From da9decdc5335ee5e8449162011dcd8b252ca722c Mon Sep 17 00:00:00 2001
From: Pietro Incardona <i-bird@private-incardon-3.mpi-cbg.de>
Date: Wed, 3 Aug 2016 16:26:56 +0200
Subject: [PATCH] Fixing for extprealloc
---
install | 26 ++++++++++++++++++++++----
src/Grid/grid_dist_id.hpp | 11 +++++------
src/Vector/vector_dist.hpp | 23 ++++-------------------
3 files changed, 31 insertions(+), 29 deletions(-)
diff --git a/install b/install
index 501786ca5..780317adf 100755
--- a/install
+++ b/install
@@ -216,6 +216,9 @@ fi
if [ -d "$i_dir/HDF5" ]; then
configure_options=" $configure_options --with-hdf5=$i_dir/HDF5/bin/h5pcc "
fi
+if [ -d "$i_dir/LIBHILBERT" ]; then
+ configure_options=" $configure_options --with-libhilbert=$i_dir/LIBHILBERT "
+fi
### MPI
@@ -250,6 +253,7 @@ EIGEN_installed=0
EIGEN_System_prv=1
HDF5_installed=0
HDF5_System_prv=1
+LIBHILBERT_installed=0
conf_err=1
if [ $install_req -eq 0 ]; then
@@ -309,6 +313,15 @@ else
./script/install_HDF5.sh $i_dir $ncore
configure_options=" $configure_options --with-hdf5=$i_dir/HDF5/bin/h5pcc "
HDF5_installed=1
+ elif [ $conf_err -eq 210 ]; then
+ echo "LIBHILBERT not found try to install"
+ if [ $LIBHILBERT_installed -eq 1 ]; then
+ echo "Error the installation of LIBHILBERT failed"
+ exit 1
+ fi
+ ./script/install_LIBHILBERT.sh $i_dir $ncore
+ configure_options=" $configure_options --with-libhilbert=$i_dir/LIBHILBERT "
+ LIBHILBERT_installed=1
elif [ $conf_err -ne 0 ]; then
echo "I do not know how to recover from this error"
exit 1
@@ -333,10 +346,10 @@ fi
### Create example.mk
install_base=$(cat install_dir)
-echo "INCLUDE_PATH=-I. -I$install_base/openfpm_numerics/include -I$install_base/openfpm_pdata/include/config -I$install_base/openfpm_pdata/include -I$install_base/openfpm_data/include -I$install_base/openfpm_vcluster/include -I$install_base/openfpm_io/include -I$install_base/openfpm_devices/include -I$i_dir/METIS/include -I$i_dir/PARMETIS/include -I$i_dir/BOOST/include -I$i_dir/HDF5/include $lin_alg_inc" > example.mk
-echo "LIBS_PATH= -L$install_base/openfpm_devices/lib -L$install_base/openfpm_pdata/lib -L$install_base/openfpm_vcluster/lib -L$i_dir/METIS/lib -L$i_dir/PARMETIS/lib -L$i_dir/BOOST/lib -L$i_dir/HDF5/lib $lin_alg_dir" >> example.mk
-echo "LIBS=-lvcluster -lofpm_pdata -lofpmmemory -lparmetis -lmetis -lboost_iostreams -lhdf5 $lin_alg_lib" >> example.mk
-echo "LIBS_SE2=-lvcluster -lofpmmemory_se2 -lparmetis -lmetis -lboost_iostreams -lhdf5 $lin_alg_lib" >> example.mk
+echo "INCLUDE_PATH=-I. -I$install_base/openfpm_numerics/include -I$install_base/openfpm_pdata/include/config -I$install_base/openfpm_pdata/include -I$install_base/openfpm_data/include -I$install_base/openfpm_vcluster/include -I$install_base/openfpm_io/include -I$install_base/openfpm_devices/include -I$i_dir/METIS/include -I$i_dir/PARMETIS/include -I$i_dir/BOOST/include -I$i_dir/HDF5/include -I$i_dir/LIBHILBERT/include $lin_alg_inc" > example.mk
+echo "LIBS_PATH= -L$install_base/openfpm_devices/lib -L$install_base/openfpm_pdata/lib -L$install_base/openfpm_vcluster/lib -L$i_dir/METIS/lib -L$i_dir/PARMETIS/lib -L$i_dir/BOOST/lib -L$i_dir/HDF5/lib -L$i_dir/LIBHILBERT/lib $lin_alg_dir" >> example.mk
+echo "LIBS=-lvcluster -lofpm_pdata -lofpmmemory -lparmetis -lmetis -lboost_iostreams -lhdf5 -llibhilbert $lin_alg_lib" >> example.mk
+echo "LIBS_SE2=-lvcluster -lofpmmemory_se2 -lparmetis -lmetis -lboost_iostreams -lhdf5 -llibhilbert $lin_alg_lib" >> example.mk
cp example.mk src/example.mk
cp example.mk example/example.mk
@@ -396,6 +409,11 @@ if [ -d "$i_dir/HDF5" ]; then
bash_library="$bash_library:$i_dir/HDF5/lib"
fi
+if [ -d "$i_dir/LIBHILBERT" ]; then
+ installation_report="$installation_report \033[92;1mLibHilbert\033[0m Installed: \033[1m $i_dir/LIBHILBERT \033[0m\n"
+ bash_library="$bash_library:$i_dir/LIBHILBERT/lib"
+fi
+
echo -e "$installation_report"
echo ""
diff --git a/src/Grid/grid_dist_id.hpp b/src/Grid/grid_dist_id.hpp
index 54d187aae..b9d3df791 100644
--- a/src/Grid/grid_dist_id.hpp
+++ b/src/Grid/grid_dist_id.hpp
@@ -1270,9 +1270,7 @@ public:
void * pointer2 = prAlloc_prp.getPointerEnd();
- v_cl.send(ig_box.get(i).prc,0,pointer/*sts.getMarkPointer(prAlloc_prp)*/,(char *)pointer2 - (char *)pointer /*sts.getMarkSize(prAlloc_prp)*/);
-
-// pointer = prAlloc_prp.getPointerEnd();
+ v_cl.send(ig_box.get(i).prc,0,pointer,(char *)pointer2 - (char *)pointer);
}
// Calculate the total information to receive from each processors
@@ -1292,12 +1290,13 @@ public:
}
}
+ size_t tot_recv = ExtPreAlloc<Memory>::calculateMem(prp_recv);
+
//! Resize the receiving buffer
- g_recv_prp_mem.resize(ExtPreAlloc<Memory>::calculateMem(prp_recv));
+ g_recv_prp_mem.resize(tot_recv);
// Create an object of preallocated memory for properties
- ExtPreAlloc<Memory> & prRecv_prp = *(new ExtPreAlloc<Memory>(req,g_recv_prp_mem));
-
+ ExtPreAlloc<Memory> & prRecv_prp = *(new ExtPreAlloc<Memory>(tot_recv,g_recv_prp_mem));
prRecv_prp.incRef();
// queue the receives
diff --git a/src/Vector/vector_dist.hpp b/src/Vector/vector_dist.hpp
index 14e767238..eeb642f1e 100644
--- a/src/Vector/vector_dist.hpp
+++ b/src/Vector/vector_dist.hpp
@@ -756,21 +756,17 @@ private:
*
* \param size_byte_prp total size for the property buffer
* \param size_byte_pos total size for the position buffer
- * \param pap_prp allocation sequence for the property buffer
- * \param pap_pos allocation sequence for the position buffer
*
*/
- template<typename prp_object> void calc_send_ghost_buf(size_t & size_byte_prp, size_t & size_byte_pos, std::vector<size_t> & pap_prp, std::vector<size_t> & pap_pos)
+ template<typename prp_object> void calc_send_ghost_buf(size_t & size_byte_prp, size_t & size_byte_pos)
{
// Calculate the total size required for the sending buffer
for (size_t i = 0; i < ghost_prc_sz.size(); i++)
{
size_t alloc_ele = openfpm::vector<prp_object, HeapMemory, typename memory_traits_lin<prp_object>::type, memory_traits_lin , openfpm::grow_policy_identity>::calculateMem(ghost_prc_sz.get(i), 0);
- pap_prp.push_back(alloc_ele);
size_byte_prp += alloc_ele;
alloc_ele = openfpm::vector<Point<dim, St>, HeapMemory, typename memory_traits_lin<Point<dim, St>>::type, memory_traits_lin, openfpm::grow_policy_identity>::calculateMem(ghost_prc_sz.get(i), 0);
- pap_pos.push_back(alloc_ele);
size_byte_pos += alloc_ele;
}
}
@@ -1137,11 +1133,7 @@ public:
size_t size_byte_prp = 0;
size_t size_byte_pos = 0;
- // allocation patterns for property and position send buffer
- std::vector<size_t> pap_prp;
- std::vector<size_t> pap_pos;
-
- calc_send_ghost_buf<prp_object>(size_byte_prp, size_byte_pos, pap_prp, pap_pos);
+ calc_send_ghost_buf<prp_object>(size_byte_prp, size_byte_pos);
// Create memory for the send buffer
@@ -1151,11 +1143,8 @@ public:
// Create and fill send buffer for particle properties
-////////////////////////////////////////////////
- size_t req = ExtPreAlloc<Memory>::calculateMem(pap_prp);
+ ExtPreAlloc<Memory> * prAlloc_prp = new ExtPreAlloc<Memory>(size_byte_prp, g_prp_mem);
- ExtPreAlloc<Memory> * prAlloc_prp = new ExtPreAlloc<Memory>(req, g_prp_mem);
-/////////////////////////////////////////////////
openfpm::vector<send_vector> g_send_prp;
fill_send_ghost_prp_buf<send_vector, prp_object, prp...>(g_send_prp, prAlloc_prp);
@@ -1165,11 +1154,7 @@ public:
openfpm::vector<send_pos_vector> g_pos_send;
if (opt != NO_POSITION)
{
-////////////////////////////////////////////////
- size_t req1 = ExtPreAlloc<Memory>::calculateMem(pap_pos);
-
- prAlloc_pos = new ExtPreAlloc<Memory>(req1, g_pos_mem);
-////////////////////////////////////////////////////////
+ prAlloc_pos = new ExtPreAlloc<Memory>(size_byte_pos, g_pos_mem);
fill_send_ghost_pos_buf(g_pos_send, prAlloc_pos);
}
--
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