ON \
        -DENABLE_MPFR=ON -DENABLE_PARTIALSAT=ON\
        -DruntimePREFIX=/usr -DCHUNKSIZE=50 -DOpenGL_GL_PREFERENCE=GLVND\
        -DENABLE_USEFUL_ERRORS=ON -DENABLE_POTENTIAL_BLOCKS=ON
```
It said `OpenMP NOT found`. But I'm sure I have installed the openmp package. After searching it on google, I modified the `trunk/CMakeLists.txt`, added ` /usr/share/cmake-3.19//Modules/` to `CMAKE_MODULE_PATH`, then this problem was solved.

```
-- Found OpenMP_C: -fopenmp (found version "4.5")
CMake Warning (dev) at /usr/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:426 (message):
  The package name passed to `find_package_handle_standard_args` (OpenMP_CXX)
  does not match the name of the calling package (OpenMP). This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  /usr/lib/cmake/vtk-8.2/vtkm/FindOpenMP.cmake:485 (find_package_handle_standard_args)
  CMakeLists.txt:683 (FIND_PACKAGE)
This warning is for project developers. Use -Wno-dev to suppress it.

-- Could NOT find OpenMP_CXX (missing: OpenP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND) (found version "4.5")
-- OpenMP NOT found
```

2. Then I began to compile, everything went fine at first, I noticed that most features were enabled:
```
-- Yade configured with following features: BoostLog RealHP mpmath PrecisionDouble MPFR VECTORIZE Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV CHOLMOD_GPU MPI TWOPHASEFLOW SPH DEFORM FEMLIKE LIQMIGRATION GL2PS LBMFLOW MASK_ARBITRARY THERMAL PARTIALSAT PROFILING PotentialParticles PotentialBlocks
-- Disabled features:
-- Using MAX_LOG_LEVEL=5, ENABLE_LOGGER=ON
-- Optimized build
-- C++ standard version: 17
```

However, when the compiling process went to around 47%, an error occured.
```
/tmp/makepkg/yade/src/trunk/pkg/common/Gl1_PotentialBlock.cpp:694:31: error: no matching function for call to 'vtkUnsignedCharArray::InsertNextTuple(unsigned char [3])'
  694 | pbColors->INSERT_NEXT_TUPLE(c);
      | ^
In file included from /usr/include/vtk/vtkIntArray.h:33,
                 from /usr/include/vtk/vtkCellTypes.h:42,
                 from /usr/include/vtk/vtkPolyData.h:64,
                 from /tmp/makepkg/yade/src/trunk/pkg/common/Gl1_PotentialBlock.hpp:15,
                 from /tmp/makepkg/yade/src/trunk/pkg/common/Gl1_PotentialBlock.cpp:9,
                 from /tmp/makepkg/yade/src/build/pkg.0.cpp:9:
/usr/include/vtk/vtkAOSDataArrayTemplate.h:214:13: note: candidate: 'vtkIdType vtkAOSDataArrayTemplate<ValueTypeT>::InsertNextTuple(const float*) [with ValueTypeT = unsigned char; vtkIdType = long long int]'
  214 | vtkIdType InsertNextTuple(const float *tuple) override;
      | ^~~~~~~~~~~~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:214:42: note: no known conversion for argument 1 from 'unsigned char [3]' to 'const float*'
  214 | vtkIdType InsertNextTuple(const float *tuple) override;
      | ~~~~~~~~~~~~~^~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:215:13: note: candidate: 'vtkIdType vtkAOSDataArrayTemplate<ValueTypeT>::InsertNextTuple(const double*) [with ValueTypeT = unsigned char; vtkIdType = long long int]'
  215 | vtkIdType InsertNextTuple(const double *tuple) override;
      | ^~~~~~~~~~~~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:215:43: note: no known conversion for argument 1 from 'unsigned char [3]' to 'const double*'
  215 | vtkIdType InsertNextTuple(const double *tuple) override;
      | ~~~~~~~~~~~~~~^~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:218:13: note: candidate: 'vtkIdType vtkAOSDataArrayTemplate<ValueTypeT>::InsertNextTuple(vtkIdType, vtkAbstractArray*) [with ValueTypeT = unsigned char; vtkIdType = long long int]'
  218 | vtkIdType InsertNextTuple(vtkIdType srcTupleIdx,
      | ^~~~~~~~~~~~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:218:13: note: candidate expects 2 arguments, 1 provided
```
I guess it is because of vtk8.2.0, `InsertNextTuple` expects 2 arguments, but the line in `trunk/pkg/common/Gl1_PotentialBlock.cpp:694:31:` only provides 1 (and other lines use this function),
```
  694 | pbColors->INSERT_NEXT_TUPLE(c);
```
But I don't know how to fix it.
Do you have any suggestions?
Thanks a lot!

Attachments:
1. PKGBUILD used to create yade package：
https://pastebin.pl/view/2c9387dc
2. make log
https://pastebin.pl/view/763f67f8

Other information that maybe helpful:
```
gcc 10.2.0-4
vtk 8.2.0-17
cmake 3.19.3-1
linux 5.10.8.arch1-1
```

Question information

Language:
English Edit question
Status:
Solved
For:
Yade Edit question
Assignee:
No assignee Edit question
Solved by:
Janek Kozicki
Solved:
Last query:
Last reply:
Revision history for this message
Robert Caulk (rcaulk) said : 		#1

Hello,

You are turning too many things on unnecessarily. Please try to compile the default compilation first. Simply:

cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk

If it isnt working, uou can try disabling PotentialParticles (I sense you do not need these).

first navigate to the yade directory and clean the build folder out. Here is the safest way to do that:

rm -r build
mkdir build

then re run the cmake command including the deactivation of potentialparticles:

cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk -DENABLE_POTENTIAL_BLOCKS=OFF -DENABLE_POTENTIAL_PARTICLES=OFF

Cheers,

Robert

Revision history for this message
Kan Su (sukanka) said : 		#2

Thanks for your reply, Robert.
I tried the default compilation options, with (and without) add `/usr/share/cmake-3.19/Modules` to `CMAKE_MODULE_PATH`. But in vain.
Then, I tried to disable potentialparticles by
```
cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk -DENABLE_POTENTIAL_BLOCKS=OFF -DENABLE_POTENTIAL_PARTICLES=OFF
```
with and without the hack above. It also failed to compile.
And it stops at around 9%, different from previous error information.

```
[ 9%] Linking CXX shared library lib64/_gts.so
[ 9%] Built target _gts
```
the error lines are listed below and full log posted at https://pastebin.pl/view/3b12616a

```
In file included from /usr/include/boost/multiprecision/cpp_int/limits.hpp:11,
                 from /usr/include/boost/multiprecision/cpp_int.hpp:2284,
                 from /usr/include/boost/multiprecision/cpp_bin_float.hpp:9,
                 from /tmp/makepkg/yade/src/trunk/lib/high-precision/RealHP.hpp:46,
                 from /tmp/makepkg/yade/src/trunk/lib/high-precision/Real.hpp:215,
                 from /tmp/makepkg/yade/src/trunk/lib/base/Math.hpp:12,
                 from /tmp/makepkg/yade/src/trunk/py/pack/_packObb.cpp:6:
/usr/include/boost/multiprecision/traits/max_digits10.hpp: In instantiation of 'const unsigned int boost::multiprecision::detail::calc_digits10<151>::value':
/usr/include/boost/multiprecision/cpp_bin_float.hpp:1918:90: required from 'constexpr const int std::numeric_limits<boost::multiprecision::number<boost::multiprecision::backends::cpp_bin_float<45, boost::multiprecision::backends::digit_base_10, void, int, 0, 0>, boost::multiprecision::et_off> >::digits10'
/tmp/makepkg/yade/src/trunk/lib/high-precision/RealHPConfig.hpp:41:70: required from 'static int yade::math::DigitsHP10<N>::value() [with int N = 3]'
/tmp/makepkg/yade/src/trunk/lib/high-precision/RealHPConfig.hpp:70:97: required from 'static int yade::math::RealHPConfig::getDigits(int) [with dig = yade::math::DigitsHP10]'
/tmp/makepkg/yade/src/trunk/lib/high-precision/RealHPConfig.hpp:76:72: required from here
/usr/include/boost/multiprecision/traits/max_digits10.hpp:51:43: in 'constexpr' expansion of 'boost::multiprecision::detail::calc_digits10<151>::digits_10(151)'
/usr/include/boost/multiprecision/traits/max_digits10.hpp:49:96: error: '(3.010299956639812e-1 * 1.5e+2)' is not a constant expression
   49 | return static_cast<unsigned>(0.301029995663981195213738894724493026768189881462108541310 * (d - 1));
      | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
```

Revision history for this message
Bruno Chareyre (bruno-chareyre) said : 		#3

Hi,
The error refers to boost/multiple precision numbers. Probably a version issue.
If turning off more module is a solution for you, the next ones are RealHP mpmath MPFR (maybe also precisionsDouble? unsure).
Bruno

Revision history for this message
Kan Su (sukanka) said : 		#4

Thanks again, Bruno.
I don't know how to turn off RealHP mpmath precisionsDouble (I didn't find such options), but I did turn off MPFR, the error message is the same.

BTW, in prevoius error message, the error is about vtk, thus I turned off VTK. But I still failed to compile, because of other errors, such as redefinition and multiple definition:

```
In file included from /tmp/makepkg/yade/src/trunk/lib.0.cpp:10:
/tmp/makepkg/yade/src/trunk/core/main/pyboot.cpp:5:74: error: redefinition of 'boost::log::v2_mt_posix::sources::severity_logger<Logging::SeverityLevel> {anonymous}::logger'
    5 | CREATE_CPP_LOCAL_LOGGER("pyboot.cpp");
      | ^
In file included from /tmp/makepkg/yade/src/trunk/lib.0.cpp:9:
/tmp/makepkg/yade/src/trunk/lib/pyutil/gil.cpp:5:74: note: 'boost::log::v2_mt_posix::sources::severity_logger<Logging::SeverityLevel> {anonymous}::logger' previously declared here
    5 | CREATE_CPP_LOCAL_LOGGER("gil.cpp")
      |

```

```
In file included from /tmp/makepkg/yade/src/trunk/pkg/pfv/PeriodicFlowEngine.cpp:16,
                 from /tmp/makepkg/yade/src/trunk/pkg.2.cpp:26:
/tmp/makepkg/yade/src/trunk/pkg/pfv/FlowEngine_FlowEngine_PeriodicInfo.hpp:52:6: error: multiple definition of 'enum yade::UseFlowSolver'
   52 | enum /* class */ UseFlowSolver {
      | ^~~~~~~~~~~~~
In file included from /tmp/makepkg/yade/src/trunk/pkg/pfv/FlowEngine.cpp:11,
                 from /tmp/makepkg/yade/src/trunk/pkg.2.cpp:24:
/tmp/makepkg/yade/src/trunk/pkg/pfv/FlowEngine_FlowEngineT.hpp:52:6: note: previous definition here
   52 | enum /* class */ UseFlowSolver {
      | ^~~~~~~~~~~~~

```

And I noticed that there is a note saying that
```
/usr/include/boost/bind.hpp:41:273: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.'
   41 | )
      |

In file included from /usr/include/CGAL/boost/graph/copy_face_graph.h:37,
                 from /usr/include/CGAL/Surface_mesh/Surface_mesh.h:53,
                 from /usr/include/CGAL/Surface_mesh.h:27,
                 from /tmp/makepkg/yade/src/trunk/lib/base/AliasCGAL.hpp:23,
                 from /tmp/makepkg/yade/src/trunk/lib/triangulation/RegularTriangulation.h:11,
                 from /tmp/makepkg/yade/src/trunk/lib/triangulation/Tenseur3.h:3,
                 from /tmp/makepkg/yade/src/trunk/lib/triangulation/KinematicLocalisationAnalyser.hpp:15,
                 from /tmp/makepkg/yade/src/trunk/lib/triangulation/KinematicLocalisationAnalyser.cpp:13,
                 from /tmp/makepkg/yade/src/build/lib.0.cpp:12:
/usr/include/boost/function_output_iterator.hpp:14:110: note: '#pragma message: This header is deprecated. Use <boost/iterator/function_output_iterator.hpp> instead.'
   14 | BOOST_HEADER_DEPRECATED("<boost/iterator/function_output_iterator.hpp>")
      |
```
I guess the problem is with my boost library

boost 1.75.0-2

Full log is posted at https://pastebin.ubuntu.com/p/sfk7gXSCFt/

I think maybe I should wait now, thanks again for your patience and advice!

Revision history for this message
Robert Caulk (rcaulk) said : 		#5

>Full log is posted at https://pastebin.ubuntu.com/p/sfk7gXSCFt/

Although I understand why you did this, please try to avoid using external links in this forum. The goal is longevity and index-ability. Both of which are compromised when we use external links.

Revision history for this message
Janek Kozicki (cosurgi) said : 		#6

> -- CHUNKSIZE is set to 50

try without chunksize.

Revision history for this message
Best Janek Kozicki (cosurgi) said : 		#7

About disabling RealHP, I have added an option for you, can you please try this:

https://gitlab.com/yade-dev/trunk/-/merge_requests/602

 and tell us if it works?

Revision history for this message
Kan Su (sukanka) said : 		#8

To Janek,

> try without chunksize.

Thanks a lot, it works when VTK is turned off.

But when VTK is turn on (I'm using vtk 8.2.0), the no matching function error occured, maybe it will be fixed by the upstream in the future?

```
/tmp/makepkg/yade/src/trunk/pkg/common/Gl1_PotentialBlock.cpp:694:31: error: no matching function for call to 'vtkUnsignedCharArray::InsertNextTuple(unsigned char [3])'
  694 | pbColors->INSERT_NEXT_TUPLE(c);
      | ^
In file included from /usr/include/vtk/vtkIntArray.h:33,
                 from /usr/include/vtk/vtkCellTypes.h:42,
                 from /usr/include/vtk/vtkPolyData.h:64,
                 from /tmp/makepkg/yade/src/trunk/pkg/common/Gl1_PotentialBlock.hpp:15,
                 from /tmp/makepkg/yade/src/trunk/pkg/common/Gl1_PotentialBlock.cpp:9,
                 from /tmp/makepkg/yade/src/build/pkg.0.cpp:9:
/usr/include/vtk/vtkAOSDataArrayTemplate.h:214:13: note: candidate: 'vtkIdType vtkAOSDataArrayTemplate<ValueTypeT>::InsertNextTuple(const float*) [with ValueTypeT = unsigned char; vtkIdType = long long int]'
  214 | vtkIdType InsertNextTuple(const float *tuple) override;
      | ^~~~~~~~~~~~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:214:42: note: no known conversion for argument 1 from 'unsigned char [3]' to 'const float*'
  214 | vtkIdType InsertNextTuple(const float *tuple) override;
      | ~~~~~~~~~~~~~^~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:215:13: note: candidate: 'vtkIdType vtkAOSDataArrayTemplate<ValueTypeT>::InsertNextTuple(const double*) [with ValueTypeT = unsigned char; vtkIdType = long long int]'
  215 | vtkIdType InsertNextTuple(const double *tuple) override;
      | ^~~~~~~~~~~~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:215:43: note: no known conversion for argument 1 from 'unsigned char [3]' to 'const double*'
  215 | vtkIdType InsertNextTuple(const double *tuple) override;
      | ~~~~~~~~~~~~~~^~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:218:13: note: candidate: 'vtkIdType vtkAOSDataArrayTemplate<ValueTypeT>::InsertNextTuple(vtkIdType, vtkAbstractArray*) [with ValueTypeT = unsigned char; vtkIdType = long long int]'
  218 | vtkIdType InsertNextTuple(vtkIdType srcTupleIdx,
      | ^~~~~~~~~~~~~~~
/usr/include/vtk/vtkAOSDataArrayTemplate.h:218:13: note: candidate expects 2 arguments, 1 provided
```

To Robert,

    Thanks for pointing out this. I'm new here, not familiar with launchpad. I used these links just to make my post shorter, and get the codes highlighted. I also selected the save forever option on the pastebin site (so others can see it).

Well, I won't use external links in this forum in the future.

Revision history for this message
Janek Kozicki (cosurgi) said : 		#9

Try to change this line:

https://gitlab.com/yade-dev/trunk/-/blob/master/pkg/common/Gl1_PotentialBlock.cpp#L665

into

#if ((VTK_MAJOR_VERSION <= 8) and (VTK_MINOR_VERSION < 2)) or (VTK_MAJOR_VERSION <= 7)

Revision history for this message
Kan Su (sukanka) said : 		#10

> Try to change this line:
>
> https://gitlab.com/yade-dev/trunk/-/blob/master/pkg/common/Gl1_PotentialBlock.cpp#L665
>
> into

> #if ((VTK_MAJOR_VERSION <= 8) and (VTK_MINOR_VERSION < 2)) or (VTK_MAJOR_VERSION <= 7)

Cheers! It works! Now I can build yade-2021.01a successfully with all features enabled.

Now this question is ansered. Thanks again Janek.

Below are the hacks:

1. add system cmake module path to CMAKE_MODULE_PATH, this fixes openmp not found
https://gitlab.com/yade-dev/trunk/-/blob/master/CMakeLists.txt#L102

```
set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cMake")
+ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} /usr/share/cmake-3.19/Modules/)
+ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} /usr/share/cmake/Modules/)
```
2. Set CHUNKSIZE=1 (default option)
3. Change this line:
 https://gitlab.com/yade-dev/trunk/-/blob/master/pkg/common/Gl1_PotentialBlock.cpp#L665

```
- #if VTK_MAJOR_VERSION < 9
+ #if ((VTK_MAJOR_VERSION <= 8) and (VTK_MINOR_VERSION < 2)) or (VTK_MAJOR_VERSION <= 7)
```

Revision history for this message
Janek Kozicki (cosurgi) said : 		#11

can you post now what prints the command

  printAllVersions()

and does it pass checks and tests:

yade --test

yade --checkall

Thanks!

Revision history for this message
Kan Su (sukanka) said : 		#12

1. printAllVersions()

```
➜ ~ yade
Welcome to Yade 2021.01a
Using python version: 3.9.1 (default, Dec 13 2020, 11:55:53)
[GCC 10.2.0]
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
TCP python prompt on localhost:9000, auth cookie `eusdks'
XMLRPC info provider on http://localhost:21000
QSettings::value: Empty key passed
QSettings::value: Empty key passed
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
[[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h" in 3D view for help), F10 both, F9 generator, F8 plot. ]]

In [1]: printAllVersions()

```
Yade version : 2021.01a
Yade features : BoostLog RealHP mpmath PrecisionDouble MPFR VECTORIZE Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV CHOLMOD_GPU MPI TWOPHASEFLOW SPH DEFORM FEMLIKE LIQMIGRATION GL2PS LBMFLOW MASK_ARBITRARY THERMAL PARTIALSAT PROFILING PotentialParticles PotentialBlocks
Yade config dir: ~/.yade
Yade precision : 53 bits, 15 decimal places, with mpmath
Yade RealHP<…> : (15, 33, 45, 60, 120, 150, 300) decimal digits in C++, (15, 33) decimal digits accessible from python
```

Libraries used :

| library | cmake | C++ |
| ------------- | --------------------- | ------------------- |
| boost | 1.75.0 | 1.75.0 |
| cgal | | 4.14.3 |
| clp | 1.17.6 | 1.17.6 |
| cmake | 3.19.3 | |
| coinutils | 2.11.4 | 2.11.4 |
| compiler | /usr/bin/c++ 10.2.0 | gcc 10.2.0 |
| eigen | 3.3.9 | 3.3.9 |
| freeglut | 3.0.0 | |
| gl | | 20190805 |
| ipython | 7.19.0 | |
| metis | | 5.1.0 |
| mpfr | 4.1.0 | 4.1.0 |
| mpi | 3.1 | ompi:4.0.5 |
| mpi4py | 3.0.3 | |
| mpmath | 1.1.0 | |
| openblas | | OpenBLAS 0.3.13 |
| python | 3.9.1 | 3.9.1 |
| qglviewer | | 2.7.2 |
| qt | | 5.15.2 |
| sqlite | | 3.34.0 |
| suitesparse | 5.8.1 | 5.8.1 |
| vtk | 8.2.0 | 8.2.0 |

```
Linux version : Arch Linux
Architecture : unknown
Little endian : True
```

```
2. It doesn't pass all checks and tests

```
➜ ~ yade --test

Using python version: 3.9.1 (default, Dec 13 2020, 11:55:53)
[GCC 10.2.0]
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.

Using PrecisionDouble with 15 digits.

Using (15, 33) decimal digits in python. Importing mpmath

testDummySomething (yade.tests.dummyTest.TestDummy) ... ok
testDummySomethingElse (yade.tests.dummyTest.TestDummy) ... ok
testMatrix3 (yade.TestEigenWrapper)
Math: Matrix3 operations ... ok
testQuaternion (yade.TestEigenWrapper)
Math: Quaternion operations ... ok
testVector2 (yade.TestEigenWrapper)
Math: Vector2 operations ... ok
testVector3 (yade.TestEigenWrapper)
Math: Vector3 operations ... ok
testClassCtors (yade.TestObjectInstantiation)
Core: correct types are instantiated ... ok
testDispatcherCtor (yade.TestObjectInstantiation)
Core: dispatcher ctors with functors ... ok
testHidden (yade.TestObjectInstantiation)
Core: Attr::hidden ... ok
testInteractionLoopCtor (yade.TestObjectInstantiation)
Core: InteractionLoop special ctor ... ok
testInvalidAttr (yade.TestObjectInstantiation)
Core: invalid attribute access raises AttributeError ... ok
testNoSave (yade.TestObjectInstantiation)
Core: Attr::noSave ... ok
testParallelEngineCtor (yade.TestObjectInstantiation)
Core: ParallelEngine special ctor ... ok
testRootDerivedCtors_attrs_few (yade.TestObjectInstantiation)
Core: class ctor's attributes ... ok
testTriggerPostLoad (yade.TestObjectInstantiation)
Core: Attr::triggerPostLoad ... ok
testWrongFunctorType (yade.TestObjectInstantiation)
Core: dispatcher and functor type mismatch is detected ... ok
testErase (yade.TestBodies)
Bodies: erased bodies are None in python ... ok
testErasedAndNewlyCreatedSphere (yade.TestBodies)
Bodies: The bug is described in LP:1001194. If the new body was created after deletion of previous, it has no bounding box ... ok
testErasedIterate (yade.TestBodies)
Bodies: Iterator silently skips erased ones ... ok
testIterate (yade.TestBodies)
Bodies: Iteration ... ok
testLen (yade.TestBodies)
Bodies: len(O.bodies) ... ok
testNegativeIndex (yade.TestBodies)
Bodies: Negative index counts backwards (like python sequences). ... ok
testSaveAllClasses (yade.TestIO)
I/O: All classes can be saved and loaded with boost::serialization ... [asustx:310005] *** Process received signal ***
[asustx:310005] Signal: Segmentation fault (11)
[asustx:310005] Signal code: (128)
[asustx:310005] Failing at address: (nil)
[asustx:310005] [ 0] /usr/lib/libc.so.6(+0x3d6a0)[0x7f80582a46a0]
[asustx:310005] [ 1] /usr/lib/yade/libyade.so(_ZNK5boost7archive6detail19pointer_iserializerINS0_15binary_iarchiveEN4yade16GridCoGridCoGeomEE15load_object_ptrERNS1_14basic_iarchiveEPvj+0x251)[0x7f805514f7d1]
[asustx:310005] [ 2] /usr/lib/libboost_serialization.so.1.75.0(+0x17c36)[0x7f804ee8ec36]
[asustx:310005] [ 3] /usr/lib/yade/libyade.so(_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveENS_10shared_ptrIN4yade12SerializableEEEE16load_object_dataERNS1_14basic_iarchiveEPvj+0x6b)[0x7f8054d7a5eb]
[asustx:310005] [ 4] /usr/lib/libboost_serialization.so.1.75.0(_ZN5boost7archive6detail14basic_iarchive11load_objectEPvRKNS1_17basic_iserializerE+0x24e)[0x7f804ee8e45e]
[asustx:310005] [ 5] /usr/lib/yade/libyade.so(_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveESt6vectorINS_10shared_ptrIN4yade12SerializableEEESaIS8_EEE16load_object_dataERNS1_14basic_iarchiveEPvj+0xed)[0x7f8054d6a51d]
[asustx:310005] [ 6] /usr/lib/libboost_serialization.so.1.75.0(_ZN5boost7archive6detail14basic_iarchive11load_objectEPvRKNS1_17basic_iserializerE+0x24e)[0x7f804ee8e45e]
[asustx:310005] [ 7] /usr/lib/yade/libyade.so(_ZN4yade5Scene9serializeIN5boost7archive15binary_iarchiveEEEvRT_j+0x31a)[0x7f8054d795ca]
[asustx:310005] [ 8] /usr/lib/libboost_serialization.so.1.75.0(_ZN5boost7archive6detail14basic_iarchive11load_objectEPvRKNS1_17basic_iserializerE+0x2a2)[0x7f804ee8e4b2]
[asustx:310005] [ 9] /usr/lib/libboost_serialization.so.1.75.0(+0x17c36)[0x7f804ee8ec36]
[asustx:310005] [10] /usr/lib/yade/libyade.so(_ZNK5boost7archive6detail11iserializerINS0_15binary_iarchiveENS_10shared_ptrIN4yade5SceneEEEE16load_object_dataERNS1_14basic_iarchiveEPvj+0x83)[0x7f8054d5a933]
[asustx:310005] [11] /usr/lib/libboost_serialization.so.1.75.0(_ZN5boost7archive6detail14basic_iarchive11load_objectEPvRKNS1_17basic_iserializerE+0x24e)[0x7f804ee8e45e]
[asustx:310005] [12] /usr/lib/yade/libyade.so(_ZN4yade5Omega14loadSimulationERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb+0x4f4)[0x7f8054d38754]
[asustx:310005] [13] /usr/lib/yade/py/yade/wrapper.so(_ZN4yade7pyOmega7loadTmpENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb+0x61)[0x7f7fc9dcd5f1]
[asustx:310005] [14] /usr/lib/yade/py/yade/wrapper.so(_ZN5boost6python7objects23caller_py_function_implINS0_6detail6callerIMN4yade7pyOmegaEFvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbENS0_21default_call_policiesENS_3mpl7vector4IvRS6_SC_bEEEEEclEP7_objectSN_+0x133)[0x7f7fc9e87bf3]
[asustx:310005] [15] /usr/lib/libboost_python39.so.1.75.0(_ZNK5boost6python7objects8function4callEP7_objectS4_+0x2bb)[0x7f805299e11b]
[asustx:310005] [16] /usr/lib/libboost_python39.so.1.75.0(+0x203b9)[0x7f805299e3b9]
[asustx:310005] [17] /usr/lib/libboost_python39.so.1.75.0(_ZN5boost6python21handle_exception_implENS_9function0IvEE+0x73)[0x7f80529a33e3]
[asustx:310005] [18] /usr/lib/libboost_python39.so.1.75.0(+0x1da63)[0x7f805299ba63]
[asustx:310005] [19] /usr/lib/libpython3.9.so.1.0(_PyObject_MakeTpCall+0x30d)[0x7f805856271d]
[asustx:310005] [20] /usr/lib/libpython3.9.so.1.0(+0x14ab49)[0x7f805857ab49]
[asustx:310005] [21] /usr/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x1187)[0x7f805855a577]
[asustx:310005] [22] /usr/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0x1aa)[0x7f805856a26a]
[asustx:310005] [23] /usr/lib/libpython3.9.so.1.0(+0x14a8e4)[0x7f805857a8e4]
[asustx:310005] [24] /usr/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3c7)[0x7f80585597b7]
[asustx:310005] [25] /usr/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0x1aa)[0x7f805856a26a]
[asustx:310005] [26] /usr/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x601)[0x7f80585599f1]
[asustx:310005] [27] /usr/lib/libpython3.9.so.1.0(+0x12828d)[0x7f805855828d]
[asustx:310005] [28] /usr/lib/libpython3.9.so.1.0(_PyFunction_Vectorcall+0x34e)[0x7f805856a40e]
[asustx:310005] [29] /usr/lib/libpython3.9.so.1.0(+0x14aae4)[0x7f805857aae4]
[asustx:310005] *** End of error message ***
[1] 310005 segmentation fault (core dumped) yade --test
```
3. yade --checkall

```
➜ ~ yade --checkall
Welcome to Yade 2021.01a
Using python version: 3.9.1 (default, Dec 13 2020, 11:55:53)
[GCC 10.2.0]
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
###################################
running: checkViscElPM.py
Status: success, time spent on this check: 0:00:00.227513
___________________________________
###################################
running: checkPolyhedraCrush.py
CGAL version is (4, 14, 3) . Will test for (cgal version > 4.9) and (cgal version < 5.1.1)
<WARNING> PolyhedraSplitter:96 virtual void yade::PolyhedraSplitter::action(): be careful, the PolyhedraSplitter returns different results depending on CGAL version! This will not produce reproducible calculations. For details see https://gitlab.com/yade-dev/trunk/issues/45
Checkpoint: force values and number of bodies are OK! Iteration 166
Status: success, time spent on this check: 0:00:00.146425
___________________________________
###################################
running: checkMPI4PYcomm.py
Master: will spawn 1 workers running: /usr/bin/yade ['/usr/lib/yade/py/yade/tests/checks/checkMPI4PYcomm.py']
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Worker1: spawned!
____ MPI comm times: ____
1e4 integers in a python list: 0.0011192798614501954
1e4 integers in a python array: 0.00014102458953857422
Status: success, time spent on this check: 0:00:00.869561
___________________________________
###################################
running: checkAvoidSelfInteractionMask.py
testing collider.avoidSelfInteractionMask
0 bb br gg gr rr
1 bb br gr
2 br gg gr
3 br gr
Status: success, time spent on this check: 0:00:00.008245
___________________________________
###################################
running: checkPotentialVTKRecorders.py
checking file: /tmp/tmpdbau6n52/potentialVTKRecorders/ppcontactPoint.10.vtu
checking file: /tmp/tmpdbau6n52/potentialVTKRecorders/ppId.10.vtu
checking file: /tmp/tmpdbau6n52/potentialVTKRecorders/pp-pb.10.vtp
checking file: /tmp/tmpdbau6n52/potentialVTKRecorders/ppvel.10.vtu
non-matching lines: 0
checking file: /tmp/tmpdbau6n52/potentialVTKRecorders/pbcontactPoint.10.vtu
 checkPotentialVTKRecorders.py failure, caught exception FileNotFoundError : [Errno 2] No such file or directory: '/usr/lib/yade/py/yade/tests/checks/data/potentialVTKRecorders/ver8.2/pbcontactPoint.10.vtu'
###################################
running: checkViscElPM2.py
Status: success, time spent on this check: 0:00:00.202520
___________________________________
###################################
running: check_TwoPhaseFlowEngine_PressureInjection.py
/usr/lib/yade/py/yade/plot.py:463: MatplotlibDeprecationWarning:
The 'verts' parameter of scatter() was deprecated in Matplotlib 3.2 and will be removed two minor releases later. If any parameter follows 'verts', they should be passed as keyword, not positionally.
  scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,s=scatterSize,color=line.get_color(),**scatterMarkerKw)
File ./vtk moved into /tmp/tmp68m2j0jl/ directory
File ./Test.txt moved into /tmp/tmp68m2j0jl/ directory
Status: success, time spent on this check: 0:00:04.922176
___________________________________
###################################
running: checkVTKRecorder.py
checkVTKRecorder
checking file: /tmp/tmpqlokk94t/vtk_testing/10.vtm
checking file: /tmp/tmpqlokk94t/vtk_testing/10/10_0.vtu
checking file: /tmp/tmpqlokk94t/vtk_testing/10/10_2.vtp
non-matching lines: 114
Status: success, time spent on this check: 0:00:00.061631
___________________________________
###################################
running: checkTestDummy.py
checkTest mechanism
Status: success, time spent on this check: 0:00:00.001004
___________________________________
###################################
Skipping checkMPISilo.py, because it is in skipScripts.
###################################
running: checkLubrication.py
Status: success, time spent on this check: 0:00:01.726180
___________________________________
###################################
running: checkLubricationWithRoughness.py
Status: success, time spent on this check: 0:00:01.767818
___________________________________
###################################
running: checkMPYcomm.py
Master: will spawn 9 workers running: /usr/bin/yade ['/usr/lib/yade/py/yade/tests/checks/checkMPYcomm.py']
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<double, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
<frozen importlib._bootstrap>:228: RuntimeWarning: to-Python converter for Eigen::Matrix<boost::multiprecision::number<boost::multiprecision::backends::float128_backend, (boost::multiprecision::expression_template_option)0>, 3, 1, 0, 3, 1> already registered; second conversion method ignored.
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
[asustx:310193] *** Process received signal ***
[asustx:310193] Signal: Segmentation fault (11)
[asustx:310193] Signal code: (128)
[asustx:310193] Failing at address: (nil)
[asustx:310193] [ 0] /usr/lib/libc.so.6(+0x3d6a0)[0x7f9c06e306a0]
[asustx:310193] [ 1] /usr/lib/yade/py/yade/_customConverters.so(_ZN4yade20custom_Se3r_from_seq9constructEP7_objectPN5boost6python9converter30rvalue_from_python_stage1_dataE+0x514)[0x7f9bf01e1af4]
[asustx:310193] [ 2] /usr/lib/libboost_python39.so.1.75.0(_ZN5boost6python9converter25rvalue_from_python_stage2EP7_objectRNS1_30rvalue_from_python_stage1_dataERKNS1_12registrationE+0x35)[0x7f9c01521565]
[asustx:310193] [ 3] /usr/lib/yade/libyade.so(_ZN4yade5State9pySetAttrERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKN5boost6python3api6objectE+0x1a7)[0x7f9c0381abd7]
[asustx:310193] [ 4] /usr/lib/yade/libyade.so(_ZN4yade12Serializable13pyUpdateAttrsERKN5boost6python4dictE+0x790)[0x7f9c037eb970]
[asustx:310193] [ 5] /usr/lib/yade/libyade.so(_ZN5boost6python7objects23caller_py_function_implINS0_6detail6callerIMN4yade12SerializableEFvRKNS0_4dictEENS0_21default_call_policiesENS_3mpl7vector3IvRS6_S9_EEEEEclEP7_objectSK_+0x6b)[0x7f9c037ec80b]
[asustx:310193] [ 6] /usr/lib/libboost_python39.so.1.75.0(_ZNK5boost6python7objects8function4callEP7_objectS4_+0x2bb)[0x7f9c0152a11b]
[asustx:310193] [ 7] /usr/lib/libboost_python39.so.1.75.0(+0x203b9)[0x7f9c0152a3b9]
[asustx:310193] [ 8] /usr/lib/libboost_python39.so.1.75.0(_ZN5boost6python21handle_exception_implENS_9function0IvEE+0x73)[0x7f9c0152f3e3]
[asustx:310193] [ 9] /usr/lib/libboost_python39.so.1.75.0(+0x1da63)[0x7f9c01527a63]
[asustx:310193] [10] /usr/lib/libpython3.9.so.1.0(_PyObject_MakeTpCall+0x30d)[0x7f9c070ee71d]
[asustx:310193] [11] /usr/lib/libpython3.9.so.1.0(+0x14ab49)[0x7f9c07106b49]
[asustx:310193] [12] /usr/lib/python3.9/lib-dynload/_pickle.cpython-39-x86_64-linux-gnu.so(+0xb96e)[0x7f9bef90a96e]
[asustx:310193] [13] /usr/lib/python3.9/lib-dynload/_pickle.cpython-39-x86_64-linux-gnu.so(+0x16d3f)[0x7f9bef915d3f]
[asustx:310193] [14] /usr/lib/python3.9/lib-dynload/_pickle.cpython-39-x86_64-linux-gnu.so(+0x10c04)[0x7f9bef90fc04]
[asustx:310193] [15] /usr/lib/python3.9/lib-dynload/_pickle.cpython-39-x86_64-linux-gnu.so(+0xf42c)[0x7f9bef90e42c]
[asustx:310193] [16] /usr/lib/python3.9/site-packages/mpi4py/MPI.cpython-39-x86_64-linux-gnu.so(+0x7f7b4)[0x7f9beb0ac7b4]
[asustx:310193] [17] /usr/lib/python3.9/site-packages/mpi4py/MPI.cpython-39-x86_64-linux-gnu.so(+0xc91c7)[0x7f9beb0f61c7]
[asustx:310193] [18] /usr/lib/python3.9/site-packages/mpi4py/MPI.cpython-39-x86_64-linux-gnu.so(+0x1360a3)[0x7f9beb1630a3]
[asustx:310193] [19] /usr/lib/python3.9/site-packages/mpi4py/MPI.cpython-39-x86_64-linux-gnu.so(+0x137888)[0x7f9beb164888]
[asustx:310193] [20] /usr/lib/libpython3.9.so.1.0(+0x14c253)[0x7f9c07108253]
[asustx:310193] [21] /usr/lib/libpython3.9.so.1.0(_PyObject_MakeTpCall+0x30d)[0x7f9c070ee71d]
[asustx:310193] [22] /usr/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x51fe)[0x7f9c070ea5ee]
[asustx:310193] [23] /usr/lib/libpython3.9.so.1.0(+0x12828d)[0x7f9c070e428d]
[asustx:310193] [24] /usr/lib/libpython3.9.so.1.0(_PyEval_EvalCodeWithName+0x51)[0x7f9c070e3c51]
[asustx:310193] [25] /usr/lib/libpython3.9.so.1.0(PyEval_EvalCode+0x23)[0x7f9c071a5b13]
[asustx:310193] [26] /usr/lib/libpython3.9.so.1.0(+0x1f0edd)[0x7f9c071acedd]
[asustx:310193] [27] /usr/lib/libpython3.9.so.1.0(+0x13ac41)[0x7f9c070f6c41]
[asustx:310193] [28] /usr/lib/libpython3.9.so.1.0(_PyEval_EvalFrameDefault+0x3c7)[0x7f9c070e57b7]
[asustx:310193] [29] /usr/lib/libpython3.9.so.1.0(+0x12828d)[0x7f9c070e428d]
[asustx:310193] *** End of error message ***
[1] 310193 segmentation fault (core dumped) yade --checkall
```

Revision history for this message
Janek Kozicki (cosurgi) said : 		#13

> [asustx:310193] Signal: Segmentation fault (11)
> [asustx:310193] Signal code: (128)
> [asustx:310193] Failing at address: (nil)
> [asustx:310193] [ 0] /usr/lib/libc.so.6(+0x3d6a0)[0x7f9c06e306a0]

It could be a compiler bug in the memory alignment of variables. In this case VECTORIZE=OFF (not using SSE instructions) would solve this. This is the reason why SSE is not enabled by default. It is still experimental.

If this does not help then maybe cmake linked with a wrong version of some library. Maybe check if you get these crashes when ENABLE_OPENMP=OFF or ENABLE_MPI=OFF, because cmake had problems finding one of these.

> Warning: freeglut versions higher than 2.8.1 are known to crash

We still have no fix for that. When you open GUI and the 3D view of the scene, it will crash.

Revision history for this message
Kan Su (sukanka) said : 		#14

Thanks a lot!

I re-complied with VECTORIZE=OFF and ran all tests and checks again.
All tests passed, but one check failed.

```
checkPotentialVTKRecorders.py failure, caught exception FileNotFoundError : [Errno 2] No such file or directory: '/usr/lib/yade/py/yade/tests/checks/data/potentialVTKRecorders/ver8.2/pbcontactPoint.10.vtu'
```

I then wen to the directory. Not that there's no file named `pbcontactPoint.10.vtu` but only one named `ppcontactPoint.10.vtu`

```
➜ yade git:(master) ✗ cd /usr/lib/yade/py/yade/tests/checks/data/potentialVTKRecorders/ver8.2/
➜ ver8.2 ll
total 52K
-rw-r--r-- 1 root root 38K Jan 21 00:09 pp-pb.10.vtp
-rw-r--r-- 1 root root 1.4K Jan 21 00:09 ppId.10.vtu
-rw-r--r-- 1 root root 2.2K Jan 21 00:09 ppcontactPoint.10.vtu
-rw-r--r-- 1 root root 2.8K Jan 21 00:09 ppvel.10.vtu
```
------
Below are the output of printAllVersions, tests and checks

```
➜ yade git:(master) ✗ yade
Welcome to Yade 2021.01a
Using python version: 3.9.1 (default, Dec 13 2020, 11:55:53)
[GCC 10.2.0]
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
TCP python prompt on localhost:9000, auth cookie `esdcsk'
XMLRPC info provider on http://localhost:21000
QSettings::value: Empty key passed
QSettings::value: Empty key passed
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
[[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h" in 3D view for help), F10 both, F9 generator, F8 plot. ]]

In [1]: printAllVersions()

```
Yade version : 2021.01a
Yade features : BoostLog RealHP mpmath PrecisionDouble MPFR Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV CHOLMOD_GPU MPI TWOPHASEFLOW SPH DEFORM FEMLIKE LIQMIGRATION GL2PS LBMFLOW MASK_ARBITRARY THERMAL PARTIALSAT PROFILING PotentialParticles PotentialBlocks
Yade config dir: ~/.yade
Yade precision : 53 bits, 15 decimal places, with mpmath
Yade RealHP<…> : (15, 33, 45, 60, 120, 150, 300) decimal digits in C++, (15, 33) decimal digits accessible from python

```
Libraries used :

| library | cmake | C++ |
| ------------- | --------------------- | ------------------- |
| boost | 1.75.0 | 1.75.0 |
| cgal | | 4.14.3 |
| clp | 1.17.6 | 1.17.6 |
| cmake | 3.19.3 | |
| coinutils | 2.11.4 | 2.11.4 |
| compiler | /usr/bin/c++ 10.2.0 | gcc 10.2.0 |
| eigen | 3.3.9 | 3.3.9 |
| freeglut | 3.0.0 | |
| gl | | 20190805 |
| ipython | 7.19.0 | |
| metis | | 5.1.0 |
| mpfr | 4.1.0 | 4.1.0 |
| mpi | 3.1 | ompi:4.0.5 |
| mpi4py | 3.0.3 | |
| mpmath | 1.1.0 | |
| openblas | | OpenBLAS 0.3.13 |
| python | 3.9.1 | 3.9.1 |
| qglviewer | | 2.7.2 |
| qt | | 5.15.2 |
| sqlite | | 3.34.0 |
| suitesparse | 5.8.1 | 5.8.1 |
| vtk | 8.2.0 | 8.2.0 |

```
Linux version : Arch Linux
Architecture : unknown
Little endian : True
```
```

```
➜ yade git:(master) ✗ yade --test
Using python version: 3.9.1 (default, Dec 13 2020, 11:55:53)
[GCC 10.2.0]
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)

Using PrecisionDouble with 15 digits.

Using (15, 33) decimal digits in python. Importing mpmath

testDummySomething (yade.tests.dummyTest.TestDummy) ... ok
testDummySomethingElse (yade.tests.dummyTest.TestDummy) ... ok
testMatrix3 (yade.TestEigenWrapper)
Math: Matrix3 operations ... ok
testQuaternion (yade.TestEigenWrapper)
Math: Quaternion operations ... ok
testVector2 (yade.TestEigenWrapper)
Math: Vector2 operations ... ok
testVector3 (yade.TestEigenWrapper)
Math: Vector3 operations ... ok
testClassCtors (yade.TestObjectInstantiation)
Core: correct types are instantiated ... ok
testDispatcherCtor (yade.TestObjectInstantiation)
Core: dispatcher ctors with functors ... ok
testHidden (yade.TestObjectInstantiation)
Core: Attr::hidden ... ok
testInteractionLoopCtor (yade.TestObjectInstantiation)
Core: InteractionLoop special ctor ... ok
testInvalidAttr (yade.TestObjectInstantiation)
Core: invalid attribute access raises AttributeError ... ok
testNoSave (yade.TestObjectInstantiation)
Core: Attr::noSave ... ok
testParallelEngineCtor (yade.TestObjectInstantiation)
Core: ParallelEngine special ctor ... ok
testRootDerivedCtors_attrs_few (yade.TestObjectInstantiation)
Core: class ctor's attributes ... ok
testTriggerPostLoad (yade.TestObjectInstantiation)
Core: Attr::triggerPostLoad ... ok
testWrongFunctorType (yade.TestObjectInstantiation)
Core: dispatcher and functor type mismatch is detected ... ok
testErase (yade.TestBodies)
Bodies: erased bodies are None in python ... ok
testErasedAndNewlyCreatedSphere (yade.TestBodies)
Bodies: The bug is described in LP:1001194. If the new body was created after deletion of previous, it has no bounding box ... ok
testErasedIterate (yade.TestBodies)
Bodies: Iterator silently skips erased ones ... ok
testIterate (yade.TestBodies)
Bodies: Iteration ... ok
testLen (yade.TestBodies)
Bodies: len(O.bodies) ... ok
testNegativeIndex (yade.TestBodies)
Bodies: Negative index counts backwards (like python sequences). ... ok
testSaveAllClasses (yade.TestIO)
I/O: All classes can be saved and loaded with boost::serialization ... Entered the initialization functionWARNING: cannot open files used for capillary law, all forces will be null. Instructions on how to download and install them is found here : https://yade-dem.org/wiki/CapillaryTriaxialTest.
ok
testEraseBodiesInInteraction (yade.TestInteractions) ... ok
testDead (yade.TestLoop)
Loop: dead engines are not run ... ok
testEnginesModificationInsideLoop (yade.TestLoop)
Loop: O.engines can be modified inside the loop transparently. ... ok
testSubstepping (yade.TestLoop)
Loop: substepping ... ok
testMatchMakerCollisions (yade.TestMatchMaker) ... ok
testMaterialReturnsState (yade.TestMaterialStateAssociativity)
Material+State: CpmMat returns CpmState when asked for newAssocState ... ok
testThrowsAtBadCombination (yade.TestMaterialStateAssociativity)
Material+State: throws when body has material and state that don't work together. ... ok
testThrowsAtNullState (yade.TestMaterialStateAssociativity)
Material+State: throws when body has material but NULL state. ... ok
testAccess (yade.TestMaterials)
Material: find by index or label; KeyError raised for invalid label. ... ok
testIterate (yade.TestMaterials)
Material: iteration over O.materials ... ok
testLen (yade.TestMaterials)
Material: len(O.materials) ... ok
testNegativeIndex (yade.TestMaterials)
Material: negative index counts backwards. ... ok
testShared (yade.TestMaterials)
Material: shared_ptr's makes change in material immediate everywhere ... ok
testSharedAfterReload (yade.TestMaterials)
Material: shared_ptr's are preserved when saving/loading ... ok
testMissingFunction (yade.TestPyRunner) ... Entered the initialization functionTraceback (most recent call last):
  File "<string>", line 1, in <module>
NameError: name 'missingFunction' is not defined
<FATAL ERROR> ThreadRunner:35 void yade::ThreadRunner::run(): Exception occured:
PyRunner error.

COMMAND: 'missingFunction()'

ERROR:
name 'missingFunction' is not defined

STACK TRACE:
Traceback (most recent call last):

  File "<string>", line 1, in <module>

NameError: name 'missingFunction' is not defined
<ERROR> yadeWrapper.cpp:1066 void yade::pyOmega::wait(): Simulation error encountered.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
NameError: name 'missingFunction' is not defined
<FATAL ERROR> ThreadRunner:35 void yade::ThreadRunner::run(): Exception occured:
PyRunner error.

COMMAND: 'missingFunction()'

ERROR:
name 'missingFunction' is not defined

STACK TRACE:
Traceback (most recent call last):

  File "<string>", line 1, in <module>

NameError: name 'missingFunction' is not defined
<ERROR> yadeWrapper.cpp:1066 void yade::pyOmega::wait(): Simulation error encountered.
ok
testPythonToCppToPythonThrow (yade.TestPyRunner) ... No suitable packing in database found, running PERIODIC compression
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/yade/py/yade/pack.py", line 522, in randomDensePack
    O.switchScene(); O.resetThisScene() ### !!
RuntimeError: Please call O.stop() first.
<FATAL ERROR> ThreadRunner:35 void yade::ThreadRunner::run(): Exception occured:
PyRunner error.

COMMAND: 'from yade import pack;pred=pack.inHyperboloid(centerBottom=(0,0,-.1),centerTop=(0,0,.1),radius=.05,skirt=.03);pack.randomDensePack(pred,spheresInCell=100,radius=8e-2)'

ERROR:
Please call O.stop() first.

STACK TRACE:
Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/usr/lib/yade/py/yade/pack.py", line 522, in randomDensePack
    O.switchScene(); O.resetThisScene() ### !!

RuntimeError: Please call O.stop() first.
<ERROR> yadeWrapper.cpp:1066 void yade::pyOmega::wait(): Simulation error encountered.
No suitable packing in database found, running PERIODIC compression
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/yade/py/yade/pack.py", line 522, in randomDensePack
    O.switchScene(); O.resetThisScene() ### !!
RuntimeError: Please call O.stop() first.
<FATAL ERROR> ThreadRunner:35 void yade::ThreadRunner::run(): Exception occured:
PyRunner error.

COMMAND: 'from yade import pack;pred=pack.inHyperboloid(centerBottom=(0,0,-.1),centerTop=(0,0,.1),radius=.05,skirt=.03);pack.randomDensePack(pred,spheresInCell=100,radius=8e-2)'

ERROR:
Please call O.stop() first.

STACK TRACE:
Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/usr/lib/yade/py/yade/pack.py", line 522, in randomDensePack
    O.switchScene(); O.resetThisScene() ### !!

RuntimeError: Please call O.stop() first.
<ERROR> yadeWrapper.cpp:1066 void yade::pyOmega::wait(): Simulation error encountered.
ok
testRaisingFunction (yade.TestPyRunner) ... Traceback (most recent call last):
  File "<string>", line 1, in <module>
RuntimeError: raised RuntimeError
<FATAL ERROR> ThreadRunner:35 void yade::ThreadRunner::run(): Exception occured:
PyRunner error.

COMMAND: 'raise RuntimeError("raised RuntimeError")'

ERROR:
raised RuntimeError

STACK TRACE:
Traceback (most recent call last):

  File "<string>", line 1, in <module>

RuntimeError: raised RuntimeError
<ERROR> yadeWrapper.cpp:1066 void yade::pyOmega::wait(): Simulation error encountered.
Traceback (most recent call last):
  File "<string>", line 1, in <module>
RuntimeError: raised RuntimeError
<FATAL ERROR> ThreadRunner:35 void yade::ThreadRunner::run(): Exception occured:
PyRunner error.

COMMAND: 'raise RuntimeError("raised RuntimeError")'

ERROR:
raised RuntimeError

STACK TRACE:
Traceback (most recent call last):

  File "<string>", line 1, in <module>

RuntimeError: raised RuntimeError
<ERROR> yadeWrapper.cpp:1066 void yade::pyOmega::wait(): Simulation error encountered.
ok
testDegenerate (yade.TestPBC)
PBC: degenerate cell raises exception ... ok
testHomotheticResizeVel (yade.TestPBC)
PBC: homothetic cell deformation adjusts particle velocity ... ok
testKineticEnergy (yade.TestPBC)
PBC: utils.kineticEnergy considers only fluctuation velocity, not the velocity gradient ... ok
testL3GeomIncidentVelocity (yade.TestPBC)
PBC: L3Geom computes incident velocity correctly ... ok
testScGeomIncidentVelocity (yade.TestPBC)
PBC: ScGeom computes incident velocity correctly ... ok
testSetBox (yade.TestPBC)
PBC: setBox modifies hSize correctly ... ok
testTrsfChange (yade.TestPBC)
PBC: chaing trsf changes hSize0, but does not modify hSize ... ok
testVelGrad (yade.TestPBC)
PBC: velGrad changes hSize, accumulates in trsf ... ok
testConsistency (yade.TestSimpleClump)
Clump: ids and flags consistency ... ok
testStaticProperties (yade.TestSimpleClump)
Clump: mass, centroid, intertia ... ok
testVelocity (yade.TestSimpleClump)
Clump: velocities of member assigned by NewtonIntegrator ... ok
testMotion (yade.tests.cohesive-chain.TestCohesiveChain)
CohesiveChain: velocity/positions tested in transient dynamics and equilibrium state ... /usr/lib/yade/py/yade/gridpfacet.py:57: UserWarning: chainedCylinder is deprecated and will be removed in the future, use GridConnection instead. See examples/grids/CohesiveGridConnectionSphere.py.
  warnings.warn('\033[1;31mchainedCylinder is deprecated and will be removed in the future, use GridConnection instead. See examples/grids/CohesiveGridConnectionSphere.py.\033[1;0m',category=UserWarning)
ok
testKinematicEngines (yade.TestKinematicEngines)
Engines: kinematic engines ... ok
testLabels (yade.TestLabelsOfEngines) ... ok
testUserCreatedInteraction (yade.TestUtils) ... ok
testLibVersions (yade.tests.libVersions.TestLibVersions) ... cmake versions: {'cmake': [(3, 19, 3), '3.19.3'], 'compiler': [(10, 2, 0), '/usr/bin/c++ 10.2.0'], 'boost': [(1, 75, 0), '1.75.0'], 'freeglut': [(3, 0, 0), '3.0.0'], 'python': [(3, 9, 1), '3.9.1'], 'eigen': [(3, 3, 9), '3.3.9'], 'vtk': [(8, 2, 0), '8.2.0'], 'suitesparse': [(5, 8, 1), '5.8.1'], 'mpi': [(3, 1, 0), '3.1'], 'ipython': [(7, 19, 0), '7.19.0'], 'clp': [(1, 17, 6), '1.17.6'], 'coinutils': [(2, 11, 4), '2.11.4'], 'mpi4py': [(3, 0, 3), '3.0.3'], 'mpfr': [(4, 1, 0), '4.1.0'], 'mpmath': [(1, 1, 0), '1.1.0']}
C++ versions: {'compiler': [(10, 2, 0), 'gcc 10.2.0'], 'boost': [(1, 75, 0), '1.75.0'], 'qt': [(5, 15, 2), '5.15.2'], 'gl': [(2019, 8, 5), '20190805'], 'qglviewer': [(2, 7, 2), '2.7.2'], 'python': [(3, 9, 1), '3.9.1'], 'eigen': [(3, 3, 9), '3.3.9'], 'sqlite': [(3, 34, 0), '3.34.0'], 'vtk': [(8, 2, 0), '8.2.0'], 'cgal': [(4, 14, 3), '4.14.3'], 'suitesparse': [(5, 8, 1), '5.8.1'], 'openblas': [(0, 0, 0), ' OpenBLAS 0.3.13 '], 'metis': [(5, 1, 0), '5.1.0'], 'mpi': [(4, 0, 5), 'ompi:4.0.5'], 'clp': [(1, 17, 6), '1.17.6'], 'coinutils': [(2, 11, 4), '2.11.4'], 'mpfr': [(4, 1, 0), '4.1.0']}

Yade version : 2021.01a
Yade features : BoostLog RealHP mpmath PrecisionDouble MPFR Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV CHOLMOD_GPU MPI TWOPHASEFLOW SPH DEFORM FEMLIKE LIQMIGRATION GL2PS LBMFLOW MASK_ARBITRARY THERMAL PARTIALSAT PROFILING PotentialParticles PotentialBlocks
Yade config dir: ~/.yade
Yade precision : 53 bits, 15 decimal places, with mpmath
Yade RealHP<…> : (15, 33, 45, 60, 120, 150, 300) decimal digits in C++, (15, 33) decimal digits accessible from python

Libraries used :

+---------------+-----------------------+---------------------+
| library | cmake | C++ |
 +===============+=======================+=====================+
| boost | 1.75.0 | 1.75.0 |
 +---------------+-----------------------+---------------------+
| cgal | | 4.14.3 |
 +---------------+-----------------------+---------------------+
| clp | 1.17.6 | 1.17.6 |
 +---------------+-----------------------+---------------------+
| cmake | 3.19.3 | |
 +---------------+-----------------------+---------------------+
| coinutils | 2.11.4 | 2.11.4 |
 +---------------+-----------------------+---------------------+
| compiler | /usr/bin/c++ 10.2.0 | gcc 10.2.0 |
 +---------------+-----------------------+---------------------+
| eigen | 3.3.9 | 3.3.9 |
 +---------------+-----------------------+---------------------+
| freeglut | 3.0.0 | |
 +---------------+-----------------------+---------------------+
| gl | | 20190805 |
 +---------------+-----------------------+---------------------+
| ipython | 7.19.0 | |
 +---------------+-----------------------+---------------------+
| metis | | 5.1.0 |
 +---------------+-----------------------+---------------------+
| mpfr | 4.1.0 | 4.1.0 |
 +---------------+-----------------------+---------------------+
| mpi | 3.1 | ompi:4.0.5 |
 +---------------+-----------------------+---------------------+
| mpi4py | 3.0.3 | |
 +---------------+-----------------------+---------------------+
| mpmath | 1.1.0 | |
 +---------------+-----------------------+---------------------+
| openblas | | OpenBLAS 0.3.13 |
 +---------------+-----------------------+---------------------+
| python | 3.9.1 | 3.9.1 |
 +---------------+-----------------------+---------------------+
| qglviewer | | 2.7.2 |
 +---------------+-----------------------+---------------------+
| qt | | 5.15.2 |
 +---------------+-----------------------+---------------------+
| sqlite | | 3.34.0 |
 +---------------+-----------------------+---------------------+
| suitesparse | 5.8.1 | 5.8.1 |
 +---------------+-----------------------+---------------------+
| vtk | 8.2.0 | 8.2.0 |
 +---------------+-----------------------+---------------------+

Linux version : Arch Linux
Architecture : unknown
Little endian : True

```
Yade version : 2021.01a
Yade features : BoostLog RealHP mpmath PrecisionDouble MPFR Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV CHOLMOD_GPU MPI TWOPHASEFLOW SPH DEFORM FEMLIKE LIQMIGRATION GL2PS LBMFLOW MASK_ARBITRARY THERMAL PARTIALSAT PROFILING PotentialParticles PotentialBlocks
Yade config dir: ~/.yade
Yade precision : 53 bits, 15 decimal places, with mpmath
Yade RealHP<…> : (15, 33, 45, 60, 120, 150, 300) decimal digits in C++, (15, 33) decimal digits accessible from python
```

Libraries used :

| library | cmake | C++ |
| ------------- | --------------------- | ------------------- |
| boost | 1.75.0 | 1.75.0 |
| cgal | | 4.14.3 |
| clp | 1.17.6 | 1.17.6 |
| cmake | 3.19.3 | |
| coinutils | 2.11.4 | 2.11.4 |
| compiler | /usr/bin/c++ 10.2.0 | gcc 10.2.0 |
| eigen | 3.3.9 | 3.3.9 |
| freeglut | 3.0.0 | |
| gl | | 20190805 |
| ipython | 7.19.0 | |
| metis | | 5.1.0 |
| mpfr | 4.1.0 | 4.1.0 |
| mpi | 3.1 | ompi:4.0.5 |
| mpi4py | 3.0.3 | |
| mpmath | 1.1.0 | |
| openblas | | OpenBLAS 0.3.13 |
| python | 3.9.1 | 3.9.1 |
| qglviewer | | 2.7.2 |
| qt | | 5.15.2 |
| sqlite | | 3.34.0 |
| suitesparse | 5.8.1 | 5.8.1 |
| vtk | 8.2.0 | 8.2.0 |

```
Linux version : Arch Linux
Architecture : unknown
Little endian : True
```

compiler version reported by by cmake is [(10, 2, 0), '/usr/bin/c++ 10.2.0'] and by C++ is [(10, 2, 0), 'gcc 10.2.0']
boost version reported by by cmake is [(1, 75, 0), '1.75.0'] and by C++ is [(1, 75, 0), '1.75.0']
python version reported by by cmake is [(3, 9, 1), '3.9.1'] and by C++ is [(3, 9, 1), '3.9.1']
eigen version reported by by cmake is [(3, 3, 9), '3.3.9'] and by C++ is [(3, 3, 9), '3.3.9']
vtk version reported by by cmake is [(8, 2, 0), '8.2.0'] and by C++ is [(8, 2, 0), '8.2.0']
suitesparse version reported by by cmake is [(5, 8, 1), '5.8.1'] and by C++ is [(5, 8, 1), '5.8.1']
mpi version reported by by cmake is [(3, 1, 0), '3.1'] and by C++ is [(4, 0, 5), 'ompi:4.0.5']

 Warning: mpi versions are different, CMAKE: (3, 1, 0) vs. C++: (4, 0, 5)
 Something suspicious is going on. Can you help with file py/libVersions.py.in?
clp version reported by by cmake is [(1, 17, 6), '1.17.6'] and by C++ is [(1, 17, 6), '1.17.6']
coinutils version reported by by cmake is [(2, 11, 4), '2.11.4'] and by C++ is [(2, 11, 4), '2.11.4']
mpfr version reported by by cmake is [(4, 1, 0), '4.1.0'] and by C++ is [(4, 1, 0), '4.1.0']
ok
testMatrix3Test (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testMatrix3cTest (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testMpmath (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testQuaternion (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testVector2 (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testVector2c (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testVector2i (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testVector3 (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testVector3c (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testVector3i (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testVector3na (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testVector4 (yade.tests.testMinieigenHP.ExtendedMinieigenTests) ... RealHP<1> RealHP<2> ok
testArray (yade.tests.testMath.SimpleTests) ... <NOFILTER> :184 void yade::testArray() [with int N = 1]: sizeof RealHP<1> in bytes: 8
<NOFILTER> :187 void yade::testArray() [with int N = 1]: sizeof float in bytes: 4
<NOFILTER> :188 void yade::testArray() [with int N = 1]: sizeof double in bytes: 8
<NOFILTER> :189 void yade::testArray() [with int N = 1]: sizeof long double in bytes: 16
<NOFILTER> :204 void yade::testArray() [with int N = 1]: calling testLoopRealHP()
<NOFILTER> :165 void yade::testConstants() [with int N = 1]: Checking ConstantsHP<1>
<NOFILTER> :165 void yade::testConstants() [with int N = 2]: Checking ConstantsHP<2>
<NOFILTER> :165 void yade::testConstants() [with int N = 3]: Checking ConstantsHP<3>
<NOFILTER> :165 void yade::testConstants() [with int N = 4]: Checking ConstantsHP<4>
<NOFILTER> :165 void yade::testConstants() [with int N = 8]: Checking ConstantsHP<8>
<NOFILTER> :165 void yade::testConstants() [with int N = 10]: Checking ConstantsHP<10>
<NOFILTER> :165 void yade::testConstants() [with int N = 20]: Checking ConstantsHP<20>
<NOFILTER> :184 void yade::testArray() [with int N = 1]: sizeof RealHP<1> in bytes: 8
<NOFILTER> :187 void yade::testArray() [with int N = 1]: sizeof float in bytes: 4
<NOFILTER> :188 void yade::testArray() [with int N = 1]: sizeof double in bytes: 8
<NOFILTER> :189 void yade::testArray() [with int N = 1]: sizeof long double in bytes: 16
<NOFILTER> :204 void yade::testArray() [with int N = 1]: calling testLoopRealHP()
<NOFILTER> :165 void yade::testConstants() [with int N = 1]: Checking ConstantsHP<1>
<NOFILTER> :165 void yade::testConstants() [with int N = 2]: Checking ConstantsHP<2>
<NOFILTER> :165 void yade::testConstants() [with int N = 3]: Checking ConstantsHP<3>
<NOFILTER> :165 void yade::testConstants() [with int N = 4]: Checking ConstantsHP<4>
<NOFILTER> :165 void yade::testConstants() [with int N = 8]: Checking ConstantsHP<8>
<NOFILTER> :165 void yade::testConstants() [with int N = 10]: Checking ConstantsHP<10>
<NOFILTER> :165 void yade::testConstants() [with int N = 20]: Checking ConstantsHP<20>
<NOFILTER> :184 void yade::testArray() [with int N = 2]: sizeof RealHP<2> in bytes: 16
<NOFILTER> :187 void yade::testArray() [with int N = 2]: sizeof float in bytes: 4
<NOFILTER> :188 void yade::testArray() [with int N = 2]: sizeof double in bytes: 8
<NOFILTER> :189 void yade::testArray() [with int N = 2]: sizeof long double in bytes: 16
<NOFILTER> :204 void yade::testArray() [with int N = 2]: calling testLoopRealHP()
<NOFILTER> :165 void yade::testConstants() [with int N = 1]: Checking ConstantsHP<1>
<NOFILTER> :165 void yade::testConstants() [with int N = 2]: Checking ConstantsHP<2>
<NOFILTER> :165 void yade::testConstants() [with int N = 3]: Checking ConstantsHP<3>
<NOFILTER> :165 void yade::testConstants() [with int N = 4]: Checking ConstantsHP<4>
<NOFILTER> :165 void yade::testConstants() [with int N = 8]: Checking ConstantsHP<8>
<NOFILTER> :165 void yade::testConstants() [with int N = 10]: Checking ConstantsHP<10>
<NOFILTER> :165 void yade::testConstants() [with int N = 20]: Checking ConstantsHP<20>
ok
testBasicHP (yade.tests.testMath.SimpleTests) ... ok
testBasicVariable (yade.tests.testMath.SimpleTests) ... ok
testCgalNumTraits (yade.tests.testMath.SimpleTests) ... pow : 0.25
sqrt : 0.7071067811865476
ok
testConstants (yade.tests.testMath.SimpleTests) ... <NOFILTER> :165 void yade::testConstants() [with int N = 1]: Checking ConstantsHP<1>
<NOFILTER> :165 void yade::testConstants() [with int N = 1]: Checking ConstantsHP<1>
<NOFILTER> :165 void yade::testConstants() [with int N = 2]: Checking ConstantsHP<2>
ok
testEigenCost (yade.tests.testMath.SimpleTests) ... ok
testInfinityNaN (yade.tests.testMath.SimpleTests) ... ok
testMathFunctions (yade.tests.testMath.SimpleTests) ... pi : 3.141592653589793
HPn.Euler() 0.5772156649015329 N= 1 MPn.euler = 0.5772156649015329
euler : 0.5772156649015329
logE2 : 0.6931471805599453
catalan : 0.915965594177219
sin : -0.8508827905700432
sinh : 1.2375852132752518
cos : -0.5253555716957192
cosh : 1.5911056407786226
tan : 1.619632181350246
tanh : 0.7778146098895282
abs : 1.039814008884047
acos : 1.5309717918361057
acosh : 1.339645391459728
asin : 0.03982453495879099
asinh : 0.9092480099645157
atan : 0.8049141358764261
atanh : 0.039835066044110516
cbrt : 1.0130990032167873
exp : 2.8286908540538747
sqrt : 1.019712708994081
exp2 : 2.0559625831384816
expm1 : 1.8286908540538744
lgamma : -0.021702159657518143
tgamma : 0.9785316378514479
erf : 0.8585787762995714
erfc : 0.1414212237004287
log : 0.03904185954844715
log10 : 0.01695566416513238
log1p : 0.7128586315840377
log2 : 0.05632549715762812
fabs : 1.039814008884047
frexp : 1.039814008884047
modf : 0.03981400888404707
pow : 1.081213173071513
csin : (6692369.337101146-3930009.0296335747j)
csinh : (-0.8169687012653108+1.1951594055882355j)
ccos : (3930009.0296336077+6692369.33710109j)
ccosh : (-1.0503385908132323+0.9296124468134137j)
ctan : (7.249493367025581e-15-1.0000000000000042j)
ctanh : (1.0008835852378306-0.25203831341181937j)
cexp : (-1.8673072920785432+2.1247718524016492j)
clog : (2.8088232316175112-1.50807951393849j)
cabs : 16.590383688254317
cconj : (1.039814008884047+16.557766085750316j)
creal : 1.039814008884047
cimag : -16.557766085750316
atan2 : 3.0788758407333865
fmod : 1.039814008884047
hypot : 16.590383688254317
max : 1.039814008884047
min : -16.557766085750316
remainder : 1.039814008884047
remquo : 1.039814008884047
ldexp : 1.5866302625794175e-05
fma : -29.52844329201143
HPn.Euler() 0.5772156649015329 N= 1 MPn.euler = 0.5772156649015329
pi : mpf('3.141592653589793238462643383279502797009')
HPn.Euler() 0.5772156649015328606065120900824024707 N= 2 MPn.euler = 0.577215664901532860606512090082402431
euler : mpf('0.5772156649015328606065120900824024706956')
logE2 : mpf('0.6931471805599453094172321214581765750954')
catalan : mpf('0.9159655941772190150546035149323841463027')
sin : mpf('0.5939454352347722584758364842187861722952')
sinh : mpf('-2830113.967446815545741980638089905292991')
cos : mpf('0.8045053262494767054593228913359127227032')
cosh : mpf('2830113.967446992217072446901569774646025')
tan : mpf('0.7382740870140492662463517318247118333016')
tanh : mpf('-0.9999999999999375744819825625915617772977')
abs : mpf('15.54897472055115491177474842955113841994')
acos : mpf('1.102882562631078742167545175247180818996')
acosh : mpf('3.498557230924345475096702268663193727015')
asin : mpf('0.4679137641638178770637765163925706758994')
asinh : mpf('-3.438174320452728365288584338745338060001')
atan : mpf('-1.506571854628382350220648463026965353011')
atanh : mpf('0.4859866403626942628538798071894969263973')
cbrt : mpf('2.495938724418268720990481545584366623995')
exp : mpf('0.0000001766713304662634798696961141768913232989')
sqrt : mpf('3.943218827373286281055206295545402135001')
exp2 : mpf('0.00002085893867528485003506738873153632439002')
expm1 : mpf('-0.9999998233286695337365201303038857860957')
lgamma : mpf('2.38601650428447065887441904334050388899')
tgamma : mpf('10.87010656077751744729777653079459114004')
erf : mpf('-1.0')
erfc : mpf('2.0')
log : mpf('2.74399470208177638696569209446805775998')
log10 : mpf('1.191701757485872925255699941784427353009')
log1p : mpf('2.806324149484195596561572928804426086999')
log2 : mpf('3.958747548918967348004721982243115694008')
fabs : mpf('15.54897472055115491177474842955113841994')
frexp : mpf('15.54897472055115491177474842955113841994')
modf : mpf('0.5489747205511549117747484295511384164022')
pow : mpf('241.7706148603388659802825590676741261994')
csin : mpc(real='-20.07936152284160973536426710899389306982', imag='125.2245697020133858127526587831764151002')
csinh : mpc(real='-2076114.713999371085036983334428566118007', imag='1923354.559890954267499482042279865616005')
ccos : mpc(real='-125.2284623875950068766831609709474848005', imag='-20.07873736249021772619096037829728466995')
ccosh : mpc(real='2076114.713999500687573468377170961636012', imag='-1923354.559890834201094749649117170746008')
ctan : mpc(real='0.000009718353047234569192245095861353986671944', imag='-0.9999704735389008820084878628476715656008')
ctanh : mpc(real='-0.9999999999999952382481640100903083020952', imag='6.224364239983127743249952158874511993992e-14')
cexp : mpc(real='0.0000001296025364850427423956610154923648935008', imag='0.0000001200664047323931626952262945820117365991')
clog : mpc(real='2.803667924256229745622505088650632037995', imag='-2.79955247765494095200272092236937079901')
cabs : mpf('16.50507524565898714157008351225418265982')
cconj : mpc(real='-15.54897472055115491177474842955113841994', imag='5.535963692486269256326495323482200316989')
creal : mpf('-15.54897472055115491177474842955113841994')
cimag : mpf('-5.535963692486269256326495323482200316989')
atan2 : mpf('-1.912836502729748905691244152549883396997')
fmod : mpf('4.477047335578616399121757782586737782953')
hypot : mpf('16.50507524565898714157008351225418265982')
max : mpf('-5.535963692486269256326495323482200316989')
min : mpf('-15.54897472055115491177474842955113841994')
remainder : mpf('-1.058916356907652857204737540895464074992')
remquo : mpf('-1.058916356907652857204737540895464074992')
ldexp : mpf('-0.4859054600172235909929608884234730754997')
fma : mpf('89.14618013923121872709942416828755663933')
ok
testRealHPDiagnostics (yade.tests.testMath.SimpleTests) ... ok
testRealHPErrors (yade.tests.testMath.SimpleTests) ... Warning: ULP error of tgamma using RealHP< 1 >, 53 bits, with arg: [(mpf('-29.72876267005694117528946662787348031998'), mpf('0.0'), mpf('0.0'))] is ULP= 5.0
ok
testWrongInput (yade.tests.testMath.SimpleTests) ... ok
testAssignment (yade.tests.enumTest.TestEnum) ... ok
testException (yade.tests.enumTest.TestEnum) ...
  Here it must throw two exceptions:
<ERROR> ArbitraryEnum_from_python<yade::UseFlowSolver>:57 static bool yade::ArbitraryEnum_from_python<ArbitraryEnum>::setArbitraryEnum(const boost::python::api::object&, ArbitraryEnum&) [with ArbitraryEnum = yade::UseFlowSolver]: enum class yade::UseFlowSolver does not have key number: -100
<ERROR> ArbitraryEnum_from_python<yade::UseFlowSolver>:65 static bool yade::ArbitraryEnum_from_python<ArbitraryEnum>::setArbitraryEnum(const boost::python::api::object&, ArbitraryEnum&) [with ArbitraryEnum = yade::UseFlowSolver]: enum class yade::UseFlowSolver does not have key called: incorrect string
ok
SpherePack_toSimulation (yade.pack)
Doctest: yade.pack.SpherePack_toSimulation ... ok
addAutoData (yade.plot)
Doctest: yade.plot.addAutoData ... ok
addData (yade.plot)
Doctest: yade.plot.addData ... ok
plot (yade.plot)
Doctest: yade.plot.plot ... /usr/lib/yade/py/yade/plot.py:463: MatplotlibDeprecationWarning:
The 'verts' parameter of scatter() was deprecated in Matplotlib 3.2 and will be removed two minor releases later. If any parameter follows 'verts', they should be passed as keyword, not positionally.
  scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,s=scatterSize,color=line.get_color(),**scatterMarkerKw)
ok
saveDataTxt (yade.plot)
Doctest: yade.plot.saveDataTxt ... ok
SpherePWaveTimeStep (yade.utils)
Doctest: yade.utils.SpherePWaveTimeStep ... ok
saveVars (yade.utils)
Doctest: yade.utils.saveVars ... ok
sphere (yade.utils)
Doctest: yade.utils.sphere ... ok
typedEngine (yade.utils)
Doctest: yade.utils.typedEngine ... ok

----------------------------------------------------------------------
Ran 90 tests in 3.582s

OK
*** ALL TESTS PASSED ***
```

```
➜ yade git:(master) ✗ yade --checkall
Welcome to Yade 2021.01a
Using python version: 3.9.1 (default, Dec 13 2020, 11:55:53)
[GCC 10.2.0]
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
###################################
running: checkViscElPM.py
Status: success, time spent on this check: 0:00:00.215001
___________________________________
###################################
running: checkPolyhedraCrush.py
CGAL version is (4, 14, 3) . Will test for (cgal version > 4.9) and (cgal version < 5.1.1)
<WARNING> PolyhedraSplitter:96 virtual void yade::PolyhedraSplitter::action(): be careful, the PolyhedraSplitter returns different results depending on CGAL version! This will not produce reproducible calculations. For details see https://gitlab.com/yade-dev/trunk/issues/45
Checkpoint: force values and number of bodies are OK! Iteration 166
Status: success, time spent on this check: 0:00:00.106797
___________________________________
###################################
running: checkMPI4PYcomm.py
Master: will spawn 1 workers running: /usr/bin/yade ['/usr/lib/yade/py/yade/tests/checks/checkMPI4PYcomm.py']
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Worker1: spawned!
____ MPI comm times: ____
1e4 integers in a python list: 0.0009484767913818359
1e4 integers in a python array: 0.00018463134765625
Status: success, time spent on this check: 0:00:00.866693
___________________________________
###################################
running: checkAvoidSelfInteractionMask.py
testing collider.avoidSelfInteractionMask
0 bb br gg gr rr
1 bb br gr
2 br gg gr
3 br gr
Status: success, time spent on this check: 0:00:00.005688
___________________________________
###################################
running: checkPotentialVTKRecorders.py
checking file: /tmp/tmp9q6r6xii/potentialVTKRecorders/ppcontactPoint.10.vtu
checking file: /tmp/tmp9q6r6xii/potentialVTKRecorders/ppId.10.vtu
checking file: /tmp/tmp9q6r6xii/potentialVTKRecorders/pp-pb.10.vtp
checking file: /tmp/tmp9q6r6xii/potentialVTKRecorders/ppvel.10.vtu
non-matching lines: 0
checking file: /tmp/tmp9q6r6xii/potentialVTKRecorders/pbcontactPoint.10.vtu
 checkPotentialVTKRecorders.py failure, caught exception FileNotFoundError : [Errno 2] No such file or directory: '/usr/lib/yade/py/yade/tests/checks/data/potentialVTKRecorders/ver8.2/pbcontactPoint.10.vtu'
###################################
running: checkViscElPM2.py
Status: success, time spent on this check: 0:00:00.203857
___________________________________
###################################
running: check_TwoPhaseFlowEngine_PressureInjection.py
/usr/lib/yade/py/yade/plot.py:463: MatplotlibDeprecationWarning:
The 'verts' parameter of scatter() was deprecated in Matplotlib 3.2 and will be removed two minor releases later. If any parameter follows 'verts', they should be passed as keyword, not positionally.
  scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,s=scatterSize,color=line.get_color(),**scatterMarkerKw)
File ./vtk moved into /tmp/tmpi9ossa_6/ directory
File ./Test.txt moved into /tmp/tmpi9ossa_6/ directory
Status: success, time spent on this check: 0:00:04.910636
___________________________________
###################################
running: checkVTKRecorder.py
checkVTKRecorder
checking file: /tmp/tmpa4ydgbiq/vtk_testing/10.vtm
checking file: /tmp/tmpa4ydgbiq/vtk_testing/10/10_0.vtu
checking file: /tmp/tmpa4ydgbiq/vtk_testing/10/10_2.vtp
non-matching lines: 113
Status: success, time spent on this check: 0:00:00.063908
___________________________________
###################################
running: checkTestDummy.py
checkTest mechanism
Status: success, time spent on this check: 0:00:00.001409
___________________________________
###################################
Skipping checkMPISilo.py, because it is in skipScripts.
###################################
running: checkLubrication.py
Status: success, time spent on this check: 0:00:01.685401
___________________________________
###################################
running: checkLubricationWithRoughness.py
Status: success, time spent on this check: 0:00:01.686242
___________________________________
###################################
running: checkMPYcomm.py
Master: will spawn 9 workers running: /usr/bin/yade ['/usr/lib/yade/py/yade/tests/checks/checkMPYcomm.py']
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Master: will spawn 7 workers running: /usr/bin/yade ['/usr/lib/yade/py/yade/tests/checks/checkMPYcomm.py']
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Master: MPYcomm disconnect
Status: success, time spent on this check: 0:00:01.950208
___________________________________
###################################
Skipping checkList.py, because it is in skipScripts.
###################################
running: checkWirePM.py
Status: success, time spent on this check: 0:00:18.645350
___________________________________
###################################
running: checkDEM-PFVPressureInjection.py
File ./vtk moved into /tmp/tmpqnowg1j8/ directory
File ./Test.txt moved into /tmp/tmpqnowg1j8/ directory
Status: success, time spent on this check: 0:00:36.676841
___________________________________
###################################
running: checkColliderCorrectness.py
checkColliderCorrectness for InsertionSortCollider
Status: success, time spent on this check: 0:00:04.174030
___________________________________
###################################
running: checkSaveLoadClumps.py
Kinetic energy OK 1.170863E-09
Kinetic energy OK 1.115568E-01
Kinetic energy OK 1.115785E-01
Kinetic energy OK 1.137640E-01
Status: success, time spent on this check: 0:01:21.928790
___________________________________
###################################
running: DEM-PFV-check.py
DEM-PFV: difference in permeability: 0.044073804895852504 vs. target 0.040399916554
DEM-PFV: difference in final pressure: 612.681692169412 vs. target 628.314160434
DEM-PFV: difference in final deformation -0.002676702421817419 vs. target -0.00258113045083
Status: success, time spent on this check: 0:00:13.519529
___________________________________
###################################
running: checkLiquidMigration.py
Status: success, time spent on this check: 0:00:00.162969
___________________________________
###################################
running: checkMPI.py
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Status: success, time spent on this check: 0:00:03.574862
___________________________________
###################################
running: checkGravityRungeKuttaCashKarp54.py
checkGravityRungeKuttaCashKarp54.py : yade precision is 15 decimal places. Will use error tolerance of: 1e-12
Note: for high precision calculations use yade.math.toHP1(...) see this:
g = yade.math.toHP1(-9.81) ## produces: -9.81
g = -9.81 ## produces: -9.81
See https://yade-dem.org/doc/HighPrecisionReal.html#string-conversions for more info.
<WARNING> GravityEngine:24 virtual void yade::GravityEngine::action(): GravityEngine is deprecated, consider using Newton::gravity instead.
Status: success, time spent on this check: 0:00:00.082296
___________________________________
###################################
running: checkGravity.py
Status: success, time spent on this check: 0:00:03.292247
___________________________________
###################################
running: checkColliderConstantness.py
checkColliderConstantness for InsertionSortCollider
Status: success, time spent on this check: 0:00:00.386369
___________________________________
###################################
running: checkWeight.py
Precalculated weight 756.093387
Obtained weight 756.093387
Status: success, time spent on this check: 0:00:00.126300
___________________________________
###################################
running: checkTestTriax.py
File ./checkTest.yade moved into /tmp/tmpyfnvko82/ directory
File ./_Unloaded_380_3.spheres moved into /tmp/tmpyfnvko82/ directory
File ./_Unloaded_380_3.xml moved into /tmp/tmpyfnvko82/ directory
File ./WallStresses moved into /tmp/tmpyfnvko82/ directory
Status: success, time spent on this check: 0:00:00.210728
___________________________________
###################################
running: checkClumpHopper.py
Iter 10000: Total number of generated spheres 1448, removed particles 0, current particles 1448, kinEnergy 13755.3
Iter 20000: Total number of generated spheres 2896, removed particles 100, current particles 2796, kinEnergy 32685.4
Iter 30000: Total number of generated spheres 3620, removed particles 484, current particles 3136, kinEnergy 24374.8
Iter 40000: Total number of generated spheres 5068, removed particles 934, current particles 4134, kinEnergy 22952.1
Status: success, time spent on this check: 0:01:34.992983
___________________________________
###################################
running: checkBlockGen.py
Adding slavesThe Block Generation is completed
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:83: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  sumVertices = sum( len(b.shape.vertices) for b in O.bodies ) #38 vertices in total
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:90: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  a = sum(len(b.shape.a) for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:91: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  b = sum(len(b.shape.b) for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:92: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  c = sum(len(b.shape.c) for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:93: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  d = sum(len(b.shape.d) for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:103: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  sumVolume = sum( b.shape.volume for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:112: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  sumMass = sum (b.state.mass for b in O.bodies)
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:123: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  x = sum( b.state.pos[0]*b.shape.volume for b in O.bodies )/sumVolume
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:124: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  y = sum( b.state.pos[1]*b.shape.volume for b in O.bodies )/sumVolume
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:125: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  z = sum( b.state.pos[2]*b.shape.volume for b in O.bodies )/sumVolume
Status: success, time spent on this check: 0:00:00.021214
___________________________________
###################################
running: checkPotentialParticles.py
Status: success, time spent on this check: 0:00:00.043495
___________________________________
###################################
running: checkPotentialBlocks.py
Status: success, time spent on this check: 0:00:00.043978
___________________________________
###################################
running: checkCapillaryModels.py
Status: success, time spent on this check: 0:00:00.044838
___________________________________
###################################
running: checkViscElEng.py
Precalculated en value 0.736356797441
Obtained en value 0.736356797441
Status: success, time spent on this check: 0:00:00.364080
___________________________________
###################################
running: checkJCFpm.py
Status: success, time spent on this check: 0:00:06.870276
___________________________________
WARNING: some checks took longer than 30 seconds.
Most time spend on a single check: 0:01:34.992983
 1 tests are failed
  checkPotentialVTKRecorders.py
```

Revision history for this message
Janek Kozicki (cosurgi) said : 		#15

> potentialVTKRecorders/ver8.2/pbcontactPoint.10.vtu

does it work if you take similar file from ver9 ?

Revision history for this message
Janek Kozicki (cosurgi) said : 		#16

I mean potentialVTKRecorders/ver9/pbcontactPoint.10.vtu

Revision history for this message
Janek Kozicki (cosurgi) said : 		#17

In fact try to take all these files from potentialVTKRecorders/ver9/ and see :)

Revision history for this message
Kan Su (sukanka) said : 		#18

Thanks, It works!

After I copied all files from potentialVTKRecorders/ver9/ to potentialVTKRecorders/ver8.2/, all checks passed!

```
 yade --checkall
Welcome to Yade 2021.01a
Using python version: 3.9.1 (default, Dec 13 2020, 11:55:53)
[GCC 10.2.0]
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
###################################
running: checkViscElPM.py
Status: success, time spent on this check: 0:00:00.194854
___________________________________
###################################
running: checkPolyhedraCrush.py
CGAL version is (4, 14, 3) . Will test for (cgal version > 4.9) and (cgal version < 5.1.1)
<WARNING> PolyhedraSplitter:96 virtual void yade::PolyhedraSplitter::action(): be careful, the PolyhedraSplitter returns different results depending on CGAL version! This will not produce reproducible calculations. For details see https://gitlab.com/yade-dev/trunk/issues/45
Checkpoint: force values and number of bodies are OK! Iteration 166
Status: success, time spent on this check: 0:00:00.104968
___________________________________
###################################
running: checkMPI4PYcomm.py
Master: will spawn 1 workers running: /usr/bin/yade ['/usr/lib/yade/py/yade/tests/checks/checkMPI4PYcomm.py']
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Worker1: spawned!
____ MPI comm times: ____
1e4 integers in a python list: 0.0005977869033813477
1e4 integers in a python array: 6.968975067138672e-05
Status: success, time spent on this check: 0:00:00.874305
___________________________________
###################################
running: checkAvoidSelfInteractionMask.py
testing collider.avoidSelfInteractionMask
0 bb br gg gr rr
1 bb br gr
2 br gg gr
3 br gr
Status: success, time spent on this check: 0:00:00.004887
___________________________________
###################################
running: checkPotentialVTKRecorders.py
checking file: /tmp/tmpiu_jfshd/potentialVTKRecorders/ppcontactPoint.10.vtu
checking file: /tmp/tmpiu_jfshd/potentialVTKRecorders/ppId.10.vtu
checking file: /tmp/tmpiu_jfshd/potentialVTKRecorders/pp-pb.10.vtp
checking file: /tmp/tmpiu_jfshd/potentialVTKRecorders/ppvel.10.vtu
non-matching lines: 0
checking file: /tmp/tmpiu_jfshd/potentialVTKRecorders/pbcontactPoint.10.vtu
checking file: /tmp/tmpiu_jfshd/potentialVTKRecorders/pbId.10.vtu
checking file: /tmp/tmpiu_jfshd/potentialVTKRecorders/pb-pb.10.vtp
checking file: /tmp/tmpiu_jfshd/potentialVTKRecorders/pbvel.10.vtu
non-matching lines: 0
Status: success, time spent on this check: 0:00:00.087385
___________________________________
###################################
running: checkViscElPM2.py
Status: success, time spent on this check: 0:00:00.202185
___________________________________
###################################
running: check_TwoPhaseFlowEngine_PressureInjection.py
/usr/lib/yade/py/yade/plot.py:463: MatplotlibDeprecationWarning:
The 'verts' parameter of scatter() was deprecated in Matplotlib 3.2 and will be removed two minor releases later. If any parameter follows 'verts', they should be passed as keyword, not positionally.
  scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,s=scatterSize,color=line.get_color(),**scatterMarkerKw)
File ./vtk moved into /tmp/tmpftqt2gzj/ directory
File ./Test.txt moved into /tmp/tmpftqt2gzj/ directory
Status: success, time spent on this check: 0:00:04.746889
___________________________________
###################################
running: checkVTKRecorder.py
checkVTKRecorder
checking file: /tmp/tmpf1dlsg0k/vtk_testing/10.vtm
checking file: /tmp/tmpf1dlsg0k/vtk_testing/10/10_0.vtu
checking file: /tmp/tmpf1dlsg0k/vtk_testing/10/10_2.vtp
non-matching lines: 113
Status: success, time spent on this check: 0:00:00.062857
___________________________________
###################################
running: checkTestDummy.py
checkTest mechanism
Status: success, time spent on this check: 0:00:00.001540
___________________________________
###################################
Skipping checkMPISilo.py, because it is in skipScripts.
###################################
running: checkLubrication.py
Status: success, time spent on this check: 0:00:01.686369
___________________________________
###################################
running: checkLubricationWithRoughness.py
Status: success, time spent on this check: 0:00:01.726809
___________________________________
###################################
running: checkMPYcomm.py
Master: will spawn 9 workers running: /usr/bin/yade ['/usr/lib/yade/py/yade/tests/checks/checkMPYcomm.py']
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Master: will spawn 7 workers running: /usr/bin/yade ['/usr/lib/yade/py/yade/tests/checks/checkMPYcomm.py']
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Master: MPYcomm disconnect
Status: success, time spent on this check: 0:00:01.828741
___________________________________
###################################
Skipping checkList.py, because it is in skipScripts.
###################################
running: checkWirePM.py
Status: success, time spent on this check: 0:00:19.050272
___________________________________
###################################
running: checkDEM-PFVPressureInjection.py
File ./vtk moved into /tmp/tmpb1nhiz36/ directory
File ./Test.txt moved into /tmp/tmpb1nhiz36/ directory
Status: success, time spent on this check: 0:00:36.501007
___________________________________
###################################
running: checkColliderCorrectness.py
checkColliderCorrectness for InsertionSortCollider
Status: success, time spent on this check: 0:00:04.306394
___________________________________
###################################
running: checkSaveLoadClumps.py
Kinetic energy OK 1.164931E-09
Kinetic energy OK 1.151232E-01
Kinetic energy OK 1.151462E-01
Kinetic energy OK 1.174632E-01
Status: success, time spent on this check: 0:01:30.646536
___________________________________
###################################
running: DEM-PFV-check.py
DEM-PFV: difference in permeability: 0.044073804895852504 vs. target 0.040399916554
DEM-PFV: difference in final pressure: 612.681692169412 vs. target 628.314160434
DEM-PFV: difference in final deformation -0.002676702421817419 vs. target -0.00258113045083
Status: success, time spent on this check: 0:00:14.210633
___________________________________
###################################
running: checkLiquidMigration.py
Status: success, time spent on this check: 0:00:00.164997
___________________________________
###################################
running: checkMPI.py
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
/usr/lib/yade/py/yade/__init__.py:76: RuntimeWarning: to-Python converter for boost::shared_ptr<yade::PartialSatClayEngine> already registered; second conversion method ignored.
  boot.initialize(plugins,config.confDir)
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Warning: freeglut versions higher than 2.8.1 are known to crash, see https://gitlab.com/yade-dev/trunk/merge_requests/160 https://gitlab.com/yade-dev/trunk/-/issues/155 https://gitlab.com/yade-dev/trunk/-/issues/107
Status: success, time spent on this check: 0:00:03.764539
___________________________________
###################################
running: checkGravityRungeKuttaCashKarp54.py
checkGravityRungeKuttaCashKarp54.py : yade precision is 15 decimal places. Will use error tolerance of: 1e-12
Note: for high precision calculations use yade.math.toHP1(...) see this:
g = yade.math.toHP1(-9.81) ## produces: -9.81
g = -9.81 ## produces: -9.81
See https://yade-dem.org/doc/HighPrecisionReal.html#string-conversions for more info.
<WARNING> GravityEngine:24 virtual void yade::GravityEngine::action(): GravityEngine is deprecated, consider using Newton::gravity instead.
Status: success, time spent on this check: 0:00:00.082308
___________________________________
###################################
running: checkGravity.py
Status: success, time spent on this check: 0:00:03.329603
___________________________________
###################################
running: checkColliderConstantness.py
checkColliderConstantness for InsertionSortCollider
Status: success, time spent on this check: 0:00:00.390193
___________________________________
###################################
running: checkWeight.py
Precalculated weight 756.093387
Obtained weight 756.093387
Status: success, time spent on this check: 0:00:00.125942
___________________________________
###################################
running: checkTestTriax.py
File ./checkTest.yade moved into /tmp/tmphgrhjn5n/ directory
File ./_Unloaded_380_3.spheres moved into /tmp/tmphgrhjn5n/ directory
File ./_Unloaded_380_3.xml moved into /tmp/tmphgrhjn5n/ directory
File ./WallStresses moved into /tmp/tmphgrhjn5n/ directory
Status: success, time spent on this check: 0:00:00.212926
___________________________________
###################################
running: checkClumpHopper.py
Iter 10000: Total number of generated spheres 1448, removed particles 0, current particles 1448, kinEnergy 13755.3
Iter 20000: Total number of generated spheres 2896, removed particles 100, current particles 2796, kinEnergy 32685.4
Iter 30000: Total number of generated spheres 3620, removed particles 484, current particles 3136, kinEnergy 24374.8
Iter 40000: Total number of generated spheres 5068, removed particles 934, current particles 4134, kinEnergy 22952.1
Status: success, time spent on this check: 0:01:29.283312
___________________________________
###################################
running: checkBlockGen.py
Adding slavesThe Block Generation is completed
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:83: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  sumVertices = sum( len(b.shape.vertices) for b in O.bodies ) #38 vertices in total
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:90: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  a = sum(len(b.shape.a) for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:91: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  b = sum(len(b.shape.b) for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:92: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  c = sum(len(b.shape.c) for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:93: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  d = sum(len(b.shape.d) for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:103: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  sumVolume = sum( b.shape.volume for b in O.bodies )
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:112: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  sumMass = sum (b.state.mass for b in O.bodies)
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:123: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  x = sum( b.state.pos[0]*b.shape.volume for b in O.bodies )/sumVolume
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:124: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  y = sum( b.state.pos[1]*b.shape.volume for b in O.bodies )/sumVolume
/usr/lib/yade/py/yade/tests/checks/checkBlockGen.py:125: DeprecationWarning: Calling np.sum(generator) is deprecated, and in the future will give a different result. Use np.sum(np.fromiter(generator)) or the python sum builtin instead.
  z = sum( b.state.pos[2]*b.shape.volume for b in O.bodies )/sumVolume
Status: success, time spent on this check: 0:00:00.042930
___________________________________
###################################
running: checkPotentialParticles.py
Status: success, time spent on this check: 0:00:00.044981
___________________________________
###################################
running: checkPotentialBlocks.py
Status: success, time spent on this check: 0:00:00.043517
___________________________________
###################################
running: checkCapillaryModels.py
Status: success, time spent on this check: 0:00:00.042101
___________________________________
###################################
running: checkViscElEng.py
Precalculated en value 0.736356797441
Obtained en value 0.736356797441
Status: success, time spent on this check: 0:00:00.403344
___________________________________
###################################
running: checkJCFpm.py
Status: success, time spent on this check: 0:00:06.237038
___________________________________
WARNING: some checks took longer than 30 seconds.
Most time spend on a single check: 0:01:30.646536
*** ALL CHECKS PASSED ***
```

Revision history for this message
Janek Kozicki (cosurgi) said : 		#19

Yade features : ... MPFR ...

| boost | 1.75.0 | 1.75.0 |
| mpfr | 4.1.0 | 4.1.0 |

> I did turn off MPFR, the error message is the same.

Did you do anything specific to workaround this compilation error:

/usr/include/boost/multiprecision/traits/max_digits10.hpp:51:43: in 'constexpr' expansion of 'boost::multiprecision::detail::calc_digits10<151>::digits_10(151)'
/usr/include/boost/multiprecision/traits/max_digits10.hpp:49:96: error: '(3.010299956639812e-1 * 1.5e+2)' is not a constant expression

This error looked like a problem with mpfr wrapper in boost, specifically in file max_digits10.hpp, but then somehow you managed to compile with MPFR ?

Revision history for this message
Janek Kozicki (cosurgi) said : 		#20

> After I copied all files from potentialVTKRecorders/ver9/ to potentialVTKRecorders/ver8.2/, all checks passed!

this is good news. We will use ver9 files for testing ver8.2

Revision history for this message
Kan Su (sukanka) said : 		#21

> > I did turn off MPFR, the error message is the same.

> Did you do anything specific to workaround this compilation error:

> This error looked like a problem with mpfr wrapper in boost, specifically in file max_digits10.hpp, but then somehow you managed to compile with MPFR ?

No. But after I followed you suggestion at #9, setting CHUNKSIZE=1 , this error disappeared.

> this is good news. We will use ver9 files for testing ver8.2

I added a hack in the PKGBUILD to use ver9 files for testing ver8.2.

BTW, I noticed that vtk8.2.0 is flagged out-of-date in arch community repo,
https://archlinux.org/packages/community/x86_64/vtk/
may be it will be updated to vtk9.0 soon.

May I mark your post at #7 as the solution? Actually I think #9 solved my problem, but I can't mark it as a solution.

Revision history for this message
Janek Kozicki (cosurgi) said : 		#22

>> Did you do anything specific to workaround this [MPFR] compilation error
> No. But after I followed you suggestion at #9, setting CHUNKSIZE=1 , this error disappeared.

Thanks for the answer, this means that we have more CHUNKSIZE related bugs.

> May I mark your post at #7 as the solution?

sure no problem :)

If you feel adventurous, maybe you would like to try building higher precision versions of yade: long double, float128, maybe even MPFR150 ?

http://yade-dem.org/doc/HighPrecisionReal.html

you only need to pass this cmake parameter for each of the builds:

REAL_DECIMAL_PLACES=18
REAL_DECIMAL_PLACES=33
REAL_DECIMAL_PLACES=150

each of these builds generate a different yade binary with different default precision of calculations.
You might want to use cmake SUFFIX=.. parameter to generate yade binaries (and .so files) with corresponding different names.

long double calculations are 1.4 times slower, float128 are 4.9 times slower, mpfr150 are 19.8 times slower.

Revision history for this message
Janek Kozicki (cosurgi) said : 		#23

> You might want to use cmake SUFFIX=

or runtimePREFIX

Revision history for this message
Kan Su (sukanka) said : 		#24

Thanks Janek Kozicki, that solved my question.