From 6a47792d66776bef5869dc2432bb1bac205c7c5b Mon Sep 17 00:00:00 2001
From: Pietro Incardona <i-bird@linux.fritz.box>
Date: Tue, 23 Feb 2016 18:42:39 -0500
Subject: [PATCH] Small changes to the install script
---
configure.ac | 6 ++---
.../PSE/0_Derivative_approx_1D/main.cpp | 11 ++++-----
install | 12 +++++-----
openfpm_data | 2 +-
openfpm_devices | 2 +-
openfpm_numerics | 2 +-
openfpm_vcluster | 2 +-
script/install_H5HUT.sh | 23 -------------------
script/install_HDF5.sh | 2 +-
src/Makefile.am | 4 ++--
src/Vector/vector_dist.hpp | 2 +-
vtk/Metis_gen_vtk.cpp | 2 +-
12 files changed, 23 insertions(+), 47 deletions(-)
delete mode 100755 script/install_H5HUT.sh
diff --git a/configure.ac b/configure.ac
index 42dc743c..9945dfa9 100755
--- a/configure.ac
+++ b/configure.ac
@@ -38,7 +38,7 @@ m4_ifdef([AX_LAPACK],,[m4_include([m4/ax_lapack.m4])])
m4_ifdef([AX_SUITESPARSE],,[m4_include([m4/ax_suitesparse.m4])])
m4_ifdef([AX_EIGEN],,[m4_include([m4/ax_eigen.m4])])
m4_ifdef([AX_LIB_HDF5],,[m4_include([m4/ax_lib_hdf5.m4])]])
-m4_ifdef([AX_H5HUT],,[m4_include([m4/ax_h5hut.m4])])
+m4_ifdef([AX_H5PART],,[m4_include([m4/ax_h5part.m4])])
CXXFLAGS+=" --std=c++11 "
NVCCFLAGS=" "
@@ -114,11 +114,11 @@ fi
#########
-## Check for H5HUT
+## Check for H5PART
save_CC=$CC
CC=$CXX
-AX_H5HUT([],[echo "Cannot detect h5hut, use the --with-h5hut option if it is not installed in the default location"
+AX_H5PART([],[echo "Cannot detect h5part, use the --with-h5part option if it is not installed in the default location"
exit 208])
CC=$save_CC
diff --git a/example/Numerics/PSE/0_Derivative_approx_1D/main.cpp b/example/Numerics/PSE/0_Derivative_approx_1D/main.cpp
index e88bdd2c..3fd936b4 100644
--- a/example/Numerics/PSE/0_Derivative_approx_1D/main.cpp
+++ b/example/Numerics/PSE/0_Derivative_approx_1D/main.cpp
@@ -204,7 +204,7 @@ int main(int argc, char* argv[])
}
//
- // ### WIKI 6 ###
+ // ### WIKI 7 ###
//
// We create a CellList with cell spacing 12 sigma
//
@@ -218,14 +218,13 @@ int main(int argc, char* argv[])
double linf = 0.0;
//
- // ### WIKI 6 ###
+ // ### WIKI 8 ###
//
// For each particle get the neighborhood of each particle
//
// This cycle is literally the formula from PSE operator approximation
- //
- //
//
+ // \$ \frac{1}{\epsilon^{2}} h (u_{q} - u_{p}) \eta_{\epsilon}(x_q - x_p) \$
//
auto it_p = vd.getDomainIterator();
@@ -288,7 +287,7 @@ int main(int argc, char* argv[])
}
//
- // ### WIKI 7 ###
+ // ### WIKI 9 ###
//
// Calculate the maximum infinity norm across processors and
// print it
@@ -301,7 +300,7 @@ int main(int argc, char* argv[])
std::cout << "Norm infinity: " << linf << "\n";
//
- // ### WIKI 8 ###
+ // ### WIKI 10 ###
//
// Deinitialize the library
//
diff --git a/install b/install
index b3eebd1e..6714ddde 100755
--- a/install
+++ b/install
@@ -138,7 +138,7 @@ LAPACK_installed=0
SUITESPARSE_installed=0
EIGEN_installed=0
HDF5_installed=0
-H5HUT_installed=0
+H5PART_installed=0
blas_options=""
conf_err=1
@@ -225,13 +225,13 @@ else
configure_options=" $configure_options --with-hdf5=$i_dir/HDF5/bin/h5pcc "
HDF5_installed=1
elif [ $conf_err -eq 208 ]; then
- echo "H5HUT not found try to install"
- if [ $H5HUT_installed -eq 1 ]; then
- echo "Error the installation of H5HUT failed"
+ echo "H5PART not found try to install"
+ if [ $H5PART_installed -eq 1 ]; then
+ echo "Error the installation of H5PART failed"
exit 1
fi
- ./script/install_H5HUT.sh $i_dir $compiler_opt
- configure_options=" $configure_options --with-h5hut=$i_dir/H5HUT/ "
+ ./script/install_H5PART.sh $i_dir $compiler_opt
+ configure_options=" $configure_options --with-h5hut=$i_dir/H5PART/ "
H5HUT_installed=1
elif [ $conf_err -ne 0 ]; then
echo "I do not know how to recover from this error"
diff --git a/openfpm_data b/openfpm_data
index d99d6e28..a3893b83 160000
--- a/openfpm_data
+++ b/openfpm_data
@@ -1 +1 @@
-Subproject commit d99d6e286199f5483327a9fd86ee84277c279310
+Subproject commit a3893b83c4dc8288dc851661f77d499d0f0742a9
diff --git a/openfpm_devices b/openfpm_devices
index 68d2e016..79ecba78 160000
--- a/openfpm_devices
+++ b/openfpm_devices
@@ -1 +1 @@
-Subproject commit 68d2e016d10ddcdf201bbc6cd4270ff0e4623d02
+Subproject commit 79ecba78fae6fce3f797c81393c9c8023a4208fe
diff --git a/openfpm_numerics b/openfpm_numerics
index 1d68c3aa..759fb600 160000
--- a/openfpm_numerics
+++ b/openfpm_numerics
@@ -1 +1 @@
-Subproject commit 1d68c3aa9ee4e7369d80320f7bf97c7dd9d6890d
+Subproject commit 759fb600260b785c9d282c10a9f1d6596767ec78
diff --git a/openfpm_vcluster b/openfpm_vcluster
index 0ed3620c..be8c849c 160000
--- a/openfpm_vcluster
+++ b/openfpm_vcluster
@@ -1 +1 @@
-Subproject commit 0ed3620ce1e91e5fa3541e01c1654dfad7515b87
+Subproject commit be8c849c9189fe90e1533125f2544258671d0916
diff --git a/script/install_H5HUT.sh b/script/install_H5HUT.sh
deleted file mode 100755
index 7f5c2ff8..00000000
--- a/script/install_H5HUT.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#! /bin/bash
-
-# check if the directory $1/H5HUT exist
-
-if [ -d "$1/H5HUT" ]; then
- echo "H5HUT already installed"
- exit 0
-fi
-
-rm H5hut-1.99.13.tar.gz
-rm -rf H5hut-1.99.13
-wget http://ppmcore.mpi-cbg.de/upload/H5hut-1.99.13.tar.gz
-tar -xf H5hut-1.99.13.tar.gz
-cd H5hut-1.99.13
-sh ./autogen.sh
-./configure --with-hdf5=$1/HDF5 --enable-parallel --prefix=$1/H5HUT
-make -j 4
-if [ $? -eq 0 ]; then
- echo "H5HUT error installing"
- exit 0
-fi
-mkdir $1/H5HUT
-make install
diff --git a/script/install_HDF5.sh b/script/install_HDF5.sh
index 87eb345e..f31f5cd1 100755
--- a/script/install_HDF5.sh
+++ b/script/install_HDF5.sh
@@ -10,7 +10,7 @@ fi
wget http://ppmcore.mpi-cbg.de/upload/hdf5-1.8.16.tar.bz2
tar -xf hdf5-1.8.16.tar.bz2
cd hdf5-1.8.16
-./configure --enable-parallel --prefix=$1/HDF5
+CC=mpicc ./configure --enable-parallel --prefix=$1/HDF5
make -j 4
mkdir $1/HDF5
make install
diff --git a/src/Makefile.am b/src/Makefile.am
index a79faae3..f9db932e 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -1,8 +1,8 @@
-LINKLIBS = $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS)
+LINKLIBS = $(METIS_LIB) $(PTHREAD_LIBS) $(OPT_LIBS) $(BOOST_LDFLAGS) $(BOOST_IOSTREAMS_LIB) $(CUDA_LIBS) $(H5PART_LIB) $(HDF5_LDFLAGS) $(HDF5_LIBS)
noinst_PROGRAMS = pdata
pdata_SOURCES = main.cpp lib/pdata.cpp test_multiple_o.cpp ../openfpm_devices/src/memory/HeapMemory.cpp ../openfpm_devices/src/memory/PtrMemory.cpp ../openfpm_vcluster/src/VCluster.cpp ../openfpm_devices/src/Memleak_check.cpp
-pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) -Wno-unused-local-typedefs
+pdata_CXXFLAGS = $(CUDA_CFLAGS) $(INCLUDES_PATH) $(METIS_INCLUDE) $(BOOST_CPPFLAGS) $(H5PART_INCLUDE) -DPARALLEL_IO $(HDF5_CPPFLAGS) -Wno-unused-local-typedefs
pdata_CFLAGS = $(CUDA_CFLAGS)
pdata_LDADD = $(LINKLIBS) -lmetis
nobase_include_HEADERS = Decomposition/CartDecomposition.hpp Decomposition/common.hpp Decomposition/Decomposition.hpp Decomposition/ie_ghost.hpp \
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index ce7b3af9..2090ca4c 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -8,6 +8,7 @@
#ifndef VECTOR_HPP_
#define VECTOR_HPP_
+#include "HDF5_XdmfWriter/HDF5_XdmfWriter.hpp"
#include "VCluster.hpp"
#include "Space/Shape/Point.hpp"
#include "Vector/vector_dist_iterator.hpp"
@@ -21,7 +22,6 @@
#include "memory/ExtPreAlloc.hpp"
#include "CSVWriter/CSVWriter.hpp"
#include "VTKWriter/VTKWriter.hpp"
-#include "H5PartWriter/H5PartWriter.hpp"
#include "Decomposition/common.hpp"
#include "Grid/grid_dist_id_iterator_dec.hpp"
#include "Vector/vector_dist_ofb.hpp"
diff --git a/vtk/Metis_gen_vtk.cpp b/vtk/Metis_gen_vtk.cpp
index c492dd0d..42b6fa72 100644
--- a/vtk/Metis_gen_vtk.cpp
+++ b/vtk/Metis_gen_vtk.cpp
@@ -39,7 +39,7 @@ int main(int argc, char ** argv)
// Write the decomposition
- VTKWriter<Graph_CSR<nm_v,nm_e>,GRAPH> vtk(g);
+ VTKWriter<Graph_CSR<nm_v,nm_e>,VTK_GRAPH> vtk(g);
vtk.write("Metis/vtk_partition.vtk");
}
--
GitLab