From 7dd825c1dbfa64fe47cf274f8ec2142e34e3771a Mon Sep 17 00:00:00 2001
From: Pietro Incardona <i-bird@localhost.localdomain>
Date: Tue, 24 May 2016 14:56:38 +0200
Subject: [PATCH] Fixing osx PETSC installation
---
example/Vector/0_simple/main.cpp | 148 +++++++++++++++----------------
script/install_PETSC.sh | 30 ++++++-
script/install_SUITESPARSE.sh | 2 +
script/pre_req | 25 ++++++
script/solve_gsed | 19 ++++
src/Grid/grid_dist_id.hpp | 1 +
src/Vector/vector_dist.hpp | 4 +-
7 files changed, 149 insertions(+), 80 deletions(-)
create mode 100755 script/solve_gsed
diff --git a/example/Vector/0_simple/main.cpp b/example/Vector/0_simple/main.cpp
index f64c635f9..83324637c 100644
--- a/example/Vector/0_simple/main.cpp
+++ b/example/Vector/0_simple/main.cpp
@@ -1,41 +1,17 @@
#include "Vector/vector_dist.hpp"
-#include "Decomposition/CartDecomposition.hpp"
/*
* ### WIKI 1 ###
*
* ## Simple example
*
- * This example show several basic functionalities of the distributed vector
+ * This example show several basic functionalities of the distributed vector, A distributed vector is nothing else than
+ * a set of particles in an N dimensional space
*
* ### WIKI END ###
*
*/
-/*
- * ### WIKI 2 ###
- *
- * We define a particle structure it contain 4 scalars one vector with 3 components
- * and a tensor of rank 2 3x3
- *
- * ### WIKI END ###
- *
- */
-
-template<typename T> class Particle
-{
-public:
-
- typedef boost::fusion::vector<T,T[3],T[3][3]> type;
-
- type data;
-
- static const unsigned int s = 0;
- static const unsigned int v = 1;
- static const unsigned int t = 2;
- static const unsigned int max_prop = 3;
-};
-
int main(int argc, char* argv[])
{
//
@@ -44,65 +20,80 @@ int main(int argc, char* argv[])
// Here we Initialize the library, than we create a uniform random generator between 0 and 1 to to generate particles
// randomly in the domain, we create a Box that define our domain, boundary conditions, and ghost
//
- openfpm_init(&argc,&argv);
- Vcluster & v_cl = create_vcluster();
- typedef Point<2,float> s;
-
- // set the seed
- // create the random generator engine
- std::srand(v_cl.getProcessUnitID());
- std::default_random_engine eg;
- std::uniform_real_distribution<float> ud(0.0f, 1.0f);
+ // initialize the library
+ openfpm_init(&argc,&argv);
+ // Here we define our domain a 2D box with internals from 0 to 1.0 for x and y
Box<2,float> domain({0.0,0.0},{1.0,1.0});
+
+ // Here we define the boundary conditions of our problem
size_t bc[2]={PERIODIC,PERIODIC};
+
+ // extended boundary around the domain, and the processor domain
Ghost<2,float> g(0.01);
//
// ### WIKI 3 ###
//
// Here we are creating a distributed vector defined by the following parameters
+ //
+ // * 2 is the Dimensionality of the space where the objects live
+ // * float is the type used for the spatial coordinate of the particles
+ // * float,float[3],float[3][3] is the information stored by each particle a scalar float, a vector float[3] and a tensor of rank 2 float[3][3]
+ // the list of properties must be put into an aggregate data astructure aggregate<prop1,prop2,prop3, ... >
//
- // * Dimensionality of the space where the objects live 2D (1° template parameters)
- // * Type of the space, float (2° template parameters)
- // * Information stored by each object (3* template parameters), in this case a Point_test store 4 scalars
- // 1 vector and an asymmetric tensor of rank 2
- //
- // Constructor instead require:
+ // vd is the instantiation of the object
+ //
+ // The Constructor instead require:
//
// * Number of particles 4096 in this case
// * Domain where is defined this structure
+ // * bc boundary conditions
+ // * g Ghost
//
// The following construct a vector where each processor has 4096 / N_proc (N_proc = number of processor)
// objects with an undefined position in space. This non-space decomposition is also called data-driven
// decomposition
//
- vector_dist<2,float, Particle<float> > vd(4096,domain,bc,g);
+ vector_dist<2,float, aggregate<float,float[3],float[3][3]> > vd(4096,domain,bc,g);
+
+ // the scalar is the element at position 0 in the aggregate
+ const int scalar = 0;
+
+ // the vector is the element at position 1 in the aggregate
+ const int vector = 1;
+
+ // the tensor is the element at position 2 in the aggregate
+ const int tensor = 2;
//
// ### WIKI 5 ###
//
- // Get an iterator that go through the particles, in an undefined position state and define its position
+ // Get an iterator that go through the 4096 particles, in an undefined position state and define its position
//
- auto it = vd.getIterator();
+ auto it = vd.getDomainIterator();
while (it.isNext())
{
auto key = it.get();
- vd.getPos(key)[0] = ud(eg);
- vd.getPos(key)[1] = ud(eg);
+ // we define x, assign a random position between 0.0 and 1.0
+ vd.getPos(key)[0] = rand() / RAND_MAX;
+
+ // we define y, assign a random position between 0.0 and 1.0
+ vd.getPos(key)[1] = rand() / RAND_MAX;
+ // next particle
++it;
}
//
// ### WIKI 6 ###
//
- // Once we define the position, we distribute them according to the default decomposition
- // The default decomposition is created even before assigning the position to the object
- // (This will probably change in future)
+ // Once we define the position, we distribute them according to the default space decomposition
+ // The default decomposition is created even before assigning the position to the object. It determine
+ // which part of space each processor manage
//
vd.map();
@@ -112,39 +103,44 @@ int main(int argc, char* argv[])
// We get the object that store the decomposition, than we iterate again across all the objects, we count them
// and we confirm that all the particles are local
//
+ //Counter we use it later
size_t cnt = 0;
+
+ // Get the space decomposition
auto & ct = vd.getDecomposition();
- it = vd.getIterator();
+ // Get a particle iterator
+ it = vd.getDomainIterator();
+
+ // For each particle ...
while (it.isNext())
{
- auto key = it.get();
-
- // The template parameter is unuseful and will probably disappear
- if (ct.isLocal(vd.getPos(key)) == false)
- std::cerr << "Error particle is not local" << "\n";
-
- // set the all the properties to some numbers
-
- // scalar
- vd.template getProp<0>(key) = 1.0;
-
- vd.template getProp<1>(key)[0] = 1.0;
- vd.template getProp<1>(key)[1] = 1.0;
- vd.template getProp<1>(key)[2] = 1.0;
-
- vd.template getProp<2>(key)[0][0] = 1.0;
- vd.template getProp<2>(key)[0][1] = 1.0;
- vd.template getProp<2>(key)[0][2] = 1.0;
- vd.template getProp<2>(key)[1][0] = 1.0;
- vd.template getProp<2>(key)[1][1] = 1.0;
- vd.template getProp<2>(key)[1][2] = 1.0;
- vd.template getProp<2>(key)[2][0] = 1.0;
- vd.template getProp<2>(key)[2][1] = 1.0;
- vd.template getProp<2>(key)[2][2] = 1.0;
-
+ // ... p
+ auto p = it.get();
+
+ // we set the properties of the particle p
+
+ // the scalar property
+ vd.template getProp<scalar>(p) = 1.0;
+
+ vd.template getProp<vector>(p)[0] = 1.0;
+ vd.template getProp<vector>(p)[1] = 1.0;
+ vd.template getProp<vector>(p)[2] = 1.0;
+
+ vd.template getProp<tensor>(p)[0][0] = 1.0;
+ vd.template getProp<tensor>(p)[0][1] = 1.0;
+ vd.template getProp<tensor>(p)[0][2] = 1.0;
+ vd.template getProp<tensor>(p)[1][0] = 1.0;
+ vd.template getProp<tensor>(p)[1][1] = 1.0;
+ vd.template getProp<tensor>(p)[1][2] = 1.0;
+ vd.template getProp<tensor>(p)[2][0] = 1.0;
+ vd.template getProp<tensor>(p)[2][1] = 1.0;
+ vd.template getProp<tensor>(p)[2][2] = 1.0;
+
+ // increment the counter
cnt++;
+ // next particle
++it;
}
@@ -156,6 +152,8 @@ int main(int argc, char* argv[])
// the variable count and finaly execute. All the operations are asynchronous, execute work like a barrier and ensure that all the
// queued operations are executed
//
+
+ auto & v_cl = create_vcluster();
v_cl.sum(cnt);
v_cl.execute();
diff --git a/script/install_PETSC.sh b/script/install_PETSC.sh
index e545127ce..d7bb78736 100755
--- a/script/install_PETSC.sh
+++ b/script/install_PETSC.sh
@@ -7,6 +7,12 @@ if [ -d "$1/PETSC" ]; then
exit 0
fi
+# Detect gcc pr clang
+
+source script/detect_gcc
+detect_gcc_or_clang g++
+
+
## If some dependencies has been installed feed them to PETSC
MUMPS_extra_libs=""
@@ -14,7 +20,7 @@ MUMPS_extra_libs=""
configure_options=""
configure_options_scalapack=""
configure_options_superlu=""
-configure_trilinos_options=" -D TPL_ENABLE_MPI=ON -D Trilinos_ENABLE_OpenMP=ON"
+configure_trilinos_options=" -D TPL_ENABLE_MPI=ON "
configure_options_hypre=""
### Here we install OpenBLAS and SUITESPARSE
@@ -84,7 +90,15 @@ if [ ! -d "$1/TRILINOS" ]; then
cd trilinos-12.6.1-Source
mkdir build
cd build
- cmake -D CMAKE_INSTALL_PREFIX:PATH=$1/TRILINOS -D CMAKE_BUILD_TYPE=RELEASE -D Trilinos_ENABLE_TESTS=OFF -D Trilinos_ENABLE_ALL_PACKAGES=ON $configure_trilinos_options ../.
+
+ ### On clang we have no openMP
+ if [ x"$dgc_compiler" == x"clang++" ]; then
+ conf_trl_openmp="-D Trilinos_ENABLE_OpenMP=OFF"
+ else
+ conf_trl_openmp="-D Trilinos_ENABLE_OpenMP=ON"
+ fi
+
+ cmake -D CMAKE_INSTALL_PREFIX:PATH=$1/TRILINOS -D CMAKE_BUILD_TYPE=RELEASE $conf_trl_openmp -D Trilinos_ENABLE_TESTS=OFF -D Trilinos_ENABLE_ALL_PACKAGES=ON $configure_trilinos_options ../.
make -j $2
if [ $? -eq 0 ]; then
@@ -139,8 +153,16 @@ if [ ! -d "$1/MUMPS" ]; then
if [ x"$platform" = x"osx" ]; then
# installation for OSX
- echo "OSX TO DO BYE"
- exit 1
+ sed -i "" -e "s|CC = cc|CC = mpicc|" Makefile.inc
+ sed -i "" -e "s|FC = f90| FC = mpif90|" Makefile.inc
+ sed -i "" -e "s|FL = f90| FL = mpif90|" Makefile.inc
+
+ sed -i "" -e "s|SCALAP = -lscalapack -lblacs|SCALAP = -L$1/SCALAPACK/lib -L$1/OPENBLAS/lib -lscalapack|" Makefile.inc
+ sed -i "" -e "s|LIBBLAS = -lblas|LIBBLAS = -lopenblas|" Makefile.inc
+
+ sed -i "" -e "s|OPTF = -O|OPTF = -fpic -O3" Makefile.inc
+ sed -i "" -e "s|OPTC = -O -I.|OPTC = -fpic -O3 -I." Makefile.inc
+ sed -i "" -e "s|OPTL = -O|OPTL = -fpic -O3" Makefile.inc
else
# Installation for linux
diff --git a/script/install_SUITESPARSE.sh b/script/install_SUITESPARSE.sh
index b96df00ad..8ad698013 100755
--- a/script/install_SUITESPARSE.sh
+++ b/script/install_SUITESPARSE.sh
@@ -1,7 +1,9 @@
#! /bin/bash
+source script/detect_gcc
source script/discover_os
+detect_gcc_or_clang g++
discover_os
# check if the directory $1/SUITESPARSE exist
diff --git a/script/pre_req b/script/pre_req
index e097e4eb8..a2efc79b4 100755
--- a/script/pre_req
+++ b/script/pre_req
@@ -68,6 +68,31 @@ if [ x"$platform" = x"linux" -a x"$pcman" = x"yum" ]; then
fi
fi
+#### if we are on OSX we install gnu-sed
+
+if [ x"platform" == x"osx" ]
+
+ command -v gsed >/dev/null 2>&1
+ if [ $? -ne 0 ]; then
+ echo >&2
+ echo -e "gsed\033[91;5;1m FAILED \033[0m"
+ echo "OpenFPM require gnu-sed but it's not installed, searching a solution... "
+ solve_gsed $platform
+ command -v gsed >/dev/null 2>&1
+ if [ $? -ne 0 ]; then
+ echo -e "gsed\033[91;5;1m FAILED \033[0m"
+ exit 1
+ else
+ echo -e "gsed\033[92;1m SUCCESS \033[0m"
+ fi
+ else
+ echo -e "gsed\033[92;1m SUCCESS \033[0m"
+ fi
+
+fi
+
+####
+
command -v cmake >/dev/null 2>&1
if [ $? -ne 0 ]; then
echo >&2
diff --git a/script/solve_gsed b/script/solve_gsed
new file mode 100755
index 000000000..7a3f74a9e
--- /dev/null
+++ b/script/solve_gsed
@@ -0,0 +1,19 @@
+
+#! /bin/bash
+
+function solve_gsed() {
+source script/show_solutions
+source script/discover_package_manager
+discover_package_manager $1
+pcman=$discover_package_manager_ret
+
+if [ x"$pcman" = x"" ]; then
+ exit 1
+fi
+
+if [ x"$1" = x"osx" ]; then
+ commands[0]="$pcman install gnu-sed"
+ possible_solutions "${commands[@]}"
+fi
+}
+
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index 7be1ed34b..7a0f96cc0 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -18,6 +18,7 @@
#include "Packer_Unpacker/Packer.hpp"
#include "Packer_Unpacker/Unpacker.hpp"
#include "Decomposition/CartDecomposition.hpp"
+#include "data_type/aggregate.hpp"
// External ghost box to send for internal ghost box fixation
template<unsigned int dim>
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 1dde07d81..0e28d613f 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -26,6 +26,7 @@
#include "Grid/grid_dist_id_iterator_dec.hpp"
#include "Vector/vector_dist_ofb.hpp"
#include "Decomposition/CartDecomposition.hpp"
+#include "data_type/aggregate.hpp"
#define V_SUB_UNIT_FACTOR 64
@@ -1015,7 +1016,7 @@ public:
{
// Get ghost and anlarge by 1%
Ghost<dim,St> g = dec.getGhost();
- g.magnify(1.01);
+ g.magnify(1.013);
return getCellList(r_cut, g);
}
@@ -1077,6 +1078,7 @@ public:
{
div[i] = static_cast<size_t>((pbox.getP2().get(i) - pbox.getP1().get(i)) / r_cut);
div[i]++;
+ pbox.setHigh(i,pbox.getLow(i) + div[i]*r_cut);
}
cell_list.Initialize(pbox, div);
--
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