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argupta
openfpm_pdata
Commits
74c330ab
Commit
74c330ab
authored
Jan 09, 2019
by
incardon
Browse files
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Plain Diff
Latest modules
parent
856eec94
Changes
10
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10 changed files
with
72 additions
and
10 deletions
+72
-10
example/Vector/3_molecular_dynamic_gpu_opt/Makefile
example/Vector/3_molecular_dynamic_gpu_opt/Makefile
+7
-3
example/Vector/7_SPH_dlb_gpu_opt/Makefile
example/Vector/7_SPH_dlb_gpu_opt/Makefile
+6
-2
example/Vector/7_SPH_dlb_gpu_opt/main.cu
example/Vector/7_SPH_dlb_gpu_opt/main.cu
+3
-1
openfpm_vcluster
openfpm_vcluster
+1
-1
src/Decomposition/CartDecomposition_ext.hpp
src/Decomposition/CartDecomposition_ext.hpp
+4
-1
src/Vector/cuda/vector_dist_cuda_funcs.cuh
src/Vector/cuda/vector_dist_cuda_funcs.cuh
+3
-0
src/Vector/tests/vector_dist_dlb_test.hpp
src/Vector/tests/vector_dist_dlb_test.hpp
+42
-0
src/Vector/vector_dist_comm.hpp
src/Vector/vector_dist_comm.hpp
+3
-0
src/lib/pdata.cpp
src/lib/pdata.cpp
+1
-2
src/lib/pdata.hpp
src/lib/pdata.hpp
+2
-0
No files found.
example/Vector/3_molecular_dynamic_gpu_opt/Makefile
View file @
74c330ab
...
...
@@ -8,9 +8,13 @@ else
CUDA_CC
=
nvcc
endif
CC_SCOREP
=
scorep
--nocompiler
--cuda
--mpp
=
mpi nvcc
CC
=
$(CUDA_CC)
#
${CC_SCOREP}
CC_MPI
=
mpic++
ifeq
($(PROFILE),ON)
CC
=
scorep
--nocompiler
--cuda
--mpp
=
mpi nvcc
CC_MPI
=
mpic++
else
CC
=
$(CUDA_CC)
CC_MPI
=
mpic++
endif
LDIR
=
OPT
=
...
...
example/Vector/7_SPH_dlb_gpu_opt/Makefile
View file @
74c330ab
...
...
@@ -13,8 +13,12 @@ else
CUDA_CC_LINK
=
nvcc
endif
CC
=
mpic++
ifeq
($(PROFILE),ON)
CUDA_CC
=
scorep
--nocompiler
--cuda
--mpp
=
mpi nvcc
CUDA_CC_LINK
=
nvcc
else
CUDA_CC_LINK
=
nvcc
endif
LDIR
=
OPT
=
...
...
example/Vector/7_SPH_dlb_gpu_opt/main.cu
View file @
74c330ab
...
...
@@ -348,7 +348,7 @@ __global__ void calc_forces_gpu(particles_type vd, NN_type NN, real_number W_dap
real_number
r2
=
norm2
(
dr
);
// if they interact
if
(
r2
<
FourH2
)
if
(
r2
<
FourH2
&&
dr
>=
1e-8
)
{
real_number
r
=
sqrt
(
r2
);
...
...
@@ -942,6 +942,8 @@ int main(int argc, char* argv[])
vd_out
.
getLastPos
()[
1
]
=
vd
.
getPos
(
p
)[
1
];
vd_out
.
getLastPos
()[
2
]
=
vd
.
getPos
(
p
)[
2
];
vd_out
.
template
getLastProp
<
0
>()
=
vd
.
template
getProp
<
type
>(
p
);
vd_out
.
template
getLastProp
<
1
>()[
0
]
=
vd
.
template
getProp
<
velocity
>(
p
)[
0
];
vd_out
.
template
getLastProp
<
1
>()[
1
]
=
vd
.
template
getProp
<
velocity
>(
p
)[
1
];
vd_out
.
template
getLastProp
<
1
>()[
2
]
=
vd
.
template
getProp
<
velocity
>(
p
)[
2
];
...
...
openfpm_vcluster
@
e105e6ef
Subproject commit
309c31433036534153366a27f8ad52c85c8dabb2
Subproject commit
e105e6ef793fa254da78c643c06bafdd858f0bb1
src/Decomposition/CartDecomposition_ext.hpp
View file @
74c330ab
...
...
@@ -218,6 +218,10 @@ public:
*/
void
setParameters
(
const
CartDecomposition
<
dim
,
T
,
Memory
,
layout_base
,
Distribution
>
&
dec
,
const
Ghost
<
dim
,
T
>
&
g
,
const
::
Box
<
dim
,
T
>
&
ext_domain
)
{
// Set the decomposition parameters
this
->
gr
.
setDimensions
(
dec
.
gr
.
getSize
());
this
->
cd
.
setDimensions
(
ext_domain
,
dec
.
gr
.
getSize
(),
0
);
this
->
box_nn_processor
=
dec
.
box_nn_processor
;
// Calculate new sub-domains for extended domain
...
...
@@ -225,7 +229,6 @@ public:
// Calculate fine_s structure for the extended domain
// update the cell decomposer and gr
// extend_fines(dec);
reconstruct_fine_s_from_extended_domain
(
ext_domain
);
// Get the old sub-sub-domain grid extension
...
...
src/Vector/cuda/vector_dist_cuda_funcs.cuh
View file @
74c330ab
...
...
@@ -12,6 +12,7 @@
#include "util/cuda/moderngpu/kernel_reduce.hxx"
#include "util/cuda/moderngpu/kernel_scan.hxx"
#include "Decomposition/common.hpp"
#include "lib/pdata.hpp"
template
<
unsigned
int
dim
,
typename
St
,
typename
decomposition_type
,
typename
vector_type
,
typename
start_type
,
typename
output_type
>
__global__
void
proc_label_id_ghost
(
decomposition_type
dec
,
vector_type
vd
,
start_type
starts
,
output_type
out
)
...
...
@@ -349,6 +350,8 @@ void remove_marked(vector_type & vd)
// first we do a scan of the property
openfpm
::
vector_gpu
<
aggregate
<
unsigned
int
>>
idx
;
idx
.
setMemory
(
mem_tmp
);
idx
.
resize
(
vd
.
size_local
());
auto
ite
=
idx
.
getGPUIterator
();
...
...
src/Vector/tests/vector_dist_dlb_test.hpp
View file @
74c330ab
...
...
@@ -239,8 +239,21 @@ template<typename vector_type> void test_dlb_vector()
}
vd
.
map
();
////////////// DEBUG ////////////////////////
vd
.
write
(
"bug_test_init_before"
);
/////////////////////////////////////////////
vd
.
template
ghost_get
<
>();
////////////// DEBUG ////////////////////////
vd
.
write
(
"bug_test_init_after"
);
/////////////////////////////////////////////
// Get the neighborhood of each particles
auto
VV
=
vd
.
getVerlet
(
0.01
);
...
...
@@ -260,10 +273,24 @@ template<typename vector_type> void test_dlb_vector()
ModelSquare
md
;
md
.
factor
=
10
;
vd
.
map
();
////////////// DEBUG ////////////////////////
vd
.
write
(
"bug_test_before_dlb"
);
/////////////////////////////////////////////
vd
.
addComputationCosts
(
md
);
vd
.
getDecomposition
().
decompose
();
vd
.
map
();
////////////// DEBUG ////////////////////////
vd
.
write
(
"bug_test_after_dlb"
);
/////////////////////////////////////////////
vd
.
addComputationCosts
(
md
);
openfpm
::
vector
<
size_t
>
loads
;
...
...
@@ -299,9 +326,24 @@ template<typename vector_type> void test_dlb_vector()
++
it
;
}
vd
.
map
();
////////////// DEBUG ////////////////////////
vd
.
write_frame
(
"bug_test_before"
,
i
);
/////////////////////////////////////////////
vd
.
template
ghost_get
<
>();
////////////// DEBUG ////////////////////////
vd
.
getDecomposition
().
write
(
"dec_test"
);
vd
.
write_frame
(
"bug_test_after"
,
i
);
/////////////////////////////////////////////
auto
VV2
=
vd
.
getVerlet
(
0.01
);
auto
it2
=
vd
.
getDomainIterator
();
...
...
src/Vector/vector_dist_comm.hpp
View file @
74c330ab
...
...
@@ -292,6 +292,9 @@ class vector_dist_comm
};
openfpm
::
vector
<
sh_box
>
reord_shift
;
box_f
.
clear
();
map_cmb
.
clear
();
box_cmb
.
clear
();
// Add local particles coming from periodic boundary, the only boxes that count are the one
// touching the border
...
...
src/lib/pdata.cpp
View file @
74c330ab
...
...
@@ -4,7 +4,7 @@
* Created on: Feb 5, 2016
* Author: Pietro Incardona
*/
#include "pdata.hpp"
#include "SubdomainGraphNodes.hpp"
const
std
::
string
nm_v
::
attributes
::
name
[]
=
{
"x"
,
"migration"
,
"computation"
,
"global_id"
,
"id"
,
"sub_id"
,
"proc_id"
,
"id"
,
"fake_v"
};
...
...
@@ -13,4 +13,3 @@ const std::string nm_part_v::attributes::name[] = {"id","sub_id"};
const
std
::
string
nm_part_e
::
attributes
::
name
[]
=
{
"id"
};
src/lib/pdata.hpp
0 → 100644
View file @
74c330ab
#include "config.h"
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