Re: [Yade-users] [Question #706851]: FreeGlut versus FREEGLUT package

[Luc OGER]

Question #706851 on Yade changed:
https://answers.launchpad.net/yade/+question/706851

Luc OGER gave more information on the question:
another strange behavior when I am trying to go behind the output
display error :

starting gdb with display crashes
then restarting with "-n" don't crash
the restarting with display works !!

see the extraction of the process (some thread are erased) :

mr078189:/home/oger/yade # gdb
GNU gdb (GDB; SUSE Linux Enterprise 15) 12.1
Copyright (C) 2022 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://bugs.opensuse.org/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.

For help, type "help".
Type "apropos word" to search for commands related to "word".
(gdb) file python3
Reading symbols from python3...
(No debugging symbols found in python3)
Missing separate debuginfos, use: zypper install 
python3-base-debuginfo-3.6.15-150300.10.48.1.x86_64
(gdb) run /opt/Yade/bin/yade-2023-06-14.git-fbf7a70 
/home/oger/prog_perso/yade/Bouncing_spheres.py
Starting program: /usr/bin/python3 /opt/Yade/bin/yade-2023-06-14.git-fbf7a70 
/home/oger/prog_perso/yade/Bouncing_spheres.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Welcome to Yade 2023-06-14.git-fbf7a70
Using python version: 3.6.15 (default, Sep 23 2021, 15:41:43) [GCC]
[Detaching after fork from child process 23433]
TCP python prompt on localhost:9000, auth cookie `ckydas'
[New Thread 0x7fffc821e700 (LWP 23435)]
[New Thread 0x7fffc799d700 (LWP 23436)]
XMLRPC info provider on http://localhost:21000


Thread 1 "python3" received signal SIGSEGV, Segmentation fault.
0x77d5439b in PyModule_GetState () from /usr/lib64/libpython3.6m.so.1.0
(gdb) s
Single stepping until exit from function PyModule_GetState,
which has no line number information.
crashHandler (sig=32767) at /home/oger/yade/trunk/core/main/pyboot.cpp:9
9   {
(gdb) b 8
Breakpoint 1 at 0x72389730: 
/data_1/oger/full_yade_local/trunk/core/main/pyboot.cpp:8. (2 locations)
(gdb) run /opt/Yade/bin/yade-2023-06-14.git-fbf7a70 -n
The program being debugged has been started already.
Start it from the beginning? (y or n) y
Starting program: /usr/bin/python3 /opt/Yade/bin/yade-2023-06-14.git-fbf7a70 -n
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Welcome to Yade 2023-06-14.git-fbf7a70
Using python version: 3.6.15 (default, Sep 23 2021, 15:41:43) [GCC]
[Detaching after fork from child process 23700]
TCP python prompt on localhost:9000, auth cookie `cdausy'
[New Thread 0x7fffca198700 (LWP 23703)]
[New Thread 0x7fffc9957700 (LWP 23704)]
XMLRPC info provider on http://localhost:21000
[New Thread 0x7fffc8c89700 (LWP 23705)]
[[ ^L clears screen, ^U kills line. F8 plot. ]]

In [1]: run /opt/Yade/bin/yade-2023-06-14.git-fbf7a70 
/home/oger/prog_perso/yade/Bouncing_spheres.py
Welcome to Yade 2023-06-14.git-fbf7a70
TCP python prompt on localhost:9001, auth cookie `descsk'
[New Thread 0x7fffba1c5700 (LWP 23732)]
[New Thread 0x7fffb99c4700 (LWP 23733)]
XMLRPC info provider on http://localhost:21001
.
[New Thread 0x7fff10ff9700 (LWP 23772)]
Running script /home/oger/prog_perso/yade/Bouncing_spheres.py
[[ ^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]: [New Thread 0x7fff09c7d700 (LWP 23781)]
[Thread 0x7fff09c7d700 (LWP 23781) exited]

[New Thread 0x7ffeebfff700 (LWP 23806)]
[Thread 0x7ffeebfff700 (LWP 23806) exited]

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Re: [Yade-users] [Question #706851]: FreeGlut versus FREEGLUT package

[Luc OGER]

Question #706851 on Yade changed:
https://answers.launchpad.net/yade/+question/706851

Luc OGER gave more information on the question:
HI
I am using either Opensuse 15.4 or 15.5 with the same result

luc

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Re: [Yade-users] [Question #706851]: FreeGlut versus FREEGLUT package

[Luc OGER]

Question #706851 on Yade changed:
https://answers.launchpad.net/yade/+question/706851

Luc OGER gave more information on the question:
other gdb detail :
run yade-2023-05-15.git-a46ea55
Starting program: /usr/bin/python3 yade-2023-05-15.git-a46ea55
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Welcome to Yade 2023-05-15.git-a46ea55
Using python version: 3.6.15 (default, Sep 23 2021, 15:41:43) [GCC]

Program received signal SIGSEGV, Segmentation fault.
0x7665d324 in std::char_traits::length (__s=0x0) at 
/usr/include/c++/7/bits/char_traits.h:320
320 return __builtin_strlen(__s);

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Re: [Yade-users] [Question #706851]: FreeGlut versus FREEGLUT package

[Luc OGER]

Question #706851 on Yade changed:
https://answers.launchpad.net/yade/+question/706851

Status: Needs information => Open

Luc OGER gave more information on the question:
Dear Jan,
here the result of catchsegv

catchsegv ./yade-2023-05-15.git-a46ea55
Welcome to Yade 2023-05-15.git-a46ea55
Using python version: 3.6.15 (default, Sep 23 2021, 15:41:43) [GCC]
SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-zGWVWW/tmp-0'
warning: Found custom handler for signal 11 (Erreur de segmentation) 
preinstalled.
Some signal dispositions inherited from the environment (SIG_DFL/SIG_IGN)
won't be propagated to spawned programs.
GNU gdb (GDB; SUSE Linux Enterprise 15) 12.1
Copyright (C) 2022 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://bugs.opensuse.org/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.

For help, type "help".
Type "apropos word" to search for commands related to "word".
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
0x7f3bf4e115f6 in wait4 () from /lib64/libc.so.6

Thread 1 (Thread 0x7f3bf4bd7740 (LWP 27293) "yade-2023-05-15"):
#0  0x7f3bf4e115f6 in wait4 () from /lib64/libc.so.6
#1  0x7f3bf4d88b57 in do_system () from /lib64/libc.so.6
#2  0x7f3bf39176ae in crashHandler (sig=11) at 
/home/oger/yade_full_install_local/trunk/core/main/pyboot.cpp:16
#3  
#4  0x7f3bf3918324 in std::char_traits::length (__s=0x0) at 
/usr/include/c++/7/bits/char_traits.h:320
#5  0x7f3bf391cfbe in 
boost::log::v2_mt_posix::basic_formatting_ostream, 
std::allocator >::operator<< (this=0x55e7bc8952b8, p=0x0) at 
/usr/include/boost/log/utility/formatting_ostream.hpp:419
#6  0x7f3bf391b8ef in 
boost::log::v2_mt_posix::basic_record_ostream::operator<< 
(this=0x55e7bc8952b8, p=0x0) at 
/usr/include/boost/log/sources/record_ostream.hpp:210
#7  0x7f3becd2c276 in yade::Omega::loadPlugins (this=0x55e7bc9b4340, 
pluginFiles=std::vector of length 14, capacity 14 = {...}) at 
/home/oger/yade_full_install_local/trunk/core/Omega.cpp:245
#8  0x7f3bf3917a67 in yadeInitialize (pp=..., 
confDir="/root/.config/yade-2023-05-15.git-a46ea55") at 
/home/oger/yade_full_install_local/trunk/core/main/pyboot.cpp:59
#9  0x7f3bf39232c9 in boost::python::detail::invoke, std::allocator > const&), 
boost::python::arg_from_python, 
boost::python::arg_from_python, std::allocator > const&> > (f=@0x55e7bc9b4228: 
0x7f3bf391776b , std::allocator > 
const&)>, ac0=..., ac1=...) at /usr/include/boost/python/detail/invoke.hpp:79
#10 0x7f3bf3922b96 in boost::python::detail::caller_arity<2u>::impl, std::allocator > const&), 
boost::python::default_call_policies, boost::mpl::vector3, 
std::allocator > const&> >::operator() (this=0x55e7bc9b4228, args_=Python 
Exception : There is no member named ob_item.
) at /usr/include/boost/python/detail/caller.hpp:216
#11 0x7f3bf392245b in 
boost::python::objects::caller_py_function_impl, std::allocator > const&), 
boost::python::default_call_policies, boost::mpl::vector3, 
std::allocator > const&> > >::operator() (this=0x55e7bc9b4220, 
args=Python Exception : There is no member named ob_item.
, kw=0x0) at /usr/include/boost/python/object/py_function.hpp:38
#12 0x7f3bf369a371 in 
boost::python::objects::py_function::operator()(_object*, _object*) const () 
from /usr/lib64/libboost_python-py3.so.1.66.0
#13 0x7f3bf36980aa in boost::python::objects::function::call(_object*, 
_object*) const () from /usr/lib64/libboost_python-py3.so.1.66.0
#14 0x7f3bf3699647 in ?? () from /usr/lib64/libboost_python-py3.so.1.66.0
#15 0x7f3bf369a052 in ?? () from /usr/lib64/libboost_python-py3.so.1.66.0
#16 0x7f3bf36b097c in boost::function0::operator()() const () from 
/usr/lib64/libboost_python-py3.so.1.66.0
#17 0x7f3bf36b0137 in 
boost::python::handle_exception_impl(boost::function0) () from 
/usr/lib64/libboost_python-py3.so.1.66.0
#18 0x7f3bf3699cd7 in ?? () from /usr/lib64/libboost_python-py3.so.1.66.0
#19 0x7f3bf3699722 in ?? () from /usr/lib64/libboost_python-py3.so.1.66.0
#20 0x7f3bf4fb9ab9 in _PyObject_FastCallDict () from 
/usr/lib64/libpython3.6m.so.1.0
#21 0x7f3bf50738aa in ?? () from /usr/lib64/libpython3.6m.so.1.0
#22 0x7f3bf5077ed5 in _PyEval_EvalFrameDefault () from 
/usr/lib64/libpython3.6m.so.1.0
#23 0x000

Re: [Yade-users] [Question #706851]: FreeGlut versus FREEGLUT package

[Luc OGER]

Question #706851 on Yade changed:
https://answers.launchpad.net/yade/+question/706851

Luc OGER gave more information on the question:
complementary investigation :

by using the debug mode I end on this error :
(gdb) run /usr/local/yade/bin/yade-2023-05-15.git-a46ea55  Bouncing_spheres.py
Starting program: /usr/bin/python3 
/usr/local/yade/bin/yade-2023-05-15.git-a46ea55  Bouncing_spheres.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Welcome to Yade 2023-05-15.git-a46ea55
Using python version: 3.6.15 (default, Sep 23 2021, 15:41:43) [GCC]
[Detaching after fork from child process 7216]
TCP python prompt on localhost:9000, auth cookie `aseyku'
[New Thread 0x7fffc0ef0700 (LWP 7219)]
[New Thread 0x7fffbbfff700 (LWP 7220)]
XMLRPC info provider on http://localhost:21000
[New Thread 0x7fff9a3c4700 (LWP 7221)]
[New Thread 0x7fff99bc3700 (LWP 7222)]
[New Thread 0x7fff991b7700 (LWP 7228)]
[New Thread 0x7fff989b6700 (LWP 7229)]
[New Thread 0x7fff8bfff700 (LWP 7230)]
[New Thread 0x7fff8b7fe700 (LWP 7231)]
[New Thread 0x7fff8affd700 (LWP 7232)]
[New Thread 0x7fff8a7fc700 (LWP 7233)]
[New Thread 0x7fff89ffb700 (LWP 7234)]
[New Thread 0x7fff897fa700 (LWP 7235)]
[New Thread 0x7fff88ff9700 (LWP 7236)]
[New Thread 0x7fff6bfff700 (LWP 7237)]
[New Thread 0x7fff6b7fe700 (LWP 7238)]
[New Thread 0x7fff6affd700 (LWP 7239)]
[New Thread 0x7fff6a7fc700 (LWP 7240)]
[New Thread 0x7fff69ffb700 (LWP 7241)]
[New Thread 0x7fff697fa700 (LWP 7242)]
[New Thread 0x7fff68ff9700 (LWP 7243)]
[New Thread 0x7fff47fff700 (LWP 7244)]
[New Thread 0x7fff477fe700 (LWP 7245)]
[New Thread 0x7fff46ffd700 (LWP 7246)]
[New Thread 0x7fff467fc700 (LWP 7247)]
[New Thread 0x7fff45ffb700 (LWP 7248)]
[New Thread 0x7fff457fa700 (LWP 7249)]
[New Thread 0x7fff44ff9700 (LWP 7250)]
[New Thread 0x7fff27fff700 (LWP 7251)]
[New Thread 0x7fff1f7fe700 (LWP 7252)]
[New Thread 0x7fff277fe700 (LWP 7253)]
[New Thread 0x7fff26ffd700 (LWP 7254)]
[New Thread 0x7fff267fc700 (LWP 7255)]
[New Thread 0x7fff25ffb700 (LWP 7256)]
[New Thread 0x7fff257fa700 (LWP 7257)]
[New Thread 0x7fff24ff9700 (LWP 7258)]
[New Thread 0x7fff1700 (LWP 7259)]
[New Thread 0x7fff1effd700 (LWP 7260)]


Thread 1 "python3" received signal SIGSEGV, Segmentation fault.
0x77d5539b in PyModule_GetState () from /usr/lib64/libpython3.6m.so.1.0

I have no idea how to go to solve this SIGSEV 

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[Yade-users] [Question #706851]: FreeGlut versus FREEGLUT package

[Luc OGER]

New question #706851 on Yade:
https://answers.launchpad.net/yade/+question/706851

hi,
during my cmake process to generate the Makefile for the latest yade version 
2023-05-15 , I got a Warning about freeglut:
CMake Warning (dev) at 
/usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (FREEGLUT)
  does not match the name of the calling package (FreeGlut).  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):
  cMake/FindFreeGlut.cmake:14 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  CMakeLists.txt:898 (FIND_PACKAGE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Found FREEGLUT: /usr/include/GL

I don't know if it is critical but, right now the GUI display is no more 
working (i.e the yade --check option is working!)

for example in debug mode the first thread is :
Thread 1 (Thread 0x7f04fc3a4dc0 (LWP 109253) "yade"):
#0  0x7f04fb7c574f in wait4 () from /lib64/libc.so.6
#1  0x7f04fb73cba7 in do_system () from /lib64/libc.so.6
#2  0x7f04f8a3d73e in crashHandler (sig=11) at 
/home/oger/yade_full_install_local/trunk/core/main/pyboot.cpp:16
#3  
#4  0x7f04fbdb5efb in PyModule_GetState () from 
/usr/lib64/libpython3.6m.so.1.0
#5  0x7f0484192783 in ?? () from 
/usr/lib64/python3.6/lib-dynload/readline.cpython-36m-x86_64-linux-gnu.so
#6  0x7f04895b2e73 in rl_initialize () from /usr/lib64/../lib64/libedit.so.0
#7  0x7f0484192909 in PyInit_readline () from 
/usr/lib64/python3.6/lib-dynload/readline.cpython-36m-x86_64-linux-gnu.so
#8  0x7f04fbe44ba3 in _PyImport_LoadDynamicModuleWithSpec () from 
/usr/lib64/libpython3.6m.so.1.0
#9  0x7f04fbe43031 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#10 0x7f04fbdb4da5 in PyCFunction_Call () from 
/usr/lib64/libpython3.6m.so.1.0
#11 0x7f04fbe2caca in _PyEval_EvalFrameDefault () from 
/usr/lib64/libpython3.6m.so.1.0
#12 0x7f04fbe25fd6 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#13 0x7f04fbe2624f in ?? () from /usr/lib64/libpython3.6m.so.1.0
#14 0x7f04fbe26455 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#15 0x7f04fbe2a9d5 in _PyEval_EvalFrameDefault () from 
/usr/lib64/libpython3.6m.so.1.0
#16 0x7f04fbe2617f in ?? () from /usr/lib64/libpython3.6m.so.1.0
#17 0x7f04fbe26455 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#18 0x7f04fbe2a9d5 in _PyEval_EvalFrameDefault () from 
/usr/lib64/libpython3.6m.so.1.0
#19 0x7f04fbe2617f in ?? () from /usr/lib64/libpython3.6m.so.1.0
#20 0x7f04fbe26455 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#21 0x7f04fbe2a9d5 in _PyEval_EvalFrameDefault () from 
/usr/lib64/libpython3.6m.so.1.0
#22 0x7f04fbe2617f in ?? () from /usr/lib64/libpython3.6m.so.1.0
#23 0x7f04fbe26455 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#24 0x7f04fbe2a9d5 in _PyEval_EvalFrameDefault () from 
/usr/lib64/libpython3.6m.so.1.0
#25 0x7f04fbe2617f in ?? () from /usr/lib64/libpython3.6m.so.1.0
#26 0x7f04fbe26455 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#27 0x7f04fbe2a9d5 in _PyEval_EvalFrameDefault () from 
/usr/lib64/libpython3.6m.so.1.0
#28 0x7f04fbe2617f in ?? () from /usr/lib64/libpython3.6m.so.1.0
#29 0x7f04fbe2e370 in _PyFunction_FastCallDict () from 
/usr/lib64/libpython3.6m.so.1.0
#30 0x7f04fbd6c9ee in _PyObject_FastCallDict () from 
/usr/lib64/libpython3.6m.so.1.0
#31 0x7f04fbd6d8c4 in _PyObject_CallMethodIdObjArgs () from 
/usr/lib64/libpython3.6m.so.1.0
#32 0x7f04fbe43d9c in PyImport_ImportModuleLevelObject () from 
/usr/lib64/libpython3.6m.so.1.0
#33 0x7f04fbe2c79f in _PyEval_EvalFrameDefault () from 
/usr/lib64/libpython3.6m.so.1.0
#34 0x7f04fbe25fd6 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#35 0x7f04fbe2624f in ?? () from /usr/lib64/libpython3.6m.so.1.0
#36 0x7f04fbe26455 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#37 0x7f04fbe2928e in _PyEval_EvalFrameDefault () from 
/usr/lib64/libpython3.6m.so.1.0
#38 0x7f04fbe25fd6 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#39 0x7f04fbe26113 in PyEval_EvalCode () from 
/usr/lib64/libpython3.6m.so.1.0
#40 0x7f04fbe4fa60 in ?? () from /usr/lib64/libpython3.6m.so.1.0
#41 0x7f04fbe51891 in PyRun_FileExFlags () from 
/usr/lib64/libpython3.6m.so.1.0
#42 0x7f04fbe519ed in PyRun_SimpleFileExFlags () from 
/usr/lib64/libpython3.6m.so.1.0
#43 0x7f04fbe68a91 in Py_Main () from /usr/lib64/libpython3.6m.so.1.0
#44 0x562b12a00c90 in main ()
[Inferior 1 (process 109253) detached]
Erreur de segmentation (core dumped)





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Re: [Yade-users] [Question #693194]: use of Law2_ScGeom_CapillaryPhys_Capillarity with variable pressure does not change results

[Luc OGER]

Question #693194 on Yade changed:
https://answers.launchpad.net/yade/+question/693194

Status: Answered => Open

Luc OGER is still having a problem:
Hi Jérôme,
here the full code and the table for the batch test with only the capillray 
pressure changes : 1000 and 5000
exactly the same particle positions (611 moving) for all of them after 1913000 
steps !!
if I am testing type = 3 it is alaso the same thing : no difference??
of course the results are different between the three cases (1 dry, 2 hertz,3 
linear) 

So I don't catch why these engine loops are not playing well?

 
table :
model_type packing_fraction pas_box theta_max converg_min cover_pack_fraction 
init_seed friction ratio Cap_Pres_Imposed
2 .55 .1 80.0 .002 0.3 625 0.5 2. 1000
2 .55 .1 80.0 .002 0.3 625 0.5 2. 5000

and the code :
# avec directory : +'/'+
# The components of the batch are:
# 1. table with parameters, one set of parameters per line (ccc.table)
# 2. readParamsFromTable which reads respective line from the parameter file
# 3. the simulation muse be run using yade-batch, not yade
#
# $ yade-batch --job-threads=1 03-oedometric-test.table 03-oedometric-test.py
#

# load parameters from file if run in batch
# default values are used if not run from batch
# gravity deposition in box, showing how to plot and save history of data,
# and how to control the simulation while it is running by calling
# python functions from within the simulation loop


#pas_box theta_max converg_min cover_pack_fraction init_seed friction ratio
#model_type bottom_cover pas_box theta_max converg_min cover_pack_fraction 
init_seed friction ratio
#3 .55 .1 80.0 .002 0.3 625 0.5 2.5 5000
readParamsFromTable(model_type=1, packing_fraction=0.6,pas_box=0.1, 
theta_max=45.0, converg_min=0.5,cover_pack_fraction=.2,init_seed=10, 
friction=0.5,ratio=2.5,Cap_Pres_Imposed=1000)
# make rMean, rRelFuzz, maxLoad accessible directly as variables later
from yade.params.table import *

# import yade modules that we will use below
from yade import pack, plot, export,math
global ratio,nombre,friction # size ratio between the glued spheres and the 
moving ones
global cover_pack_fraction ,converg_min, init_seed,nombre_moving # coverage 
percent for moving spheres
global  i_pas, 
box_size,pas_box,rayon,step0,step1,step2,step_precedent,gravity_y,gravity_z,theta_max,theta_max,nom_file,filename_yade,traitement_file,str_Angle
global angle_actif,angle

#some parameters passed by batch_table:

batch : friction= 0.5
batch : theta_max   = 30.0
batch : pas_box = 0.1
batch : ratio = 3   # size ratio between the glued spheres and the moving 
ones
batch : cover_pack_fraction = 0.2 # coverage percent for moving spheres
batch : init_seed=10
batch : packing_fraction = 70./100.
batch : model_type = 1   
#some parameters:
shear_modulus   = 1e5
poisson_ratio   = 0.3
young_modulus   = 2*shear_modulus*(1+poisson_ratio)
local_damping   = 0.01
viscous_normal  = 0.021
viscous_shear   = 0.8*viscous_normal
position_init   = numpy.arange(1200*4, dtype=float)
position_init   = position_init.reshape((1200,4))
numpy.zeros_like(position_init)
Cap_Pressure = 0.0  #valeur initiale 
angle   = math.atan(friction)   # value in radians for friction 
Angle
angle_init  = math.atan(0.10)
angle_actif = angle_init
# initialisation coordonnees initiales
#newTable("position_init",1200,4) # Create a new table with 5 rows and 3 column
#creating a material (FrictMat):
#frictionAngle(=.5)
# Contact friction angle (in radians). Hint : use ‘radians(degreesValue)’ in 
python scripts.

id_SphereMat=O.materials.append(FrictMat(young=young_modulus,poisson=poisson_ratio,density=2500,frictionAngle=angle_actif,label="glass_beads"))
SphereMat=O.materials[id_SphereMat]

   
#1 = >hertz model sans capillary forces
if model_type == 1:#hertz model with capillary forces
converg_min = converg_min
elif model_type == 2: #hertz model with capillary forces
converg_min = 10.0*converg_min
else:   #for linear model only
converg_min = 10*converg_min
box_size = 4.0
i_pas = 0 

step0 = 0
step1 = 0
step2 = 0
step_precedent = 0
mask1=0b01
mask2=0b10
mask3=0b11

gravity_y = 9.81*sin( pas_box*i_pas*3.14/180.0)
gravity_z = 9.81*cos( pas_box*i_pas*3.14/180.0)

O.reset

# create rectangular box from facets
O.bodies.append(geom.facetBox((box_size/2.0,box_size/2.0,box_size*0.62),(box_size/2.0,box_size/2.0,box_size*0.62),wallMask=31))

# create empty sphere packing
# sphere packing is not equivalent to particles in simulation, it contains only 
the pure geometry

rayon = 0.025
height = 5. * rayon
nombre= int(packing_fraction*(box_size*box_size)/(rayon*rayon*3.14159) )
print("nombre = ",nombre)
print("friction angle = ",angle_actif)
print("Model type (1 sec- 2 hertz, 3 lineaire) = ",model_type)
sp=pack.SpherePack()
# generate random

Re: [Yade-users] [Question #693194]: use of Law2_ScGeom_CapillaryPhys_Capillarity with variable pressure does not change results

[Luc OGER]

Question #693194 on Yade changed:
https://answers.launchpad.net/yade/+question/693194

Status: Answered => Open

Luc OGER is still having a problem:
Hi Jerôme,

my engine is exactly the same as in the reference [*]:
 #for linear model only
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()], 
avoidSelfInteractionMask = mask2),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_CapillaryPhys()],#for 
linear model only
[Law2_ScGeom_FrictPhys_CundallStrack()],#for 
linear model only
),

Law2_ScGeom_CapillaryPhys_Capillarity(capillaryPressure=Cap_Pressure),#for 
linear model only

NewtonIntegrator(damping=local_damping,gravity=(0,-gravity_y,-gravity_z),label='Newton_integrator'),
# call the checkUnbalanced function (defined below) every 2 
seconds

PyRunner(command='checkUnbalanced()',iterPeriod=1000,label='checker'),
]

I guess that the computeThings() is only for obtaining intermediate
output? and does not play a rol ein the fcap calculation?

In my problem, my main concern is the transiont between the packing preparation 
where the capillary pressure is set to zero in order to have identical packing 
structure then set to the defined Cap_Pressure.
In my guess, this will not create new contact so no new need of fcap caluation?

maybe I am wrong somewhere?

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[Yade-users] [Question #693194]: use of Law2_ScGeom_CapillaryPhys_Capillarity with variable pressure does not change results

[Luc OGER]

New question #693194 on Yade:
https://answers.launchpad.net/yade/+question/693194

Hello,
I am trying a simple test case with rolling  large spheres on top of small ones 
by using the two 'classical capillary exemples present in the directory :
./examples/capillaryLaplaceYoung/CapillaryPhys-example.py

in both cases changing the capillaryPressure in 
Law2_ScGeom_CapillaryPhys_Capillarity(capillaryPressure=) produces the same 
results !!
in complement in some previous answers in the Yade-help you are talking about 
two 'similar' laws :
Law2_ScGeom_CapillaryPhys_Capillarity and 
Law2_ScGeom_CapillaryPhys_Capillarity1 

so what is the actual situation and which one we have to use in order to see 
some differences?

thanks in adance for your help

Luc

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Re: [Yade-users] [Question #692681]: result indeterminism and MPI=OFF

[Luc OGER]

Question #692681 on Yade changed:
https://answers.launchpad.net/yade/+question/692681

Status: Answered => Solved

Luc OGER confirmed that the question is solved:
Dear Jan

in my first rapid test, the change to iterPeriod  solves my problem

thanks

Luc

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Re: [Yade-users] [Question #692681]: result indeterminism and MPI=OFF

[Luc OGER]

Question #692681 on Yade changed:
https://answers.launchpad.net/yade/+question/692681

Luc OGER gave more information on the question:
with the cmake..
 cmake -DENABLE_MPI=OFF -DOpenGL_GL_PREFERENCE=GLVND 
-DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=../install 
-DPYTHON_VERSION=3 -DDISABLE_SAVE_TEMPS=1 -W ../trunk

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Re: [Yade-users] [Question #692681]: result indeterminism and MPI=OFF

[Luc OGER]

Question #692681 on Yade changed:
https://answers.launchpad.net/yade/+question/692681

Status: Needs information => Open

Luc OGER gave more information on the question:
here the cmake command

and the py code
#Result indeterminism
#It is naturally expected that running the same simulation several times will 
give exactly the same results: although the computation is done 
#with finite precision, round-off errors would be deterministically the same at 
every run. While this is true for single-threaded computation 
#where exact order of all operations is given by the simulation itself, it is 
not true anymore in multi-threaded computation which is described in detail in 
later sections.
#The straight-forward manner of parallel processing in explicit DEM is given by 
the possibility of treating interactions in arbitrary order. 
#Strain and stress is evaluated for each interaction independently, but forces 
from interactions have to be summed up. If summation order is also arbitrary 
#(in Yade, forces are accumulated for each thread in the order interactions are 
processed, then summed together), then the results can be slightly different. 
For instance

#(1/10.)+(1/13.)+(1/17.)=0.23574660633484162
#(1/17.)+(1/13.)+(1/10.)=0.23574660633484165

#As forces generated by interactions are assigned to bodies in quasi-random 
order, summary force Fi
#on the body can be different between single-threaded and multi-threaded 
computations, but also between different runs of multi-threaded computation 
with exactly the same parameters. 
#Exact thread scheduling by the kernel is not predictable since it depends on 
asynchronous events (hardware interrupts) and other unrelated tasks running on 
the system; 
#and it is thread scheduling that ultimately determines summation order of 
force contributions from interactions.


# The components of the batch are:
# 1. table with parameters, one set of parameters per line (ccc.table)
# 2. readParamsFromTable which reads respective line from the parameter file
# 3. the simulation muse be run using yade-batch, not yade
#
# $ yade-batch --job-threads=1 03-oedometric-test.table 03-oedometric-test.py
#

# load parameters from file if run in batch
# default values are used if not run from batch
# gravity deposition in box, showing how to plot and save history of data,
# and how to control the simulation while it is running by calling
# python functions from within the simulation loop


#pas_box theta_max converg_min cover_pack_fraction init_seed friction ratio
#model_type bottom_cover pas_box theta_max converg_min cover_pack_fraction 
init_seed friction ratio
#.1 55. .002 0.1 210 0.4 4
readParamsFromTable(model_type=1, packing_fraction=0.5,pas_box=0.5, 
theta_max=5.0, nb_cycles=3,converg_min=0.5,nb_layers=10,init_seed=10, 
friction=0.15,ratio=1)
# make rMean, rRelFuzz, maxLoad accessible directly as variables later
from yade.params.table import *

# import yade modules that we will use below
from yade import pack, plot, export,math
global ratio,nombre,position_prec,position_init # size ratio between the glued 
spheres and the moving ones
global converg_min, init_seed,nombre_moving,z_max # coverage percent for moving 
spheres
global  i_pas, 
box_size,pas_box,rayon,step0,step1,step2,step_precedent,gravity_y,gravity_z,theta_max,theta_max,nom_file,filename_yade,traitement_file,str_Angle,
 nb_cycles,numero_cycle,num_Angle


#some parameters passed by batch_table:

batch : friction= 0.5
batch : theta_max   = 30.0
batch : pas_box = 0.1
batch : ratio = 3   # size ratio between the glued spheres and the moving 
ones
batch : cover_pack_fraction = 0.2 # coverage percent for moving spheres
batch : init_seed=10
batch : packing_fraction = 70./100.
batch : model_type = 1   

#some parameters:
shear_modulus   = 1e5
poisson_ratio   = 0.3
young_modulus   = 2*shear_modulus*(1+poisson_ratio)
local_damping   = 0.01
viscous_normal  = 0.021
viscous_shear   = 0.8*viscous_normal
angle   = math.atan(friction)
# initialisation coordonnees initiales
#newTable("position_init",600,4) # Create a new table with 5 rows and 3 column
#creating a material (FrictMat):
id_SphereMat=O.materials.append(FrictMat(young=young_modulus,poisson=poisson_ratio,density=2500,frictionAngle=angle,label="glass_beads"))
SphereMat=O.materials[id_SphereMat]
 
box_size = 1.0
i_pas = 0 
step0=0
mask1=0b01
num_Angle= pas_box*i_pas
gravity_y = 9.81*sin( num_Angle*3.14/180.0)
gravity_z = 9.81*cos( num_Angle*3.14/180.0)

O.reset

nom_file=str(model_type)+"_"+str(packing_fraction)+"_"+str(theta_max)+"_"+str(nb_cycles)+"_"+str(nb_layers)+"_"+str(ratio)+'_'+str(friction)+'_'+str(pas_box)+'_'+str(converg_min)+'_'+str(init_seed)
filename_yade=nom_file+'.yade'
rayon = 0.025
height = 5.0*rayon*nb_layers
# create rectangular box from facets
O.bodies.append(geom.facetBox((box_size/2.0,box_size/2.0,height),(box_s

[Yade-users] [Question #692681]: result indeterminism and MPI=OFF

[Luc OGER]

New question #692681 on Yade:
https://answers.launchpad.net/yade/+question/692681

Helle,

I am trying to 'compare' several runs made with different evolutions of 
parameters with time, wich implies the same 'initial' behavior ,
so according to 
https://yade-dem.org/doc/formulation.html?highlight=indeterminism#result-indeterminism
 using a single thread version of Yade would give the same results

so I have compiled with ENABLE_MPI=OFF and seed defined in the makeCloud  
identical... BUT I got different results already just after the gravity 
deposition output after having launched twice the same py code though my batch 
command.

What I have missed to obtain my goal?

Luc




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[Yade-users] [Question #692478]: Interrogation about generation of capillary files byMatlab program

[Luc OGER]

New question #692478 on Yade:
https://answers.launchpad.net/yade/+question/692478

Hi,

in order to test a different contact angle for my  simulation with capillary 
interaction I am using the Matalb programs writeCapFile.m and its two linked 
ones. 
I started first by using the inital case theta=0 and I am surprised by the non 
continuous evolution of the calculated maximum suction versus the rRatio:
see the matlab output:
 For r = 1, maximum suction found: final uc = 9230
 For r = 1.1, maximum suction found: final uc = 16749
 For r = 1.25, maximum suction found: final uc = 19036
 For r = 1.5, maximum suction found: final uc = 22843
-
 For r = 1.75, maximum suction found: final uc = 26389
 For r = 2, maximum suction found: final uc = 21154
--
 For r = 3, maximum suction found: final uc = 31738
 For r = 4, maximum suction found: final uc = 41922
 For r = 5, maximum suction found: final uc = 51901
 For r = 10, maximum suction found: final uc = 88968

The jump down during the evolution between 1.75 and 2 is quite strange  it 
is like two different slopes

is it two different ways of calculating the data ?
how this fact can influence the output files M(r=...) ?

thanks in advance for your explanation 

Luc


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Re: [Yade-users] [Question #691593]: avoid this message : "The constructor with a shareWidget is deprecated, use the regular contructor instead."

[Luc OGER]

Question #691593 on Yade changed:
https://answers.launchpad.net/yade/+question/691593

Luc OGER posted a new comment:
here my modification which avoid the warning and still generates a
graphical view :


GLViewer.cpp
line 64-65:

GLViewer::GLViewer(int _viewId, const shared_ptr& _renderer, 
QOpenGLWidget* parent)
: QGLViewer(/*parent*/ (QWidget*) parent)

GLViewer.hpp
line 92:
GLViewer(int viewId, const shared_ptr& renderer, 
QOpenGLWidget* Widget = 0);

OpenGLManager.cpp
line 56:

views.push_back(shared_ptr(boost::make_shared(0, renderer, 
/*QopenGLWidget*/ (QOpenGLWidget*)0)));

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Re: [Yade-users] [Question #691593]: avoid this message : "The constructor with a shareWidget is deprecated, use the regular contructor instead."

[Luc OGER]

Question #691593 on Yade changed:
https://answers.launchpad.net/yade/+question/691593

Luc OGER posted a new comment:
just some complementary inormation:
"After Qt 5.3's introduction of QQuickWidget, Qt 5.4 adds QOpenGLWidget, the 
long-awaited replacement for the legacy QGLWidget" from 
https://www.qt.io/blog/2014/09/10/qt-weekly-19-qopenglwidget

so I will try to modify /gui/qt5/GLViewer.cpp according to the new
specification by eliminating the shareWidget

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Re: [Yade-users] [Question #691593]: avoid this message : "The constructor with a shareWidget is deprecated, use the regular contructor instead."

[Luc OGER]

Question #691593 on Yade changed:
https://answers.launchpad.net/yade/+question/691593

Status: Open => Solved

Luc OGER confirmed that the question is solved:
Dear Jérôme

thanks for the hint where to find the 'solution': it is effectively
inside the libQGLviewer 2.7.0 to 2.7.2 library, especially inside the
qglviewer.cpp:

#ifndef DOXYGEN
/*! These contructors are deprecated since version 2.7.0, since they are not
 * supported by QOpenGlWidget */

/*! Constructor. See \c QGLWidget documentation for details.

All viewer parameters (display flags, scene parameters, associated objects...)
are set to their default values. See the associated documentation.

If the \p shareWidget parameter points to a valid \c QGLWidget, the QGLViewer
will share the OpenGL context with \p shareWidget (see isSharing()). */
QGLViewer::QGLViewer(QWidget *parent, const QGLWidget *shareWidget,
 Qt::WindowFlags flags)
: QOpenGLWidget(parent, flags) {
  Q_UNUSED(shareWidget)
  qWarning("The constructor with a shareWidget is deprecated, use the regular "
   "contructor instead.");
  defaultConstructor();
}

now I will try to find a solution

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[Yade-users] [Question #691593]: avoid this message : "The constructor with a shareWidget is deprecated, use the regular contructor instead."

[Luc OGER]

New question #691593 on Yade:
https://answers.launchpad.net/yade/+question/691593

Dear sir,

It i not a crucial point... but I want to avoid having this warning message at 
each run of a yade script:"The constructor with a shareWidget is deprecated, 
use the regular contructor instead."
I am using the latest compiled version of yade from june : 
2020-06-23.git-f03a37c on  Opensuse 15.1

how and where to modifiy things to do it?

Luc 

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:
the last result without -DENABLE_MPI=OFF on OPENSUSE 15.1:
0b00 bb br gg gr rr
0b10 br gg gr
0b01 bb br gr
0b11 br gr


so the error link to MPI option is prooved!!

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:
complementary information: the two previous yade were made with UBUNTU
19!

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:
new information:

with the  Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz Irecent computer)  got the 
same kind of answer :
with -DENABLE_MPI=OFF : bad results
without DENABLE_MPI : same "good" results such as mask = 0b01 : bb br gr

i don't know how to interpret this facts

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:
I have just done a basic test with two different cmake option on my
UBUNTU 19 machine : enable-mpi=off or not

here the two answer for the #20 mask py program:
CASE 1: with MPI:
 /home/oger/full-yade-local/install_with_MPI/bin/yade-2019-08-30.git-a2f1fbf 
mask_test.py
Welcome to Yade 2019-08-30.git-a2f1fbf
Using python version: 3.7.3 (default, Apr  3 2019, 05:39:12)
[GCC 8.3.0]
TCP python prompt on localhost:9000, auth cookie `cssdyk'
XMLRPC info provider on http://localhost:21000
Running script mask_test.py
br gg gr
[[ ^L clears screen, ^U kills line. F12 controller, F11 3D view (press "h" in 
3D view for help), F10 both, F9 generator, F8 plot. ]]

CASE 2 WITHOUT MPI:
oger@hp-1021:~/programme_perso/yade$ 
/home/oger/full-yade-local/install/bin/yade-2019-08-30.git-a2f1fbf mask_test.py
Welcome to Yade 2019-08-30.git-a2f1fbf
Using python version: 3.7.3 (default, Apr  3 2019, 05:39:12)
[GCC 8.3.0]
TCP python prompt on localhost:9000, auth cookie `eskacd'
XMLRPC info provider on http://localhost:21000
Running script mask_test.py
bb br gb gg gr rr
[[ ^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 all other OPENSUSE machines I have always put -DENABLE_MPI=OFF

which can epxlain the problemfor the solution it is another story!

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:

here the bug for the new intel AND also the old one: same list!!
bugs: cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds 
swapgs

full old intel cpuinfo:

processor   : 7
vendor_id   : GenuineIntel
cpu family  : 6
model   : 42
model name  : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
stepping: 7
microcode   : 0x2f
cpu MHz : 1725.371
cache size  : 8192 KB
physical id : 0
siblings: 8
core id : 3
cpu cores   : 4
apicid  : 7
initial apicid  : 7
fpu : yes
fpu_exception   : yes
cpuid level : 13
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov 
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm 
constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid 
aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr 
pdcm pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx lahf_lm 
epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid xsaveopt 
dtherm ida arat pln pts md_clear flush_l1d
bugs: cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds 
swapgs
bogomips: 6784.67
clflush size: 64
cache_alignment : 64
address sizes   : 36 bits physical, 48 bits virtual
power management:


processor   : 7
vendor_id   : GenuineIntel
cpu family  : 6
model   : 94
model name  : Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
stepping: 3
microcode   : 0xcc
cpu MHz : 800.039
cache size  : 6144 KB
physical id : 0
siblings: 8
core id : 3
cpu cores   : 4
apicid  : 7
initial apicid  : 7
fpu : yes
fpu_exception   : yes
cpuid level : 22
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov 
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb 
rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology 
nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq dtes64 monitor ds_cpl 
vmx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe 
popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch 
cpuid_fault epb invpcid_single pti ssbd ibrs ibpb stibp tpr_shadow vnmi 
flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms 
invpcid rtm mpx rdseed adx smap clflushopt intel_pt xsaveopt xsavec xgetbv1 
xsaves dtherm ida arat pln pts hwp hwp_notify hwp_act_window hwp_epp md_clear 
flush_l1d
bugs: cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds 
swapgs
bogomips: 5184.00
clflush size: 64
cache_alignment : 64
address sizes   : 39 bits physical, 48 bits virtual
power management:
full new intel cpuinfo:

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:
Here the cmake comannd which is really the simplest one :
cmake DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=../install 
-DPYTHON_VERSION=3 -DDISABLE_SAVE_TEMPS=1 -DENABLE_MPI=OFF ../trunk

and I have tried to compile and run yade on several machines, but the 
"simplest" comparison test is the following :
on the same laptop with new Intel processor (see #35) both Opensuse 15.1 and 
Ubuntu 19 generates the same bitmask error (see#28)

on th same old PC with older intel processor  (see #35) the openuse 15.1
gave the answer as #28 BUT the UBUNTU 19 gave the answer #35

Sorry but I am unable to answer to the #39 request as i don't know how
and where to look for...

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Re: [Yade-users] [Question #683511]: meaning of ENABLE_MASK_ARBITRARY

[Luc OGER]

Question #683511 on Yade changed:
https://answers.launchpad.net/yade/+question/683511

Status: Needs information => Open

Luc OGER gave more information on the question:
i am still trying to understand why with some CPU environment the use of
collider.avoidSelfInteractionMask is funcitonning well or not (see
https://answers.launchpad.net/yade/+question/682290)

So I founded this option but without knowing how it is working

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[Yade-users] [Question #683511]: meaning of ENABLE_MASK_ARBITRARY

[Luc OGER]

New question #683511 on Yade:
https://answers.launchpad.net/yade/+question/683511

I need some explanation:

In order to understand why the use of the mask is not functionning in some 
recent CPU envrionment (see 682290), I am looking inside the code of 
collider.cpp or body.cpp and I founded the ifdef option of  YADE_MASK_ARBITRARY.
I guess that this option is controled by  ENABLE_MASK_ARBITRARY cmake option 
but I did not founded what is his use and his need.

could you provied me some hints or links to the place for th explanation




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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:
Strange behaviour :
2 UBUNTU 19 environments on two differents machines:
the same compiler option and the same yade-2019-08-26 
result 
--on an old machine (cpu family : 6
model   : 42
model name  : Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz
stepping: 7
microcode   : 0x2f
cpu MHz : 1725.371
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov 
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm 
constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid 
aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr 
pdcm pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx lahf_lm 
epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid xsaveopt 
dtherm ida arat pln pts md_clear flush_l1d)
the mask seems too work

--- on the new machine (cpu family  : 6
model   : 94
model name  : Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
stepping: 3
microcode   : 0xcc
cpu MHz : 800.039) the 
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov 
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb 
rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology 
nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq dtes64 monitor ds_cpl 
vmx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe 
popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch 
cpuid_fault epb invpcid_single pti ssbd ibrs ibpb stibp tpr_shadow vnmi 
flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms 
invpcid rtm mpx rdseed adx smap clflushopt intel_pt xsaveopt xsavec xgetbv1 
xsaves dtherm ida arat pln pts hwp hwp_notify hwp_act_window hwp_epp md_clear 
flush_l1d)
the result are similar to the bad previous series : full or no interactions??
this confirm the processor coompilation problem as suggested by Janek

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Status: Answered => Open

Luc OGER is still having a problem:
Hi,

i have compiled yade-2019-08-25.git-0f74746 and run again the test #20... and 
this time the results is quite different!:
mask=0b00 : bb br gg gr rr
mask=0b01 : bb br gr
mask=0b10 : br gg gr
mask=0b11 : br gr

I will check my program now!

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER posted a new comment:
I have tried with two very different machines:
laptop : hp envy and server Dell R960
BUT I got the same answer???

here the CPUINFO:

server Dell :
processor   : 127
vendor_id   : GenuineIntel
cpu family  : 6
model   : 79
model name  : Intel(R) Xeon(R) CPU E7-4850 v4 @ 2.10GHz
stepping: 1
microcode   : 0xb2e
cpu MHz : 2094.877
cache size  : 40960 KB
physical id : 3
siblings: 32
core id : 15
cpu cores   : 16
apicid  : 127
initial apicid  : 127
fpu : yes
fpu_exception   : yes
cpuid level : 20
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov 
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb 
rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology 
nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est 
tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt 
tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch 
cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti ssbd ibrs ibpb stibp 
tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep 
bmi2 erms invpcid rtm cqm rdt_a rdseed adx smap intel_pt xsaveopt cqm_llc 
cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts flush_l1d
bugs: cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf
bogomips: 4191.91
clflush size: 64
cache_alignment : 64
address sizes   : 46 bits physical, 48 bits virtual

Laptop HP-ENVY:
processor   : 7
vendor_id   : GenuineIntel
cpu family  : 6
model   : 94
model name  : Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz
stepping: 3
microcode   : 0xcc
cpu MHz : 2600.000
cache size  : 6144 KB
physical id : 0
siblings: 8
core id : 3
cpu cores   : 4
apicid  : 7
initial apicid  : 7
fpu : yes
fpu_exception   : yes
cpuid level : 22
wp  : yes
flags   : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov 
pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb 
rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology 
nonstop_tsc cpuid aperfmperf tsc_known_freq pni pclmulqdq dtes64 monitor ds_cpl 
vmx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe 
popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch 
cpuid_fault epb invpcid_single pti ssbd ibrs ibpb stibp tpr_shadow vnmi 
flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid 
rtm mpx rdseed adx smap clflushopt intel_pt xsaveopt xsavec xgetbv1 xsaves 
dtherm ida arat pln pts hwp hwp_notify hwp_act_window hwp_epp md_clear flush_l1d
bugs: cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds
bogomips: 5184.00
clflush size: 64
cache_alignment : 64
address sizes   : 39 bits physical, 48 bits virtual

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER posted a new comment:
it is only a "basic" one :
cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_PREFIX=../install 
-DPYTHON_VERSION=3  -DDISABLE_SAVE_TEMPS=1 -DENABLE_MPI=OFF ../trunk


and to extend some tests :
here the results with 2 or 3 bit long for the mask!!
if mb,mg,mr = 0b10, 0b01, 0b11
0b00 : bb br gb gg gr rr
0b10 : bb br gb gg gr rr
0b01 :
0b11 :


if mb,mg,mr = 0b100, 0b010, 0b110
0b000 : bb br gb gg gr rr
0b010 : bb br gb gg gr rr
0b100 : bb br gb gg gr rr
0b110 : bb br gb gg gr rr

0b001 : 
0b011 : 
0b101 : 
0b111 : 

if mb,mg,mr = 0b101, 0b011, 0b111
0b000 : bb br gb gg gr rr
0b010 : bb br gb gg gr rr
0b100 : bb br gb gg gr rr
0b110 : bb br gb gg gr rr

0b001 : 
0b011 : 
0b101 : 
0b111 : 

so results only controled from bit in position 0 at right side

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:
I have run #20
and the answer is strange :
Mask=0b00 : bb br gb gg gr rr
Mask=0b10 : bb br gb gg gr rr

Mask = 0b01 or 0b11 = no line ouput ??

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Status: Needs information => Open

Luc OGER gave more information on the question:
Same as reply in#9 every sphere passed through or every sphere interact
with all the others

OK I will try tu write as #19 20

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Status: Needs information => Open

Luc OGER gave more information on the question:
I have installed UBUNTU 19 on one USB HDD and compiled the last yade:, 
yade-2019-08-11
Then I have run my py code... And I got exactly the same behavior !!!

So I agree with Jan'remark about the luck?

I will modify the collidermask use and position in the ode

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Status: Answered => Open

Luc OGER is still having a problem:
I am using only the basic cmake option plus MPI=OFF only

I have tried with several vesion or Yade but alwaays with OpenSuse 15.1

after my vacations i will install a linux UBUNTU to test and so avoid
this kind of problem

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Status: Answered => Open

Luc OGER is still having a problem:
aSIMask=0b00 full interaction
aSIMask=0b01 full no interaction
aSIMask=0b10 full interaction
aSIMask=0b11 full no interaction

full no interaction = means all the spheres on top of the bottom fixed
one are not interacting with this bottom one and are falling down
outside the system

full interaction = means all the spheres are bouncing with all the ones
like the standard 2spheres bouncing case.


I have no special interaction depending on the avoidSelfInteractionMask choice 

PS I don't catch the meaning and the issue of the 10 lines after O.step()???
I have no problem of position or duplicated according to the initial display of 
the full sphere setup.

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:
I have just tried with yade-2019-08-08.git-775ae74 and I got the same
problem!!

I guess that some compiler options are not going well in some  bit test?

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Status: Answered => Open

Luc OGER is still having a problem:
It is a july version 
Like 12-07

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Luc OGER gave more information on the question:
Dear Bruno,

 As I don't know what is this function "avoidSelf_after_reloading" I
have not played with it.

how i can check its value or its rule?

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Status: Answered => Open

Luc OGER is still having a problem:
When I run it on my computer this is not what I get :
in the 5th column with  avoidSelf=1 all the three balls on top of the blue 
fixed one passed through this one
and it is identical for the 5 colums series of events : every thing passed 
through...

this is what I don't catch especially if it is working on your version
of Yade

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Re: [Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

Question #682290 on Yade changed:
https://answers.launchpad.net/yade/+question/682290

Status: Answered => Open

Luc OGER is still having a problem:
sorry for the creation of this long discussion but i am still not happy with 
the results of this Collider.avoidSelfInteractionMask functionnality:
according to the comment by Jérome (06-08-2019) if the 
Collider.avoidSelfInteractionMask=0b01 the blue would interact with themselves
but when I modified the line with the collider to 0b01 and run my example, in 
the 5th column the blue one on the column is not interacting with the fixed 
blue one at the bottom

it was part of the analysis and the bottom of the initial post witht th
four possible choices for the collider and the full no or yes
interaction for all of them??? = not really linked to the bit mask
position

back here:
and the result for collider.avoidSelfInteractionMask
0b00 full interaction
0b01 full no interaction
0b10 full interaction
0b11 full no interaction

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[Yade-users] [Question #682290]: the correct use of collider.avoidSelfInteractionMask ?

[Luc OGER]

New question #682290 on Yade:
https://answers.launchpad.net/yade/+question/682290

Hello,

 I am trying to setup properly the possible interaction between different group 
of sphere: some can interact with other, some cannot interact with themselves

here the basic code
# basic simulation showing sphere falling ball gravity,
# bouncing against another sphere representing the support

# DATA COMPONENTS

# add 2 particles to the simulation
# they the default material (utils.defaultMat)
mask1=0b10
mask2=0b01
mask3=0b11

O.bodies.append([
# fixed: particle's positionin space will not change (support)
sphere(center=(0,0,0),radius=.5,fixed=True,mask=mask1,color=(0,0,1)),   
#fond immobile
sphere(center=(0,0,2),radius=.5,fixed=False,mask=mask2,color=(0,1,0)),
# these particles are free, subject to dynamics
sphere(center=(0,0,4),radius=.5,fixed=False,mask=mask3,color=(1,0,0)),
sphere(center=(0,0,6),radius=.5,fixed=False,mask=mask3,color=(1,0,0)),
# fixed: particle's positionin space will not change (support)
sphere(center=(3,0,0),radius=.5,fixed=True,mask=mask1,color=(0,0,1)),   
#fond immobile
sphere(center=(3,0,2),radius=.5,fixed=False,mask=mask3,color=(1,0,0)),
# these particles are free, subject to dynamics
sphere(center=(3,0,4),radius=.5,fixed=False,mask=mask2,color=(0,1,0)),
sphere(center=(3,0,6),radius=.5,fixed=False,mask=mask2,color=(0,1,0)),
# fixed: particle's positionin space will not change (support)
sphere(center=(6,0,0),radius=.5,fixed=True,mask=mask3,color=(1,0,0)),   
#fond immobile
sphere(center=(6,0,2),radius=.5,fixed=False,mask=mask1,color=(0,0,1)),
# these particles are free, subject to dynamics
sphere(center=(6,0,4),radius=.5,fixed=False,mask=mask3,color=(1,0,0)),
sphere(center=(6,0,6),radius=.5,fixed=False,mask=mask2,color=(0,1,0)),
# fixed: particle's positionin space will not change (support)
sphere(center=(9,0,0),radius=.5,fixed=True,mask=mask2,color=(0,1,0)),   
#fond immobile
sphere(center=(9,0,2),radius=.5,fixed=False,mask=mask1,color=(0,0,1)),
# these particles are free, subject to dynamics
sphere(center=(9,0,4),radius=.5,fixed=False,mask=mask3,color=(1,0,0)),
sphere(center=(9,0,6),radius=.5,fixed=False,mask=mask2,color=(0,1,0)),
# fixed: particle's positionin space will not change (support)
sphere(center=(12,0,0),radius=.5,fixed=True,mask=mask1,color=(0,0,1)),  
 #fond immobile
sphere(center=(12,0,2),radius=.5,fixed=False,mask=mask1,color=(0,0,1)),
# these particles are free, subject to dynamics
sphere(center=(12,0,4),radius=.5,fixed=False,mask=mask3,color=(1,0,0)),
sphere(center=(12,0,6),radius=.5,fixed=False,mask=mask2,color=(0,1,0)),






])

# FUNCTIONAL COMPONENTS
collider.avoidSelfInteractionMask = 0b00


# simulation loop -- see presentation for the explanation
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb()]),
InteractionLoop(
[Ig2_Sphere_Sphere_ScGeom()],# collision geometry
[Ip2_FrictMat_FrictMat_FrictPhys()], # collision "physics"
[Law2_ScGeom_FrictPhys_CundallStrack()]   # contact law -- 
apply forces
),
# Apply gravity force to particles. damping: numerical dissipation of 
energy.
NewtonIntegrator(gravity=(0,0,-9.81),damping=0.1)

]

# set timestep to a fraction of the critical timestep
# the fraction is very small, so that the simulation is not too fast
# and the motion can be observed
O.dt=.5e-4*PWaveTimeStep()

# save the simulation, so that it can be reloaded later, for experimentation
O.saveTmp()

so the three masks are :
mask1=0b10  blue
mask2=0b01  green
mask3=0b11  red

and the result for  collider.avoidSelfInteractionMask
0b00full interaction
0b01full no interaction
0b10full interaction
0b11full no interaction

 according to the definiton of the mask "This mask is used to avoid the 
interactions inside a group of particles. To do so, the particles must have the 
exact same mask and that mask should have one bit in common with this 
avoidSelfInteractionMask as for their binary representations" this should not 
be ful or zero interactions???

where I made a mistake?


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[Yade-users] [Question #680628]: InsertNextTupleValue errror in Gl1_PotentialParticle.cpp

[Luc OGER]

New question #680628 on Yade:
https://answers.launchpad.net/yade/+question/680628

When I try to compile the yade-daily package with VTK 8, I got 5 errors inside 
the Gl1_PotentialParticle.cpp file in the pkg/common
 directory
for the lines 431 472 479 551 552 
I change the four last ones in InsertNextTuple without the term Value as 
classical VTK new package issue but for the line 431 the problem still remains:
what is the exact solution?
 

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[Yade-users] [Question #680624]: why python 3.6 when I define python2 as executable

[Luc OGER]

New question #680624 on Yade:
https://answers.launchpad.net/yade/+question/680624


I am trying to install the latest daily package but during the cmake command I 
got some strange warnings 

here the cmake command:
cmake -DUSE_QT5=ON -DPYTHON_EXECUTABLE=/usr/bin/python2 
-DCMAKE_VERBOSE_MAKEFILE=ON  -Wno-dev -Wno-deprecated -Wno-int-in-bool-context 
-DENABLE_LBMFLOW=OFF -DENABLE_TWOPHASEFLOW=OFF -DENABLE_PFVFLOW=OFF 
-DQGLVIEWER_INCLUDE_DIR=/usr/local/include/QGLViewer -DLocal
Boost=1.66.0 -DDEBUG=ON ../trunk

then the warnings messages : 
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/python3.6 (found version "3.6.5") 
Python version 3.6.5 found, try to import dependencies...
CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:1612 (message):
  No header defined for python-py36; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:62 (FIND_PACKAGE)
  CMakeLists.txt:178 (FIND_PYTHON_PACKAGES)


CMake Warning at /usr/share/cmake/Modules/FindBoost.cmake:1612 (message):
  No header defined for python3-py36; skipping header check
Call Stack (most recent call first):
  cMake/YadePythonHelpers.cmake:62 (FIND_PACKAGE)
  CMakeLists.txt:178 (FIND_PYTHON_PACKAGES)


Failed to import dependencies for Python version 3.6.5. NOT 
FOUND:libboost-python
-- Found PythonInterp: /usr/bin/python2.7 (found version "2.7.14") 
Python version 2.7.14 found, try to import dependencies...
-- Found NumPy: version "1.14.0" 
/usr/lib64/python2.7/site-packages/numpy/core/include
-- Found IPython: /usr/lib/python2.7/site-packages/IPython  
-- Found matplotlib: /usr/lib64/python2.7/site-packages/matplotlib  
-- Found pygraphviz: /usr/lib64/python2.7/site-packages/pygraphviz  
-- Found Xlib: /usr/lib/python2.7/site-packages/Xlib  
-- Found minieigen: /usr/lib64/python2.7/site-packages/minieigen.so  
-- Found future: /usr/lib/python2.7/site-packages/future  
-- Found past: /usr/lib/python2.7/site-packages/past  
-- Found Tkinter: /usr/lib64/python2.7/lib-tk/Tkinter.pyc  

why looking at python >2.7 if I have define the executable?

Do I have to insert a new option in the cmake command line?


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Re: [Yade-users] [Question #679428]: unable to display sphere with latest version

[Luc OGER]

Question #679428 on Yade changed:
https://answers.launchpad.net/yade/+question/679428

Status: Answered => Open

Luc OGER is still having a problem:

I have erased all links to qt4 and compile libQGLViewer for qt5 and qmake-qt5
The program still crashes at the same "view 3D" choice

the last line is :
/tmp/yade-Debt3H/tmp-0:3: Error in sourced command file:
Invalid thread ID: info
(gdb)
i don't even understand the term info for the thread ID ???

if I ask for the "info thread" i got this: Id   Target Id   
Frame
* 1Thread 0x7f0ffc4084c0 (LWP 30222) "yade-2019-04-26" 0x7f0ffb8d1dd7 
in waitpid () from /lib64/libc.so.6
  2Thread 0x7f0fd827b700 (LWP 30227) "WorkerThread"0x7f0ffbbd6246 
in do_futex_wait.constprop () from /lib64/libpthread.so.0
  3Thread 0x7f0fd7a7a700 (LWP 30228) "WorkerThread"0x7f0ffbbd6246 
in do_futex_wait.constprop () from /lib64/libpthread.so.0
  4Thread 0x7f0fc4b1a700 (LWP 30229) "yade-2019-04-26" 0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  5Thread 0x7f0fbcd1c700 (LWP 30230) "llvmpipe-0"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  6Thread 0x7f0fbc51b700 (LWP 30231) "llvmpipe-1"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  7Thread 0x7f0fbbd1a700 (LWP 30232) "llvmpipe-2"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  8Thread 0x7f0fbb519700 (LWP 30233) "llvmpipe-3"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  9Thread 0x7f0fbad18700 (LWP 30234) "llvmpipe-4"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  10   Thread 0x7f0fba517700 (LWP 30235) "llvmpipe-5"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  11   Thread 0x7f0fb9d16700 (LWP 30236) "llvmpipe-6"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  12   Thread 0x7f0fb9515700 (LWP 30237) "llvmpipe-7"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  13   Thread 0x7f0f9a303700 (LWP 30435) "QXcbEventReader" 0x7f0ffb8fa0bb 
in poll () from /lib64/libc.so.6
  14   Thread 0x7f0f98bf1700 (LWP 30436) "yade-2019-04-26" 0x7f0ffbbd6246 
in do_futex_wait.constprop () from /lib64/libpthread.so.0
  15   Thread 0x7f0f87bf4700 (LWP 30437) "QDBusConnection" 0x7f0ffb8fa0bb 
in poll () from /lib64/libc.so.6
  16   Thread 0x7f0f8733a700 (LWP 30438) "llvmpipe-0"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  17   Thread 0x7f0f86b39700 (LWP 30439) "llvmpipe-1"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  18   Thread 0x7f0f86338700 (LWP 30440) "llvmpipe-2"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  19   Thread 0x7f0f85b37700 (LWP 30441) "llvmpipe-3"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  20   Thread 0x7f0f85336700 (LWP 30442) "llvmpipe-4"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  21   Thread 0x7f0f84b35700 (LWP 30443) "llvmpipe-5"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  22   Thread 0x7f0f6700 (LWP 30444) "llvmpipe-6"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  23   Thread 0x7f0f6f7fe700 (LWP 30445) "llvmpipe-7"  0x7f0ffbbd38ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  24   Thread 0x7f0f6effd700 (LWP 30452) "yade-2019-04-26" 0x7f0ffb8fbf33 
in select () from /lib64/libc.so.6


this looks to be a problem for a pthread but I have no idea where to look 
inside ou avoid this?

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Re: [Yade-users] [Question #679428]: unable to display sphere with latest version

[Luc OGER]

Question #679428 on Yade changed:
https://answers.launchpad.net/yade/+question/679428

Status: Answered => Open

Luc OGER is still having a problem:
new research for solving my problem: here the debug answer with latest
verison 15/04/2019 with qt5 and python 2.7 on Opnsuse 15.0

DEBUG /home/oger/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring 
plugin ZECollider
DEBUG /home/oger/Yade/trunk/pkg/dem/FlatGridCollider.cpp:44 initIndices: 
sphereIdx=1
DEBUG /home/oger/Yade/trunk/pkg/dem/FlatGridCollider.cpp:44 initIndices: 
sphereIdx=1
TCP python prompt on localhost:9000, auth cookie `kecyds'
XMLRPC info provider on http://localhost:21000
DEBUG /home/oger/Yade/trunk/pkg/common/OpenGLRenderer.cpp:66 initgl: 
(re)initializing GL for gldraw methods.

qt5ct: using qt5ct plugin
Running script 01-bouncing-sphere.py
INFO  /home/oger/Yade/trunk/core/Omega.cpp:265 saveSimulation: Saving file 
:memory:
[[ ^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]: QXcbConnection: XCB error: 145 (Unknown), sequence: 171, resource id: 
0, major code: 139 (Unknown), minor code: 20
inotify_add_watch("/home/oger/.config/qt5ct") failed: "No such file or 
directory"


In [2]: INFO  /home/oger/Yade/trunk/gui/qt5/GLViewer.cpp:350 centerScene: 
Select with shift, press 'm' to move.
DEBUG /home/oger/Yade/trunk/gui/qt5/GLViewer.cpp:359 centerScene: scene's bound 
not yet calculated or has zero or nan dimension(s), attempt get that from 
bodies' positions.
DEBUG /home/oger/Yade/trunk/gui/qt5/GLViewer.cpp:370 centerScene: Got scene box 
min=0 0 0 and max=0 0 2
DEBUG /home/oger/Yade/trunk/gui/qt5/GLViewer.cpp:374 centerScene: Scene 
center=0 0 1, halfSize=0 0 1, radius=1
INFO  /home/oger/Yade/trunk/gui/qt5/GLViewer.cpp:350 centerScene: Select with 
shift, press 'm' to move.
DEBUG /home/oger/Yade/trunk/gui/qt5/GLViewer.cpp:359 centerScene: scene's bound 
not yet calculated or has zero or nan dimension(s), attempt get that from 
bodies' positions.
DEBUG /home/oger/Yade/trunk/gui/qt5/GLViewer.cpp:370 centerScene: Got scene box 
min=0 0 0 and max=0 0 2
DEBUG /home/oger/Yade/trunk/gui/qt5/GLViewer.cpp:374 centerScene: Scene 
center=0 0 1, halfSize=0 0 1, radius=1
SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-YVDdwH/tmp-0'
GNU gdb (GDB; openSUSE Leap 15.0) 8.2
Copyright (C) 2018 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://bugs.opensuse.org/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.

For help, type "help".
Type "apropos word" to search for commands related to "word".
[New LWP 12572]
[New LWP 12573]

[New LWP 12594]
[New LWP 13036]
Missing separate debuginfo for /usr/bin/python2.7


/tmp/yade-YVDdwH/tmp-0:3: Error in sourced command file:
Invalid thread ID: info
(gdb)
infp threads

  Id   Target Id   Frame
* 1Thread 0x7fe0619c34c0 (LWP 12567) "yade-2019-04-15" 0x7fe060e8cd97 
in waitpid () from /lib64/libc.so.6
  2Thread 0x7fe03d83e700 (LWP 12572) "WorkerThread"0x7fe060eb6ef3 
in select () from /lib64/libc.so.6
  3Thread 0x7fe03d03d700 (LWP 12573) "WorkerThread"0x7fe060eb6ef3 
in select () from /lib64/libc.so.6
  4Thread 0x7fe02a1be700 (LWP 12574) "yade-2019-04-15" 0x7fe06118e8ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  5Thread 0x7fe02231c700 (LWP 12575) "llvmpipe-0"  0x7fe06118e8ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  6Thread 0x7fe021b1b700 (LWP 12576) "llvmpipe-1"  0x7fe06118e8ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  7Thread 0x7fe02131a700 (LWP 12577) "llvmpipe-2"  0x7fe06118e8ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  8Thread 0x7fe01cb19700 (LWP 12578) "llvmpipe-3"  0x7fe06118e8ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  9Thread 0x7fe020b19700 (LWP 12579) "llvmpipe-4"  0x7fe06118e8ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  10   Thread 0x7fe020318700 (LWP 12580) "llvmpipe-5"  0x7fe06118e8ad 
in pthread_cond_wait@@GLIBC_2.3.2 () from /lib64/libpthread.so.0
  11   Thread 0x7fe01fb17700 (LWP 12581) "llvmpipe-6"  0x7fe06

[Yade-users] [Question #680316]: wrong path autogens for two include hpp

[Luc OGER]

New question #680316 on Yade:
https://answers.launchpad.net/yade/+question/680316

hello,

when I try to compile the latest yade trunk (15-04-2019) I got two worng 
generated path :

here the rror 
Building CXX object 
gui/CMakeFiles/_GLViewer.dir/_GLViewer_autogen/mocs_compilation.cpp.o
cd /home/oger/Yade/build_april-qt5/gui && /usr/bin/c++  
-DBOOST_MATH_DISABLE_FLOAT128=1 -DQT_CORE_LIB -DQT_GUI_LIB -DQT_OPENGL_LIB 
-DQT_WIDGETS_LIB -DQT_XML_LIB -DSUITESPARSE_VERSION_4 -DYADE_ODEINT 
-D_GLViewer_EXPORTS 
-I/home/oger/Yade/build_april-qt5/gui/_GLViewer_autogen/include 
-I/home/oger/Yade/trunk -I/usr/lib64/python2.7/site-packages/numpy/core/include 
-I/usr/include/python2.7 -I/usr/include/eigen3 -I/usr/include/vtk-8.1 
-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include 
-I/usr/include/suitesparse -I/home/oger/Yade/build_april-qt5 
-I/usr/local/include/QGLViewer -isystem /usr/include/qt5 -isystem 
/usr/include/qt5/QtWidgets -isystem /usr/include/qt5/QtGui -isystem 
/usr/include/qt5/QtCore -isystem /usr/lib64/qt5/mkspecs/linux-g++ -isystem 
/usr/include/qt5/QtXml -isystem /usr/include/qt5/QtOpenGL  -fPIC -O2 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security 
-Wall -std=c++11 -DYADE_VTK -DYADE_OPENMP -fopenmp -DYADE_GTS 
-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include 
-DQGLVIEWER_FOUND -DYADE_OPENGL -DYADE_QT5  -DYADE_CGAL  -DLINSOLV 
-DFLOW_ENGINE -DYADE_GL2PS -g -fPIC   -ftrack-macro-expansion=0 -save-temps 
-fstack-protector-strong -DYADE_DEBUG -g -DEIGEN_DONT_VECTORIZE 
-DEIGEN_DONT_ALIGN -DEIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT 
-DCGAL_DISABLE_ROUNDING_MATH_CHECK -frounding-math -fPIC -std=gnu++11 -o 
CMakeFiles/_GLViewer.dir/_GLViewer_autogen/mocs_compilation.cpp.o -c 
/home/oger/Yade/build_april-qt5/gui/_GLViewer_autogen/mocs_compilation.cpp
In file included from 
/home/oger/Yade/build_april-qt5/gui/_GLViewer_autogen/mocs_compilation.cpp:2:0:
/home/oger/Yade/build_april-qt5/gui/_GLViewer_autogen/OXRBQHTNNB/moc_GLViewer.cpp:9:10:
 fatal error: ../../../../../../Yade/trunk/gui/qt5/GLViewer.hpp: Aucun fichier 
ou dossier de ce type
 #include "../../../../../../Yade/trunk/gui/qt5/GLViewer.hpp"
  ^~~
compilation terminated.

clearly for the moc_GLViewer.cpp and moc_OpenGLManager.cpp we have the path 
errors:
more gui/_GLViewer_autogen/OXRBQHTNNB/moc_GLViewer.cpp |grep hpp
** Meta object code from reading C++ file 'GLViewer.hpp'
#include "../../../../../../Yade/trunk/gui/qt5/GLViewer.hpp"

 more gui/_GLViewer_autogen/OXRBQHTNNB/moc_OpenGLManager.cpp|grep hpp
** Meta object code from reading C++ file 'OpenGLManager.hpp'
#include "../../../../../../Yade/trunk/gui/qt5/OpenGLManager.hpp"

instead of something like:
   more gui/_GLViewer_autogen/OXRBQHTNNB/moc_OpenGLManager.cpp|grep hpp
** Meta object code from reading C++ file 'OpenGLManager.hpp'
#include "../../../../../Yade/trunk/gui/qt5/OpenGLManager.hpp"

one less '../" will be good 
I have corrected insside the two files and I can compile but I guess that he 
solution is to correct during the make process!
but where??


Luc

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Re: [Yade-users] [Question #679750]: Omega output with Debug mode?

[Luc OGER]

Question #679750 on Yade changed:
https://answers.launchpad.net/yade/+question/679750

Status: Answered => Solved

Luc OGER confirmed that the question is solved:
I finally founded the problem about the DEBUG mode:

after testing so many runs of the yade in the debug mode, the /tmp
folder was saturated and no more space was available to create a new
/tmp/yade-TzyaFx/tmp-0 or similar directories..

sorry for the waste ofyour time  for my own mystake!!

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Re: [Yade-users] [Question #679750]: Omega output with Debug mode?

[Luc OGER]

Question #679750 on Yade changed:
https://answers.launchpad.net/yade/+question/679750

Luc OGER posted a new comment:
no sign of any ptrace message.

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Re: [Yade-users] [Question #679750]: Omega output with Debug mode?

[Luc OGER]

Question #679750 on Yade changed:
https://answers.launchpad.net/yade/+question/679750

Luc OGER posted a new comment:
it is the same !!!

here the begin of the previous debug version :

command : /usr/local/bin/yade-2019-03-14.git-8b073f5

results:

Welcome to Yade 2019-03-14.git-8b073f5
DEBUG /home/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
DEBUG /home/Yade/trunk/core/Omega.cpp:209 loadPlugins: Loading plugin 
/usr/local/lib64/yade-2019-03-14.git-8b073f5/libyade.so
DEBUG /home/Yade/trunk/core/Omega.cpp:134 buildDynlibDatabase: called with 324 
plugins.
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin 
Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin 
AxialGravityEngine
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin 
BicyclePedalEngine
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin 
Bo1_Box_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin 
Bo1_ChainedCylinder_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin 
Bo1_Cylinder_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin 
Bo1_DeformableElement_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin 
Bo1_Facet_Aabb
DEBUG /home/Yade/trunk/core/Omega.cpp:140 buildDynlibDatabase: Factoring plugin 
Bo1_GridConnection_Aabb
and so on...

and in both cases the libyade.so exists :
% ll /usr/local/lib64/yade-2019-04-01.git-aa31ef3/
total 1521428
-rwxr-xr-x 1 root root 1557894336  3 avril 16:07 libyade.so
drwxr-xr-x 3 root root   4096  3 avril 16:31 py

% ll /usr/local/lib64/yade-2019-03-14.git-8b073f5/
total 1521372
-rwxr-xr-x 1 root root 1557865488 28 mars  17:26 libyade.so
drwxr-xr-x 3 root root   4096 28 mars  17:51 py

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Re: [Yade-users] [Question #679750]: Omega output with Debug mode?

[Luc OGER]

Question #679750 on Yade changed:
https://answers.launchpad.net/yade/+question/679750

Luc OGER posted a new comment:
everything before % is the part of the folder name so without interest
here

the only command and result are :
/usr/local/bin/yade-2019-04-01.git-aa31ef3
Welcome to Yade 2019-04-01.git-aa31ef3
DEBUG /home/oger/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
Incident de segmentation (core dumped)

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Re: [Yade-users] [Question #679750]: Omega output with Debug mode?

[Luc OGER]

Question #679750 on Yade changed:
https://answers.launchpad.net/yade/+question/679750

Luc OGER posted a new comment:
same crash:

programme_yade/bouncing_ss_interaction% 
/usr/local/bin/yade-2019-04-01.git-aa31ef3
Welcome to Yade 2019-04-01.git-aa31ef3
DEBUG /home/oger/Yade/trunk/core/Omega.hpp:106 Omega: Constructing Omega.
Incident de segmentation (core dumped)
programme_yade/bouncing_ss_interaction%

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Re: [Yade-users] [Question #679428]: unable to display sphere with latest version

[Luc OGER]

Question #679428 on Yade changed:
https://answers.launchpad.net/yade/+question/679428

Status: Answered => Open

Luc OGER is still having a problem:
Dear Bruno,

I agreed that the missing debug info is due to nissing debug package in
the OS but it is just a list of warning linked to the gdb stop due to an
error during the visualization process.

My problem is to try to discover where to look to find the problem : yade in 
batch mode  is working well; !
I have tried to compile previous versionbut 2018-02a and b cannot be compiled 
with my opensuse 15.0 as the CGAL package has a different number of argument 
for some functions..
the 2019.01 generates the same crash as the daily one

I know that november versionswere working well but I don't know how to
get back a specific old daily git package (if possible?) to try again
and check when the development starts to crash.

Luc

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[Yade-users] [Question #679428]: unable to display sphere with latest version

[Luc OGER]

New question #679428 on Yade:
https://answers.launchpad.net/yade/+question/679428

i am using the latest git version of Yade and compiled it on Opensuse 15.0 
without any error but alot of warnings...as ususal!

but recently I got  aproblem for having a display of the spheres

here the final lines in the debug mode when I run yade 01-bopuncing case and 
prss display 3D:
Missing separate debuginfo for 
/usr/lib64/kde4/plugins/imageformats/kimg_xview.so
Try: zypper install -C 
"debuginfo(build-id)=a85fc879980a1489d22bab033684de284a79320c"
0x7f8380cf2d97 in waitpid () from /lib64/libc.so.6
/tmp/yade-q0wBU7/tmp-0:3: Error in sourced command file:
Invalid thread ID: info

I did not catched where I have to look to solve this new problem?

Thanks in advance for your help

Luc

here the cmake log of the yade generation:
isce-suse:/home/Yade/build # cmake -DUSE_QT5=OFF 
-DPYTHON_EXECUTABLE=/usr/bin/python2  -DCMAKE_VERBOSE_MAKEFILE=ON 
-DLocalBoost=1.166 -Wno-dev -Wno-deprecated -Wno-int-in-bool-context 
-DENABLE_LBMFLOW=OFF -DENABLE_TWOPHASEFLOW=OFF -DENABLE_PFVFLOW=OFF 
-DQGLVIEWER_INCLUDE_DIR=/usr/local/include/QGLViewer -DLocalBoost=1.66.0 
-DDEBUG=ON ../trunk
-- The C compiler identification is GNU 7.3.1
-- The CXX compiler identification is GNU 7.3.1
-- 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
-- Found PythonInterp: /usr/bin/python2 (found version "2.7.14")
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.8.7")
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2")
-- Version is set to 2019-03-14.git-8b073f5
-- Found OpenGL: /usr/lib64/libOpenGL.so
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GL2PS: /usr/lib64/libgl2ps.so
-- Found CGAL: /usr/include, /usr/lib64/libCGAL.so
-- Found NumPy: version "1.14.0" 
/usr/lib64/python2.7/site-packages/numpy/core/include
-- Found Loki: /usr/include
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- GCC Version >= 4.9. Adding -fstack-protector-strong
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.66.0
-- Found the following Boost libraries:
--   python
--   thread
--   filesystem
--   iostreams
--   regex
--   serialization
--   system
--   date_time
--   chrono
--   atomic
--   Boost_VERSION: 106600
--   Boost_LIB_VERSION: 1_66
--   Boost_INCLUDE_DIRS: /usr/include
--   Boost_LIBRARIES: 
/usr/lib64/libboost_python.so/usr/lib64/libboost_thread.so/usr/lib64/libboost_filesystem.so/usr/lib64/libboost_iostreams.so/usr/lib64/libboost_regex.so/usr/lib64/libboost_serialization.so/usr/lib64/libboost_system.so/usr/lib64/libboost_date_time.so/usr/lib64/libboost_chrono.so/usr/lib64/libboost_atomic.so
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0")
-- Found BZip2: /usr/lib64/libbz2.so (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found PythonLibs: /usr/lib64/libpython2.7.so (found version "2.7.14")
-- Found Eigen3, version: 3.3.4
-- Disable vectorization
-- Found VTK
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib64/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
-- Found GLUT: /usr/lib64/libglut.so
-- USE QT4
-- Found QGLVIEWER-qt4: /usr/local/include/QGLViewer
-- Found Qt4: /usr/bin/qmake (found version "4.8.7")
-- Found GUI-LIBS
-- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
-- Found GMP: /usr/include
-- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
-- Found CGAL
-- SuiteSparse version 4.5.5 

Re: [Yade-users] [Question #676748]: fixed=True how it is iworking?

[Luc OGER]

Question #676748 on Yade changed:
https://answers.launchpad.net/yade/+question/676748

Status: Answered => Solved

Luc OGER confirmed that the question is solved:
thanks Robert,

with dynamic it is working!!

so fixed is no more supported?

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[Yade-users] [Question #676748]: fixed=True how it is iworking?

[Luc OGER]

New question #676748 on Yade:
https://answers.launchpad.net/yade/+question/676748

Hi,
I am reading a first layer of spheres sitting on a plate that I want to glue  
before doing a deposition of other.
I am using fixer=True inside O.bodies.append without  success.

During the run these spheres can move??

what is my problem in the definition of them?

here part of the code:
O.load("1st-step.yade")
print "len-load-O.bodies = ",len(O.bodies)

O.materials[0].frictionAngle=radians(15.0)

sp=pack.SpherePack()

for c,r in sp: 
O.bodies.append(sphere(c,r,fixed=True))
O.bodies[0].mask = 0b01 # 1

sp.toSimulation()

PS i am usin the yade daily 12-05



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Re: [Yade-users] [Question #676672]: list index out of range for plot.saveDataTxt ?

[Luc OGER]

Question #676672 on Yade changed:
https://answers.launchpad.net/yade/+question/676672

Status: Answered => Solved

Luc OGER confirmed that the question is solved:
Thanks Robert for the reply.

I catch my problem:
I was using this command without any argument before to save all data as 
pointed out in the variables explanaition "If None (default), all variables in 
plot.plot are saved."
but to speed up this new code i have commented out all the other plot 
functions!!

so I will try other option

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[Yade-users] [Question #676672]: list index out of range for plot.saveDataTxt ?

[Luc OGER]

New question #676672 on Yade:
https://answers.launchpad.net/yade/+question/676672

I am trying to setup a double set of loose packing on on top of the other as 
prelimnary condition for simulations.
Os I have made a first program to make the fixed first packing and save the 
xyzr coodinates thne generate a second one on top which fall down on the first 
one without ny problem ... but the command plot.saveDataTxt generate an error 
message "list index out of range"

i don't understand why?

%%
here the output of the code :
Running script gravity-2-3rd-step-2packs.py
len-load-O.bodies =  7649
len-O.bodies =  7649
nombre_moving= 282
len-tot-O.bodies =  7931

then  part of my code :
%
O.load("1st-step.yade")
print "len-load-O.bodies = ",len(O.bodies)

O.materials[0].frictionAngle=radians(15.0)

sp=pack.SpherePack()

for c,r in sp: 
O.bodies.append(sphere(c,r,fixed=True))
O.bodies[0].mask = 0b01 # 1
num_small = len(O.bodies)   
print "len-O.bodies = ",num_small

sp.toSimulation()


nombre_moving = 
int(cover_pack_fraction*(box_size*box_size)/(ratio*rayon*ratio*rayon*3.14159) )
print "nombre_moving=", nombre_moving
# generate randomly spheres with uniform radius distribution
sp.makeCloud((0,0,2.2*rayon),(box_size,box_size,(3.2+.2)*rayon*ratio),rMean=rayon*ratio,rRelFuzz=.005*ratio,num=
 nombre_moving)
for c,r in sp: 
if  O.bodies[0].mask == 0b01:  continue # 1
O.bodies[0].mask == 0b10# 2
# add the sphere pack to the simulation
sp.toSimulation()

num_tot = len(O.bodies) 
print "len-tot-O.bodies = ",num_tot
collider.avoidSelfInteractionMask = 0b10


# simulation loop 
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
InteractionLoop(
# handle sphere+sphere and facet+sphere collisions
[Ig2_Sphere_Sphere_L3Geom(),Ig2_Facet_Sphere_L3Geom()],
[Ip2_FrictMat_FrictMat_FrictPhys(frictAngle=0.0)],
[Law2_L3Geom_FrictPhys_ElPerfPl()]
),
#   GravityEngine(gravity=(0,0,-9.81)),
#   NewtonIntegrator(damping=0.4),
# 

NewtonIntegrator(damping=0.4,gravity=(0,-gravity_y,-gravity_z),label='Newton_integrator'),
# call the checkUnbalanced function (defined below) every 2 seconds
PyRunner(command='checkUnbalanced()',realPeriod=2,label='checker'),
]

#without friction 
O.materials[0].frictionAngle=0

# timesteps
O.dt=.5*utils.PWaveTimeStep()

# enable energy tracking; any simulation parts supporting it
# can create and update arbitrary energy types, which can be
# accessed as O.energy['energyName'] subsequently
O.trackEnergy=True


def checkUnbalanced():
 global converg_min,iter_max,step1
# if step1>0: PyRunner(command='add_moving_sphere()')
 if utils.unbalancedForce()https://launchpad.net/~yade-users
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Re: [Yade-users] [Question #675971]: interacting or non interacting spheres

[Luc OGER]

Question #675971 on Yade changed:
https://answers.launchpad.net/yade/+question/675971

Luc OGER posted a new comment:
Dear Bruno,

thanks for your answer, I agree with you that the first solution is
based on permanent reconstruction of two bodies interactions in order to
switch the flag, and I was not so clear on how to implement it

Your solution looks easier and closer to what I was expecting:
"automatic kind of detection". If I have perfectly understood the Mask
idea : I will avoid interaction between two bodies having the same
Mask=2 but I will have interaction between a body with Mask=1 and body
with Mask=2 as I expect!

And, to answer at the last point: I also agree that during the
deposition step this non interaction between large spheres is not
crucial: I can keep the normal behaviour. it is just an help for the
size of the bottom plane if the size of large sphere is large and I want
to have enough statistics.

BUT the mean reason of this non-interaction is during the titlting or the 
oscillating process: as I am looking at the percentage of sphere which have 
moved versus mechanical parameters (inclinaison rate or frequency-amplitude of 
oscillation) , these movements have to be direct not generated by a billiard 
collision with a previous large sphere already in movement.
 
so I will try and let you know if it is working

Regards

Luc

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[Yade-users] [Question #675971]: interacting or non interacting spheres

[Luc OGER]

New question #675971 on Yade:
https://answers.launchpad.net/yade/+question/675971

Dear all,

I need some help in order to improve my way of doing statistical analysis. I 
want to deposit individual spheres with large diameter on a rough surface made 
with small monosize sphere layer. this step is before tilting or vibrating the 
structure with capillary forces insde it.
  
The bottom layer is built by glued immobile spheres and the individual large 
spheres are deposited on top of them but I don't want interaction between these 
large spheres (i.e. one large does not see the other large ones but see the 
bottom layer)

I can make a deposit of few large spheres with a packing fraction less than 5% 
which can limit the large sphere interactions but I will need a large bottom 
surface, the other way is to avoid interaction between the large ones by 
defining some key parameters? this is what I am looking for: is it possible and 
how?
Indeed, this soluton will help me to do a smaller global system.

Thanks in advance for your help

Luc

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Re: [Yade-users] [Question #673172]: InsertNextTupleValue does not exist in VTK 8.1?

[Luc OGER]

Question #673172 on Yade changed:
https://answers.launchpad.net/yade/+question/673172

Luc OGER posted a new comment:
inisde the CMakefilelist.txt
this is the change:


IF(ENABLE_VTK)
  IF(${VTK_MAJOR_VERSION} GREATER 5)
TARGET_LINK_LIBRARIES(yade ${VTK_LIBRARIES})
ADD_DEFINITIONS("-DYADE_VTK6")
IF(${VTK_MAJOR_VERSION} GREATER 7)
ADD_DEFINITIONS("-DYADE_VTK8")
MESSAGE(STATUS "VTK version >7 is found")
ELSE(${VTK_MAJOR_VERSION} GREATER 7)
MESSAGE(STATUS "VTK version >5  and <8 is found")
ENDIF(${VTK_MAJOR_VERSION} GREATER 7)
   ELSE(${VTK_MAJOR_VERSION} GREATER 5)
TARGET_LINK_LIBRARIES(yade vtkHybrid)
  ENDIF(${VTK_MAJOR_VERSION} GREATER 5)
ENDIF(ENABLE_VTK)

i have also modifed VTKrecorder.cpp according to YADE_VTK8 variable but
I don't know how to send it...

Luc

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[Yade-users] [Question #673172]: InsertNextTupleValue does not exist in VTK 8.1?

[Luc OGER]

New question #673172 on Yade:
https://answers.launchpad.net/yade/+question/673172

Hi,

in my Linux distribution (Suse Leap 15.0) the standard VTK package is in 
version8.1 which does not contained  InsertNextTupleValue any more: the new 
name  is only InsertNextTuple.

i have changed manually all the named function inside the cpp file but if I do 
a new git I will have to do it again. Is it a better solution to keep the 
compilation of the last development of Yade easy to manage?

thanks in advance 

Luc

see:
trunk/pkg/dem/VTKRecorder.cpp:511:20: error: ‘class vtkDoubleArray’ has no 
member named ‘InsertNextTupleValue’; did you mean ‘InsertNextTuple’?
 intrAbsForceT->InsertNextTupleValue(fs);
InsertNextTuple


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[Yade-users] [Question #669686]: TwoPhaseFlowEngine.cpp : compilation error

[Luc OGER]

New question #669686 on Yade:
https://answers.launchpad.net/yade/+question/669686

I am using an OPENSUSE OS leap 42.3 and I have able to compile all git veriosn 
upt o May 15 but the last one generates error during the 
TwoPhaseFlowEngine.cpp.o generation; here the cmake and the error message.
I guess that some variable declaration are not made by default?
when I start from scratch : new trunk and build folder, this is the result:

cmake -Wno-error=deprecated -DCMAKE_VERBOSE_MAKEFILE=ON -DUSE_QT5=OFF  
-DENABLE_GTS=ON  -DENABLE_VTK=ON ../trunk
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- 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
-- Found PythonInterp: /usr/bin/python (found version "2.7.13") 
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.8.6") 
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.28") 
-- Version is set to 2018-05-24.git-0e4dac9
-- Found OpenGL: /usr/lib64/libGL.so  
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Found GL2PS: /usr/lib64/libgl2ps.so  
-- Found CGAL: /usr/include, /usr/lib64/libCGAL.so
-- Found NumPy: version "1.8.0" 
/usr/lib64/python2.7/site-packages/numpy/core/include
-- Found Loki: /usr/include  
-- GCC Version >= 4.8. Adding -ftrack-macro-expansion=0
-- GCC Version >= 4.8. Adding -save-temps
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Boost version: 1.61.0
-- Found the following Boost libraries:
--   python
--   thread
--   filesystem
--   iostreams
--   regex
--   serialization
--   system
--   date_time
--   chrono
--   atomic
--   Boost_VERSION: 106100
--   Boost_LIB_VERSION: 1_61
--   Boost_INCLUDE_DIRS: /usr/include
--   Boost_LIBRARIES: 
/usr/lib64/libboost_python-mt.so/usr/lib64/libboost_thread-mt.so/usr/lib64/libboost_filesystem-mt.so/usr/lib64/libboost_iostreams-mt.so/usr/lib64/libboost_regex-mt.so/usr/lib64/libboost_serialization-mt.so/usr/lib64/libboost_system-mt.so/usr/lib64/libboost_date_time-mt.so/usr/lib64/libboost_chrono-mt.so/usr/lib64/libboost_atomic-mt.so
-- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") 
-- Found BZip2: /usr/lib64/libbz2.so (found version "1.0.6") 
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.8") 
-- Found PythonLibs: /usr/lib64/libpython2.7.so (found version "2.7.13") 
-- Found Eigen3, version: 3.2.9
-- Disable vectorization
-- Found VTK
-- Found OpenMP
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Checking for one of the modules 'glib-2.0'
-- Found GLib2: glib-2.0 /usr/include/glib-2.0;/usr/lib64/glib-2.0/include
-- Looking for include file glib/gregex.h
-- Looking for include file glib/gregex.h - not found
-- Found GTS
-- Found GLUT: /usr/lib64/libglut.so  
-- USE QT4
-- Found QGLVIEWER-qt4: /usr/include/QGLViewer  
-- Found Qt4: /usr/bin/qmake (found version "4.8.6") 
-- Found GUI-LIBS
-- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
-- Found GMP: /usr/include  
-- GMP libs: /usr/lib64/libgmp.so /usr/lib64/libgmpxx.so
-- Found CGAL
-- Could NOT find Cholmod (missing:  CHOLMOD_LIBRARIES CHOLMOD_INCLUDE_DIR 
AMD_LIBRARY CAMD_LIBRARY COLAMD_LIBRARY CCOLAMD_LIBRARY) 
-- Found OpenBlas: /usr/lib64/libblas.so  
-- Found Metis: /usr/include  
-- Missing dependency for LINSOLV, disabled
-- Found GL2PS
LBMFLOW is still experimental, building and running LBM engine are at your own 
risk!
Yade will be installed to /usr/local
-- Suffix is set to -2018-05-24.git-0e4dac9
-- LIBRARY_OUTPUT_PATH is set to lib64
-- runtimePREFIX is set to /usr/local
-- Could NOT find gts (missing:  PY_gts) 
-- Use embedded version of gts. Please, consider installing the corresponding 
package
-- 

Re: [Yade-users] [Question #668315]: mininum timesteps after change to calculate the convergene accuracy

[Luc OGER]

Question #668315 on Yade changed:
https://answers.launchpad.net/yade/+question/668315

Status: Answered => Open

Luc OGER is still having a problem:
this is not exactly my case:
for me, the spheres are only subjected to a gravity field : no external 
compression at all and I am awaiting for a "quasistatic equilibrium" before 
changing and the imposed change of the gravity is of the order of 10-4
which meant that the calcul of the 'new unbalancedForce is only changed 
immediatly by 10-6 order of magnitude before changing more after some time
i have tried gravity (0.01,0 ,0) then (0.02,0,0) and looked at the immediat 
difference and after few timesteps

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Re: [Yade-users] [Question #668315]: mininum timesteps after change to calculate the convergene accuracy

[Luc OGER]

Question #668315 on Yade changed:
https://answers.launchpad.net/yade/+question/668315

Status: Answered => Open

Luc OGER is still having a problem:
Dear Jerome,

When I tilted the gravity field, the full simulation needs 'some timesteps" 
before giving a new correct unbalancedforce calculation (otherwise the 
threshold test is immediatly still valid); checking every 500 steps will 
produce the same problem of initial recalculation of the new equilibrium of all 
the forces. 
so this is the reason of the waiting of 5000 timesteps BEFOREchecking the 
unbalance, but it looks like that it is  too small when I check the quality of 
the results!

so your comment about "you can use plenty of other values instead of 500" is 
what exactly I was looking for : how to approach the correct order of magnitude 
without doing a lot of test runs depending of the number of spheres, the 
friction coefificent, the stiffness and so on
doing that at random is right now a waste of time.

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Re: [Yade-users] [Question #668315]: mininum timesteps after change to calculate the convergene accuracy

[Luc OGER]

Question #668315 on Yade changed:
https://answers.launchpad.net/yade/+question/668315

Status: Needs information => Open

Luc OGER gave more information on the question:
Hello Robert
thanks for trying to help me

in more detail, I am filling abox by classical gravity depositon than
slowly titlt the box and look at the sphere displacements.

as the first 'step' made a correct converging force balance, the change of the 
gravity direction is not playing immediately enough change in the 
balancedforcecalculation to reach the 'new equilibrium', so I have used the 
same idea as in your oedometrixc sample case
i hope that I am enough clear?

 So here one lineof the table for my batch run then the full code py. 
table:
pas_box theta_max converg_min nb_layer init_seed
.050 35. .01 20 10

py code:
# gravity deposition, continuing with oedometric test after stabilization
# shows also how to run parametric studies with yade-batch

# The components of the batch are:
# 1. table with parameters, one set of parameters per line (ccc.table)
# 2. readParamsFromTable which reads respective line from the parameter file
# 3. the simulation muse be run using yade-batch, not yade
#
# $ yade-batch --job-threads=1 03-oedometric-test.table 03-oedometric-test.py
#

# load parameters from file if run in batch
# default values are used if not run from batch
# gravity deposition in box, showing how to plot and save history of data,
# and how to control the simulation while it is running by calling
# python functions from within the simulation loop
#pas_box theta_max converg_min
#.05 35. .01
readParamsFromTable(pas_box=0.05, theta_max=35.0, 
converg_min=0.01,nb_layer=20.0,init_seed=10)
# make rMean, rRelFuzz, maxLoad accessible directly as variables later
from yade.params.table import *


# import yade modules that we will use below
from yade import pack, plot, export
  
  
box_size = 5.0
# create rectangular box from facets
O.bodies.append(geom.facetBox((box_size/2.0,box_size/2.0,box_size*0.62),(box_size/2.0,box_size/2.0,box_size*0.62),wallMask=31))

# create empty sphere packing
# sphere packing is not equivalent to particles in simulation, it contains only 
the pure geometry
packing_fraction = 60./100.
global  i_pas, 
pas_box,step0,gravity_y,gravity_z,theta_max,converg_min,nb_layer,init_seed
i_pas = 0 
pas_box=.0250
step0 = 0
nb_layer=20.0
gravity_y = 9.81*sin( pas_box*i_pas*3.14/180.0)
gravity_z = 9.81*cos( pas_box*i_pas*3.14/180.0)

rayon = 0.025
height = 5. * rayon*nb_layer
nombre= int(packing_fraction*(box_size*box_size*nb_layer)/(rayon*rayon*3.14159) 
)
print(nombre)
print(i_pas*pas_box)
sp=pack.SpherePack()
# generate randomly spheres with uniform radius distribution
sp.makeCloud((0,0,0),(box_size,box_size,height),rMean=rayon,rRelFuzz=.005,num= 
nombre,seed=init_seed)
# add the sphere pack to the simulation
sp.toSimulation()


# if the unbalanced forces goes below .05, the packing
# is considered stabilized, therefore we stop collected
# data history and stop
def checkUnbalanced():
 global i_pas, pas_box, step0,gravity_y,gravity_z,theta_max,converg_min
   # at the very start, unbalanced force can be low as there is only few 
contacts, but it does not mean the packing is stable
 if O.iter<(step0+5000): return 
 if utils.unbalancedForce()theta_max :
O.pause()
#plot.saveDataTxt('bbb.txt.bz2')

nom_file=str(i_pas)+"_"+str(pas_box)+"_"+str(nb_layer)+"_"+str(converg_min)
filename1='./output_'+nom_file+'.txt'
# sauvegarde fichier txt
export.textExt(filename1,format='x_y_z_r',comment='x y z r')
filename2='./output_'+nom_file+'.vtk'
export.text2vtk(filename1,filename2)


# simulation loop 
O.engines=[
ForceResetter(),
InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]),
InteractionLoop(
# handle sphere+sphere and facet+sphere collisions
[Ig2_Sphere_Sphere_ScGeom(),
 Ig2_Facet_Sphere_ScGeom()],
[Ip2_FrictMat_FrictMat_FrictPhys(frictAngle=radians(15.0))],
[Law2_ScGeom_FrictPhys_CundallStrack()]
),


NewtonIntegrator(damping=0.4,gravity=(0,-gravity_y,-gravity_z),label='Newton_integrator'),
# call the checkUnbalanced function (defined below) every 2 seconds
PyRunner(command='checkUnbalanced()',realPeriod=5),
# call the addPlotData function every 200 steps
PyRunner(command='addPlotData()',iterPeriod=200)
]

#without friction 
O.materials[0].frictionAngle=radians(15.0)
# timesteps
O.dt=.5*PWaveTimeStep()

# enable energy tracking; any simulation parts supporting it
# can create and update arbitrary energy types, which can be
# accessed as O.energy['energyName'] subsequently
O.trackEnergy=True


# collect history of data which will be plotted
def addPlotData():
 global  i_pas, pas_box
# print( pas_box*i_pas,sin( pas_box*i_pas*3.14/180.0),cos( 

[Yade-users] [Question #668315]: mininum timesteps after change to calculate the convergene accuracy

[Luc OGER]

New question #668315 on Yade:
https://answers.launchpad.net/yade/+question/668315

Dear all,

I am doing a simple and slow tilting process of a box filled with monosize 
spheres. For that, I am increasing by step the angle of the gravity and 
calculated after that the unbalancedForce.
In real experiments the system will move by successive avalanches depending of 
the friction coefficient between grains.
In my simulation it is not the case as I guess the number of timestep before 
doing the calculation of the new unbalancedforce minium is too small : I am 
using 5000 !
my question is how to define or calculate or adjust this nimimal value 
depending of the parameter of my expriments: number of grains, friciton 
coefficient, and so on...

thanks for some clue for my problem.

details of the program:
def checkUnbalanced():
 global i_pas, pas_box, step0,gravity_y,gravity_z,theta_max,converg_min
   # at the very start, unbalanced force can be low as there is only few 
contacts, but it does not mean the packing is stable
 if O.iter<(step0+5000): return 
 if utils.unbalancedForce()https://launchpad.net/~yade-users
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Re: [Yade-users] [Question #665225]: Could not find minieigen (missing: PY_minieigen)

[Luc OGER]

Question #665225 on Yade changed:
https://answers.launchpad.net/yade/+question/665225

Status: Open => Answered

Luc OGER proposed the following answer:
Hi Jipeiqi,

in my recollection, some prebuild package can be installed in a different place 
as some manually installed one : I had the problem with libQGLviewer... and I 
was unable to link it correctly
so i suggest
- you to try the intallation of the link[1] package
- you try to install the git-trunk latest distribution version 
"yade-2018-03." it is always better for a compiling version to have the 
up-to-date solution.

otherwise you can add the "-DCMAKE_VERBOSE_MAKEFILE=ON" in the cmake
command to get more detail in the log file.

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Re: [Yade-users] [Question #665225]: Could not find minieigen (missing: PY_minieigen)

[Luc OGER]

Question #665225 on Yade changed:
https://answers.launchpad.net/yade/+question/665225

Luc OGER posted a new comment:
hi Jipeiqi

just to completed the link [1] was the correct one for my opensuse case.
launching directly the "setup.py" command is doing the job!

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Re: [Yade-users] [Question #665225]: Could not find minieigen (missing: PY_minieigen)

[Luc OGER]

Question #665225 on Yade changed:
https://answers.launchpad.net/yade/+question/665225

Status: Open => Answered

Luc OGER proposed the following answer:
hi Jipeiqi

in my case :
in /usr/lib64/python2.7/site-packages or  /usr/lib64/python/site-packages (same 
as virtual link for python)
I have 
> ll  | grep mini
-rw-r--r--1 root root 1265   12 févr. 09:31 
minieigen-0.5.3-py2.7.egg-info
-rwxr-xr-x 1 root root 89733144 12 févr. 09:31 minieigen.so

which means that your installation of minieigen is corrupt and can
explain the rest of the compilation problem.

so erase the minieigen files and start from scratch

PS : check which python is the main one : version 2.x or 3.x generally
the new OS can start to install part of btoh!

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Re: [Yade-users] [Question #665225]: Could not find minieigen (missing: PY_minieigen)

[Luc OGER]

Question #665225 on Yade changed:
https://answers.launchpad.net/yade/+question/665225

Status: Open => Answered

Luc OGER proposed the following answer:
as I am compiling very often yade on several opensuse systems, I had to
install minieigen_0.5.3 at each  beginning, I suggested to make a clean
basic installation on minieigen WITHOUT any change in the library or
include path.

Indeed all the process of Yade or extra library linking are based on
some default paths. Changing one location can change a lot the full
hierarchy...

in my case python setup.py  install for minieigen is working without any
problem and after the position of the package inside python egg is well
recognize.

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Re: [Yade-users] [Question #664417]: Install Yade on CentOs 6.9

[Luc OGER]

Question #664417 on Yade changed:
https://answers.launchpad.net/yade/+question/664417

Status: Open => Answered

Luc OGER proposed the following answer:
Dear Azim

I had the same problem before!! tthe trunk solution is more up-to-date!
so here my script for the installation on my Opensuse machine:

# more update.csh
cd trunk
git pull https://github.com/yade/trunk.git
cd ../build
# -DUSE_QT5=ON -DENABLE_VTK=ON -DENABLE_GTS=ON 
-DCMAKE_INSTALL_PREFIX=/usr/local all by default
cmake  -DCMAKE_VERBOSE_MAKEFILE=ON -Wno-deprecated -Wno-dev  ../trunk
make
make install

after the cmake the log must have no warning or error, otherwise one or
more packages have to be put first!

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Re: [Yade-users] [Question #664240]: Law2_L3Geom_FrictPhys_HertzMindlin exists or not?

[Luc OGER]

Question #664240 on Yade changed:
https://answers.launchpad.net/yade/+question/664240

Status: Answered => Solved

Luc OGER confirmed that the question is solved:
Thanks Bruno for this fast answer

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[Yade-users] [Question #664240]: Law2_L3Geom_FrictPhys_HertzMindlin exists or not?

[Luc OGER]

New question #664240 on Yade:
https://answers.launchpad.net/yade/+question/664240

in the online documentation 2 references to this function is made but I did not 
found any detail of it???
is it replace by another function name?


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Re: [Yade-users] [Question #663627]: DUSE_QT5=OFF but libQt5Xml & libQt5Core on use

[Luc OGER]

Question #663627 on Yade changed:
https://answers.launchpad.net/yade/+question/663627

Status: Needs information => Open

Luc OGER gave more information on the question:
I am using OpenSuse Leap 42.3
and I am using QT5=OFFas in my distribution as for example: somme command are 
not equivalent
 qmake command is linked to the qt4 
qmake-qt5 is the 'new version for qt5 and also for some other command.

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[Yade-users] [Question #663627]: DUSE_QT5=OFF but libQt5Xml & libQt5Core on use

[Luc OGER]

New question #663627 on Yade:
https://answers.launchpad.net/yade/+question/663627

I am trying to use the latest version of Yade (2018-1-25)  but the run crashes..
in the cmake I am using DUSE_QT5=OFF which gives:
-- Found QGLVIEWER-qt4: /usr/include/QGLViewer
-- Found Qt4: /usr/bin/qmake (found version "4.8.7") (twice)

I had no error during the make and make install

BUT during the crash I got this error lines :
Welcome to Yade 2018-01-25.git-719987b
*** Error in `/usr/bin/python': realloc(): invalid pointer: 0x7f300eeb4820 
***
=== Backtrace: =
/lib64/libc.so.6(+0x721af)[0x7f301b05e1af]
/lib64/libc.so.6(+0x77706)[0x7f301b063706]
/lib64/libc.so.6(realloc+0x2a9)[0x7f301b067cd9]
/usr/lib64/libQt5Core.so.5(_ZN9QListData12realloc_growEi+0x54)[0x7f30031622d4]
and also the lionks to these other libraraires:
/usr/lib64/libQt5Gui.so.5.6.2
/usr/lib64/libQt5Widgets.so.5.6.2
 /usr/lib64/libQt5OpenGL.so.5.6.2

so how to solve this problem?


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Re: [Yade-users] [Question #658070]: from start: Segmentation fault (core dumped)

[Luc OGER]

Question #658070 on Yade changed:
https://answers.launchpad.net/yade/+question/658070

Status: Answered => Solved

Luc OGER confirmed that the question is solved:
thanks Bruno

Finally with the debug option and gdb I got the answer about the segmentation 
fault:
gdb
GNU gdb (GDB; openSUSE Leap 42.3) 8.0
Copyright (C) 2017 Free Software Foundation, Inc.
(gdb) file python
Reading symbols from python...(no debugging symbols found)...done.
(gdb) run yade-2017-09-11.git-949a2d9
Starting program: /usr/bin/python yade-2017-09-11.git-949a2d9

Welcome to Yade 2017-09-11.git-949a2d9 
.
Program received signal SIGSEGV, Segmentation fault.
0x7fffe4dd294c in ?? () from /usr/lib64/libQtGui.so.4

I have compiled yade with the QT5=ON option BUT the program is still looking at 
the /usr/lib64/libQtGui.so.4 which is linked to the QT4 version!
I think that is a problem inside the cmake script ?

indeed the /usr/lib64/libQt5Gui.so.5 and the /usr/lib64/libQt5Gui.so.4
are both present in the computer.

So I moved down to QT4 and the yade program is running well!

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Re: [Yade-users] [Question #658070]: from start: Segmentation fault (core dumped)

[Luc OGER]

Question #658070 on Yade changed:
https://answers.launchpad.net/yade/+question/658070

Status: Answered => Open

Luc OGER is still having a problem:
IYes t is the case and here part of the Cmake output:
-- ===
-- Yade configured with following features: Odeint VTK OpenMP GTS GUI-Qt5 CGAL 
PFVFLOW GL2PS LBMFLOW
-- Disabled features: LINSOLV SPH DEFORM LIQMIGRATION MASK_ARBITRARY PROFILING 
PotentialParticles PotentialBlocks
-- Debug build
-- ===

and one of the first c++ in the make output :
[  3%] Building CXX object gui/CMakeFiles/_GLViewer.dir/qt5/GLViewer.cpp.o
cd /home/oger/Yade/build/gui && /usr/bin/c++   -DBOOST_MATH_DISABLE_FLOAT128=1 
-DQT_CORE_LIB -DQT_GUI_LIB -DQT_OPENGL_LIB -DQT_WIDGETS_LIB -DQT_XML_LIB 
-DYADE_ODEINT -D_GLViewer_EXPORTS -I/home/oger/Yade/trunk 
-I/usr/lib64/python2.7/site-packages/numpy/core/include 
-I/usr/include/python2.7 -I/usr/include/eigen3 -I/usr/include/vtk-7.0 
-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/home/oger/Yade/build 
-I/usr/include/QGLViewer -isystem /usr/include/qt5 -isystem 
/usr/include/qt5/QtWidgets -isystem /usr/include/qt5/QtGui -isystem 
/usr/include/qt5/QtCore -isystem /usr/lib64/qt5/mkspecs/linux-g++ -isystem 
/usr/include/qt5/QtXml -isystem /usr/include/qt5/QtOpenGL  -fPIC -O2 
--param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security 
-Wall -std=c++11 -DYADE_VTK -DYADE_OPENMP -fopenmp -DYADE_GTS 
-I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include 
-DQGLVIEWER_FOUND -DYADE_OPENGL -DYADE_QT5  -DYADE_CGAL -DFLOW_ENGINE 
-DYADE_GL2PS -DLBM_ENGINE -g -fPIC
-ftrack-macro-expansion=0 -save-temps -fstack-protector -DYADE_DEBUG -g 
-DEIGEN_DONT_VECTORIZE -DEIGEN_DONT_ALIGN 
-DEIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT -DCGAL_DISABLE_ROUNDING_MATH_CHECK 
-frounding-math -fPIC -o CMakeFiles/_GLViewer.dir/qt5/GLViewer.cpp.o -c 
/home/oger/Yade/trunk/gui/qt5/GLViewer.cpp


where -g is:
-DLBM_ENGINE -g -fPIC   -ftrack-macro-expansion=0 -save-temps -fstack-protector 
-DYADE_DEBUG -g 

So I don't know how to look???

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[Yade-users] [Question #658070]: from start: Segmentation fault (core dumped)

[Luc OGER]

New question #658070 on Yade:
https://answers.launchpad.net/yade/+question/658070

I have just updated  Opoensuse leap from 42.2 and  42.3 and I got a strange 
problem :
I am still able to compile the yade code without error-crash  BUT I got 
immediately the " Segmentation fault (core dumped)" message without more 
comment or explanation.

I compiled after the the DEBUG option but the results is the same : no 
information, no way to found where is the problem??
could you give me some hints where and to find the problem.

Thanks

Luc


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[Yade-users] [Question #648259]: rotation of gravity or box?

[Luc OGER]

New question #648259 on Yade:
https://answers.launchpad.net/yade/+question/648259

I want to simulate a very slow inclinaison process of a box filled with spheres 
in order to observe the precursors of the avalanche process.
for that I can first fill a box with spheres and after do a rotation either of 
the gravity field (change gravity in x and z) or of the box by changing the 
orientation of all the walls.

but of course the way to calculate all the interactions between spheres, 
gravity and walls can generate different amplitudes of errors; so my question :
according to the internal calculation of Yade, is it better to tilt the gravity 
or the walls?  

thanks for the answer.


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[Yade-users] [Question #300740]: -Wdeprecated_declarations: where to put it?

[Luc OGER]

New question #300740 on Yade:
https://answers.launchpad.net/yade/+question/300740

during the make process of a dialy yade compilation, I got a huge number of 
lines saying that some declarations are deprecated.
the compiler suggets to include the option -Wdeprecated_declarations,  but 
where to put it in order to avoid all these warnings?

exemple :
/usr/include/eigen3/Eigen/src/Core/Functors.h:977:28: warning: 'template class std::binder1st' is deprecated [-Wdeprecated-declarations]
 struct functor_traits
or
usr/include/boost/type_traits/detail/ice_eq.hpp:17:70: note: #pragma message: 
NOTE: Use of this header (ice_eq.hpp) is deprecated
 # pragma message("NOTE: Use of this header (ice_eq.hpp) is deprecated")

PS I am using Opensuse 42 tumbleweed with gcc version 6 and python 3




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Re: [Yade-users] [Question #268697]: installation of YADE with suse distribution

[Luc OGER]

Question #268697 on Yade changed:
https://answers.launchpad.net/yade/+question/268697

Luc OGER posted a new comment:
I am using for a long time the yade distribution with OPENSUSE 13.2
x86_64 without any problem up to now!

But this new update series of packages such the move from qt4 to qt5
generates also for me the same kind of warnings:

I guess that some changes of the qt4/GLviewer to qt5/glviewer in some paths is 
needed?
 gui/qt4/GLViewer.cpp  |5 +-
 gui/qt4/GLViewer.hpp  |4 +
 gui/qt4/GLViewerDisplay.cpp   |8 +
 gui/qt4/build |4 -
 gui/qt5/GLViewer.cpp  |  488 
++
 gui/qt5/GLViewer.hpp  |  163 
++
 gui/qt5/GLViewerDisplay.cpp

why both are in the distribution?

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Re: [Yade-users] [Question #266166]: PY_minieigen missing?

[Luc OGER]

Question #266166 on Yade changed:
https://answers.launchpad.net/yade/+question/266166

Luc OGER posted a new comment:
here the first warning :
In file included from /usr/include/eigen3/Eigen/Cholesky:24:0,
 from /usr/include/eigen3/Eigen/QR:8,
 from /usr/include/eigen3/Eigen/SVD:4,
 from /usr/include/eigen3/Eigen/Geometry:8,
 from /home/oger/Yade/trunk/lib/base/Math.hpp:98,
 from /home/oger/Yade/trunk/core/Omega.hpp:20,
 from /home/oger/Yade/trunk/gui/qt4/GLViewer.hpp:6,
 from /home/oger/Yade/trunk/gui/qt4/GLViewer.cpp:11:
/usr/include/eigen3/Eigen/src/Cholesky/LDLT.h: In member function ‘void 
Eigen::internal::solve_retvalEigen::LDLTMatrixType, _UpLo, 
Rhs::evalTo(Dest) const’:
/usr/include/eigen3/Eigen/src/Cholesky/LDLT.h:505:39: warning: typedef ‘Scalar’ 
locally defined but not used [-Wunused-local-typedefs]
 typedef typename LDLTType::Scalar Scalar;
   ^
and the same warning message for a lot of building CXX

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Re: [Yade-users] [Question #266166]: PY_minieigen missing?

[Luc OGER]

Question #266166 on Yade changed:
https://answers.launchpad.net/yade/+question/266166

Luc OGER confirmed that the question is solved:
Thanks Anton Gladky, that solved my question.

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Re: [Yade-users] [Question #266166]: PY_minieigen missing?

[Luc OGER]

Question #266166 on Yade changed:
https://answers.launchpad.net/yade/+question/266166

Status: Answered = Solved

Luc OGER confirmed that the question is solved:

thanks again for both of you.

I have used the package  from the pypi link and installed the python_minieigen. 
The new configuration went ok during the cmake then the make process.

I only got a lot of warning about a Scalar definition inside a
subroutine involving eigen.

then my first run works well after that.

Luc

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[Yade-users] [Question #266166]: PY_minieigen missing?

[Luc OGER]

New question #266166 on Yade:
https://answers.launchpad.net/yade/+question/266166

i just downloaded and tried to compile  the latest Yade package (through pull) 
then during the Cmake script in order to check the library packge I got an 
error :
CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:136 
(message):
  Could NOT find minieigen (missing: PY_minieigen)
Call Stack (most recent call first):
  /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:343 
(_FPHSA_FAILURE_MESSAGE)
  cMake/FindPythonModule.cmake:22 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  CMakeLists.txt:452 (find_python_module)

it was working before but the last pull erase a lot of file linked to mineigen :
 py/mathWrap/miniEigen.cpp | 474
and
40 files changed, 176 insertions(+), 746 deletions(-)
 delete mode 100644 py/mathWrap/miniEigen.cpp

so how I can solved this problem?

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Re: [Yade-users] [Question #266166]: PY_minieigen missing?

[Luc OGER]

Question #266166 on Yade changed:
https://answers.launchpad.net/yade/+question/266166

Status: Answered = Open

Luc OGER is still having a problem:
Thanks for the two fast answers;

but the problem still exists for me, as the package python-minieigen
exists only in the UBUNTU distribution!!

no other linux distribution provides this kind of package...

in my case I am using the latest opensuse 13.2 and nothing close to this
package is available even around the official distribution. really too
bad!!!

so which function, libraries or other things are needed through this python 
library ?
or putting back the old miinieigen library can be able to solve the 
dependancies?

Luc

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Re: [Yade-users] [Question #263739]: isotropic compression at controled pressure

[Luc OGER]

Question #263739 on Yade changed:
https://answers.launchpad.net/yade/+question/263739

Status: Answered = Open

Luc OGER is still having a problem:
I made several tests to see if putting some max_vel solved my problem,
it seems that it is not what I was expected.

but to understand more my queston, I have to described what I was looking for :
I want to look at the consequence at the anisotropy linked to the gravity 
deposition process. So my first step is doing a packing from spheres 
distributed randmoly inside big vertical box , letting them settling down, (in 
order to get a quasi cubic dense packing) putting the top wall at the upper 
point of the packing and then doing an isotropic compression by pressure 
control on all the walls but one by one. 
Indeed, the top wall starts with zero pressure and has to move alone to reach 
some pressure similar to the mean values of the others before moving the other 
walls. Otherwise I will reorganise too much the structure before compressing.

i hope my description is clear enough for the understanding.

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Re: [Yade-users] [Question #263739]: isotropic compression at controled pressure

[Luc OGER]

Question #263739 on Yade changed:
https://answers.launchpad.net/yade/+question/263739

Status: Answered = Open

Luc OGER is still having a problem:
thanks for the fast reply.

I don't want to reach quickly the isotropic goal as some local
reorganisaiton for the contacts between spheres is part of my studies,
indeed the particles are frictionless which allow rotations and sliding
during the slow compression process.

so I guess that this solution (copy from your answer) will be the good one 
coupled with a small max_vel if the change of the triaxgoal loop only occurs 
when it is reached ?: Number effect  is unclear for me in this example :
If what you want is to increase the isotropic confinement progressively:
for k in range(N):
triax.goal1=triax.goal2=triax.goal3=isoP*float(k)/float(N)
   O.run(number,True)

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[Yade-users] [Question #263739]: isotropic compression at controled pressure

[Luc OGER]

New question #263739 on Yade:
https://answers.launchpad.net/yade/+question/263739

I am new in the use of Yade and it is not clear for me how to define some 
parameters for the TriaxialStresscontroller class in order to  make a triaxial 
compression with identical pressures in all the walls.
In my understanding of the class I can controled the strain rate and/or the 
wall displacements but not the pressure on all the walls to have the same value 
during the isotropic compression.

so my question :
is it possible ? and if yes how I can do that?

thanks in advance.


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Re: [Yade-users] [Question #263739]: isotropic compression at controled pressure

[Luc OGER]

Question #263739 on Yade changed:
https://answers.launchpad.net/yade/+question/263739

Status: Answered = Open

Luc OGER is still having a problem:
Luc Thanks for the fast answer

but  this example is not exactly that I was expecting :
 I want to compress by the walls not by growxing the spheres and as the time to 
get equilibrium when moving the walls is crucial I want to select the rate to 
this iso-compression.

if I understand mask=7 and all goal identical are more linked to final
results not to the progressive intermediate steps.

Luc

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Re: [Yade-users] [Question #261610]: libQGLviewer version is compatible?

[Luc OGER]

Question #261610 on Yade changed:
https://answers.launchpad.net/yade/+question/261610

Status: Answered = Solved

Luc OGER confirmed that the question is solved:
thanks for your response. 
it was not an Opensuse issue:

By looking more carefully through the web site of libQGLviewer I found that the 
new developpemnt version uses qreal instead of float for some variables since 
2.6.0 : 
http://www.libqglviewer.com/changeLog.html
The entire API now consistently uses the qreal (i.e double) type for floating 
point numbers.
This should not break code compatibility since types will mostly get 
automatically converted.
Update your code if you use one of the getX(qreal  x) methods, which take a 
reference as a parameter, which type needs to be changed to qreal.

so I downloaded a version prior to 2.6.0 and I was able to compile with
this library.

But I guess that any new user of Yade which will follow the normal link
will have the same problem!

an improvment of the YADE code or the CMAKE will be needed soon

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[Yade-users] [Question #261610]: libQGLviewer version is compatible?

[Luc OGER]

New question #261610 on Yade:
https://answers.launchpad.net/yade/+question/261610

In order to install the yade package on my Linux opensuse 13.2 I need to 
install specific libraries such as libQGLviewer.
for special cases like this library, YaST from Opensuse does not provide an 
official one so I have used the one obtained from the link in the installation 
yade page, but this link points to libQGLviewer web page which allows us to 
downlaod the latest available library which is in version 2.6.1.

but this library uses variable in qreal mode which genetares compilation error 
: the first error is about zNear for gui/qt4/glviewer.cpp line 11  which is in 
float in the cpp program!

I have corrected this first error but a lot of following ones occur after 
that

so which solution is the best one :
-using an older library for libQGLviewer but how old???
- changing some parameter in the cmake or in the Makefiles
- or other solutions???


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[Yade-users] [Question #261428]: (French) libQGLviewer version compatible???

[Luc OGER]

A question was asked in a language (French) spoken by
none of the registered Yade answer contacts.

https://answers.launchpad.net/yade/+question/261428

je viens de me lancer dans l'installation de Yade 2015 sou slnux opensuse 13.2 
et donc je recupère les packages complémentaires obligatoire pour certaines 
fonctionnalités.
ainis pour avoir le GUI il faut avoir libQGLvierwer!
en suivant le lien j'ai téléchargé la dernière version 2.61 que j'ai compilé et 
installé sans problème (libQGLViewer.so - libQGLViewer.so.2.6.1) mais le make 
de yade me génère plein d'erreur lié à cette librairie???

la première est sur zNear dans camera.f qui a un format qrela sur la lib et 
float sur yade.
puis ensuite : /data/Yade/trunk/gui/qt4/GLViewerDisplay.cpp:87:60: error: no 
matching function for call to ‘qglviewer::ManipulatedFrame::getPosition
etc

donc quelle solution ??
installé une ancienne librairie libQGviewerL et dans ce cas laquelle?
modifié certains paramètre dans le make : où?
modifié certains fichiers.h dans yade? où?
ou qq chose d'autre???

d'avance merci


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