From 6ce99624e9d8a4dc489e25992160f0e8ad363e21 Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Sat, 4 Nov 2017 19:29:11 +0100
Subject: [PATCH] Improving documentation
---
CHANGELOG.md | 11 +++
src/Vector/se_class3_vector.hpp | 116 ++++++++++++++++++++++++++++----
src/Vector/vector_dist.hpp | 62 +++++++----------
3 files changed, 139 insertions(+), 50 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5d9c39333..de399263a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,17 @@
# Change Log
All notable changes to this project will be documented in this file.
+## [1.1.0]
+
+### Added
+
+- Interface for Multi-vector dynamic load balancing
+
+### Fixed
+
+- Installation/detection of PETSC
+- 2D Fixing IO in binary for vector
+
## [1.0.0] 13 September 2017
### Added
diff --git a/src/Vector/se_class3_vector.hpp b/src/Vector/se_class3_vector.hpp
index 85497c7cc..3611174f9 100644
--- a/src/Vector/se_class3_vector.hpp
+++ b/src/Vector/se_class3_vector.hpp
@@ -100,42 +100,75 @@ struct init_prop
}
};
-// Unknown type
+//! Type check in case of unknown type
template<typename tcheck, bool foundamental>
struct typeCheck
{
- //! It check if the type is Nan, data type to check
+ /*! \brief It check if the type is Nan, data type to check
+ *
+ * \param data to check
+ *
+ * \return true if is Nan
+ *
+ */
static bool isNan(const tcheck & data)
{
return false;
}
- //! It check is the type is infinity, data type to checl
+ /*! \brief It check if the type is Infinity, data type to check
+ *
+ * \param data to check
+ *
+ * \return false if is infinity
+ *
+ */
static bool isInf(const tcheck & data)
{
return false;
}
};
-// Unknown type
+//! Type check in case of supported type
template<typename tcheck>
struct typeCheck<tcheck,true>
{
+ /*! \brief It check if the type is Nan, data type to check
+ *
+ * \param data to check
+ *
+ * \return true if is Nan
+ *
+ */
static bool isNan(const tcheck & data)
{
return std::isnan(data);
}
+ /*! \brief It check if the type is Infinity, data type to check
+ *
+ * \param data to check
+ *
+ * \return true if is infinity
+ *
+ */
static bool isInf(const tcheck & data)
{
return std::isinf(data);
}
};
-// Array
+//! Type check in case of supported array type
template<typename tcheck, bool foundamental, unsigned int N1>
struct typeCheck<tcheck[N1], foundamental>
{
+ /*! \brief It check if the type is Nan, data type to check
+ *
+ * \param data to check
+ *
+ * \return true if is Nan
+ *
+ */
static bool isNan(tcheck (& data)[N1])
{
bool nn = false;
@@ -149,6 +182,13 @@ struct typeCheck<tcheck[N1], foundamental>
return nn;
}
+ /*! \brief It check if the type is Infinity, data type to check
+ *
+ * \param data to check
+ *
+ * \return true if is infinity
+ *
+ */
static bool isInf(tcheck (& data)[N1])
{
bool nn = false;
@@ -163,10 +203,17 @@ struct typeCheck<tcheck[N1], foundamental>
}
};
-// Array2d
+//! Type check in case of supported 2D array type
template<typename tcheck, bool foundamental, unsigned int N1, unsigned int N2>
struct typeCheck<tcheck[N1][N2], foundamental>
{
+ /*! \brief It check if the type is Nan, data type to check
+ *
+ * \param data to check
+ *
+ * \return true if is Nan
+ *
+ */
static bool isNan(tcheck (& data)[N1][N2])
{
bool nn = false;
@@ -183,6 +230,13 @@ struct typeCheck<tcheck[N1][N2], foundamental>
return nn;
}
+ /*! \brief It check if the type is Infinity, data type to check
+ *
+ * \param data to check
+ *
+ * \return true if is infinity
+ *
+ */
static bool isInf(tcheck (& data)[N1][N2])
{
bool nn = false;
@@ -219,7 +273,8 @@ struct propCheckNAN
/*! \brief constructor
*
- * \param
+ * \param data vector to check for Nan properties
+ * \param id element to check
*
*/
inline propCheckNAN(const vector & data, size_t id)
@@ -252,7 +307,7 @@ struct propCheckNAN
/*! \brief this class is a functor for "for_each" algorithm
*
* This class is a functor for "for_each" algorithm. For each
- * property it check that there are not NAN properties
+ * property it check that there are not infinity properties
*
* \param T boost::fusion::vector
*
@@ -269,7 +324,7 @@ struct propCheckINF
/*! \brief constructor
*
- * \param check the the property is infinity
+ * \param data vector to check
* \param id element
*
*/
@@ -389,6 +444,13 @@ class se_class3_vector
//! last write
size_t l_wrt;
+ /*! \brief It check if the particle is in the internal ghost area
+ *
+ * \param p particle to check
+ *
+ * \return true if the particle is in that area
+ *
+ */
bool isLocalHalo(const Point<dim,T> & p)
{
for (size_t i = 0; i < dec.getNLocalSub(); i++)
@@ -448,7 +510,13 @@ class se_class3_vector
return type;
}
- template<unsigned int ... prp> void create_NNP( const size_t (& gg)[sizeof...(prp)+1] )
+ /*! \brief Fill non_NP with the properties that are not synchronized
+ *
+ * \param gg vector of properties synchronized
+ *
+ */
+ template<unsigned int ... prp>
+ void create_NNP( const size_t (& gg)[sizeof...(prp)+1] )
{
non_NP.clear();
@@ -470,6 +538,13 @@ class se_class3_vector
}
+ /*! \brief Get property name
+ *
+ * \param i property
+ *
+ * \return the property name
+ *
+ */
std::string getPrpName(size_t i) const
{
if (i == Np_real)
@@ -480,17 +555,30 @@ class se_class3_vector
public:
- //! Constructor all properties are uninitialized
+ /*! Constructor all properties are uninitialized
+ *
+ * \param dec decomposition
+ * \param vd vector we are cheking with SE_CLASS3 checks
+ *
+ */
se_class3_vector(Decomposition & dec, vector & vd)
- :dec(dec),vd(vd)
+ :dec(dec),vd(vd),l_wrt(-1)
{
}
+ /*! \brief return the status of the ghosts
+ *
+ * \return the status of the ghosts
+ *
+ */
template<unsigned int prp> size_t isGhostSync()
{
return sync[GHOST][prp];
}
+ /*! \brief Initialize the se_class2 structure
+ *
+ */
void Initialize()
{
auto it = vd.getDomainIterator_no_se3();
@@ -702,6 +790,10 @@ class se_class3_vector
}
}
+ /*! \brief Operation to do after map
+ *
+ *
+ */
void map_post()
{
for (size_t j = 0 ; j < Np_real + 1 ; j++)
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 979760c7a..77e6c99db 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -913,11 +913,13 @@ public:
* \tparam CellL CellList type to construct
*
* \param r_cut interation radius, or size of each cell
+ * \param no_se3 avoid SE_CLASS3 checking
*
* \return the Cell list
*
*/
- template<typename CellL = CellList_gen<dim, St, Process_keys_lin, Mem_fast, shift<dim, St> > > CellL getCellList(St r_cut, bool no_se3 = false)
+ template<typename CellL = CellList_gen<dim, St, Process_keys_lin, Mem_fast, shift<dim, St> > >
+ CellL getCellList(St r_cut, bool no_se3 = false)
{
#ifdef SE_CLASS3
if (no_se3 == false)
@@ -943,7 +945,8 @@ public:
* \return the Cell list
*
*/
- template<typename CellL = CellList_gen<dim, St, Process_keys_hilb, Mem_fast, shift<dim, St> > > CellL getCellList_hilb(St r_cut)
+ template<typename CellL = CellList_gen<dim, St, Process_keys_hilb, Mem_fast, shift<dim, St> > >
+ CellL getCellList_hilb(St r_cut)
{
#ifdef SE_CLASS3
se3.getNN();
@@ -964,6 +967,7 @@ public:
* \tparam CellL CellList type to construct
*
* \param cell_list Cell list to update
+ * \param no_se3 avoid se class 3 checking
*
*/
template<typename CellL> void updateCellList(CellL & cell_list, bool no_se3 = false)
@@ -1045,11 +1049,13 @@ public:
*
* \param r_cut interation radius, or size of each cell
* \param enlarge In case of padding particles the cell list must be enlarged, like a ghost this parameter say how much must be enlarged
+ * \param no_se3 avoid se_class3 cheking default false
*
* \return the CellList
*
*/
- template<typename CellL = CellList_gen<dim, St, Process_keys_lin, Mem_fast, shift<dim, St> > > CellL getCellList(St r_cut, const Ghost<dim, St> & enlarge, bool no_se3 = false)
+ template<typename CellL = CellList_gen<dim, St, Process_keys_lin, Mem_fast, shift<dim, St> > >
+ CellL getCellList(St r_cut, const Ghost<dim, St> & enlarge, bool no_se3 = false)
{
#ifdef SE_CLASS3
if (no_se3 == false)
@@ -1525,11 +1531,15 @@ public:
}
/*! \brief Get an iterator that traverse the particles in the domain
+ * using a cell list
*
- * \return an iterator
+ * \param NN Cell-list
+ *
+ * \return an iterator over the particles
*
*/
- template<typename CellList> ParticleIt_Cells<dim,CellList> getDomainIteratorCells(CellList & NN)
+ template<typename CellList> ParticleIt_Cells<dim,CellList>
+ getDomainIteratorCells(CellList & NN)
{
#ifdef SE_CLASS3
se3.getIterator();
@@ -1741,9 +1751,7 @@ public:
* from the particles
*
* \param md Model to use
- * \param vd vector to add for the computational cost
- * \param ts It is an optional parameter approximately should be the number of ghost get between two
- * rebalancing at first decomposition this number can be ignored (default = 1) because not used
+ * \param vd external vector to add for the computational cost
*
*/
template <typename Model=ModelLin>inline void addComputationCosts(const self & vd, Model md=Model())
@@ -1766,6 +1774,14 @@ public:
}
}
+ /*! \brief Add the computation cost on the decomposition coming
+ * from the particles
+ *
+ * \param md Model to use
+ * \param ts It is an optional parameter approximately should be the number of ghost get between two
+ * rebalancing at first decomposition this number can be ignored (default = 1) because not used
+ *
+ */
template <typename Model=ModelLin> void finalizeComputationCosts(Model md=Model(), size_t ts = 1)
{
Decomposition & dec = getDecomposition();
@@ -1808,36 +1824,6 @@ public:
addComputationCosts(*this,md);
finalizeComputationCosts(md,ts);
-
-/* CellDecomposer_sm<dim, St, shift<dim,St>> cdsm;
-
- Decomposition & dec = getDecomposition();
- auto & dist = getDecomposition().getDistribution();
-
- cdsm.setDimensions(dec.getDomain(), dec.getDistGrid().getSize(), 0);
-
- for (size_t i = 0; i < dist.getNOwnerSubSubDomains() ; i++)
- dec.setSubSubDomainComputationCost(dist.getOwnerSubSubDomain(i) , 1);
-
- auto it = getDomainIterator();
-
- while (it.isNext())
- {
- size_t v = cdsm.getCell(this->getPos(it.get()));
-
- md.addComputation(dec,*this,v,it.get().getKey());
-
- ++it;
- }
-
- dec.computeCommunicationAndMigrationCosts(ts);
-
- // Go throught all the sub-sub-domains and apply the model
-
- for (size_t i = 0 ; i < dist.getNOwnerSubSubDomains(); i++)
- md.applyModel(dec,dist.getOwnerSubSubDomain(i));
-
- dist.setDistTol(md.distributionTol());*/
}
/*! \brief Save the distributed vector on HDF5 file
--
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