Xfiles issueshttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues2018-04-25T07:45:54Zhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/34geom: distance computation in distributed context with ann or brute force2018-04-25T07:45:54ZAlexis SALZMANgeom: distance computation in distributed context with ann or brute forceCommit 3b05590 introduce a way to compute distance to a surface in distributed context with CGAL. The same should be done with ANN at least and maybe for brute force. Test case functional_xDistanceNearestPointDist should be modified in c...Commit 3b05590 introduce a way to compute distance to a surface in distributed context with CGAL. The same should be done with ANN at least and maybe for brute force. Test case functional_xDistanceNearestPointDist should be modified in consequence.Parallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/32kill xPhysSurf ?2018-09-07T11:44:16ZGrégory LEGRAINkill xPhysSurf ?the (old) xPhysSurf is (in practice) deprecated in favor of xPhysSurfByTagging.
We should move it to attic.
Though, it necessitates some fixes in some testcases and classes...the (old) xPhysSurf is (in practice) deprecated in favor of xPhysSurfByTagging.
We should move it to attic.
Though, it necessitates some fixes in some testcases and classes...Grégory LEGRAINGrégory LEGRAINhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/31xDoubleManager/xValManger distributed concept2018-05-18T07:23:37ZAlexis SALZMANxDoubleManager/xValManger distributed conceptHas mentioned in commit d1f3ed5561e76ed4c2b318220128f5af68a19cc0 the partition manager introduced in double manager may be generalized to xValManager.
Make a template version of xValKeyDataManager would be certainly a must. But how ...Has mentioned in commit d1f3ed5561e76ed4c2b318220128f5af68a19cc0 the partition manager introduced in double manager may be generalized to xValManager.
Make a template version of xValKeyDataManager would be certainly a must. But how genPartitionManager would be done in xValManager. In a rather specific way as it is in xDoubleManager where xMesh::partman_t is expected. Or will it be generic wit a template type for mesh partition manager. In this case maybe it will be a bit touchy to deal with a generic partman to create xValManager partion manager (for example at no stage we want to introduce AOMD struff) ...
First check that this concept is good and then pass some time on this generalization ...Parallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/26CGAL interface not compatible with CGAL 4.112018-05-18T07:23:37ZGrégory LEGRAINCGAL interface not compatible with CGAL 4.11AABBPrimitiveExtension.h seems incompatible with new CGAL implementation
`pas de concordance pour l'appel à « (CGAL::Cartesian_base_no_ref_count<double, CGAL::Simple_cartesian<double> >::Construct_projected_point_3 {aka CGAL::CartesianK...AABBPrimitiveExtension.h seems incompatible with new CGAL implementation
`pas de concordance pour l'appel à « (CGAL::Cartesian_base_no_ref_count<double, CGAL::Simple_cartesian<double> >::Construct_projected_point_3 {aka CGAL::CartesianKernelFunctors::Construct_projected_point_3<CGAL::Simple_cartesian<double> >}) (CGAL::internal::Primitive_helper<CGAL::AABB_traits<CGAL::Simple_cartesian<double>, CGAL::AABB_point_primitive<CGAL::Simple_cartesian<double>, __gnu_cxx::__normal_iterator<CGAL::Point_3<CGAL::Simple_cartesian<double> >*, std::vector<CGAL::Point_3<CGAL::Simple_cartesian<double> > > > > >, false>::Datum_type, const Point&) »
Point closest_point = geom_traits.construct_projected_point_3_object()(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
internal::Primitive_helper<AT>::get_datum(pr,m_traits), p);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
`
It complains that the point to point case (whici is de fined in AABBPrimitiveExtension. if I am correct) is missing.
Good to know when we will update the version which is available on the platformGrégory LEGRAINGrégory LEGRAINhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/25Keeping boost iostream isolated2018-05-18T07:23:37ZAlexis SALZMANKeeping boost iostream isolatedDiscussion around cmake point out that with some effort (little ?) we may hide boost iostram (used for gzip output) from Xfem interface.
That may also be treated as an extra interface in xInterface.
In one hand treating it in Xfem corr...Discussion around cmake point out that with some effort (little ?) we may hide boost iostram (used for gzip output) from Xfem interface.
That may also be treated as an extra interface in xInterface.
In one hand treating it in Xfem correspond to where it is used for now, in the other adding it as an Xinterface gives a way to use it everywhere.http://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/24treillis with _DEBUG_ macro enable2018-05-18T07:23:37ZAlexis SALZMANtreillis with _DEBUG_ macro enableIn Treillis, in mVector and mPoint (at least) if _DEBUG_ macro is enable code does not compile.
Bug correction needed.
For now don't turn on USE_DEBUG_FLAG option in cmake (which is not only a printing stuff as message suggest)In Treillis, in mVector and mPoint (at least) if _DEBUG_ macro is enable code does not compile.
Bug correction needed.
For now don't turn on USE_DEBUG_FLAG option in cmake (which is not only a printing stuff as message suggest)http://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/21Removing xFitToVertexKeyManager in xFitToVertices class2018-05-18T07:23:38ZAlexis SALZMANRemoving xFitToVertexKeyManager in xFitToVertices classFollowing commit 5d34c604 the key manager xFitToVertexKeyManager should be remove and usage replace by new keyManagerSendOrReceiveFollowing commit 5d34c604 the key manager xFitToVertexKeyManager should be remove and usage replace by new keyManagerSendOrReceivehttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/19xStringManager2018-07-10T07:56:27ZAlexis SALZMANxStringManagerIn adb708519561c2fdcbb458207f6d1fe63d818050 we had a function which need to communicate keys (xValKey) in between proc. Due to lack of synchronization in xStringManager this have been done with string !!!<br>
If, in xKeyInfo in particu...In adb708519561c2fdcbb458207f6d1fe63d818050 we had a function which need to communicate keys (xValKey) in between proc. Due to lack of synchronization in xStringManager this have been done with string !!!<br>
If, in xKeyInfo in particular, association of string with “int” is not done in the same order in all proc we cannot rely on “int” value to communicate. A way to bypass this problem is to set explicitly this association at the beginning of your application (and by implementation in the same order for all proc). But it is difficult to be sure that we did set all mandatory association and it's hard for beginners to figure out which association must be set...<br>
<br>
The ideal solution from a user point of view is that xStringManager do appropriate communication to insure uniqueness of association string<=> integer.<br>
<br>
From a performance point of view a solution must be find to achieve this goal but with as minimal communication as possible. <br>
<br>
It is a tricky problem despite it's apparent simplicity. We are in asynchronous context and there is no reason that call to xStringManager methods are done at the same time !! Synchronization just for that ... please don't think about it. Windowing ??? Maybe.
---
An alternative is to consider that the id (integer) associated to a string in xStringManager is no more depending on order in which it is created but depends only on the string itself.
The T nb = s_.size(); would be replace by
T nb = static_cast<T>(str_hash(s)); with str_hash being std::hash\<std::string\> str_hash;
The c++11 hash class is expected to give no collision in regard of the set of string used in xfem. Unfortunately, in Xfem, xKeyInfo is using a T of type "int" which is smaller then the size_t type returned by C++11 hash operator. So this first casting, that appears here with static_cast call, is a first concern: does the casting will not increase artificially collision ?
And when we see that xValKey itself is using short, this last casting will or will not increase collision ?
Due to those last interrogation it looks difficult to relies on a collision free hash function at xStringManager level but it would have solve the issue without any communication ....
One can thing of creating a hash function that do return a short:
short hash(std::string & str)
{
unsigned short h = 0;
unsigned short mx=std::numeric_limits<unsigned short>::max();
for (auto c : str)
{
h = ((( h << 5 ) + h ) + c)%mx; /* hash * 33 + c : I added this dirty %mx but in fact I think it is not mandatory */
}
return static_cast<short>(h);
}
This hash function base on djb2 algorithm (k=33) first reported by Dan Bernstein many years ago in comp.lang.c may give no collision in our context. But then the fact that xValkey is using short and xKeyInfo int remain a problem as using this short hash function for T being a int is quite ugly ...
Parallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/16xCFL getDt2018-05-18T07:23:38ZAlexis SALZMANxCFL getDtFrom Kevin Moreau this is weird to divide by 1 and by 2 ! missing parenthesis (i.e. divinding by 0.5) or volonteer (i.e. divinding by 2.)
<br>
double xCFL::getDt(xRegion s) {<br>
return ((xCFL::getLength(s))/1./2.);<br>
}From Kevin Moreau this is weird to divide by 1 and by 2 ! missing parenthesis (i.e. divinding by 0.5) or volonteer (i.e. divinding by 2.)
<br>
double xCFL::getDt(xRegion s) {<br>
return ((xCFL::getLength(s))/1./2.);<br>
}http://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/15xExport2018-07-23T12:35:49ZAlexis SALZMANxExportSome PARALEL oldies must be treated in a new way :
<ul><li>xExport must have their comunicator given has argument with MPI_COM_WORD as default</li>
<li>multi file must be refplaced by some MPIO/hdf5 mecanism</li>
</ul>
To start, us...Some PARALEL oldies must be treated in a new way :
<ul><li>xExport must have their comunicator given has argument with MPI_COM_WORD as default</li>
<li>multi file must be refplaced by some MPIO/hdf5 mecanism</li>
</ul>
To start, using one file per proc with right extention will be simple and it will force user to use unique name for their Export calls. Passing to MPIO will then be transparent ( i.e. in implementation).Parallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/14newMeshDataId vs lookupMeshDataId2018-05-18T07:23:38ZAlexis SALZMANnewMeshDataId vs lookupMeshDataIdIt looks like lookupMeshDataId have been used in many place in xfem. But it is not so clear to me that newMeshDataId would have not been the right choice in some cases.
To checkIt looks like lookupMeshDataId have been used in many place in xfem. But it is not so clear to me that newMeshDataId would have not been the right choice in some cases.
To checkhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/11Boost2018-05-18T07:23:38ZAlexis SALZMANBoostCommit 297718b and GemUtil commit 12aa2c6 introduce new BOOST_SPECIAL_INCLUDE_PATH variable.
It have been used sucessfully with Xfem and SplitMesh/test. But it had to be done on all CMAKE of eXlibris where it have to.
It replace prope...Commit 297718b and GemUtil commit 12aa2c6 introduce new BOOST_SPECIAL_INCLUDE_PATH variable.
It have been used sucessfully with Xfem and SplitMesh/test. But it had to be done on all CMAKE of eXlibris where it have to.
It replace properly what was done in eXlibrisType.
Boost version checking mechanism may have to be adapted.
http://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/9Fast marching2019-03-01T08:16:34ZAlexis SALZMANFast marchingpass in parallelpass in parallelParallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/8Remove PARDIST/PARSEQ/PARALEL2018-09-07T11:43:49ZAlexis SALZMANRemove PARDIST/PARSEQ/PARALELRemove those compiler macro definition.
For AOMD put special guard to avoid usage of this library in parallelRemove those compiler macro definition.
For AOMD put special guard to avoid usage of this library in parallelParallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/7Guard2018-09-07T13:20:35ZAlexis SALZMANGuardSet guard on every point where parallel is an issue.
See commit 282fdb3Set guard on every point where parallel is an issue.
See commit 282fdb3Parallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/6xSubmesh2018-09-07T11:39:13ZAlexis SALZMANxSubmeshpass it in new parralel environementpass it in new parralel environementParallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/5xLevelset2018-09-07T11:39:13ZAlexis SALZMANxLevelsetIt have to be treated
A first guard have been set for gradiant computationIt have to be treated
A first guard have been set for gradiant computationParallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/4xData2018-09-07T11:39:13ZAlexis SALZMANxDataIn xData when reading mesh things are :
<ul><li>if sequential name corespond to a file, proc O read this files and the others do nothing</li>
<li>if sequential name does not corespond to any files, distributed name is tried. The idear ...In xData when reading mesh things are :
<ul><li>if sequential name corespond to a file, proc O read this files and the others do nothing</li>
<li>if sequential name does not corespond to any files, distributed name is tried. The idear is then that if no file correspond for a proc, an empty mesh is created.
In this way a mesh distributed on 3 files will potentially be read by 3 proc only, the others proc simply creating empty mesh. Loadbalancing planned to equilibrate mesh on all proc aftewards.</li>
</ul>
The problem is that case with no mesh for all proc is not covered. TODO.
A global flag communication is simple (if on all proc flag is null there is problem) but is there somting smarter ?? Parallel integrationhttp://git.gem.ec-nantes.fr/eXlibris/Xfiles/-/issues/2xPhysSurfByTaging2018-09-07T11:39:13ZAlexis SALZMANxPhysSurfByTagingFinish parallel.
Work fine for now with mecanical test case but does not work with functional.
entity tag prb
Finish parallel.
Work fine for now with mecanical test case but does not work with functional.
entity tag prb
Parallel integrationAlexis SALZMANAlexis SALZMAN