Re: [Yade-dev] makeing yade single-threaded by default

[Bruno Chareyre]

Please Luc, use launchpad questions.
"-j 1" should start jobs one after the other, no? Did you find
simultaneous jobs running in that case?

Bruno



On 27/04/11 01:36, luc scholtes wrote:
> OK, thank you guys for your input. Now comes the second part of my
> question... ;-)
>
> How to run YADE in batch mode such as only one calculation runs at a
> time? In the current default mode, running YADE in batch mode launches
> several calculations simultaneously (as much as the number of
> available cores if I understood well), but I would like to allow only
> one calculation at the same time, in an "iterative manner", one after
> the other. The -j option does not seem to allow that...
>
> Cheers
>
>   Luc
>
> 2011/4/19 Anton Gladky  >
>
> Hi, luc,
>
> If you start yade without -j option, it will use just 1 thread. As
> Klaus already said, you can start yade with -j6 to start yade in 6
> threads.
>
> But you should be careful. If you do not use a large number of
> particles, more threads can lead you to decreasing of calculation
> speed. That is why yade starts now by default in 1 thread mode not to
> confuse new users.
>
> Anton
>
>
>
>
> On Tue, Apr 19, 2011 at 4:39 AM, luc scholtes
> mailto:lscholte...@gmail.com>> wrote:
> > Hi guys,
> >
> > sorry to wake up so late, but, I tried to find info concerning
> the -j/
> > --jobs option and could not really sort it all due to my lack of
> Linux
> > oriented knowledge... As I understand, YADE now run 1 thread
> (job?) per
> > core. Nonetheless, what would be the command to make it run 1
> thread over
> > several/all cores in order to speed up the calculation (if it is
> the right
> > thing to do for this purpose)?
> >
> > Thanks in advance
> >
> >   Luc
> >
> > 2011/1/30 Anton Gladky  >
> >>
> >> Hi,
> >>
> >> In most of my simulations I use 1 thread/core and find it the most
> >> optimal solution. Also it helps to get completely identical results
> >> excluding openmp-instability. And only on a very large simulations
> >> (>10^5 particles) it is reasonable to use 2-3 threads, no more.
> >>
> >> So, I personally agree.
> >>
> >> Anton
> >>
> >>
> >>
> >>
> >> 2011/1/29 Václav Šmilauer mailto:e...@doxos.eu>>:
> >> > Hi there,
> >> >
> >> > due to numerous performance problems when Yade uses the
> default number
> >> > of
> >> > threads (one thread per core), I think it would be better to
> make run
> >> > single-threaded by default, so that unknowledgeable people are
> not hit.
> >> > Those who know assign the right number of threads anyway.
> >> >
> >> > It would concern both the main program, and also the batch
> system, which
> >> > would still use all cores, but 1 core/job.
> >> >
> >> > Thoughts?
> >> >
> >> > v.
> >> >
> >> > ___
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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2835: A section on devpt tools and check tests in programmer manual.

[noreply]

revno: 2835
committer: Bruno Chareyre 
branch nick: trunk
timestamp: Wed 2011-04-27 14:37:04 +0200
message:
  A section on devpt tools and check tests in programmer manual.
modified:
  doc/sphinx/prog.rst


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=== modified file 'doc/sphinx/prog.rst'
--- doc/sphinx/prog.rst	2011-04-15 06:20:10 +
+++ doc/sphinx/prog.rst	2011-04-27 12:37:04 +
@@ -201,6 +201,38 @@
 
 See scons manpage for meaning of parameters passed to build functions, such as ``SHLIBPREFIX``.
 
+Development tools
+=
+
+Integrated Development Environment and other tools
+---
+A frequently used IDE is Kdevelop. We recommend using this software for navigating in the sources, compiling and debugging. Other usefull tools for debugging and profiling are Valgrind and KCachegrind. A series a wiki pages are dedicated to these tools in the `development section `__ of the wiki.
+
+Hosting and versioning
+--
+The Yade project is kindly hosted at `launchpad `__, which is used for source code, bug tracking, planning, package downloads and more. Our repository `can be http-browsed `__.
+
+The versioning software used is `Bazaar `__, for wich a short tutorial can be found in a `Yade's wiki pages `__. Bazaar is a distributed revision control system. It is available packaged for all major linux distributions.
+
+Build robot
+---
+A build robot hosted at `3SR lab. `__ is tracking souce code changes.
+Each time a change in the source code is commited to the main development branch via bazaar. The "buildbot" downloads and compiles the new version, and start a series of tests.
+
+If a compilation error has been introduced, it will be notified to the yade-dev mailing list and to the commiter, thus helping to fix problems quickly.
+If the compilation is successfull, the buildbot starts unit regression tests and "check tests" (see below) and report the results. If all tests are passed, a new version of the documentation is generated and uploaded to the website in `html `__ and `pdf `__ format. As a consequence, those two links always point to the documentation (the one you are reading now) of the last successfull build, and the delay between commits and documentation updates are very short (minutes).
+The buildbot activity and logs can be `browsed online `__.
+
+Check tests
+---
+Check tests perform comparisons of simulation results between different versions of yade, as discussed in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg05784.html and the whole thread. They differ with regression tests in the sense that they simulate more complex situations and combinations of different engines, and usually don't have a mathematical proof (though there is no restriction on the latest). They compare the values obtained in version N with values obtained in a previous version or any other "expected" results. The reference values must be hardcoded in the script itself or in data files provided with the script. Check tests are based on regular yade scripts, so that users can easily commit their own scripts to trunk in order to get some automatized testing after commits from other developers.
+
+Since the check tests history will be mostly based on standard output generated by "yade --checks", a meaningfull checkTest should include some "print" command telling if something went wrong. If the script itself fails for some reason and can't generate an output, the log will contain "scriptName failure". If the script defines differences on obtained and awaited data, it should print some useful information about the problem and increase the value of global variable resultStatus. After this occurs, the automatic test will stop the execution with error message.
+
+An example check test can be found in checkTestTriax.py. It shows results comparison, output, and how to define the path to data files using "checksPath".
+Users are encouraged to add their own scripts into the scripts/test/checks/ folder. Discussion of some specific checktests design in users question is welcome.
+A check test should never need more than a few seconds to run. If your typical script needs more, try and reduce the number of element or the number of steps.
+
 Conventions
 
 
@@ -267,7 +299,6 @@
 
 .. [#opengldispatchers] Not considering OpenGL dispatchers, which 

[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2836: - doc smallfix

[noreply]

revno: 2836
committer: Bruno Chareyre 
branch nick: trunk
timestamp: Wed 2011-04-27 14:42:25 +0200
message:
  - doc smallfix
modified:
  doc/sphinx/prog.rst


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=== modified file 'doc/sphinx/prog.rst'
--- doc/sphinx/prog.rst	2011-04-27 12:37:04 +
+++ doc/sphinx/prog.rst	2011-04-27 12:42:25 +
@@ -217,7 +217,7 @@
 Build robot
 ---
 A build robot hosted at `3SR lab. `__ is tracking souce code changes.
-Each time a change in the source code is commited to the main development branch via bazaar. The "buildbot" downloads and compiles the new version, and start a series of tests.
+Each time a change in the source code is commited to the main development branch via bazaar, the "buildbot" downloads and compiles the new version, and start a series of tests.
 
 If a compilation error has been introduced, it will be notified to the yade-dev mailing list and to the commiter, thus helping to fix problems quickly.
 If the compilation is successfull, the buildbot starts unit regression tests and "check tests" (see below) and report the results. If all tests are passed, a new version of the documentation is generated and uploaded to the website in `html `__ and `pdf `__ format. As a consequence, those two links always point to the documentation (the one you are reading now) of the last successfull build, and the delay between commits and documentation updates are very short (minutes).

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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2835: A section on devpt tools and check tests in programmer manual.

[Jerome Duriez]

Thanks Bruno,

I have still a small remark :

Check tests definition relys still (partly) on comparison with 
regression tests. The fact that regression tests are never explained 
anywhere did not help me to get clearly the (different ?) uses of all 
these tests...


Le 27/04/2011 14:39, nore...@launchpad.net a écrit :


revno: 2835
committer: Bruno Chareyre
branch nick: trunk
timestamp: Wed 2011-04-27 14:37:04 +0200
message:
   A section on devpt tools and check tests in programmer manual.
modified:
   doc/sphinx/prog.rst


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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2837: - improved section on regression test

[noreply]

revno: 2837
committer: Bruno Chareyre 
branch nick: trunk
timestamp: Wed 2011-04-27 15:04:26 +0200
message:
  - improved section on regression test
modified:
  doc/sphinx/prog.rst


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=== modified file 'doc/sphinx/prog.rst'
--- doc/sphinx/prog.rst	2011-04-27 12:42:25 +
+++ doc/sphinx/prog.rst	2011-04-27 13:04:26 +
@@ -223,8 +223,21 @@
 If the compilation is successfull, the buildbot starts unit regression tests and "check tests" (see below) and report the results. If all tests are passed, a new version of the documentation is generated and uploaded to the website in `html `__ and `pdf `__ format. As a consequence, those two links always point to the documentation (the one you are reading now) of the last successfull build, and the delay between commits and documentation updates are very short (minutes).
 The buildbot activity and logs can be `browsed online `__.
 
+Regression tests
+
+Yade contains two types of regression tests, some are unit tests while others are testing more complex simulations. Altough both types can be considered regression tests, the usage is that we name the first simply "regression tests", while the latest are called "check tests".
+Both series of tests can ran at yade startup by passing the options "test" or "check" ::
+
+	yade --test
+	yade --check
+
+Unit regression tests
+^
+Unit regression tests are testing well the output of individual functors and engines in well defined conditions. They are defined in the folder :ysrc:`py/tests/`.
+The purpose of unit testing is to make sure that the behaviour of the most important classes remains correct during code development. Since they test classes one by one, unit tests can't detect
+
 Check tests

+^^^
 Check tests perform comparisons of simulation results between different versions of yade, as discussed in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg05784.html and the whole thread. They differ with regression tests in the sense that they simulate more complex situations and combinations of different engines, and usually don't have a mathematical proof (though there is no restriction on the latest). They compare the values obtained in version N with values obtained in a previous version or any other "expected" results. The reference values must be hardcoded in the script itself or in data files provided with the script. Check tests are based on regular yade scripts, so that users can easily commit their own scripts to trunk in order to get some automatized testing after commits from other developers.
 
 Since the check tests history will be mostly based on standard output generated by "yade --checks", a meaningfull checkTest should include some "print" command telling if something went wrong. If the script itself fails for some reason and can't generate an output, the log will contain "scriptName failure". If the script defines differences on obtained and awaited data, it should print some useful information about the problem and increase the value of global variable resultStatus. After this occurs, the automatic test will stop the execution with error message.

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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2835: A section on devpt tools and check tests in programmer manual.

[Bruno Chareyre]

I see your remark only now. I think the problem is already adressed in 2837.
Tell me if it's not clear.

Bruno

On 27/04/11 14:53, Jerome Duriez wrote:
> Thanks Bruno,
>
> I have still a small remark :
>
> Check tests definition relys still (partly) on comparison with
> regression tests. The fact that regression tests are never explained
> anywhere did not help me to get clearly the (different ?) uses of all
> these tests...
>
> Le 27/04/2011 14:39, nore...@launchpad.net a écrit :
>> 
>> revno: 2835
>> committer: Bruno Chareyre
>> branch nick: trunk
>> timestamp: Wed 2011-04-27 14:37:04 +0200
>> message:
>>A section on devpt tools and check tests in programmer manual.
>> modified:
>>doc/sphinx/prog.rst
>>
>>
>> -- 
>> lp:yade
>> https://code.launchpad.net/~yade-dev/yade/trunk
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[Yade-dev] [Bug 761411] Re: No information about regression and check tests in manual

[Chareyre]

Fixed in r2835
https://www.yade-dem.org/doc/prog.html#development-tools

** Changed in: yade
   Status: New => Fix Released

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https://bugs.launchpad.net/bugs/761411

Title:
  No information about regression and check tests in manual

Status in Yet Another Dynamic Engine:
  Fix Released

Bug description:
  It would be good to add an information about regression and check
  tests into the manual (Sphinx).

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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2838: - fix (in fact workaround...) bad display of double minus (--) in sphinx.

[noreply]

revno: 2838
committer: Bruno Chareyre 
branch nick: trunk
timestamp: Wed 2011-04-27 15:14:07 +0200
message:
  - fix (in fact workaround...) bad display of double minus (--) in sphinx.
modified:
  doc/sphinx/prog.rst


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=== modified file 'doc/sphinx/prog.rst'
--- doc/sphinx/prog.rst	2011-04-27 13:04:26 +
+++ doc/sphinx/prog.rst	2011-04-27 13:14:07 +
@@ -240,7 +240,7 @@
 ^^^
 Check tests perform comparisons of simulation results between different versions of yade, as discussed in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg05784.html and the whole thread. They differ with regression tests in the sense that they simulate more complex situations and combinations of different engines, and usually don't have a mathematical proof (though there is no restriction on the latest). They compare the values obtained in version N with values obtained in a previous version or any other "expected" results. The reference values must be hardcoded in the script itself or in data files provided with the script. Check tests are based on regular yade scripts, so that users can easily commit their own scripts to trunk in order to get some automatized testing after commits from other developers.
 
-Since the check tests history will be mostly based on standard output generated by "yade --checks", a meaningfull checkTest should include some "print" command telling if something went wrong. If the script itself fails for some reason and can't generate an output, the log will contain "scriptName failure". If the script defines differences on obtained and awaited data, it should print some useful information about the problem and increase the value of global variable resultStatus. After this occurs, the automatic test will stop the execution with error message.
+Since the check tests history will be mostly based on standard output generated by "yade ---check", a meaningfull checkTest should include some "print" command telling if something went wrong. If the script itself fails for some reason and can't generate an output, the log will contain "scriptName failure". If the script defines differences on obtained and awaited data, it should print some useful information about the problem and increase the value of global variable resultStatus. After this occurs, the automatic test will stop the execution with error message.
 
 An example check test can be found in checkTestTriax.py. It shows results comparison, output, and how to define the path to data files using "checksPath".
 Users are encouraged to add their own scripts into the scripts/test/checks/ folder. Discussion of some specific checktests design in users question is welcome.

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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2835: A section on devpt tools and check tests in programmer manual.

[Jerome Duriez]

2837 makes things again clearer indeed, thanks. I just think that "ran" 
should be replaced by "run" or "be ran" in "


Both series of tests can ran

, and it seems to me that a sentence does not have an end :

Since they test classes one by one, unit tests can't detect


(According to what I read in the commit mail). Due to this second need 
of change I did not perform the first one myself.



Le 27/04/2011 15:12, Bruno Chareyre a écrit :

I see your remark only now. I think the problem is already adressed in 2837.
Tell me if it's not clear.

Bruno

On 27/04/11 14:53, Jerome Duriez wrote:

Thanks Bruno,

I have still a small remark :

Check tests definition relys still (partly) on comparison with
regression tests. The fact that regression tests are never explained
anywhere did not help me to get clearly the (different ?) uses of all
these tests...

Le 27/04/2011 14:39, nore...@launchpad.net a écrit :


revno: 2835
committer: Bruno Chareyre
branch nick: trunk
timestamp: Wed 2011-04-27 14:37:04 +0200
message:
A section on devpt tools and check tests in programmer manual.
modified:
doc/sphinx/prog.rst


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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2839: - typos

[noreply]

revno: 2839
committer: Bruno Chareyre 
branch nick: trunk
timestamp: Wed 2011-04-27 15:54:26 +0200
message:
  - typos
modified:
  doc/sphinx/prog.rst


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=== modified file 'doc/sphinx/prog.rst'
--- doc/sphinx/prog.rst	2011-04-27 13:14:07 +
+++ doc/sphinx/prog.rst	2011-04-27 13:54:26 +
@@ -226,14 +226,14 @@
 Regression tests
 
 Yade contains two types of regression tests, some are unit tests while others are testing more complex simulations. Altough both types can be considered regression tests, the usage is that we name the first simply "regression tests", while the latest are called "check tests".
-Both series of tests can ran at yade startup by passing the options "test" or "check" ::
+Both series of tests can be ran at yade startup by passing the options "test" or "check" ::
 
 	yade --test
 	yade --check
 
 Unit regression tests
 ^
-Unit regression tests are testing well the output of individual functors and engines in well defined conditions. They are defined in the folder :ysrc:`py/tests/`.
+Unit regression tests are testing the output of individual functors and engines in well defined conditions. They are defined in the folder :ysrc:`py/tests/`.
 The purpose of unit testing is to make sure that the behaviour of the most important classes remains correct during code development. Since they test classes one by one, unit tests can't detect
 
 Check tests

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Re: [Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2835: A section on devpt tools and check tests in programmer manual.

[Bruno Chareyre]

>
> , and it seems to me that a sentence does not have an end :
>
> Since they test classes one by one, unit tests can't detect
>
Ah yes indeed... Thanks.

B


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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2840: End a sentence... (thanks Jerome)

[noreply]

revno: 2840
committer: Bruno Chareyre 
branch nick: trunk
timestamp: Wed 2011-04-27 15:58:19 +0200
message:
  End a sentence... (thanks Jerome)
modified:
  doc/sphinx/prog.rst


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=== modified file 'doc/sphinx/prog.rst'
--- doc/sphinx/prog.rst	2011-04-27 13:54:26 +
+++ doc/sphinx/prog.rst	2011-04-27 13:58:19 +
@@ -234,7 +234,7 @@
 Unit regression tests
 ^
 Unit regression tests are testing the output of individual functors and engines in well defined conditions. They are defined in the folder :ysrc:`py/tests/`.
-The purpose of unit testing is to make sure that the behaviour of the most important classes remains correct during code development. Since they test classes one by one, unit tests can't detect
+The purpose of unit testing is to make sure that the behaviour of the most important classes remains correct during code development. Since they test classes one by one, unit tests can't detect problems coming from the interaction between different engines in a typical simulation. That is why check tests have been introduced. 
 
 Check tests
 ^^^

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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2841: - Fix retriangulation issue

[noreply]

revno: 2841
committer: Emanuele Catalano https://code.launchpad.net/~yade-dev/yade/trunk

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=== modified file 'lib/triangulation/FlowBoundingSphere.cpp'
--- lib/triangulation/FlowBoundingSphere.cpp	2011-04-22 09:09:28 +
+++ lib/triangulation/FlowBoundingSphere.cpp	2011-04-27 15:15:04 +
@@ -784,7 +784,7 @@
 	 cout << "WARNING! if !areaR2Permeability, facetFluidSurfacesRatio will not be defined correctly. Don't use that." EpsVolPercent_RTRG || retriangulationLastIter>1) && retriangulationLastIter>10) {
 			Update_Triangulation = true;
@@ -177,7 +177,7 @@
 void FlowEngine::clearImposedPressure() { flow->imposedP.clear();}
 
 Real FlowEngine::getFlux(int cond) {
-	if (cond>=flow->imposedP.size()) LOG_ERROR("Getting flux with cond higher than imposedP size.");
+	if (cond>=(int)flow->imposedP.size()) LOG_ERROR("Getting flux with cond higher than imposedP size.");
 	CGT::RTriangulation& Tri = flow->T[flow->currentTes].Triangulation();
 	double flux=0;
 	CGT::Cell_handle cell= Tri.locate(flow->imposedP[cond].first);
@@ -252,7 +252,6 @@
 		flow->Initialize_pressures(P_zero);// FIXME : why, if we are going to interpolate after that?
 		flow->Interpolate (flow->T[!flow->currentTes], flow->T[flow->currentTes]);
  		if (WaveAction) flow->ApplySinusoidalPressure(flow->T[flow->currentTes].Triangulation(), Sinus_Amplitude, Sinus_Average, 30);
-
 	}
 	Initialize_volumes();
 }

=== modified file 'pkg/dem/FlowEngine.hpp'
--- pkg/dem/FlowEngine.hpp	2011-04-22 09:09:28 +
+++ pkg/dem/FlowEngine.hpp	2011-04-27 15:15:04 +
@@ -56,7 +56,7 @@
 		void Average_real_cell_velocity();
 		Real getFlux(int cond);
 		void saveVtk() {flow->save_vtk_file();}
-		vector AvFlVelOnSph(int id_sph) {flow->Average_Fluid_Velocity_On_Sphere(id_sph);}
+		vector AvFlVelOnSph(int id_sph) {return flow->Average_Fluid_Velocity_On_Sphere(id_sph);}
 		python::list getConstrictions() {
 			vector csd=flow->getConstrictions(); python::list pycsd;
 			for (unsigned int k=0;k___
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Re: [Yade-dev] [Bug 761411] Re: No information about regression and check tests in manual

[Anton Gladky]

Thanks, Bruno!

Anton



On Wed, Apr 27, 2011 at 3:10 PM, Chareyre <761...@bugs.launchpad.net> wrote:
> Fixed in r2835
> https://www.yade-dem.org/doc/prog.html#development-tools
>
> ** Changed in: yade
>       Status: New => Fix Released
>
> --
> You received this bug notification because you are a direct subscriber
> of the bug.
> https://bugs.launchpad.net/bugs/761411
>
> Title:
>  No information about regression and check tests in manual
>
> Status in Yet Another Dynamic Engine:
>  Fix Released
>
> Bug description:
>  It would be good to add an information about regression and check
>  tests into the manual (Sphinx).
>
> To unsubscribe from this bug, go to:
> https://bugs.launchpad.net/yade/+bug/761411/+subscribe
>

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https://bugs.launchpad.net/bugs/761411

Title:
  No information about regression and check tests in manual

Status in Yet Another Dynamic Engine:
  Fix Released

Bug description:
  It would be good to add an information about regression and check
  tests into the manual (Sphinx).

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[Yade-dev] [Branch ~yade-dev/yade/trunk] Rev 2842: - more explicit notes on citing (I realized it was not clear while reviewing a paper citing yade ...

[noreply]

revno: 2842
committer: Bruno Chareyre 
branch nick: trunk
timestamp: Wed 2011-04-27 19:21:19 +0200
message:
  - more explicit notes on citing (I realized it was not clear while reviewing 
a paper citing yade ;-))
  - again small fixes in the "development tools" section
modified:
  doc/sphinx/citing.rst
  doc/sphinx/prog.rst


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=== modified file 'doc/sphinx/citing.rst'
--- doc/sphinx/citing.rst	2011-02-14 13:35:11 +
+++ doc/sphinx/citing.rst	2011-04-27 17:21:19 +
@@ -6,26 +6,30 @@
 
 In order to let users cite Yade consistently in publications, we provide a list of bibliographic references for the different parts of the documentation, as in the citation model pushed by `CGAL `_. This way of acknowledging Yade is also a way to make developments and documentation of Yade more attractive for researchers, who are evaluated on the basis of citations of their work by others. We therefore kindly ask users to cite Yade as accurately as possible in their papers. A more detailed discussion of the citation model and its application to Yade can be found `here `_.
 
-If new developments are presented and explained in self-contained papers, we will be glad to include them in the documentation and to reference them in the list below. Any other substantial improvement is welcome and can be discussed in the `yade-dev `_ mailing list.
+If new developments are presented and explained in self-contained papers (at the end of a PhD, typically), we will be glad to include them in the documentation and to reference them in the list below. Any other substantial improvement is welcome and can be discussed in the `yade-dev `_ mailing list.
 
 Citing chapters of Yade Documentation
 ^
-The first edition of Yade documentation is seen as a collection with three volumes (or "chapters"), also provided as `bibtex entries `_:
-
-* The reference documentation includes details on equations and algorithms found at the highest levels of Yade. Citation of, namely, contact laws, boundary conditions controllers, pre- and post-processing modules, is using `(pdf version) `_:
+The first edition of Yade documentation is seen as a collection with the three volumes (or "chapters") listed below, also provided as `bibtex entries `_. Please cite the chapter that is the most relevant in your case. For instance, a paper using one of the documented contact laws will cite the reference documentation [yade:reference]_; if programing concepts are discussed, Yade's manual [yade:manual]_ will be cited; the theoretical background [yade:background]_ can be used as the refence for contact detection, time-step determination, or periodic boundary conditions.
+
+If it is not possible to choose the right chapter (but please try), you may cite the documentation [yade:doc]_ as a whole.
+
+* The reference documentation includes details on equations and algorithms found at the highest levels of Yade (contact laws, boundary conditions controllers, pre- and post-processing modules,...) `(pdf version) `_:
 	V. Šmilauer, E. Catalano, B. Chareyre, S. Dorofeenko, J. Duriez, A. Gladky, J. Kozicki, C. Modenese, L. Scholtès, L. Sibille, J. Stránský, and K. Thoeni, “Yade Reference Documentation,” in Yade Documentation (V. Šmilauer, ed.), The Yade Project, 1st ed., 2010. http://yade-dem.org/doc/.
 
 * Software design, user's and programmer's manuals are in `(pdf version) `_:
 	V. Šmilauer, A. Gladky, J. Kozicki, C. Modenese, and J. Stránský, “Yade Using and Programming,” in Yade Documentation (V. Šmilauer, ed.), The Yade Project, 1st ed., 2010. http://yade-dem.org/doc/.
 
 * Fundamentals of the DEM as implemented in Yade are explained in `(pdf version) `_:
-	V. Šmilauer and B. Chareyre, “Yade Dem Formulation,” in Yade Documentation (V. Šmilauer, ed.), The Yade Project, 1st ed., 2010. http://yade-dem.org/doc/formulation.html.
+	V. Šmilauer and B. Chareyre, “Yade Dem Formulation”, in Yade Documentation (V. Šmilauer, ed.), The Yade Project, 1st ed., 2010. http://yade-dem.org/doc/formulation.html.
 
+* The documentation as a whole:
+	V. Å milauer, E. Catalano, B. Chareyre, S. Dorofeenko, J. Duriez, A. G

[Yade-dev] [Bug 764344] Re: Replace wiki main page by sphinx main page

[Chareyre]

Quick note:

We have this page for documentation: https://yade-dem.org/doc/
and this one for main page: https://yade-dem.org (currently wiki page)

It would be good to keep the page at https://yade-dem.org/doc/ as it is now 
(not including more stuff), since this url is used to cite yade's documentation.
So, the best would be to define the new sphinx main as a third html target in 
conf.py, with a different index.html template.
This third target would contain what's is in https://yade-dem.org/doc/, but it 
would also add "yade community" and others a discussed before.

I played a little with conf.py, index.html, and others before, so tell
me if I can help.

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https://bugs.launchpad.net/bugs/764344

Title:
  Replace wiki main page by sphinx main page

Status in Yet Another Dynamic Engine:
  New

Bug description:
  Sphinx main page should be opened by https://yade-dem.org/ address.

  Some changes in sphinx are needed.

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[Yade-dev] problem with import scipy.linalg

[Chiara Modenese]

Hey guys,

I tried to include these three lines in a py script to be run in Yade,
namely:

from numpy import *
import scipy
import scipy.linalg

The third line gives segmentation fault. I am not sure why. I attach below
the output from debug mode. Not sure if anyone can help, but maybe you had
the same problem and found a workaround to it.

Chiara

***
TCP python prompt on localhost:9000, auth cookie `syduek'
XMLRPC info provider on http://localhost:21000
Running script q.py
SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-wdKR2U/tmp-0'
GNU gdb (Ubuntu/Linaro 7.2-1ubuntu11) 7.2
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later 
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 "i686-linux-gnu".
For bug reporting instructions, please see:
.
Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
/tmp/yade-wdKR2U/tmp-0:1: Error in sourced command file:
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Re: [Yade-dev] problem with import scipy.linalg

[Chiara Modenese]

Sorry, do not bother guys, I have just seen that using numpy.linalg other
than scipy.linalg works, instead. Just to let you know in case you need it.

On 27 April 2011 17:50, Chiara Modenese  wrote:

> Hey guys,
>
> I tried to include these three lines in a py script to be run in Yade,
> namely:
>
> from numpy import *
> import scipy
> import scipy.linalg
>
> The third line gives segmentation fault. I am not sure why. I attach below
> the output from debug mode. Not sure if anyone can help, but maybe you had
> the same problem and found a workaround to it.
>
> Chiara
>
> ***
> TCP python prompt on localhost:9000, auth cookie `syduek'
> XMLRPC info provider on http://localhost:21000
> Running script q.py
> SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-wdKR2U/tmp-0'
> GNU gdb (Ubuntu/Linaro 7.2-1ubuntu11) 7.2
> Copyright (C) 2010 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 "i686-linux-gnu".
> For bug reporting instructions, please see:
> .
> Could not attach to process.  If your uid matches the uid of the target
> process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
> again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
> /tmp/yade-wdKR2U/tmp-0:1: Error in sourced command file:
>
>
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Re: [Yade-dev] problem with import scipy.linalg

[Anton Gladky]

So, your problem is resolved?

Anton




On Wed, Apr 27, 2011 at 8:04 PM, Chiara Modenese  wrote:
> Sorry, do not bother guys, I have just seen that using numpy.linalg other
> than scipy.linalg works, instead. Just to let you know in case you need it.
>
> On 27 April 2011 17:50, Chiara Modenese  wrote:
>>
>> Hey guys,
>>
>> I tried to include these three lines in a py script to be run in Yade,
>> namely:
>>
>> from numpy import *
>> import scipy
>> import scipy.linalg
>>
>> The third line gives segmentation fault. I am not sure why. I attach below
>> the output from debug mode. Not sure if anyone can help, but maybe you had
>> the same problem and found a workaround to it.
>>
>> Chiara
>>
>> ***
>> TCP python prompt on localhost:9000, auth cookie `syduek'
>> XMLRPC info provider on http://localhost:21000
>> Running script q.py
>> SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-wdKR2U/tmp-0'
>> GNU gdb (Ubuntu/Linaro 7.2-1ubuntu11) 7.2
>> Copyright (C) 2010 Free Software Foundation, Inc.
>> License GPLv3+: GNU GPL version 3 or later
>> 
>> 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 "i686-linux-gnu".
>> For bug reporting instructions, please see:
>> .
>> Could not attach to process.  If your uid matches the uid of the target
>> process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
>> again as the root user.  For more details, see
>> /etc/sysctl.d/10-ptrace.conf
>> /tmp/yade-wdKR2U/tmp-0:1: Error in sourced command file:
>>
>
>
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