error in running an example. showing 3D error

Asked by ehsan benabbas on 2019-08-01

Hello
I have installed yade-2019-07-08.git-e27605e , the source code version, and using ubunu 18.04 on a virtual machine software called VMWare. my host OS for VMWare is Windows 10 and my linux (Ubuntu 18.04) has been install on VMWare.
I try to run an example when I go to the directory of the .py file by the following command:

/home/ehsan/myYade/install/bin/yade-2019-07-08.git-e27605e filename.py

The problem is when I click on "Show 3D" on the Yade window, all windows will be closed and I get the following error:

In [1]: The constructor with a shareWidget is deprecated, use the regular contructor instead.
Segmentation fault (core dumped)

Thus, I cannot see the 3D result of the code.
Do you know what's my problem?
Thanks

Question information

Language:
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Status:
Answered
For:
Yade Edit question
Assignee:
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Last query:
2019-08-12
Last reply:
2019-08-12
Jan Stránský (honzik) said : #1

> Thus, I cannot see the 3D result of the code.

you can see the 3D results in an external program, like Paraview

> Do you know what's my problem?

please provide the commands you used for compilation and the output of cmake command (for the beginning :-)

cheers
Jan

ehsan benabbas (ehsanben) said : #2

Thanks Jan

The Yade window I mentioned is a window that will be open after running any code, in this window we have a option which is "show 3D" . If Paraview is another software or package which shows the result of my code, could you please provide me more information about that?

I installed the whole code successfully. Compilation and cmake commands belong to installation processthat I have done it already, so I cannot show you that in this stage. But, I'm sure I installed the source code correctly and have done it by using wiki installation.

To be more specific, I don't have any problem to run my codes, the only problem I have is after running a code, when I select the "show 3D" bottom, all windows are closed.

Jan Stránský (honzik) said : #3

Instant replay: please provide the commands you used for compilation and the output of cmake command
Even if you did everything correctly, it is needed to give you a meaningful answer.. help us to help you :-)

> If Paraview is another software or package which shows the result of my code, could you please provide me more information about that?

[1]

cheers
Jan

[1] https://yade-dem.org/doc/user.html#id3

ehsan benabbas (ehsanben) said : #4

thank you for your replies Jan

Ok. here it is:

cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk
 which for me was like this:
cmake -DCMAKE_INSTALL_PREFIX=/home/ehsan/myYade/install /home/ehsan/trunk
This is the command I used for compilation when I was in the directory : /home/ehsan/myYade/build
and I didn't get any error. do you mean I use this command again and copy here the output? if yes, doesn't it make any problem for my current yade?

Sorry, I don't know what you mean by output of cmake, do you mean I just tyoe cmake in terminal and copy here the output or you mean another task?

please be more specific for providing information, because I'm just new with both linux and yade.

Thanks again,
Ehsan

Jan Stránský (honzik) said : #5

> output of cmake, do you mean I just tyoe cmake in terminal and copy here the output

yes. But it should be a fresh run, i.e. from clean directory.
So just create a directory, e.g. yade-cmake-test, run:
###
cd yade-cmake-test
make -DCMAKE_INSTALL_PREFIX=/home/ehsan/myYade/install /home/ehsan/trunk
###
in terminal and copy here the output.
You can then delete the yade-cmake-test directory

cheers
Jan

ehsan benabbas (ehsanben) said : #6

Thank you. Ok, I did what you said and here it is the output:

ehsan@ehsan:~$ cd ~/yade-cmake-test
ehsan@ehsan:~/yade-cmake-test$ cmake -DCMAKE_INSTALL_PREFIX=/home/ehsan/myYade/install /home/ehsan/trunk
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Version is set to 2019-07-08.git-e27605e
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
Loop on the following python versions and check available dependencies:3.8;3.7;3.6;3.5;3.4;3.3;3.2;3.1;3.0;2.7;2.6
-- Found PythonInterp: /usr/bin/python (found version "2.7.15")
-- Found PythonInterp: /usr/local/bin/python3.7 (found version "3.7.4")
Python version 3.7.4 found, try to import dependencies...
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python-py37; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:62 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python3-py37; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:62 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)

CMake Warning (dev) at /usr/share/cmake-3.10/Modules/FindBoost.cmake:911 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted. Run "cmake --help-policy CMP0054" for policy
  details. Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "chrono" will no longer be dereferenced when the
  policy is set to NEW. Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
  cMake/YadePythonHelpers.cmake:68 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)
This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python-py3; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:68 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)

Failed to import dependencies for Python version 3.7.4. NOT FOUND:libboost-python
-- Found PythonInterp: /usr/bin/python3.6 (found version "3.6.8")
Python version 3.6.8 found, try to import dependencies...
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python-py36; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:62 (FIND_PACKAGE)
  CMakeLists.txt:179 (FIND_PYTHON_PACKAGES)

-- Found NumPy: version "1.17.0" /home/ehsan/.local/lib/python3.6/site-packages/numpy/core/include
-- Found IPython: /usr/local/lib/python3.6/dist-packages/IPython
-- Found matplotlib: /usr/local/lib/python3.6/dist-packages/matplotlib
-- Found pygraphviz: /usr/lib/python3/dist-packages/pygraphviz
-- Found Xlib: /usr/lib/python3/dist-packages/Xlib
-- Found minieigen: /usr/lib/python3/dist-packages/minieigen.cpython-36m-x86_64-linux-gnu.so
-- Found future: /usr/lib/python3/dist-packages/future
-- Found past: /usr/lib/python3/dist-packages/past
-- Found tkinter: /usr/lib/python3.6/tkinter
-- Boost_VERSION: 106501
-- Boost_LIB_VERSION: 1_65_1
-- Boost_INCLUDE_DIRS: /usr/include
-- Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python-py36.so/usr/lib/x86_64-linux-gnu/libboost_thread.so/usr/lib/x86_64-linux-gnu/libboost_filesystem.so/usr/lib/x86_64-linux-gnu/libboost_iostreams.so/usr/lib/x86_64-linux-gnu/libboost_regex.so/usr/lib/x86_64-linux-gnu/libboost_serialization.so/usr/lib/x86_64-linux-gnu/libboost_system.so/usr/lib/x86_64-linux-gnu/libboost_date_time.so/usr/lib/x86_64-linux-gnu/libboost_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so/usr/lib/x86_64-linux-gnu/libpthread.so
Found all python dependencies with version 3.6.8, will compile yade with that.
-- Found Loki: /usr/include
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
-- Found Eigen3, version: 3.3.4
-- Disable vectorization
-- The imported target "vtkRenderingPythonTkWidgets" references the file
   "/usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-6.3/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtk" references the file
   "/usr/bin/vtk"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-6.3/VTKTargets.cmake"
but not all the files it references.

-- Found VTK
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so
-- Found GLUT: /usr/lib/x86_64-linux-gnu/libglut.so
-- USE QT5
-- Found QGLVIEWER-qt5: /usr/include/QGLViewer
-- Found GUI-Qt5-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found GMP: /usr/include/x86_64-linux-gnu
-- Found CGAL: /usr/include, /usr/lib/x86_64-linux-gnu/libCGAL.so
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
-- SuiteSparse version 5.1.2 found, CHOLMOD direct solver for CPU activated.
-- Found Cholmod: /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas: /usr/lib/x86_64-linux-gnu/libopenblas.so
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- Found Metis: /usr/include
-- Found Cholmod in /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas in /usr/lib/x86_64-linux-gnu/libopenblas.so
-- Found Metis in /usr/lib/x86_64-linux-gnu/libmetis.so
-- Found MPI_C: /usr/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- MPI found
-- Found GL2PS: /usr/lib/x86_64-linux-gnu/libgl2ps.so
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found Threads: TRUE
-- A library with BLAS API found.
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Found OpenBlas
-- Found Lapack
-- Found CLP: /usr/include/coin, /usr/lib/x86_64-linux-gnu/libClp.so
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Found CLP
Yade will be installed to /home/ehsan/myYade/install
-- Suffix is set to -2019-07-08.git-e27605e
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/ehsan/myYade/install
-- Could NOT find gts (missing: PY_gts)
-- Use embedded version of gts. Please, consider installing the corresponding package
-- VTK version >5 and <8 is found
-- ===========================================================
-- Yade configured with following features: Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW LINSOLV MPI TWOPHASEFLOW GL2PS LBMFLOW PotentialParticles PotentialBlocks
-- Disabled features: CHOLMOD_GPU SPH DEFORM LIQMIGRATION MASK_ARBITRARY THERMAL PROFILING
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ehsan/yade-cmake-test

Jan Stránský (honzik) said : #7

Thanks,
I don't know the answer, but others can give better some based on your information.
cheers
Jan

Janek Kozicki (cosurgi) said : #8

Please provide output of printAllVersions(), https://yade-dem.org/doc/yade.libVersions.html

Chareyre (bruno-chareyre-9) said : #9

Hi, did you try other 3D programs inside vmware? What's the result of
command «glxgears» for instance?
Bruno

Le jeu. 1 août. 2019 23:17, ehsan benabbas <
<email address hidden>> a écrit :

> New question #682504 on Yade:
> https://answers.launchpad.net/yade/+question/682504
>
> Hello
> I have installed yade-2019-07-08.git-e27605e , the source code version,
> and using ubunu 18.04 on a virtual machine software called VMWare. my host
> OS for VMWare is Windows 10 and my linux (Ubuntu 18.04) has been install on
> VMWare.
> I try to run an example when I go to the directory of the .py file by the
> following command:
>
> /home/ehsan/myYade/install/bin/yade-2019-07-08.git-e27605e filename.py
>
> The problem is when I click on "Show 3D" on the Yade window, all windows
> will be closed and I get the following error:
>
> In [1]: The constructor with a shareWidget is deprecated, use the regular
> contructor instead.
> Segmentation fault (core dumped)
>
> Thus, I cannot see the 3D result of the code.
> Do you know what's my problem?
> Thanks
>
> --
> You received this question notification because your team yade-users is
> an answer contact for Yade.
>
> _______________________________________________
> Mailing list: https://launchpad.net/~yade-users
> Post to : <email address hidden>
> Unsubscribe : https://launchpad.net/~yade-users
> More help : https://help.launchpad.net/ListHelp
>
>
>

ehsan benabbas (ehsanben) said : #10

Thanks Jan

Dear Jane, hope the following is the output you want:

ehsan@ehsan:~$ /home/ehsan/myYade/install/bin/yade-2019-07-08.git-e27605e
Welcome to Yade 2019-07-08.git-e27605e
Using python version: 3.6.8 (default, Jan 14 2019, 11:02:34)
[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]]
TCP python prompt on localhost:9000, auth cookie `sdscau'
XMLRPC info provider on http://localhost:21000
[[ ^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]: from yade.libVersions import *

In [2]: getAllVersionsCmake()
Out[2]:
{'cmake': [(3, 10, 2), '3.10.2'],
 'gcc': [(7, 4, 0), '7.4.0'],
 'boost': [(1, 65, 1), '106501'],
 'python': [(3, 6, 8), '3.6.8'],
 'eigen': [(3, 3, 4), '3.3.4'],
 'vtk': [(6, 3, 0), '6.3.0'],
 'suitesparse': [(5, 1, 2), '5.1.2'],
 'mpi': [(3, 1, 0), '3.1'],
 'numpy': [(1, 17, 0), '1.17.0'],
 'ipython': [(7, 7, 0), '7.7.0'],
 'sphinx': [(2, 1, 2), '2.1.2-final-0'],
 'mpi4py': [(3, 0, 2), '3.0.2']}

In [3]:

ehsan benabbas (ehsanben) said : #11

Hi Chareyre

I'm not sure if I get what you mean 100%, but, I have Ubuntu Linux on my VMWare and I think every single 3D program we can use on Ubuntu, I can use here as well.

And I'm not familiar with glxgears, so could you please tell me what should I do now?

Thanks,
Ehsan

ehsan benabbas (ehsanben) said : #12

Dear Chareyre,

I tried the command you mentioned and a window showed up which contained 3 wheels with different sizes and colors. They were moving soft and without any issue. So, here it is the output:

ehsan@ehsan:~$ glxgears
Running synchronized to the vertical refresh. The framerate should be
approximately the same as the monitor refresh rate.
299 frames in 5.0 seconds = 59.707 FPS
301 frames in 5.0 seconds = 59.991 FPS
301 frames in 5.0 seconds = 59.997 FPS
300 frames in 5.0 seconds = 59.990 FPS
301 frames in 5.0 seconds = 60.004 FPS

Janek Kozicki (cosurgi) said : #13

I asked about printAllVersions(), not getAllVersionsCmake() ;)

ehsan benabbas (ehsanben) said : #15

Is this the output you asked?

In [36]: printAllVersions()
    ...:

```
Yade version : 2019-07-08.git-e27605e
Yade features : Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW LINSOLV MPI TWOPHASEFLOW GL2PS LBMFLOW PotentialParticles PotentialBlocks
Yade config dir: ~/.yade-2019-07-08.git-e27605e
```

Libraries used :

| library | cmake | C++ |
| ------------- | --------------- | ------------------- |
| boost | 106501 | 1.65.1 |
| cgal | | 4.11 |
| clp | | 1.16.11 |
| cmake | 3.10.2 | |
| eigen | 3.3.4 | 3.3.4 |
| freeglut | | 13.4.1 |
| gcc | 7.4.0 | 7.4.0 |
| gl | | 20180725 |
| ipython | 7.7.0 | |
| metis | | 5.1.0 |
| mpi | 3.1 | ompi:2.1.1 |
| mpi4py | 3.0.2 | |
| numpy | 1.17.0 | |
| openblas | | OpenBLAS 0.2.20 |
| python | 3.6.8 | 3.6.8 |
| qglviewer | | 2.7.1 |
| qt | | 5.9.5 |
| sphinx | 2.1.2-final-0 | |
| sqlite | | 3.22.0 |
| suitesparse | 5.1.2 | 5.1.2 |
| vtk | 6.3.0 | 6.3.0 |

Linux version: Ubuntu 18.04.2 LTS

In [37]:

Janek Kozicki (cosurgi) said : #16

OK, thank you. Please try the latest version, 023af5ccb. There was a bug regarding 3D display [1] fixed in the same week as when you have downloaded yade.

[1] https://gitlab.com/yade-dev/trunk/merge_requests/160

ehsan benabbas (ehsanben) said : #17

Jane thank you so much for your solution. just a quick question. do I need to uninstall my current version of Yade and install the version you provided? is there any way to update it?

Janek Kozicki (cosurgi) said : #18

Without knowing the details how you have installed the current version I don't know how to answer this question. I guess that you can have installed both of them without conflicts. Fortunately the 023af5 will be part of the name, so you will be able to recognize which version you are running.

Janek Kozicki (cosurgi) said : #19

Or if you want to save space, you can uninstall the old one, your call :)

ehsan benabbas (ehsanben) said : #20

well, I have installed it by source code as the instruction of wiki webpage. I was worried maybe I need to uninstall all packages, so in that case, I can easily install your version without uninstalling other packages and run it.

Thank you so much dear Jane,
 I'm going to try your version.

ehsan benabbas (ehsanben) said : #21

To download and use my current version, I used the following command in terminal to get the trunk folder:

git clone <email address hidden>:yade-dev/trunk.git

unfortunately I cannot find the clone in the link you provided above
could you please tell me how should I do that?

Janek Kozicki (cosurgi) said : #22

Ah, you need to go through some basic git tutorial. You can start here: https://git-scm.com/book/en/v1/Getting-Started and
https://yade-dem.org/doc/github.html

The command which you need to run in terminal in the directory where you previously did "git clone ...." is the command "git pull".

good luck :)

ehsan benabbas (ehsanben) said : #23

I did all of those step for the current version I have. Do I need to again go through all of those steps (for git) for the version you provided?

Janek Kozicki (cosurgi) said : #24

after you do "git pull" you can confirm that you have a new source code version with command "git status", then you can compile (again) it and run it.

So yes. You need to :)

ehsan benabbas (ehsanben) said : #25

thank you for your kind explanations, sorry I ask many questions. just to make sure, I need to download the version you said, extract it (the trunk folder of your version). go to the directory of this new trunk and then go for git pull. am I right?

Janek Kozicki (cosurgi) said : #26

No. You go to the directory where you have done "git clone <email address hidden>:yade-dev/trunk.git", then "cd trunk", then "git pull"

The "git pull" will download latest version.

ehsan benabbas (ehsanben) said : #27

Oh ok thanks, so I did it already. now I need to compile it again. ok, thank you

ehsan benabbas (ehsanben) said : #28

I got a problem, I did the git pull and git push, then did the cmake command and after that tried for make command. make command took like 20 hours and didn't finish (that was strange) and I got an error about connecting a new screen and virtual machine (VMWare) cannot do that. I had no choice unless closing the whole VMWare and open it again. I said ok maybe it's installed now, so I went to the directory of examples and used the following command to run an example:

ehsan@ehsan:~/Desktop/yexp$ /home/ehsan/myYade/install/bin/yade-2019-07-08.git-e27605e 3dpostprocessing.py
Welcome to Yade 2019-07-08.git-e27605e
Using python version: 3.6.8 (default, Jan 14 2019, 11:02:34)
[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]]
TCP python prompt on localhost:9000, auth cookie `aessuy'
XMLRPC info provider on http://localhost:21000
Running script 3dpostprocessing.py
The constructor with a shareWidget is deprecated, use the regular contructor instead.
Segmentation fault (core dumped)
ehsan@ehsan:~/Desktop/yexp$

that I got a new error.

Janek Kozicki (cosurgi) said : #29

About vmware I can't help you. But 2019-07-08.git-e27605e is the old version.

ehsan benabbas (ehsanben) said : #30

when I do the "git pull", it says every thing is up to date

ehsan@ehsan:~$ cd /home/ehsan/trunk
ehsan@ehsan:~/trunk$ git pull --rebase upstream master
From gitlab.com:yade-dev/trunk
 * branch master -> FETCH_HEAD
Already up to date.
Current branch master is up to date.
ehsan@ehsan:~/trunk$ git push
Everything up-to-date
ehsan@ehsan:~/trunk$

now, I just deleted all file in myYade/build directory and installation folder as well and want to go for make again. hope this works.

ehsan benabbas (ehsanben) said : #31

Cmake command was successful. Hope the make command be finished without any error.

this is the output of cmake:
ehsan@ehsan:~/myYade/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/ehsan/myYade/install /home/ehsan/trunk
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Version is set to 2019-08-08.git-775ae74
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
-- Found PythonInterp: /usr/bin/python (found version "2.7.15")
-- Found NumPy: version "1.13.3" /usr/lib/python2.7/dist-packages/numpy/core/include
-- Log filtering: enabled
-- Enabling boost::log library and DEBUG=OFF. Logging will work nicely, backtraces will not have debug info, files will be small.
Loop on the following python versions and check available dependencies:3.8;3.7;3.6;3.5;3.4;3.3;3.2;3.1;3.0;2.7;2.6
-- Found PythonInterp: /usr/local/bin/python3.7 (found version "3.7.4")
Python version 3.7.4 found, try to import dependencies...
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python-py37; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:67 (FIND_PACKAGE)
  CMakeLists.txt:258 (FIND_PYTHON_PACKAGES)

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python3-py37; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:67 (FIND_PACKAGE)
  CMakeLists.txt:258 (FIND_PYTHON_PACKAGES)

CMake Warning (dev) at /usr/share/cmake-3.10/Modules/FindBoost.cmake:911 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted. Run "cmake --help-policy CMP0054" for policy
  details. Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "chrono" will no longer be dereferenced when the
  policy is set to NEW. Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindBoost.cmake:1558 (_Boost_MISSING_DEPENDENCIES)
  cMake/YadePythonHelpers.cmake:77 (FIND_PACKAGE)
  CMakeLists.txt:258 (FIND_PYTHON_PACKAGES)
This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python-py3; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:77 (FIND_PACKAGE)
  CMakeLists.txt:258 (FIND_PYTHON_PACKAGES)

Failed to import dependencies for Python version 3.7.4. NOT FOUND:libboost-python
-- Found PythonInterp: /usr/bin/python3.6 (found version "3.6.8")
Python version 3.6.8 found, try to import dependencies...
CMake Warning at /usr/share/cmake-3.10/Modules/FindBoost.cmake:1626 (message):
  No header defined for python-py36; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:67 (FIND_PACKAGE)
  CMakeLists.txt:258 (FIND_PYTHON_PACKAGES)

-- Found NumPy: version "1.17.0" /home/ehsan/.local/lib/python3.6/site-packages/numpy/core/include
-- Found IPython: /usr/local/lib/python3.6/dist-packages/IPython
-- Found matplotlib: /usr/local/lib/python3.6/dist-packages/matplotlib
-- Found pygraphviz: /usr/lib/python3/dist-packages/pygraphviz
-- Found Xlib: /usr/lib/python3/dist-packages/Xlib
-- Found minieigen: /usr/lib/python3/dist-packages/minieigen.cpython-36m-x86_64-linux-gnu.so
-- Found future: /usr/lib/python3/dist-packages/future
-- Found past: /usr/lib/python3/dist-packages/past
-- Found tkinter: /usr/lib/python3.6/tkinter
-- Boost_VERSION: 106501
-- Boost_LIB_VERSION: 1_65_1
-- Boost_INCLUDE_DIRS: /usr/include
-- Boost_LIBRARIES: /usr/lib/x86_64-linux-gnu/libboost_python-py36.so/usr/lib/x86_64-linux-gnu/libboost_thread.so/usr/lib/x86_64-linux-gnu/libboost_filesystem.so/usr/lib/x86_64-linux-gnu/libboost_iostreams.so/usr/lib/x86_64-linux-gnu/libboost_regex.so/usr/lib/x86_64-linux-gnu/libboost_serialization.so/usr/lib/x86_64-linux-gnu/libboost_system.so/usr/lib/x86_64-linux-gnu/libboost_date_time.so/usr/lib/x86_64-linux-gnu/libboost_log.so/usr/lib/x86_64-linux-gnu/libboost_chrono.so/usr/lib/x86_64-linux-gnu/libboost_atomic.so/usr/lib/x86_64-linux-gnu/libboost_log_setup.so/usr/lib/x86_64-linux-gnu/libpthread.so
Found all python dependencies with version 3.6.8, will compile yade with that.
-- Found Loki: /usr/include
-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
-- Found Eigen3, version: 3.3.4
-- Disable vectorization
-- The imported target "vtkRenderingPythonTkWidgets" references the file
   "/usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-6.3/VTKTargets.cmake"
but not all the files it references.

-- The imported target "vtk" references the file
   "/usr/bin/vtk"
but this file does not exist. Possible reasons include:
* The file was deleted, renamed, or moved to another location.
* An install or uninstall procedure did not complete successfully.
* The installation package was faulty and contained
   "/usr/lib/cmake/vtk-6.3/VTKTargets.cmake"
but not all the files it references.

-- Found VTK
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib/x86_64-linux-gnu/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so
-- Found GLUT: /usr/lib/x86_64-linux-gnu/libglut.so
-- USE QT5
-- Found QGLVIEWER-qt5: /usr/include/QGLViewer
-- Found GUI-Qt5-LIBS
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found GMP: /usr/include/x86_64-linux-gnu
-- Found CGAL: /usr/include, /usr/lib/x86_64-linux-gnu/libCGAL.so
-- GMP libs: /usr/lib/x86_64-linux-gnu/libgmp.so /usr/lib/x86_64-linux-gnu/libgmpxx.so
-- Found CGAL
-- SuiteSparse version 5.1.2 found, CHOLMOD direct solver for CPU activated.
-- Found Cholmod: /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas: /usr/lib/x86_64-linux-gnu/libopenblas.so
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- Found Metis: /usr/include
-- Found Cholmod in /usr/lib/x86_64-linux-gnu/libcholmod.so
-- Found OpenBlas in /usr/lib/x86_64-linux-gnu/libopenblas.so
-- Found Metis in /usr/lib/x86_64-linux-gnu/libmetis.so
-- Found MPI_C: /usr/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- MPI found
-- Found GL2PS: /usr/lib/x86_64-linux-gnu/libgl2ps.so
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own risk!
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found Threads: TRUE
-- A library with BLAS API found.
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Found OpenBlas
-- Found Lapack
-- Found CLP: /usr/include/coin, /usr/lib/x86_64-linux-gnu/libClp.so
-- BLAS_INCLUDE_DIR=/usr/include/x86_64-linux-gnu
-- A library with BLAS API found.
-- A library with LAPACK API found.
-- Found CLP
-- md5sum of freegult /usr/include/GL/freeglut_std.h is: 791a2febd8584ec530cdd7676191b6d5
-- freegult version is 2.8.1
Yade will be installed to /home/ehsan/myYade/install
-- Suffix is set to -2019-08-08.git-775ae74
-- LIBRARY_OUTPUT_PATH is set to lib/x86_64-linux-gnu
-- runtimePREFIX is set to /home/ehsan/myYade/install
-- Could NOT find gts (missing: PY_gts)
-- Use embedded version of gts. Please, consider installing the corresponding package
-- VTK version >5 and <8 is found
-- ===========================================================
-- Yade configured with following features: BoostLog Odeint VTK OpenMP GTS GUI-Qt5 CGAL PFVFLOW PFVFLOW LINSOLV MPI TWOPHASEFLOW FEMLIKE GL2PS LBMFLOW THERMAL PotentialParticles PotentialBlocks
-- Disabled features: CHOLMOD_GPU SPH DEFORM LIQMIGRATION MASK_ARBITRARY PROFILING
-- Using MAX_LOG_LEVEL=5, ENABLE_LOGGER=ON
-- Optimized build
-- ===========================================================
-- Configuring done
-- Generating done
-- Build files have been written to: /home/ehsan/myYade/build
ehsan@ehsan:~/myYade/build$

Janek Kozicki (cosurgi) said : #32

Suffix is set to -2019-08-08.git-775ae74 looks good. Now compile this one.

ehsan benabbas (ehsanben) said : #33

please help me with the following error
I did the make command for the new version after git pull, and left the PC for more than 1 day, finally I got this error:

[ 48%] Building CXX object CMakeFiles/yade.dir/pkg/dem/PDFEngine.cpp.o
[ 49%] Building CXX object CMakeFiles/yade.dir/pkg/dem/PeriIsoCompressor.cpp.o
[ 49%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o
In file included from /usr/include/eigen3/Eigen/Core:471:0,
                 from /home/ehsan/trunk/lib/base/Math.hpp:90,
                 from /home/ehsan/trunk/core/Omega.hpp:20,
                 from /home/ehsan/trunk/pkg/dem/Polyhedra.hpp:13,
                 from /home/ehsan/trunk/pkg/dem/Polyhedra.cpp:9:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h: In instantiation of ‘void Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr, nr, ConjugateLhs, ConjugateRhs>::operator()(const DataMapper&, const LhsScalar*, const RhsScalar*, Index, Index, Index, Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar, Index, Index, Index, Index) [with LhsScalar = double; RhsScalar = double; Index = long int; DataMapper = Eigen::internal::blas_data_mapper<double, long int, 0, 0>; int mr = 1; int nr = 4; bool ConjugateLhs = false; bool ConjugateRhs = false; Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar = double]’:
/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix.h:195:22: required from ‘static void Eigen::internal::product_triangular_matrix_matrix<Scalar, Index, Mode, true, LhsStorageOrder, ConjugateLhs, RhsStorageOrder, ConjugateRhs, 0, Version>::run(Index, Index, Index, const Scalar*, Index, const Scalar*, Index, Scalar*, Index, const Scalar&, Eigen::internal::level3_blocking<Scalar, Scalar>&) [with Scalar = double; Index = long int; int Mode = 5; int LhsStorageOrder = 0; bool ConjugateLhs = false; int RhsStorageOrder = 0; bool ConjugateRhs = false; int Version = 0]’
/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix.h:427:12: required from ‘static void Eigen::internal::triangular_product_impl<Mode, LhsIsTriangular, Lhs, false, Rhs, false>::run(Dest&, const Lhs&, const Rhs&, const typename Dest::Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; int Mode = 5; bool LhsIsTriangular = true; Lhs = const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>; typename Dest::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:712:14: required from ‘static void Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::TriangularShape, Eigen::DenseShape, ProductTag>::scaleAndAddTo(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; Lhs = Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>; int ProductTag = 3; Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::TriangularShape, Eigen::DenseShape, ProductTag>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:361:27: required from ‘static void Eigen::internal::generic_product_impl_base<Lhs, Rhs, Derived>::scaleAndAddTo(Dst&, const Lhs&, const Rhs&, const Scalar&) [with Dst = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; Lhs = Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>; Derived = Eigen::internal::generic_product_impl<Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>, Eigen::Matrix<double, -1, -1, 0, 2, 3>, Eigen::TriangularShape, Eigen::DenseShape, 3>; Eigen::internal::generic_product_impl_base<Lhs, Rhs, Derived>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:357:18: required from ‘static void Eigen::internal::generic_product_impl_base<Lhs, Rhs, Derived>::subTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; Lhs = Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>; Derived = Eigen::internal::generic_product_impl<Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>, Eigen::Matrix<double, -1, -1, 0, 2, 3>, Eigen::TriangularShape, Eigen::DenseShape, 3>]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:178:42: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/eigen3/Eigen/src/Householder/HouseholderSequence.h:333:46: required from ‘void Eigen::HouseholderSequence<VectorsType, CoeffsType, Side>::applyThisOnTheLeft(Dest&, Workspace&) const [with Dest = Eigen::Matrix<double, 3, 3>; Workspace = Eigen::Matrix<double, 1, 3>; VectorsType = Eigen::Matrix<double, 3, 2, 0, 3, 2>; CoeffsType = Eigen::Matrix<double, 2, 1>; int Side = 1]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:237:9: required from ‘bool Eigen::internal::qr_preconditioner_impl<MatrixType, 2, 0, true>::run(Eigen::JacobiSVD<MatrixType, 2>&, const MatrixType&) [with MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:684:5: required from ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>& Eigen::JacobiSVD<MatrixType, QRPreconditioner>::compute(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>; int QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType, QRPreconditioner>::MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:548:14: required from ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>::JacobiSVD(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>; int QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType, QRPreconditioner>::MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>]’
/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:596:36: required from ‘Derived& Eigen::QuaternionBase<Derived>::setFromTwoVectors(const Eigen::MatrixBase<OtherDerived>&, const Eigen::MatrixBase<OtherDerived>&) [with Derived1 = Eigen::Matrix<double, 3, 1>; Derived2 = Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 3, 1> > >; Derived = Eigen::Quaternion<double>]’
/home/ehsan/trunk/pkg/dem/Polyhedra.cpp:438:78: required from here
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:1584:135: warning: declaration of ‘SResPacketHalf’ shadows a previous local [-Wshadow=compatible-local]
 ket_traits<SResPacket>::half,SResPacket>::type SResPacketHalf;
                                                ^~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:1529:62: note: shadowed declaration is here
 def typename unpacket_traits<SResPacket>::half SResPacketHalf;
                                                ^~~~~~~~~~~~~~
c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
CMakeFiles/yade.dir/build.make:2246: recipe for target 'CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o' failed
make[2]: *** [CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o] Error 4
CMakeFiles/Makefile2:137: recipe for target 'CMakeFiles/yade.dir/all' failed
make[1]: *** [CMakeFiles/yade.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
ehsan@ehsan:~/myYade/build$

ehsan benabbas (ehsanben) said : #34

So, isn't it possible to delete the previous trunk file as well as myYade folder, and download (clone) the new trunk floder (the newest version you said) to avoid git pull step and then try to compile the code? because the problem has showed up from the time I updated (git pull) my old trunk. After that I couldn't finish make command to install Yade.

Thank you for your asnwers

Jan Stránský (honzik) said : #35

Hello,

> c++: internal compiler error: Killed (program cc1plus)

from this error and your description of the length of compilation I would guess you run out of memory. How much RAM is dedicated to the virtual machine?

> isn't it possible to delete the previous trunk file as well as myYade folder, and download (clone) the new trunk floder (the newest version you said) to avoid git pull step

yes, of course it is possible :-)

But please note that git pull and cloning the newest version is basically the same (if you do not make changes to files) so I doubt git pull is the issue here..

cheers
Jan

ehsan benabbas (ehsanben) said : #36

I think I need to install Ubuntu Linux separately as an OS, not on a Virtual Machine. This is because I deleted the trunk folder and all files inside the myYade/build directory, cloned the trunk again, and got same error for make command again. This is the error:

[ 49%] Building CXX object CMakeFiles/yade.dir/pkg/dem/PeriIsoCompressor.cpp.o
[ 49%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o
In file included from /usr/include/eigen3/Eigen/Core:471:0,
                 from /home/ehsan/trunk/lib/base/Math.hpp:90,
                 from /home/ehsan/trunk/core/Omega.hpp:20,
                 from /home/ehsan/trunk/pkg/dem/Polyhedra.hpp:13,
                 from /home/ehsan/trunk/pkg/dem/Polyhedra.cpp:9:
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h: In instantiation of ‘void Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr, nr, ConjugateLhs, ConjugateRhs>::operator()(const DataMapper&, const LhsScalar*, const RhsScalar*, Index, Index, Index, Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar, Index, Index, Index, Index) [with LhsScalar = double; RhsScalar = double; Index = long int; DataMapper = Eigen::internal::blas_data_mapper<double, long int, 0, 0>; int mr = 1; int nr = 4; bool ConjugateLhs = false; bool ConjugateRhs = false; Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr, nr, ConjugateLhs, ConjugateRhs>::ResScalar = double]’:
/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix.h:195:22: required from ‘static void Eigen::internal::product_triangular_matrix_matrix<Scalar, Index, Mode, true, LhsStorageOrder, ConjugateLhs, RhsStorageOrder, ConjugateRhs, 0, Version>::run(Index, Index, Index, const Scalar*, Index, const Scalar*, Index, Scalar*, Index, const Scalar&, Eigen::internal::level3_blocking<Scalar, Scalar>&) [with Scalar = double; Index = long int; int Mode = 5; int LhsStorageOrder = 0; bool ConjugateLhs = false; int RhsStorageOrder = 0; bool ConjugateRhs = false; int Version = 0]’
/usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix.h:427:12: required from ‘static void Eigen::internal::triangular_product_impl<Mode, LhsIsTriangular, Lhs, false, Rhs, false>::run(Dest&, const Lhs&, const Rhs&, const typename Dest::Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; int Mode = 5; bool LhsIsTriangular = true; Lhs = const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>; typename Dest::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:712:14: required from ‘static void Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::TriangularShape, Eigen::DenseShape, ProductTag>::scaleAndAddTo(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; Lhs = Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>; int ProductTag = 3; Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::TriangularShape, Eigen::DenseShape, ProductTag>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:361:27: required from ‘static void Eigen::internal::generic_product_impl_base<Lhs, Rhs, Derived>::scaleAndAddTo(Dst&, const Lhs&, const Rhs&, const Scalar&) [with Dst = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; Lhs = Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>; Derived = Eigen::internal::generic_product_impl<Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>, Eigen::Matrix<double, -1, -1, 0, 2, 3>, Eigen::TriangularShape, Eigen::DenseShape, 3>; Eigen::internal::generic_product_impl_base<Lhs, Rhs, Derived>::Scalar = double]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:357:18: required from ‘static void Eigen::internal::generic_product_impl_base<Lhs, Rhs, Derived>::subTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; Lhs = Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>; Derived = Eigen::internal::generic_product_impl<Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>, Eigen::Matrix<double, -1, -1, 0, 2, 3>, Eigen::TriangularShape, Eigen::DenseShape, 3>]’
/usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:178:42: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/usr/include/eigen3/Eigen/src/Householder/HouseholderSequence.h:333:46: required from ‘void Eigen::HouseholderSequence<VectorsType, CoeffsType, Side>::applyThisOnTheLeft(Dest&, Workspace&) const [with Dest = Eigen::Matrix<double, 3, 3>; Workspace = Eigen::Matrix<double, 1, 3>; VectorsType = Eigen::Matrix<double, 3, 2, 0, 3, 2>; CoeffsType = Eigen::Matrix<double, 2, 1>; int Side = 1]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:237:9: required from ‘bool Eigen::internal::qr_preconditioner_impl<MatrixType, 2, 0, true>::run(Eigen::JacobiSVD<MatrixType, 2>&, const MatrixType&) [with MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:684:5: required from ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>& Eigen::JacobiSVD<MatrixType, QRPreconditioner>::compute(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>; int QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType, QRPreconditioner>::MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>]’
/usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:548:14: required from ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>::JacobiSVD(const MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>; int QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType, QRPreconditioner>::MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>]’
/usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:596:36: required from ‘Derived& Eigen::QuaternionBase<Derived>::setFromTwoVectors(const Eigen::MatrixBase<OtherDerived>&, const Eigen::MatrixBase<OtherDerived>&) [with Derived1 = Eigen::Matrix<double, 3, 1>; Derived2 = Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>, const Eigen::Matrix<double, 3, 1>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 3, 1> > >; Derived = Eigen::Quaternion<double>]’
/home/ehsan/trunk/pkg/dem/Polyhedra.cpp:438:78: required from here
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:1584:135: warning: declaration of ‘SResPacketHalf’ shadows a previous local [-Wshadow=compatible-local]
 ional<SwappedTraits::LhsProgress>=8,typename unpacket_traits<SResPacket>::half,SResPacket>::type SResPacketHalf;
                                                                                                  ^~~~~~~~~~~~~~
/usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:1529:62: note: shadowed declaration is here
           typedef typename unpacket_traits<SResPacket>::half SResPacketHalf;
                                                              ^~~~~~~~~~~~~~
c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
CMakeFiles/yade.dir/build.make:2246: recipe for target 'CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o' failed
make[2]: *** [CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o] Error 4
CMakeFiles/Makefile2:137: recipe for target 'CMakeFiles/yade.dir/all' failed
make[1]: *** [CMakeFiles/yade.dir/all] Error 2
Makefile:129: recipe for target 'all' failed
make: *** [all] Error 2
ehsan@ehsan:~/myYade/build$

Just a quick question to make sure about the trunk file. If I install a new linux and go with the following command:
git clone <email address hidden>:yade-dev/trunk.git

In this case, will I get the newest version you suggested? or again I will need to use git pull to make it updated?

Thank you so much for all your answers.
Bests,
Ehsan

Chareyre (bruno-chareyre-9) said : #37

Hi, «git clone» always picks latest version.
Your compile error is probably not due to vmware.
Bruno

Le lun. 12 août. 2019 17:13, ehsan benabbas <
<email address hidden>> a écrit :

> Question #682504 on Yade changed:
> https://answers.launchpad.net/yade/+question/682504
>
> Status: Needs information => Open
>
> ehsan benabbas gave more information on the question:
> I think I need to install Ubuntu Linux separately as an OS, not on a
> Virtual Machine. This is because I deleted the trunk folder and all
> files inside the myYade/build directory, cloned the trunk again, and got
> same error for make command again. This is the error:
>
> [ 49%] Building CXX object
> CMakeFiles/yade.dir/pkg/dem/PeriIsoCompressor.cpp.o
> [ 49%] Building CXX object CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o
> In file included from /usr/include/eigen3/Eigen/Core:471:0,
> from /home/ehsan/trunk/lib/base/Math.hpp:90,
> from /home/ehsan/trunk/core/Omega.hpp:20,
> from /home/ehsan/trunk/pkg/dem/Polyhedra.hpp:13,
> from /home/ehsan/trunk/pkg/dem/Polyhedra.cpp:9:
> /usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h: In
> instantiation of ‘void Eigen::internal::gebp_kernel<LhsScalar, RhsScalar,
> Index, DataMapper, mr, nr, ConjugateLhs, ConjugateRhs>::operator()(const
> DataMapper&, const LhsScalar*, const RhsScalar*, Index, Index, Index,
> Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr,
> nr, ConjugateLhs, ConjugateRhs>::ResScalar, Index, Index, Index, Index)
> [with LhsScalar = double; RhsScalar = double; Index = long int; DataMapper
> = Eigen::internal::blas_data_mapper<double, long int, 0, 0>; int mr = 1;
> int nr = 4; bool ConjugateLhs = false; bool ConjugateRhs = false;
> Eigen::internal::gebp_kernel<LhsScalar, RhsScalar, Index, DataMapper, mr,
> nr, ConjugateLhs, ConjugateRhs>::ResScalar = double]’:
> /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix.h:195:22:
> required from ‘static void
> Eigen::internal::product_triangular_matrix_matrix<Scalar, Index, Mode,
> true, LhsStorageOrder, ConjugateLhs, RhsStorageOrder, ConjugateRhs, 0,
> Version>::run(Index, Index, Index, const Scalar*, Index, const Scalar*,
> Index, Scalar*, Index, const Scalar&,
> Eigen::internal::level3_blocking<Scalar, Scalar>&) [with Scalar = double;
> Index = long int; int Mode = 5; int LhsStorageOrder = 0; bool ConjugateLhs
> = false; int RhsStorageOrder = 0; bool ConjugateRhs = false; int Version =
> 0]’
> /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixMatrix.h:427:12:
> required from ‘static void Eigen::internal::triangular_product_impl<Mode,
> LhsIsTriangular, Lhs, false, Rhs, false>::run(Dest&, const Lhs&, const
> Rhs&, const typename Dest::Scalar&) [with Dest =
> Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; int Mode = 5;
> bool LhsIsTriangular = true; Lhs = const Eigen::Block<Eigen::Matrix<double,
> 3, 2, 0, 3, 2>, -1, -1, false>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2,
> 3>; typename Dest::Scalar = double]’
> /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:712:14: required
> from ‘static void Eigen::internal::generic_product_impl<Lhs, Rhs,
> Eigen::TriangularShape, Eigen::DenseShape,
> ProductTag>::scaleAndAddTo(Dest&, const Lhs&, const Rhs&, const Scalar&)
> [with Dest = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; Lhs
> = Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0,
> 3, 2>, -1, -1, false>, 5>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>;
> int ProductTag = 3; Eigen::internal::generic_product_impl<Lhs, Rhs,
> Eigen::TriangularShape, Eigen::DenseShape, ProductTag>::Scalar = double]’
> /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:361:27: required
> from ‘static void Eigen::internal::generic_product_impl_base<Lhs, Rhs,
> Derived>::scaleAndAddTo(Dst&, const Lhs&, const Rhs&, const Scalar&) [with
> Dst = Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; Lhs =
> Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3,
> 2>, -1, -1, false>, 5>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>;
> Derived = Eigen::internal::generic_product_impl<Eigen::TriangularView<const
> Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>,
> Eigen::Matrix<double, -1, -1, 0, 2, 3>, Eigen::TriangularShape,
> Eigen::DenseShape, 3>; Eigen::internal::generic_product_impl_base<Lhs, Rhs,
> Derived>::Scalar = double]’
> /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:357:18: required
> from ‘static void Eigen::internal::generic_product_impl_base<Lhs, Rhs,
> Derived>::subTo(Dst&, const Lhs&, const Rhs&) [with Dst =
> Eigen::Block<Eigen::Matrix<double, 3, 3>, -1, -1, false>; Lhs =
> Eigen::TriangularView<const Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3,
> 2>, -1, -1, false>, 5>; Rhs = Eigen::Matrix<double, -1, -1, 0, 2, 3>;
> Derived = Eigen::internal::generic_product_impl<Eigen::TriangularView<const
> Eigen::Block<Eigen::Matrix<double, 3, 2, 0, 3, 2>, -1, -1, false>, 5>,
> Eigen::Matrix<double, -1, -1, 0, 2, 3>, Eigen::TriangularShape,
> Eigen::DenseShape, 3>]’
> /usr/include/eigen3/Eigen/src/Core/ProductEvaluators.h:178:42: [
> skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to
> disable ]
> /usr/include/eigen3/Eigen/src/Householder/HouseholderSequence.h:333:46:
> required from ‘void Eigen::HouseholderSequence<VectorsType, CoeffsType,
> Side>::applyThisOnTheLeft(Dest&, Workspace&) const [with Dest =
> Eigen::Matrix<double, 3, 3>; Workspace = Eigen::Matrix<double, 1, 3>;
> VectorsType = Eigen::Matrix<double, 3, 2, 0, 3, 2>; CoeffsType =
> Eigen::Matrix<double, 2, 1>; int Side = 1]’
> /usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:237:9: required from ‘bool
> Eigen::internal::qr_preconditioner_impl<MatrixType, 2, 0,
> true>::run(Eigen::JacobiSVD<MatrixType, 2>&, const MatrixType&) [with
> MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>]’
> /usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:684:5: required from
> ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>&
> Eigen::JacobiSVD<MatrixType, QRPreconditioner>::compute(const MatrixType&,
> unsigned int) [with _MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>; int
> QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType,
> QRPreconditioner>::MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>]’
> /usr/include/eigen3/Eigen/src/SVD/JacobiSVD.h:548:14: required from
> ‘Eigen::JacobiSVD<MatrixType, QRPreconditioner>::JacobiSVD(const
> MatrixType&, unsigned int) [with _MatrixType = Eigen::Matrix<double, 2, 3,
> 0, 2, 3>; int QRPreconditioner = 2; Eigen::JacobiSVD<MatrixType,
> QRPreconditioner>::MatrixType = Eigen::Matrix<double, 2, 3, 0, 2, 3>]’
> /usr/include/eigen3/Eigen/src/Geometry/Quaternion.h:596:36: required
> from ‘Derived& Eigen::QuaternionBase<Derived>::setFromTwoVectors(const
> Eigen::MatrixBase<OtherDerived>&, const Eigen::MatrixBase<OtherDerived>&)
> [with Derived1 = Eigen::Matrix<double, 3, 1>; Derived2 =
> Eigen::CwiseBinaryOp<Eigen::internal::scalar_quotient_op<double, double>,
> const Eigen::Matrix<double, 3, 1>, const
> Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const
> Eigen::Matrix<double, 3, 1> > >; Derived = Eigen::Quaternion<double>]’
> /home/ehsan/trunk/pkg/dem/Polyhedra.cpp:438:78: required from here
> /usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:1584:135:
> warning: declaration of ‘SResPacketHalf’ shadows a previous local
> [-Wshadow=compatible-local]
> ional<SwappedTraits::LhsProgress>=8,typename
> unpacket_traits<SResPacket>::half,SResPacket>::type SResPacketHalf;
>
> ^~~~~~~~~~~~~~
> /usr/include/eigen3/Eigen/src/Core/products/GeneralBlockPanelKernel.h:1529:62:
> note: shadowed declaration is here
> typedef typename unpacket_traits<SResPacket>::half
> SResPacketHalf;
>
> ^~~~~~~~~~~~~~
> c++: internal compiler error: Killed (program cc1plus)
> Please submit a full bug report,
> with preprocessed source if appropriate.
> See <file:///usr/share/doc/gcc-7/README.Bugs> for instructions.
> CMakeFiles/yade.dir/build.make:2246: recipe for target
> 'CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o' failed
> make[2]: *** [CMakeFiles/yade.dir/pkg/dem/Polyhedra.cpp.o] Error 4
> CMakeFiles/Makefile2:137: recipe for target 'CMakeFiles/yade.dir/all'
> failed
> make[1]: *** [CMakeFiles/yade.dir/all] Error 2
> Makefile:129: recipe for target 'all' failed
> make: *** [all] Error 2
> ehsan@ehsan:~/myYade/build$
>
>
> Just a quick question to make sure about the trunk file. If I install a
> new linux and go with the following command:
> git clone <email address hidden>:yade-dev/trunk.git
>
> In this case, will I get the newest version you suggested? or again I
> will need to use git pull to make it updated?
>
> Thank you so much for all your answers.
> Bests,
> Ehsan
>
> --
> You received this question notification because your team yade-users is
> an answer contact for Yade.
>
> _______________________________________________
> Mailing list: https://launchpad.net/~yade-users
> Post to : <email address hidden>
> Unsubscribe : https://launchpad.net/~yade-users
> More help : https://help.launchpad.net/ListHelp
>

Jan Stránský (honzik) said : #38

Hello,

> How much RAM is dedicated to the virtual machine?

for future reference, please tell us the value.

Thanks
Jan

Can you help with this problem?

Provide an answer of your own, or ask ehsan benabbas for more information if necessary.

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