From cd9afeba15984fccc18e326aa01b6e2c06ddb12d Mon Sep 17 00:00:00 2001
From: Pietro Incardona <incardon@mpi-cbg.de>
Date: Tue, 11 Jul 2017 01:08:34 +0200
Subject: [PATCH] Latest modules
---
CHANGELOG.md | 3 +-
example/Grid/0_simple/main.cpp | 58 ++++----
example/Grid/1_stencil/main.cpp | 26 ++--
example/Grid/2_solve_eq/main.cpp | 42 +++---
example/Grid/3_gray_scott/main.cpp | 18 +--
example/Grid/3_gray_scott_3d/main.cpp | 6 +-
.../0_2D_incompressible/main_eigen.cpp | 2 +-
.../0_2D_incompressible/main_petsc.cpp | 8 +-
.../1_3D_incompressible/main_eigen.cpp | 2 +-
.../1_3D_incompressible/main_petsc.cpp | 2 +-
example/Vector/7_SPH_dlb/main.cpp | 117 +++++++++++++++-
install | 17 ++-
openfpm_numerics | 2 +-
script/install_MPI.sh | 12 +-
script/install_PETSC.sh | 125 ++++++++++++------
script/install_Parmetis.sh | 12 ++
script/install_SUITESPARSE.sh | 41 +++---
script/remove_old | 74 ++++++++++-
script/show_solutions | 29 ++++
src/Grid/grid_dist_id.hpp | 2 +-
src/Vector/vector_dist.hpp | 2 +-
21 files changed, 440 insertions(+), 160 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1538ddad3..443ecd0d5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -34,7 +34,8 @@ All notable changes to this project will be documented in this file.
become
CellList<3, double, Mem_fast<3, double>, shift<3, double>>
- getIterator in CellList changed getCellIterator
-- Gris iterator types has changes (one additional template parameter)
+- Grid iterator types has changes (one additional template parameter)
+- FDScheme the constructor now has one parameter less (Parameter number 4 has been removed) (see Stokes_Flow examples in Numerics)
## [0.8.0] 28 February 2016
diff --git a/example/Grid/0_simple/main.cpp b/example/Grid/0_simple/main.cpp
index 64411b39e..30ae5a947 100644
--- a/example/Grid/0_simple/main.cpp
+++ b/example/Grid/0_simple/main.cpp
@@ -4,13 +4,15 @@
/*! \page grid Grid
*
* \subpage grid_0_simple
+ * \subpage grid_1_save_load
* \subpage Grid_1_stencil
* \subpage Grid_2_solve_eq
* \subpage Grid_3_gs
+ * \subpage Grid_3_gs_3D
*
*/
-/*! \page grid_0_simple Grid 0 simple
+/*! \page grid_0_simple Simple usage
[TOC]
@@ -29,7 +31,7 @@
int main(int argc, char* argv[])
{
- /*! \page grid_0_simple Grid 0 simple
+ /*! \page grid_0_simple Simple usage
*
* ## Initialization ## {#e0_s_initialization}
*
@@ -55,18 +57,18 @@ int main(int argc, char* argv[])
size_t sz[3] = {100,100,100};
// Ghost part
- Ghost<3,float> g(0.01);
+ Ghost<3,float> g(0.1);
//! \cond [initialization] \endcond
- /*! \page grid_0_simple Grid 0 simple
+ /*! \page grid_0_simple Simple usage
*
* ## Grid instantiation ## {#e0_s_grid_inst}
*
- * Here we are creating a distributed grid in defined by the following parameters
+ * Here we are creating a distributed grid defined by the following parameters
*
* * 3 dimensionality of the grid
- * * float Type used for the spatial coordinates
+ * * float type used for the spatial coordinates
* * each grid point contain a vector of dimension 3 (float[3]),
* * float[3] is the information stored by each grid point a float[3]
* the list of properties must be put into an aggregate data structure aggregate<prop1,prop2,prop3, ... >
@@ -88,13 +90,12 @@ int main(int argc, char* argv[])
//! \cond [grid instantiation] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* ## Loop over grid points ## {#e0_s_loop_gp}
*
* Get an iterator that go through all the grid points. In this
- * example we use iterators. Iterators are convenient way to explore/iterate data-structures in an
- * convenient and easy way.
+ * example we use iterators. Iterators are convenient way to explore/iterate data-structures.
*
* \snippet Grid/0_simple/main.cpp get iterator
* \snippet Grid/0_simple/main.cpp get iterator2
@@ -115,7 +116,7 @@ int main(int argc, char* argv[])
//! \cond [get iterator] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* ## Grid coordinates ## {#e0_s_grid_coord}
*
@@ -135,7 +136,7 @@ int main(int argc, char* argv[])
//! \cond [local grid] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* **Short explanation**
*
@@ -144,7 +145,7 @@ int main(int argc, char* argv[])
*/
/*!
*
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
\htmlonly <a href="#" onclick="if (document.getElementById('long-explanation-div').style.display == 'none') {document.getElementById('long-explanation-div').style.display = 'block'} else {document.getElementById('long-explanation-div').style.display = 'none'}" >Long Explanation</a> \endhtmlonly
*
@@ -185,7 +186,7 @@ int main(int argc, char* argv[])
PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
<ul>
-<li>Global/Real coordinates are (3,2)</li>
+<li>Global/Real coordinates (3,2)</li>
<li>Local grid coordinates are Sub-domain = 0, grid position = (0,0)</li>
</ul>
<p>Here we convert the local grid coordinates, into global coordinates. key_g internally store 3 integers that identify the position of the grid point in global coordinates</p>
@@ -193,7 +194,7 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
</div>
\endhtmlonly
*/
- /*! \page grid_0_simple Grid 0 simple
+ /*! \page grid_0_simple Simple usage
*
* \snippet Grid/0_simple/main.cpp global coord
*
@@ -206,7 +207,7 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
//! \cond [global coord] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* ## Assign properties ## {#grid_assign}
*
@@ -230,8 +231,6 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
//! \cond [get iterator2] \endcond
- //! ...
-
// next point
++dom;
}
@@ -239,7 +238,7 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
//! \cond [get iterator2] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* Each sub-domain has an extended part, that is materially contained in
* another processor. The function ghost_get guarantee (after return) that this extended part
@@ -256,7 +255,7 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
//! \cond [ghost get] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* count contain the number of points the local processor contain, if we are interested to count the total number across the processor
* we can use the function sum, to sum numbers across processors. First we have to get an instance of Vcluster, queue an operation of sum with
@@ -285,7 +284,7 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
//! \cond [reduce] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* ## VTK and visualization ## {#e0_s_VTK_vis}
*
@@ -293,6 +292,10 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
* The function write by default produce VTK files. One for each processor that can be visualized
* with the programs like paraview
*
+ * \htmlonly
+ * <img src="http://ppmcore.mpi-cbg.de/web/images/examples/0_simple_grid/0_simple_grid_init.jpg"/>
+ * \endhtmlonly
+ *
* \snippet Grid/0_simple/main.cpp write
*
*/
@@ -304,7 +307,7 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
//! \cond [write] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* ## Decomposition ## {#grid_dec}
*
@@ -313,6 +316,15 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
*
* \snippet Grid/0_simple/main.cpp out_dec
*
+ * \htmlonly
+ * <img src="http://ppmcore.mpi-cbg.de/web/images/examples/0_simple_grid/0_simple_grid_dec.jpg"/>
+ * \endhtmlonly
+ *
+ * Here we see the decomposition in 3D for 2 processors. The red box in wire-frame is the processor 0
+ * subdomain. The blu one is the processor 1 sub-domain. The red solid box is the extended part for processor 0
+ * the blu solid part is the extended part for processor 1
+ *
+ *
*/
//! \cond [out_dec] \endcond
@@ -322,7 +334,7 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
//! \cond [out_dec] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* ## Finalize ## {#finalize}
*
@@ -339,7 +351,7 @@ PX,Y Processor X, sub-domain Y</pre><p>The point # has</p>
//! \cond [finalize] \endcond
/*!
- * \page grid_0_simple Grid 0 simple
+ * \page grid_0_simple Simple usage
*
* # Full code # {#code}
*
diff --git a/example/Grid/1_stencil/main.cpp b/example/Grid/1_stencil/main.cpp
index b91d2f113..551e0dccd 100644
--- a/example/Grid/1_stencil/main.cpp
+++ b/example/Grid/1_stencil/main.cpp
@@ -3,7 +3,7 @@
#include "Decomposition/CartDecomposition.hpp"
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
*
* # Stencil example and ghost # {#e1_st}
@@ -15,7 +15,7 @@
*/
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* Define some convenient constants and types
*
@@ -37,7 +37,7 @@ constexpr size_t B = 0;
int main(int argc, char* argv[])
{
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* ## Initialization ## {#e1_st_init}
*
@@ -66,7 +66,7 @@ int main(int argc, char* argv[])
//! \cond [parameters] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* ## Grid create ## {#e1_st_inst}
*
@@ -89,7 +89,7 @@ int main(int argc, char* argv[])
//! \cond [grid] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* ## Loop over grid points ## {#e1_s_loop_gp}
*
@@ -112,7 +112,7 @@ int main(int argc, char* argv[])
//! \cond [iterator] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* Inside the cycle we get the local grid key
*
@@ -129,7 +129,7 @@ int main(int argc, char* argv[])
//! \cond [local key] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* We convert the local grid position, into global position, key_g contain 3 integers that identify the position
* of the grid point in global coordinates
@@ -147,7 +147,7 @@ int main(int argc, char* argv[])
//! \cond [global key] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* we write on the grid point of position (i,j,k) the value i*i + j*j + k*k on the property A.
* Mathematically is equivalent to the function
@@ -172,7 +172,7 @@ int main(int argc, char* argv[])
//! \cond [iterator2] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* ## Ghost ## {#e1_s_ghost}
*
@@ -191,7 +191,7 @@ int main(int argc, char* argv[])
//! \cond [ghost] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* Get again another iterator, iterate across all the domain points, calculating a Laplace stencil. Write the
* result on B
@@ -220,7 +220,7 @@ int main(int argc, char* argv[])
//! \cond [laplacian] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
*
* Finally we want a nice output to visualize the information stored by the distributed grid
@@ -238,7 +238,7 @@ int main(int argc, char* argv[])
//! \cond [output] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* Deinitialize the library
*
@@ -253,7 +253,7 @@ int main(int argc, char* argv[])
//! \cond [finalize] \endcond
/*!
- * \page Grid_1_stencil Grid 1 stencil
+ * \page Grid_1_stencil Stencil example
*
* # Full code # {#code}
*
diff --git a/example/Grid/2_solve_eq/main.cpp b/example/Grid/2_solve_eq/main.cpp
index cfa128458..743cf7253 100644
--- a/example/Grid/2_solve_eq/main.cpp
+++ b/example/Grid/2_solve_eq/main.cpp
@@ -2,7 +2,7 @@
#include "data_type/aggregate.hpp"
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* [TOC]
*
@@ -14,7 +14,11 @@
*
* \f$u(x,y) = 0 \f$
*
- * at the boundary
+ * at the boundary. This lead to the solution shown in the picture
+ *
+ * \htmlonly
+ * <img src="http://ppmcore.mpi-cbg.de/web/images/examples/2_solve_eq/solution.jpg"/>
+ * \endhtmlonly
*
*
* ## Field initialization ## {#e2_se_finit}
@@ -26,7 +30,7 @@
void init(grid_dist_id<2,double,aggregate<double> > & g_dist, const size_t (& sz)[2])
{
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* In order to initialize the field U, first we get an iterator that cover
* domain + Ghost to iterate all the grid points.
@@ -47,7 +51,7 @@ void init(grid_dist_id<2,double,aggregate<double> > & g_dist, const size_t (& sz
//! \cond [iterator] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* Get the local grid key
*
@@ -64,7 +68,7 @@ void init(grid_dist_id<2,double,aggregate<double> > & g_dist, const size_t (& sz
//! \cond [local key] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
*
* Here we convert the local grid position, into global position.
@@ -84,7 +88,7 @@ void init(grid_dist_id<2,double,aggregate<double> > & g_dist, const size_t (& sz
//! \cond [global key] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* Initialize to 0, domain + boundary
*
@@ -129,7 +133,7 @@ constexpr int y = 1;
int main(int argc, char* argv[])
{
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* ## Initialization ##
*
@@ -148,7 +152,7 @@ int main(int argc, char* argv[])
//! \cond [ofp_init] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* ## Grid instantiation and initialization ##
*
@@ -174,7 +178,7 @@ int main(int argc, char* argv[])
//! \cond [ofp_par] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* Create a distributed grid in 2D (1° template parameter) space in with double precision (2° template parameter)
* each grid point contain a scalar (double),
@@ -202,7 +206,7 @@ int main(int argc, char* argv[])
//! \cond [grid inst] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* Initialize U and fill the boundary conditions
*
@@ -219,7 +223,7 @@ int main(int argc, char* argv[])
//! \cond [grid init] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* ## %Ghost synchronization ##
*
@@ -238,7 +242,7 @@ int main(int argc, char* argv[])
//! \cond [ghost sync] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* ## Red-Black alghorithm ##
*
@@ -257,7 +261,7 @@ int main(int argc, char* argv[])
for (size_t i = 0 ; i < 10000 ; i++)
{
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* Get an iterator that go through the points of the grid (No ghost)
* To compute one iteration.
@@ -312,7 +316,7 @@ int main(int argc, char* argv[])
//! \cond [gs_it] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
*
* Once an iteration is done we have to synchronize the ghosts
@@ -336,7 +340,7 @@ int main(int argc, char* argv[])
}
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* The full Algorithm look like this
*
@@ -400,7 +404,7 @@ int main(int argc, char* argv[])
//! \cond [sol stat] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* ## VTK Write and visualization ##
*
@@ -422,7 +426,7 @@ int main(int argc, char* argv[])
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
* ## Finalize ##
*
@@ -439,9 +443,9 @@ int main(int argc, char* argv[])
//! \cond [finalize] \endcond
/*!
- * \page Grid_2_solve_eq Grid 2 solve eq
+ * \page Grid_2_solve_eq Solve equation
*
- * # Full code # {#code}
+ * # Full code # {#e2_solve_eq_code}
*
* \include Grid/2_solve_eq/main.cpp
*
diff --git a/example/Grid/3_gray_scott/main.cpp b/example/Grid/3_gray_scott/main.cpp
index 180d9c95c..0cded15e3 100644
--- a/example/Grid/3_gray_scott/main.cpp
+++ b/example/Grid/3_gray_scott/main.cpp
@@ -3,7 +3,7 @@
#include "timer.hpp"
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs Gray Scott 2D
*
* # Solving a gray scott-system # {#e3_gs_gray_scott}
*
@@ -34,7 +34,7 @@ constexpr int y = 1;
//! \cond [constants] \endcond
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs Gray Scott 2D
*
* We also define an init function. This function initialize the species U and V. In the following we are going into the
* detail of this function
@@ -52,7 +52,7 @@ void init(grid_dist_id<2,double,aggregate<double,double> > & Old, grid_dist_id<2
//! \cond [init fun] \endcond
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs Gray Scott 2D
*
* Here we initialize for the full domain. U and V itarating across the grid points. For the calculation
* We are using 2 grids one Old and New. We initialize Old with the initial condition concentration of the
@@ -86,7 +86,7 @@ void init(grid_dist_id<2,double,aggregate<double,double> > & Old, grid_dist_id<2
//! \cond [init uv] \endcond
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs Gray Scott 2D
*
* After we initialized the full grid, we create a perturbation in the domain with different values.
* We do in the part of space: 1.55 < x < 1.85 and 1.55 < y < 1.85. Or more precisely on the points included
@@ -125,7 +125,7 @@ void init(grid_dist_id<2,double,aggregate<double,double> > & Old, grid_dist_id<2
int main(int argc, char* argv[])
{
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs Gray Scott 2D
*
* ## Initialization ##
*
@@ -185,7 +185,7 @@ int main(int argc, char* argv[])
//! \cond [init lib] \endcond
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs Gray Scott 2D
*
* Here we create 2 distributed grid in 2D Old and New. In particular because we want that
* the second grid is distributed across processors in the same way we pass the decomposition
@@ -210,7 +210,7 @@ int main(int argc, char* argv[])
//! \cond [init grid] \endcond
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs Gray Scott 2D
*
* We use the function init to initialize U and V on the grid Old
*
@@ -225,7 +225,7 @@ int main(int argc, char* argv[])
//! \cond [init uvc] \endcond
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs Gray Scott 2D
*
* ## Time stepping ##
*
@@ -323,7 +323,7 @@ int main(int argc, char* argv[])
//! \cond [time stepping] \endcond
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs Gray Scott 2D
*
* ## Finalize ##
*
diff --git a/example/Grid/3_gray_scott_3d/main.cpp b/example/Grid/3_gray_scott_3d/main.cpp
index 22249b10c..e6cb92350 100644
--- a/example/Grid/3_gray_scott_3d/main.cpp
+++ b/example/Grid/3_gray_scott_3d/main.cpp
@@ -3,7 +3,7 @@
#include "timer.hpp"
/*!
- * \page Grid_3_gs Grid 3 Gray Scott in 3D
+ * \page Grid_3_gs_3D Grid 3 Gray Scott in 3D
*
* # Solving a gray scott-system in 3D # {#e3_gs_gray_scott}
*
@@ -107,7 +107,7 @@ int main(int argc, char* argv[])
//! \cond [init lib] \endcond
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs_3D Grid 3 Gray Scott
*
* Here we create 2 distributed grid in 2D Old and New. In particular because we want that
* the second grid is distributed across processors in the same way we pass the decomposition
@@ -208,7 +208,7 @@ int main(int argc, char* argv[])
//! \cond [time stepping] \endcond
/*!
- * \page Grid_3_gs Grid 3 Gray Scott
+ * \page Grid_3_gs_3D Grid 3 Gray Scott
*
* ## Finalize ##
*
diff --git a/example/Numerics/Stoke_flow/0_2D_incompressible/main_eigen.cpp b/example/Numerics/Stoke_flow/0_2D_incompressible/main_eigen.cpp
index ce342fd20..d75754c39 100644
--- a/example/Numerics/Stoke_flow/0_2D_incompressible/main_eigen.cpp
+++ b/example/Numerics/Stoke_flow/0_2D_incompressible/main_eigen.cpp
@@ -300,7 +300,7 @@ int main(int argc, char* argv[])
Ghost<2,long int> stencil_max(1);
// Finite difference scheme
- FDScheme<lid_nn> fd(pd, stencil_max, domain, g_dist.getGridInfo(), g_dist);
+ FDScheme<lid_nn> fd(pd, stencil_max, domain, g_dist);
//! \cond [fd scheme] \endcond
diff --git a/example/Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp b/example/Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp
index 6f5ae88b6..96ce2eded 100644
--- a/example/Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp
+++ b/example/Numerics/Stoke_flow/0_2D_incompressible/main_petsc.cpp
@@ -291,7 +291,7 @@ int main(int argc, char* argv[])
Ghost<2,long int> stencil_max(1);
// Finite difference scheme
- FDScheme<lid_nn> fd(pd, stencil_max, domain, g_dist.getGridInfo(), g_dist);
+ FDScheme<lid_nn> fd(pd, stencil_max, domain, g_dist);
//! \cond [fd scheme] \endcond
@@ -383,17 +383,13 @@ int main(int argc, char* argv[])
// Create a PETSC solver
petsc_solver<double> solver;
- // Warning try many solver and collect statistics require a lot of time
- // To just solve you can comment this line
- solver.best_solve();
-
// Set the maxumum nunber if iterations
solver.setMaxIter(1000);
solver.setRestart(200);
// Give to the solver A and b, return x, the solution
- auto x = solver.solve(fd.getA(),fd.getB());
+ auto x = solver.try_solve(fd.getA(),fd.getB());
//! \cond [solver] \endcond
diff --git a/example/Numerics/Stoke_flow/1_3D_incompressible/main_eigen.cpp b/example/Numerics/Stoke_flow/1_3D_incompressible/main_eigen.cpp
index 79e55d6d5..5b66ef69a 100644
--- a/example/Numerics/Stoke_flow/1_3D_incompressible/main_eigen.cpp
+++ b/example/Numerics/Stoke_flow/1_3D_incompressible/main_eigen.cpp
@@ -318,7 +318,7 @@ int main(int argc, char* argv[])
Ghost<3,long int> stencil_max(1);
// Finite difference scheme
- FDScheme<lid_nn> fd(pd, stencil_max, domain, g_dist.getGridInfo(), g_dist);
+ FDScheme<lid_nn> fd(pd, stencil_max, domain, g_dist);
//! \cond [fd scheme] \endcond
diff --git a/example/Numerics/Stoke_flow/1_3D_incompressible/main_petsc.cpp b/example/Numerics/Stoke_flow/1_3D_incompressible/main_petsc.cpp
index 58d08d63f..6b4bc29b1 100644
--- a/example/Numerics/Stoke_flow/1_3D_incompressible/main_petsc.cpp
+++ b/example/Numerics/Stoke_flow/1_3D_incompressible/main_petsc.cpp
@@ -319,7 +319,7 @@ int main(int argc, char* argv[])
Ghost<3,long int> stencil_max(1);
// Finite difference scheme
- FDScheme<lid_nn> fd(pd, stencil_max, domain, g_dist.getGridInfo(), g_dist);
+ FDScheme<lid_nn> fd(pd, stencil_max, domain, g_dist);
//! \cond [fd scheme] \endcond
diff --git a/example/Vector/7_SPH_dlb/main.cpp b/example/Vector/7_SPH_dlb/main.cpp
index a3dbb163c..25485a1f5 100644
--- a/example/Vector/7_SPH_dlb/main.cpp
+++ b/example/Vector/7_SPH_dlb/main.cpp
@@ -876,6 +876,107 @@ void euler_int(particles & vd, double dt)
/*! \cond [verlet_int] \endcond */
+/*!
+ *
+ * \page Vector_7_sph_dlb Vector 7 SPH Dam break simulation with Dynamic load balancing
+ *
+ * ### Probes/sensors {#e7_sph_prob_sens}
+ *
+ * This function show how to create a pressure sensor/probe on a set of specified points. To do this
+ * from the cell-list we just get an iterator across the neighborhood points of the sensors and we
+ * calculate the pressure profile. On the other hand because the sensor is in the processor domain
+ * of only one processor, only one processor must do this calculation. We will use the function isLocal
+ * to determine which processor contain the probe and only such processor will do the calculation.
+ *
+ * \warning This type of calculation is suitable if the number of probes is small (like 10) and pressure is not
+ * calculated every time step. In case the number of
+ * probes is comparable to the number of particles or the pressure is calculated every time-step than we suggest
+ * to create a set of "probe" particles
+ *
+ *
+ * \snippet Vector/7_SPH_dlb/main.cpp sens_press
+ *
+ *
+ */
+
+/*! \cond [sens_press] \endcond */
+
+template<typename Vector, typename CellList>
+inline void sensor_pressure(Vector & vd,
+ CellList & NN,
+ openfpm::vector<openfpm::vector<double>> & press_t,
+ openfpm::vector<Point<3,double>> & probes)
+{
+ Vcluster & v_cl = create_vcluster();
+
+ press_t.add();
+
+ for (size_t i = 0 ; i < probes.size() ; i++)
+ {
+ float press_tmp = 0.0f;
+ float tot_ker = 0.0;
+
+ // if the probe is inside the processor domain
+ if (vd.getDecomposition().isLocal(probes.get(i)) == true)
+ {
+ // Get the position of the probe i
+ Point<3,double> xp = probes.get(i);
+
+ // get the iterator over the neighbohood particles of the probes position
+ auto itg = NN.template getNNIterator<NO_CHECK>(NN.getCell(probes.get(i)));
+ while (itg.isNext())
+ {
+ auto q = itg.get();
+
+ // Only the fluid particles are importants
+ if (vd.template getProp<type>(q) != FLUID)
+ {
+ ++itg;
+ continue;
+ }
+
+ // Get the position of the neighborhood particle q
+ Point<3,double> xq = vd.template getPos(q);
+
+ // Calculate the contribution of the particle to the pressure
+ // of the probe
+ double r = sqrt(norm2(xp - xq));
+
+ double ker = Wab(r) * (MassFluid / rho_zero);
+
+ // Also keep track of the calculation of the summed
+ // kernel
+ tot_ker += ker;
+
+ // Add the total pressure contribution
+ press_tmp += vd.template getProp<Pressure>(q) * ker;
+
+ // next neighborhood particle
+ ++itg;
+ }
+
+ // We calculate the pressure normalizing the
+ // sum over all kernels
+ if (tot_ker == 0.0)
+ press_tmp = 0.0;
+ else
+ press_tmp = 1.0 / tot_ker * press_tmp;
+
+ }
+
+ // This is not necessary in principle, but if you
+ // want to make all processor aware of the history of the calculated
+ // pressure we have to execute this
+ v_cl.sum(press_tmp);
+ v_cl.execute();
+
+ // We add the calculated pressure into the history
+ press_t.last().add(press_tmp);
+ }
+}
+
+/*! \cond [sens_press] \endcond */
+
int main(int argc, char* argv[])
{
/*!
@@ -884,7 +985,8 @@ int main(int argc, char* argv[])
*
* ## Main function {#e7_sph_main}
*
- * Here we Initialize the library, we create a Box that define our domain, boundary conditions and ghost
+ * Here we Initialize the library, we create a Box that define our domain, boundary conditions and ghost. We also create
+ * a vector that contain two probes to measure pressure
*
* \see \ref e0_s_init
*
@@ -897,6 +999,13 @@ int main(int argc, char* argv[])
// initialize the library
openfpm_init(&argc,&argv);
+ // It contain for each time-step the value detected by the probes
+ openfpm::vector<openfpm::vector<double>> press_t;
+ openfpm::vector<Point<3,double>> probes;
+
+ probes.add({0.8779,0.3,0.02});
+ probes.add({0.754,0.31,0.02});
+
// Here we define our domain a 2D box with internals from 0 to 1.0 for x and y
Box<3,double> domain({-0.05,-0.05,-0.05},{1.7010,0.7065,0.5025});
size_t sz[3] = {207,90,66};
@@ -1254,8 +1363,8 @@ int main(int argc, char* argv[])
*
* The main loop do time integration. It calculate the pressure based on the
* density, than calculate the forces, than we calculate delta time, and finally update position
- * and velocity. After 200 time-step we do a rebalancing. And we save the configuration
- * every 0.01 seconds
+ * and velocity. After 200 time-step we do a re-balancing. We save the configuration
+ * and we calculate the pressure on the probe position every 0.01 seconds
*
* \snippet Vector/7_SPH_dlb/main.cpp main loop
*
@@ -1320,6 +1429,8 @@ int main(int argc, char* argv[])
if (write < t*100)
{
+ // calculate the pressure at the sensor points
+ sensor_pressure(vd,NN,press_t,probes);
vd.write("Geometry",write);
write++;
diff --git a/install b/install
index 3a6b2fcf5..9c2dd0071 100755
--- a/install
+++ b/install
@@ -23,7 +23,7 @@ nomake=0
update_openfpm=0
upgrade_openfpm=0
-while getopts :di:smhc:nu FLAG; do
+while getopts di:smhc:nu FLAG; do
case $FLAG in
d)
echo "Disable depencencies installation"
@@ -197,6 +197,21 @@ if [ ! -d "$i_dir/PETSC" -o ! -d "$i_dir/EIGEN" ]; then
fi
fi
+#### License and Copyright disclamer
+
+echo -e "\033[1;34m Licenses \033[0m"
+echo -e "\033[1;34m OpenFPM install several dependencies automatically. Some of them impose restriction and the user must explicitly accept it \033[0m"
+echo -e "\033[1;33m PARMETIS: \033[0m \033[1m http://glaros.dtc.umn.edu/gkhome/metis/parmetis/download (Copyright and License) \033[0m"
+echo -e ""
+
+if [ $sq -eq 0 ]; then
+ unset commands
+ commands[0]="Accept and continue"
+ possible_solutions_no_continue "${commands[@]}"
+fi
+
+####
+
lin_alg_dir=""
lin_alg_lib=""
lin_alg_inc=""
diff --git a/openfpm_numerics b/openfpm_numerics
index 173b92abc..408a41dd8 160000
--- a/openfpm_numerics
+++ b/openfpm_numerics
@@ -1 +1 @@
-Subproject commit 173b92abc7585e0a3099b69301b21c2b0accc362
+Subproject commit 408a41dd88bfb703c09ab031e2210047582a8e1c
diff --git a/script/install_MPI.sh b/script/install_MPI.sh
index 36f0c7e47..d7f4d4e96 100755
--- a/script/install_MPI.sh
+++ b/script/install_MPI.sh
@@ -6,11 +6,11 @@ if [ -d "$1/MPI" ]; then
echo "MPI already installed"
exit 0
fi
-rm -rf openmpi-1.10.2
-rm openmpi-1.10.2.tar.bz2
-wget http://ppmcore.mpi-cbg.de/upload/openmpi-1.10.2.tar.bz2
-tar -xvf openmpi-1.10.2.tar.bz2
-cd openmpi-1.10.2
+rm -rf openmpi-2.1.1
+rm openmpi-2.1.1.tar.bz2
+wget http://ppmcore.mpi-cbg.de/upload/openmpi-2.1.1.tar.bz2
+tar -xvf openmpi-2.1.1.tar.bz2
+cd openmpi-2.1.1
#
# --disable-mca-dso \
@@ -30,5 +30,5 @@ make -j $2
make install
# Mark the installation
-echo 1 > $1/MPI/version
+echo 2 > $1/MPI/version
diff --git a/script/install_PETSC.sh b/script/install_PETSC.sh
index 16ba425d5..c01bc4b2a 100755
--- a/script/install_PETSC.sh
+++ b/script/install_PETSC.sh
@@ -96,15 +96,15 @@ else
fi
if [ ! -d "$1/TRILINOS" ]; then
- rm trilinos-12.6.1-Source.tar.gz
- rm -rf trilinos-12.6.1-Source
- wget http://ppmcore.mpi-cbg.de/upload/trilinos-12.6.1-Source.tar.gz
+ rm trilinos-12.10.1-Source.tar.bz2
+ rm -rf trilinos-12.10.1-Source
+ wget http://ppmcore.mpi-cbg.de/upload/trilinos-12.10.1-Source.tar.bz2
if [ $? -ne 0 ]; then
echo -e "\033[91;5;1m FAILED Installation require an Internet connection \033[0m"
exit 1
fi
- tar -xf trilinos-12.6.1-Source.tar.gz
- cd trilinos-12.6.1-Source
+ tar -xf trilinos-12.10.1-Source.tar.bz2
+ cd trilinos-12.10.1-Source
mkdir build
cd build
@@ -125,6 +125,8 @@ if [ ! -d "$1/TRILINOS" ]; then
make -j $2
if [ $? -eq 0 ]; then
make install
+ # Mark the installation
+ echo 1 > $1/TRILINOS/version
configure_options="$configure_options --with-trilinos=yes -with-trilinos-dir=$1/TRILINOS"
fi
else
@@ -215,48 +217,57 @@ fi
## SuperLU installation
if [ ! -d "$1/SUPERLU_DIST" ]; then
- rm superlu_dist_4.3.tar.gz
- rm -rf SuperLU_DIST_4.3
- wget http://ppmcore.mpi-cbg.de/upload/superlu_dist_4.3.tar.gz
+ rm superlu_dist_5.1.3.tar.gz
+ rm -rf SuperLU_DIST_5.1.3
+ wget http://ppmcore.mpi-cbg.de/upload/superlu_dist_5.1.3.tar.gz
if [ $? -ne 0 ]; then
echo -e "\033[91;5;1m FAILED Installation require an Internet connection \033[0m"
exit 1
fi
- tar -xf superlu_dist_4.3.tar.gz
- cd SuperLU_DIST_4.3
+ tar -xf superlu_dist_5.1.3.tar.gz
+ cd SuperLU_DIST_5.1.3
+
+ mkdir build
+ cd build
+
+ cmake .. -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_INSTALL_PREFIX="$1/SUPERLU_DIST" -DCMAKE_EXE_LINKER_FLAGS="-L$1/METIS/lib -lmetis" -DTPL_PARMETIS_INCLUDE_DIRS="$1/PARMETIS/include/;$1/METIS/include/" -DTPL_PARMETIS_LIBRARIES="$1/PARMETIS/lib/libparmetis.a"
# Installation for linux
- $sed_command -i "/DSuperLUroot\s\+=\s\${HOME}\/Release_Codes\/SuperLU_DIST_4.3/c\DSuperLUroot = ../" make.inc
- $sed_command -i "/BLASLIB\s\+=/c\BLASLIB = $1/OPENBLAS/lib/libopenblas.a" make.inc
- $sed_command -i "/LOADOPTS\s\+=\s-openmp/c\LOADOPTS = -fopenmp" make.inc
- $sed_command -i "/PARMETIS_DIR\s\+=\/project\/projectdirs\/mp127\/parmetis-4.0.3-g/c\PARMETIS_DIR := $1/PARMETIS" make.inc
+# $sed_command -i "/DSuperLUroot\s\+=\s\${HOME}\/Release_Codes\/SuperLU_DIST_4.3/c\DSuperLUroot = ../" make.inc
+# $sed_command -i "/BLASLIB\s\+=/c\BLASLIB = $1/OPENBLAS/lib/libopenblas.a" make.inc
+# $sed_command -i "/LOADOPTS\s\+=\s-openmp/c\LOADOPTS = -fopenmp" make.inc
+# $sed_command -i "/PARMETIS_DIR\s\+=\/project\/projectdirs\/mp127\/parmetis-4.0.3-g/c\PARMETIS_DIR := $1/PARMETIS" make.inc
- $sed_command -i "/METISLIB\s:=\s-L\${PARMETIS_DIR}\/build\/Linux-x86_64\/libmetis\s-lmetis/c\METISLIB := -L$1/METIS/lib -lmetis" make.inc
- $sed_command -i "/PARMETISLIB\s:=\s-L\${PARMETIS_DIR}\/build\/Linux-x86_64\/libparmetis\s-lparmetis/c\PARMETISLIB := -L$1/PARMETIS/lib -lparmetis" make.inc
+# $sed_command -i "/METISLIB\s:=\s-L\${PARMETIS_DIR}\/build\/Linux-x86_64\/libmetis\s-lmetis/c\METISLIB := -L$1/METIS/lib -lmetis" make.inc
+# $sed_command -i "/PARMETISLIB\s:=\s-L\${PARMETIS_DIR}\/build\/Linux-x86_64\/libparmetis\s-lparmetis/c\PARMETISLIB := -L$1/PARMETIS/lib -lparmetis" make.inc
- $sed_command -i "/I_PARMETIS\s:=\s-I\${PARMETIS_DIR}\/include\s-I\${PARMETIS_DIR}\/metis\/include/c\I_PARMETIS := -I$1/PARMETIS/include -I$1/METIS/include" make.inc
- $sed_command -i "/CC\s\+=\scc/c\CC = mpicc" make.inc
- $sed_command -i "/FORTRAN\s\+=\sftn/c\FORTRAN = mpif90" make.inc
+# $sed_command -i "/I_PARMETIS\s:=\s-I\${PARMETIS_DIR}\/include\s-I\${PARMETIS_DIR}\/metis\/include/c\I_PARMETIS := -I$1/PARMETIS/include -I$1/METIS/include" make.inc
+# $sed_command -i "/CC\s\+=\scc/c\CC = mpicc" make.inc
+# $sed_command -i "/FORTRAN\s\+=\sftn/c\FORTRAN = mpif90" make.inc
- if [ x"$CXX" == x"clang++" ]; then
- $sed_command -i "/CFLAGS\s\+=\s-fast\s-m64\s-std=c99\s-Wall\s-openmp\s\\\/c\CFLAGS =-fpic -O3 -m64 -std=c99 -Wall \$(I_PARMETIS) -DDEBUGlevel=0 -DPRNTlevel=0 -DPROFlevel=0" make.inc
- else
- $sed_command -i "/CFLAGS\s\+=\s-fast\s-m64\s-std=c99\s-Wall\s-openmp\s\\\/c\CFLAGS =-fpic -O3 -m64 -std=c99 -Wall -fopenmp \$(I_PARMETIS) -DDEBUGlevel=0 -DPRNTlevel=0 -DPROFlevel=0" make.inc
- fi
- $sed_command -i "/\s\$(I_PARMETIS)\s-DDEBUGlevel=0\s-DPRNTlevel=0\s-DPROFlevel=0\s\\\/c\ " make.inc
+# if [ x"$CXX" == x"clang++" ]; then
+# $sed_command -i "/CFLAGS\s\+=\s-fast\s-m64\s-std=c99\s-Wall\s-openmp\s\\\/c\CFLAGS =-fpic -O3 -m64 -std=c99 -Wall \$(I_PARMETIS) -DDEBUGlevel=0 -DPRNTlevel=0 -DPROFlevel=0" make.inc
+# else
+# $sed_command -i "/CFLAGS\s\+=\s-fast\s-m64\s-std=c99\s-Wall\s-openmp\s\\\/c\CFLAGS =-fpic -O3 -m64 -std=c99 -Wall -fopenmp \$(I_PARMETIS) -DDEBUGlevel=0 -DPRNTlevel=0 -DPROFlevel=0" make.inc
+# fi
+# $sed_command -i "/\s\$(I_PARMETIS)\s-DDEBUGlevel=0\s-DPRNTlevel=0\s-DPROFlevel=0\s\\\/c\ " make.inc
make
if [ $? -eq 0 ]; then
- mkdir $1/SUPERLU_DIST
- mkdir $1/SUPERLU_DIST/include
- cp -r lib $1/SUPERLU_DIST
- cp SRC/*.h $1/SUPERLU_DIST/include
+
+ make install
+ echo 1 > $1/SUPERLU_DIST/version
+
+# mkdir $1/SUPERLU_DIST
+# mkdir $1/SUPERLU_DIST/include
+# cp -r lib $1/SUPERLU_DIST
+# cp SRC/*.h $1/SUPERLU_DIST/include
if [ x"$CXX" == x"icpc" ]; then
configure_options="$configure_options"
else
- configure_options="$configure_options --with-superlu_dist=yes --with-superlu_dist-lib=$1/SUPERLU_DIST/lib/libsuperlu_dist_4.3.a --with-superlu_dist-include=$1/SUPERLU_DIST/include/"
+ configure_options="$configure_options --with-superlu_dist=yes --with-superlu_dist-lib=$1/SUPERLU_DIST/lib/libsuperlu_dist.a --with-superlu_dist-include=$1/SUPERLU_DIST/include/"
fi
fi
@@ -265,22 +276,22 @@ else
if [ x"$CXX" == x"icpc" ]; then
configure_options="$configure_options"
else
- configure_options="$configure_options --with-superlu_dist=yes --with-superlu_dist-lib=$1/SUPERLU_DIST/lib/libsuperlu_dist_4.3.a --with-superlu_dist-include=$1/SUPERLU_DIST/include/"
+ configure_options="$configure_options --with-superlu_dist=yes --with-superlu_dist-lib=$1/SUPERLU_DIST/lib/libsuperlu_dist.a --with-superlu_dist-include=$1/SUPERLU_DIST/include/"
fi
fi
## HYPRE installation
if [ ! -d "$1/HYPRE" ]; then
- rm hypre-2.11.0.tar.gz
- rm -rf hypre-2.11.0
- wget http://ppmcore.mpi-cbg.de/upload/hypre-2.11.0.tar.gz
+ rm hypre-2.11.2.tar.gz
+ rm -rf hypre-2.11.2
+ wget http://ppmcore.mpi-cbg.de/upload/hypre-2.11.2.tar.gz
if [ $? -ne 0 ]; then
echo -e "\033[91;5;1m FAILED Installation require an Internet connection \033[0m"
exit 1
fi
- tar -xf hypre-2.11.0.tar.gz
- cd hypre-2.11.0
+ tar -xf hypre-2.11.2.tar.gz
+ cd hypre-2.11.2
cd src
@@ -289,6 +300,7 @@ if [ ! -d "$1/HYPRE" ]; then
if [ $? -eq 0 ]; then
make install
+ echo 1 > $1/HYPRE/version
configure_options="$configure_options --with-hypre=yes -with-hypre-dir=$1/HYPRE"
fi
@@ -296,21 +308,46 @@ else
echo "HYPRE already installed"
configure_options="$configure_options --with-hypre=yes -with-hypre-dir=$1/HYPRE"
fi
-
-rm petsc-lite-3.6.4.tar.gz
-rm -rf petsc-3.6.4
-wget http://ppmcore.mpi-cbg.de/upload/petsc-lite-3.6.4.tar.gz
+# Install NETCFD
+
+if [ ! -d "$1/NETCDF" ]; then
+ rm netcdf-4.4.1.1.tar.gz
+ rm -rf netcdf-4.4.1.1
+ wget http://ppmcore.mpi-cbg.de/upload/netcdf-4.4.1.1.tar.gz
+ if [ $? -ne 0 ]; then
+ echo -e "\033[91;5;1m FAILED Installation require an Internet connection \033[0m"
+ exit 1
+ fi
+ tar -xf netcdf-4.4.1.1.tar.gz
+ cd netcdf-4.4.1.1
+
+ ./configure CC=mpicc CPPFLAGS=-I$1/HDF5/include LDFLAGS=-L$1/HDF5/lib --disable-shared --prefix=$1/NETCDF
+ make -j $2
+
+ if [ $? -eq 0 ]; then
+ make install
+ configure_options="$configure_options --with-netcdf=yes -with-netcdf-dir=$1/NETCDF --with-hdf5=yes --with-hdf5-dir=$1/HDF5"
+ fi
+
+else
+ echo "NETCDF already installed"
+ configure_options="$configure_options --with-netcdf=yes -with-netcdf-dir=$1/NETCDF --with-hdf5=yes --with-hdf5-dir=$1/HDF5"
+fi
+
+rm petsc-lite-3.7.6.tar.gz
+rm -rf petsc-3.7.6
+wget http://ppmcore.mpi-cbg.de/upload/petsc-lite-3.7.6.tar.gz
if [ $? -ne 0 ]; then
echo -e "\033[91;5;1m FAILED Installation require an Internet connection \033[0m"
exit 1
fi
-tar -xf petsc-lite-3.6.4.tar.gz
-cd petsc-3.6.4
+tar -xf petsc-lite-3.7.6.tar.gz
+cd petsc-3.7.6
-echo "./configure --with-cxx-dialect=C++11 $petsc_openmp --with-mpi-dir=$mpi_dir $configure_options --with-mumps-lib="$MUMPS_extra_lib" --prefix=$1/PETSC --with-debugging=0"
+echo "./configure COPTFLAGS="-O3 -g" CXXOPTFLAGS="-O3 -g" FOPTFLAGS="-O3 -g" --with-cxx-dialect=C++11 $petsc_openmp --with-mpi-dir=$mpi_dir $configure_options --with-mumps-lib="$MUMPS_extra_lib" --prefix=$1/PETSC --with-debugging=0"
-./configure --with-cxx-dialect=C++11 $petsc_openmp --with-mpi-dir=$mpi_dir $configure_options --with-mumps-lib="$MUMPS_extra_lib" --prefix=$1/PETSC --with-debugging=0
+python2 configure COPTFLAGS="-O3 -g" CXXOPTFLAGS="-O3 -g" FOPTFLAGS="-O3 -g" --with-cxx-dialect=C++11 $petsc_openmp --with-mpi-dir=$mpi_dir $configure_options --with-mumps-lib="$MUMPS_extra_lib" --prefix=$1/PETSC --with-debugging=0
make all test
make install
diff --git a/script/install_Parmetis.sh b/script/install_Parmetis.sh
index f1b425993..17cd3a99d 100755
--- a/script/install_Parmetis.sh
+++ b/script/install_Parmetis.sh
@@ -13,6 +13,18 @@ rm -rf parmetis-4.0.3
wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz
tar -xf parmetis-4.0.3.tar.gz
cd parmetis-4.0.3
+# Change to 64 bit parmetis
+
+if [ x"$platform" == x"osx" ]; then
+ sed_command=gsed
+else
+ sed_command=sed
+fi
+
+$sed_command -i "/#define\sIDXTYPEWIDTH\s32/c\#define IDXTYPEWIDTH 64" metis/include/metis.h
+
+sed #define IDXTYPEWIDTH 32
+
make config prefix=$1/PARMETIS
make -j $2
if [ $? -ne 0 ]; then
diff --git a/script/install_SUITESPARSE.sh b/script/install_SUITESPARSE.sh
index d2a4500f8..94ad89608 100755
--- a/script/install_SUITESPARSE.sh
+++ b/script/install_SUITESPARSE.sh
@@ -12,9 +12,9 @@ if [ -d "$1/SUITESPARSE" ]; then
exit 0
fi
-wget http://ppmcore.mpi-cbg.de/upload/SuiteSparse-4.4.5.tar.gz
+wget http://ppmcore.mpi-cbg.de/upload/SuiteSparse-4.5.5.tar.gz
rm -rf SuiteSparse
-tar -xf SuiteSparse-4.4.5.tar.gz
+tar -xf SuiteSparse-4.5.5.tar.gz
if [ $? != 0 ]; then
echo "Fail to download SuiteSparse"
exit 1
@@ -26,10 +26,8 @@ cd SuiteSparse
if [ x"$platform" = x"osx" ]; then
# installation for OSX
- sed -i "" -e "s|INSTALL_LIB = \/usr\/local\/lib|INSTALL_LIB = "$1"\/SUITESPARSE\/lib|" SuiteSparse_config/SuiteSparse_config_Mac.mk
- sed -i "" -e "s|INSTALL_INCLUDE = \/usr\/local\/include|INSTALL_INCLUDE = "$1"\/SUITESPARSE\/include|" SuiteSparse_config/SuiteSparse_config_Mac.mk
- sed -i "" -e "s| LAPACK = -llapack|LAPACK = |" SuiteSparse_config/SuiteSparse_config_Mac.mk
- sed -i "" -e "s| BLAS = -lopenblas|BLAS = -L"$1"/OPENBLAS/lib -lopenblas|" SuiteSparse_config/SuiteSparse_config_Mac.mk
+# sed -i "" -e "s| LAPACK = -llapack|LAPACK = |" SuiteSparse_config/SuiteSparse_config_Mac.mk
+# sed -i "" -e "s| BLAS = -lopenblas|BLAS = -L"$1"/OPENBLAS/lib -lopenblas|" SuiteSparse_config/SuiteSparse_config_Mac.mk
### Overwrite SuiteSparse_config.mk
@@ -37,34 +35,33 @@ if [ x"$platform" = x"osx" ]; then
mv SuiteSparse_config/SuiteSparse_config_Mac.mk SuiteSparse_config/SuiteSparse_config.mk
else
+
# Installation for linux
if [ x"$CXX" == x"icpc" ]; then
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/$1/OPENBLAS/lib"
- sed -i "/\sLIB\s=\s-lm\s-lrt/c\LIB = -shared-intel -lm -lrt -lifcore" SuiteSparse_config/SuiteSparse_config.mk
- sed -i "/INSTALL_LIB\s=\s\/usr\/local\/lib/c\INSTALL_LIB = $1\/SUITESPARSE\/lib" SuiteSparse_config/SuiteSparse_config.mk
- sed -i "/INSTALL_INCLUDE\s=\s\/usr\/local\/include/c\INSTALL_INCLUDE = $1\/SUITESPARSE\/include" SuiteSparse_config/SuiteSparse_config.mk
- sed -i "/\sLAPACK\s=\s-llapack/c\LAPACK = " SuiteSparse_config/SuiteSparse_config.mk
- sed -i "/\sBLAS\s=\s\-lopenblas/c\BLAS = -L$1/OPENBLAS/lib -lopenblas -lpthread" SuiteSparse_config/SuiteSparse_config.mk
- else
- sed -i "/INSTALL_LIB\s=\s\/usr\/local\/lib/c\INSTALL_LIB = $1\/SUITESPARSE\/lib" SuiteSparse_config/SuiteSparse_config.mk
- sed -i "/INSTALL_INCLUDE\s=\s\/usr\/local\/include/c\INSTALL_INCLUDE = $1\/SUITESPARSE\/include" SuiteSparse_config/SuiteSparse_config.mk
- sed -i "/\sLAPACK\s=\s-llapack/c\LAPACK = " SuiteSparse_config/SuiteSparse_config.mk
- sed -i "/\sBLAS\s=\s\-lopenblas/c\BLAS = -L$1/OPENBLAS/lib -lopenblas -lpthread" SuiteSparse_config/SuiteSparse_config.mk
+ STS_LIB="-shared-intel -lrt -lifcore"
fi
+# sed -i "/\sLIB\s=\s-lm\s-lrt/c\LIB = -shared-intel -lm -lrt -lifcore" SuiteSparse_config/SuiteSparse_config.mk
+# sed -i "/\sLAPACK\s=\s-llapack/c\LAPACK = " SuiteSparse_config/SuiteSparse_config.mk
+# sed -i "/\sBLAS\s=\s\-lopenblas/c\BLAS = -L$1/OPENBLAS/lib -lopenblas -lpthread" SuiteSparse_config/SuiteSparse_config.mk
+# else
+# sed -i "/\sLAPACK\s=\s-llapack/c\LAPACK = " SuiteSparse_config/SuiteSparse_config.mk
+# sed -i "/\sBLAS\s=\s\-lopenblas/c\BLAS = -L$1/OPENBLAS/lib -lopenblas -lpthread" SuiteSparse_config/SuiteSparse_config.mk
+# fi
fi
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$1/OPENBLAS/lib"
-make
+echo "Compiling SuiteSparse without CUDA (old variable $CUDA)"
+make "CUDA=no" "BLAS=-L$1/OPENBLAS/lib -lopenblas" "LAPACK="
if [ $? != 0 ]; then
echo "Fail to compile SuiteSparse"
exit 1
fi
-mkdir $1/SUITESPARSE
-mkdir $1/SUITESPARSE/lib
-mkdir $1/SUITESPARSE/include
-make install
+make install "CUDA=no" "INSTALL=$1/SUITESPARSE" "INSTALL_LIB=$1/SUITESPARSE/lib" "INSTALL_INCLUDE=$1/SUITESPARSE/include" "BLAS=-L$1/OPENBLAS/lib -lopenblas" "LAPACK="
+# Mark the installation
+echo 1 > $1/SUITESPARSE/version
rm -rf SuiteSparse
-rm SuiteSparse-4.4.5.tar.gz
+rm SuiteSparse-4.5.5.tar.gz
diff --git a/script/remove_old b/script/remove_old
index 1159c8654..4d9e78f4d 100755
--- a/script/remove_old
+++ b/script/remove_old
@@ -117,12 +117,71 @@ function remove_old()
fi
fi
+ if [ -d $1/TRILINOS ]; then
+ version=$(cat $1/TRILINOS/version)
+ if [ x"$version" != x"1" ]; then
+ echo -e "\033[1;34;5m ------------------------------------------------------------------------------------------- \033[0m"
+ echo -e "\033[1;34;5m Trilinos has been updated to version 12.10.1, the component will be updated automatically \033[0m"
+ echo -e "\033[1;34;5m ------------------------------------------------------------------------------------------- \033[0m"
+ sleep 5
+ rm -rf $1/TRILINOS
+ rm -rf $1/PETSC
+ fi
+ fi
+
+ if [ -d $1/SUITESPARSE ]; then
+ version=$(cat $1/SUITESPARSE/version)
+ if [ x"$version" != x"1" ]; then
+ echo -e "\033[1;34;5m ------------------------------------------------------------------------------------------- \033[0m"
+ echo -e "\033[1;34;5m SuiteSparse has been updated to version 4.5.5, the component will be updated automatically \033[0m"
+ echo -e "\033[1;34;5m ------------------------------------------------------------------------------------------- \033[0m"
+ sleep 5
+ rm -rf $1/SUITESPARSE
+ rm -rf $1/PETSC
+ fi
+ fi
+
+ if [ -d $1/SUPERLU_DIST ]; then
+ version=$(cat $1/SUPERLU_DIST/version)
+ if [ x"$version" != x"1" ]; then
+ echo -e "\033[1;34;5m ---------------------------------------------------------------------------------------------------------- \033[0m"
+ echo -e "\033[1;34;5m SuperLU (Distributed) has been updated to version 5.2.1, the component will be updated automatically \033[0m"
+ echo -e "\033[1;34;5m ---------------------------------------------------------------------------------------------------------- \033[0m"
+ sleep 5
+ rm -rf $1/SUPERLU_DIST
+ rm -rf $1/PETSC
+ fi
+ fi
+
+ if [ -d $1/HYPRE ]; then
+ version=$(cat $1/HYPRE/version)
+ if [ x"$version" != x"1" ]; then
+ echo -e "\033[1;34;5m ------------------------------------------------------------------------------------------- \033[0m"
+ echo -e "\033[1;34;5m HYPRE has been updated to version 2.11.2, the component will be updated automatically \033[0m"
+ echo -e "\033[1;34;5m ------------------------------------------------------------------------------------------- \033[0m"
+ sleep 5
+ rm -rf $1/HYPRE
+ rm -rf $1/PETSC
+ fi
+ fi
+
+ if [ -d $1/PETSC ]; then
+ version=$(cat $1/PETSC/version)
+ if [ x"$version" != x"1" ]; then
+ echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
+ echo -e "\033[1;34;5m PETSC has been updated to version 3.7.6, the component will be updated automatically \033[0m"
+ echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
+ sleep 5
+ rm -rf $1/PETSC
+ fi
+ fi
+
if [ -d $1/MPI ]; then
version=$(cat $1/MPI/version)
- if [ x"$version" != x"1" ]; then
- echo -e "\033[1;34;5m ---------------------------------------------------------------------- \033[0m"
- echo -e "\033[1;34;5m MPI has been updated, the component will be updated automatically \033[0m"
- echo -e "\033[1;34;5m ---------------------------------------------------------------------- \033[0m"
+ if [ x"$version" != x"2" ]; then
+ echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
+ echo -e "\033[1;34;5m MPI has been updated to version 2.1.1, the component will be updated automatically \033[0m"
+ echo -e "\033[1;34;5m -------------------------------------------------------------------------------------- \033[0m"
sleep 5
rm -rf $1/MPI/include
rm -rf $1/MPI/lib
@@ -132,9 +191,16 @@ function remove_old()
rm -rf $1/MPI
rm -rf $1/HDF5
+ rm -rf $1/PARMETIS
+ rm -rf $1/PETSC
+ rm -rf $1/TRILINOS
+ rm -rf $1/HYPRE
+ rm -rf $1/MUMPS
+ rm -rf $1/SUPERLU_DIST
fi
fi
+
if [ -d $1/EIGEN ]; then
version=$(cat $1/EIGEN/version)
if [ x"$version" != x"1" ]; then
diff --git a/script/show_solutions b/script/show_solutions
index 74b1c333e..aaa14302e 100755
--- a/script/show_solutions
+++ b/script/show_solutions
@@ -35,3 +35,32 @@ function possible_solutions {
possible_solutions_command=${commands[$possible_solutions_ret]}
}
+function possible_solutions_no_continue {
+
+ if [ $sq -eq 1 ]; then
+ return
+ fi
+
+ sol=1
+ echo "Possible solutions:"
+ for com in "$@"
+ do
+ echo "$sol $com"
+ sol=`expr $sol + 1`
+ done
+ echo "$sol exit the script"
+ echo -e "\033[1;34;5mChoose the solution:\033[0m"
+ read choose
+ if [ x"$choose" = x"$sol" ]; then
+ exit 1
+ fi
+ possible_solutions_ret=`expr $choose - 1`
+ echo "Executing: ${command[$possible_solutions_ret]}"
+ if [ -a input_install ]; then
+ eval ${commands[$possible_solutions_ret]} < input_install
+ else
+ eval ${commands[$possible_solutions_ret]}
+ fi
+ possible_solutions_command=${commands[$possible_solutions_ret]}
+}
+
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index 0c48616d6..d78cd80d1 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -1491,7 +1491,7 @@ public:
Point<dim,St> offset = getOffset(i);
vtk_g.add(loc_grid.get(i),offset,cd_sm.getCellBox().getP2(),gdb_ext.get(i).Dbox);
}
- vtk_g.write(output + "_" + std::to_string(v_cl.getProcessUnitID()) + "_" + std::to_string(i) + ".vtk","grids",ft);
+ vtk_g.write(output + "_" + std::to_string(v_cl.getProcessUnitID()) + "_" + std::to_string(i) + ".vtk",prp_names,"grids",ft);
return true;
}
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 9e291e5d9..84cc89cda 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -844,7 +844,7 @@ public:
#ifdef SE_CLASS1
if ((opt & BIND_DEC_TO_GHOST))
{
- if (ghost.getLow(dim-1) == 0.0)
+ if (getDecomposition().getGhost().getLow(dim-1) == 0.0)
{
std::cerr << __FILE__ << ":" << __LINE__ << " Error the vector has been constructed without BIND_DEC_TO_GHOST, If you construct a vector without BIND_DEC_TO_GHOST the ghost must be full without reductions " << std::endl;
ACTION_ON_ERROR(VECTOR_DIST_ERROR_OBJECT);
--
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