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Francois Tessier
TAPIOCA
Commits
ef46bc18
Commit
ef46bc18
authored
Oct 30, 2017
by
Francois Tessier
Browse files
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Browse Files
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Plain Diff
Global declaration of tiers of memory for aggregation and output file in HACC-IO
parent
ff95772e
Changes
4
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Inline
Side-by-side
Showing
4 changed files
with
64 additions
and
36 deletions
+64
-36
examples/HACC-IO/miniHACC-AoS-R.cpp
examples/HACC-IO/miniHACC-AoS-R.cpp
+9
-6
examples/HACC-IO/miniHACC-AoS-W.cpp
examples/HACC-IO/miniHACC-AoS-W.cpp
+1
-1
examples/HACC-IO/miniHACC-AoS.cpp
examples/HACC-IO/miniHACC-AoS.cpp
+21
-17
examples/HACC-IO/run_check_haswell.sh
examples/HACC-IO/run_check_haswell.sh
+33
-12
No files found.
examples/HACC-IO/miniHACC-AoS-R.cpp
View file @
ef46bc18
...
@@ -11,6 +11,9 @@
...
@@ -11,6 +11,9 @@
#define BLUE "\x1b[34m"
#define BLUE "\x1b[34m"
#define RESET "\x1b[0m"
#define RESET "\x1b[0m"
mem_t
memAggr
=
NVR
;
mem_t
memTarg
=
HDD
;
int
main
(
int
argc
,
char
*
argv
[])
int
main
(
int
argc
,
char
*
argv
[])
{
{
int
world_numtasks
,
world_myrank
,
mycolor
,
mykey
,
sub_numtasks
,
sub_myrank
,
i
,
file_id
;
int
world_numtasks
,
world_myrank
,
mycolor
,
mykey
,
sub_numtasks
,
sub_myrank
,
i
,
file_id
;
...
@@ -29,9 +32,8 @@ int main (int argc, char * argv[])
...
@@ -29,9 +32,8 @@ int main (int argc, char * argv[])
MPI_Init
(
&
argc
,
&
argv
);
MPI_Init
(
&
argc
,
&
argv
);
MPI_Comm_size
(
MPI_COMM_WORLD
,
&
world_numtasks
);
MPI_Comm_size
(
MPI_COMM_WORLD
,
&
world_numtasks
);
MPI_Comm_rank
(
MPI_COMM_WORLD
,
&
world_myrank
);
MPI_Comm_rank
(
MPI_COMM_WORLD
,
&
world_myrank
);
mycolor
=
tp
.
topology
.
BridgeNodeId
();
mycolor
=
tp
.
topology
.
BridgeNodeId
();
//mycolor = 42;
mykey
=
world_myrank
;
mykey
=
world_myrank
;
MPI_Comm_split
(
MPI_COMM_WORLD
,
mycolor
,
mykey
,
&
sub_comm
);
MPI_Comm_split
(
MPI_COMM_WORLD
,
mycolor
,
mykey
,
&
sub_comm
);
...
@@ -43,7 +45,7 @@ int main (int argc, char * argv[])
...
@@ -43,7 +45,7 @@ int main (int argc, char * argv[])
file_id
=
0
;
file_id
=
0
;
if
(
argv
[
2
]
!=
NULL
)
if
(
argv
[
2
]
!=
NULL
)
file_id
=
atoi
(
argv
[
2
]
);
file_id
=
atoi
(
argv
[
2
]
);
#ifdef BGQ
#ifdef BGQ
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-AOS-%08d-%d.dat"
,
mycolor
,
file_id
);
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-AOS-%08d-%d.dat"
,
mycolor
,
file_id
);
#elif XC40
#elif XC40
...
@@ -140,8 +142,8 @@ int main (int argc, char * argv[])
...
@@ -140,8 +142,8 @@ int main (int argc, char * argv[])
}
}
tp
.
Init
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
sub_comm
);
tp
.
Init
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
sub_comm
);
tp
.
setAggregationTier
(
2
,
DDR
,
"/scratch/tmp"
);
tp
.
setAggregationTier
(
2
,
memAggr
,
"/scratch/tmp"
);
tp
.
setTargetTier
(
HDD
,
file_size
,
output
);
tp
.
setTargetTier
(
memTarg
,
file_size
,
output
);
/*****************/
/*****************/
start_time
=
MPI_Wtime
();
start_time
=
MPI_Wtime
();
...
@@ -197,7 +199,8 @@ int main (int argc, char * argv[])
...
@@ -197,7 +199,8 @@ int main (int argc, char * argv[])
||
(
vx
[
i
]
!=
vx_r
[
i
])
||
(
vy
[
i
]
!=
vy_r
[
i
])
||
(
vz
[
i
]
!=
vz_r
[
i
])
||
(
vx
[
i
]
!=
vx_r
[
i
])
||
(
vy
[
i
]
!=
vy_r
[
i
])
||
(
vz
[
i
]
!=
vz_r
[
i
])
||
(
phi
[
i
]
!=
phi_r
[
i
])
||
(
pid
[
i
]
!=
pid_r
[
i
])
||
(
mask
[
i
]
!=
mask_r
[
i
]))
||
(
phi
[
i
]
!=
phi_r
[
i
])
||
(
pid
[
i
]
!=
pid_r
[
i
])
||
(
mask
[
i
]
!=
mask_r
[
i
]))
{
{
fprintf
(
stdout
,
RED
"[ERROR]"
RESET
" Wrong value for particle %d
\n
"
,
i
);
fprintf
(
stdout
,
RED
"[ERROR]"
RESET
"[%02d] Wrong value for particle %d (%.2f, %.2f, %.2f, %.2f, %.2f, %.2f, %.2f, %lld, %u )
\n
"
,
world_myrank
,
i
,
xx_r
[
i
],
yy_r
[
i
],
zz_r
[
i
],
vx_r
[
i
],
vy_r
[
i
],
vz_r
[
i
],
phi_r
[
i
],
pid_r
[
i
],
mask_r
[
i
]
);
MPI_Abort
(
MPI_COMM_WORLD
,
-
1
);
MPI_Abort
(
MPI_COMM_WORLD
,
-
1
);
}
}
}
}
...
...
examples/HACC-IO/miniHACC-AoS-W.cpp
View file @
ef46bc18
...
@@ -45,7 +45,7 @@ int main (int argc, char * argv[])
...
@@ -45,7 +45,7 @@ int main (int argc, char * argv[])
file_id
=
atoi
(
argv
[
2
]
);
file_id
=
atoi
(
argv
[
2
]
);
#ifdef BGQ
#ifdef BGQ
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-
SOA
-%08d-%d.dat"
,
mycolor
,
file_id
);
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-
AOS
-%08d-%d.dat"
,
mycolor
,
file_id
);
#elif XC40
#elif XC40
snprintf
(
output
,
100
,
"/lus/theta-fs0/projects/Performance/ftessier/HACC/HACC-AOS-%08d-%d.dat"
,
mycolor
,
file_id
);
snprintf
(
output
,
100
,
"/lus/theta-fs0/projects/Performance/ftessier/HACC/HACC-AOS-%08d-%d.dat"
,
mycolor
,
file_id
);
#else
#else
...
...
examples/HACC-IO/miniHACC-AoS.cpp
View file @
ef46bc18
...
@@ -11,6 +11,9 @@
...
@@ -11,6 +11,9 @@
#define BLUE "\x1b[34m"
#define BLUE "\x1b[34m"
#define RESET "\x1b[0m"
#define RESET "\x1b[0m"
mem_t
memAggr
=
NVR
;
mem_t
memTarg
=
HDD
;
int
main
(
int
argc
,
char
*
argv
[])
int
main
(
int
argc
,
char
*
argv
[])
{
{
int
world_numtasks
,
world_myrank
,
mycolor
,
mykey
,
sub_numtasks
,
sub_myrank
,
i
,
file_id
;
int
world_numtasks
,
world_myrank
,
mycolor
,
mykey
,
sub_numtasks
,
sub_myrank
,
i
,
file_id
;
...
@@ -22,7 +25,7 @@ int main (int argc, char * argv[])
...
@@ -22,7 +25,7 @@ int main (int argc, char * argv[])
MPI_Comm
sub_comm
;
MPI_Comm
sub_comm
;
MPI_Status
status
;
MPI_Status
status
;
char
output
[
100
];
char
output
[
100
];
Tapioca
tp
;
Tapioca
tp
,
tp2
;
int64_t
chunkCount
[
9
],
chunkOffset
[
9
];
int64_t
chunkCount
[
9
],
chunkOffset
[
9
];
int
chunkSize
[
9
];
int
chunkSize
[
9
];
...
@@ -122,8 +125,8 @@ int main (int argc, char * argv[])
...
@@ -122,8 +125,8 @@ int main (int argc, char * argv[])
}
}
tp
.
Init
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
sub_comm
);
tp
.
Init
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
sub_comm
);
tp
.
setAggregationTier
(
5
,
NVR
,
"/scratch/tmp
"
);
tp
.
setAggregationTier
(
2
,
memAggr
,
"/scratch/tmp-write
"
);
tp
.
setTargetTier
(
HDD
,
file_size
,
output
);
tp
.
setTargetTier
(
memTarg
,
file_size
,
output
);
/*****************/
/*****************/
start_time
=
MPI_Wtime
();
start_time
=
MPI_Wtime
();
...
@@ -190,9 +193,9 @@ int main (int argc, char * argv[])
...
@@ -190,9 +193,9 @@ int main (int argc, char * argv[])
/*****************/
/*****************/
/* INIT TAPIOCA */
/* INIT TAPIOCA */
/*****************/
/*****************/
tp
.
Init
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
sub_comm
);
tp
2
.
Init
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
sub_comm
);
tp
.
setAggregationTier
(
4
,
NVR
,
"/scratch/tmp
"
);
tp
2
.
setAggregationTier
(
2
,
memAggr
,
"/scratch/tmp-read
"
);
tp
.
setTargetTier
(
HDD
,
file_size
,
output
);
tp
2
.
setTargetTier
(
memTarg
,
file_size
,
output
);
/*****************/
/*****************/
start_time
=
MPI_Wtime
();
start_time
=
MPI_Wtime
();
...
@@ -202,31 +205,31 @@ int main (int argc, char * argv[])
...
@@ -202,31 +205,31 @@ int main (int argc, char * argv[])
offset
=
scan_size
*
particle_size
;
offset
=
scan_size
*
particle_size
;
tp
.
Read
(
offset
,
xx_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
2
.
Read
(
offset
,
xx_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
yy_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
2
.
Read
(
offset
,
yy_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
zz_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
2
.
Read
(
offset
,
zz_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
vx_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
2
.
Read
(
offset
,
vx_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
vy_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
2
.
Read
(
offset
,
vy_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
vz_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
2
.
Read
(
offset
,
vz_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
phi_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
2
.
Read
(
offset
,
phi_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
pid_r
,
num_particles
,
MPI_LONG_LONG
,
&
status
);
tp
2
.
Read
(
offset
,
pid_r
,
num_particles
,
MPI_LONG_LONG
,
&
status
);
offset
+=
num_particles
*
sizeof
(
int64_t
);
offset
+=
num_particles
*
sizeof
(
int64_t
);
tp
.
Read
(
offset
,
mask_r
,
num_particles
,
MPI_UNSIGNED_SHORT
,
&
status
);
tp
2
.
Read
(
offset
,
mask_r
,
num_particles
,
MPI_UNSIGNED_SHORT
,
&
status
);
end_time
=
MPI_Wtime
();
end_time
=
MPI_Wtime
();
tot_time
=
end_time
-
start_time
;
tot_time
=
end_time
-
start_time
;
...
@@ -238,7 +241,7 @@ int main (int argc, char * argv[])
...
@@ -238,7 +241,7 @@ int main (int argc, char * argv[])
io_bw
,
(
double
)
tot_size
/
(
1024
*
1024
),
max_time
*
1000
);
io_bw
,
(
double
)
tot_size
/
(
1024
*
1024
),
max_time
*
1000
);
}
}
tp
.
Finalize
();
tp
2
.
Finalize
();
/*****************/
/*****************/
/* VERIFICATION */
/* VERIFICATION */
...
@@ -248,7 +251,8 @@ int main (int argc, char * argv[])
...
@@ -248,7 +251,8 @@ int main (int argc, char * argv[])
||
(
vx
[
i
]
!=
vx_r
[
i
])
||
(
vy
[
i
]
!=
vy_r
[
i
])
||
(
vz
[
i
]
!=
vz_r
[
i
])
||
(
vx
[
i
]
!=
vx_r
[
i
])
||
(
vy
[
i
]
!=
vy_r
[
i
])
||
(
vz
[
i
]
!=
vz_r
[
i
])
||
(
phi
[
i
]
!=
phi_r
[
i
])
||
(
pid
[
i
]
!=
pid_r
[
i
])
||
(
mask
[
i
]
!=
mask_r
[
i
]))
||
(
phi
[
i
]
!=
phi_r
[
i
])
||
(
pid
[
i
]
!=
pid_r
[
i
])
||
(
mask
[
i
]
!=
mask_r
[
i
]))
{
{
fprintf
(
stdout
,
RED
"[ERROR]"
RESET
"[%03d] Wrong value for particle %d
\n
"
,
world_myrank
,
i
);
fprintf
(
stdout
,
RED
"[ERROR]"
RESET
"[%02d] Wrong value for particle %d (%.2f, %.2f, %.2f, %.2f, %.2f, %.2f, %.2f, %lld, %u )
\n
"
,
world_myrank
,
i
,
xx_r
[
i
],
yy_r
[
i
],
zz_r
[
i
],
vx_r
[
i
],
vy_r
[
i
],
vz_r
[
i
],
phi_r
[
i
],
pid_r
[
i
],
mask_r
[
i
]
);
MPI_Abort
(
MPI_COMM_WORLD
,
-
1
);
MPI_Abort
(
MPI_COMM_WORLD
,
-
1
);
}
}
}
}
...
...
examples/HACC-IO/run_check_haswell.sh
View file @
ef46bc18
...
@@ -13,6 +13,7 @@ export TAPIOCA_COMMSPLIT=true
...
@@ -13,6 +13,7 @@ export TAPIOCA_COMMSPLIT=true
export
TAPIOCA_STRATEGY
=
TOPOLOGY_AWARE
export
TAPIOCA_STRATEGY
=
TOPOLOGY_AWARE
export
TAPIOCA_NBAGGR
=
4
export
TAPIOCA_NBAGGR
=
4
export
TAPIOCA_BUFFERSIZE
=
16777216
export
TAPIOCA_BUFFERSIZE
=
16777216
#export TAPIOCA_BUFFERSIZE=33554432
export
TAPIOCA_PIPELINING
=
true
export
TAPIOCA_PIPELINING
=
true
export
PAMID_VERBOSE
=
1
export
PAMID_VERBOSE
=
1
...
@@ -28,28 +29,48 @@ function outputFile ()
...
@@ -28,28 +29,48 @@ function outputFile ()
printenv
| egrep
"TAPIOCA_"
printenv
| egrep
"TAPIOCA_"
PARTICLES
=
200000
#rm $TARGET/*
#rm $TARGET/*
#mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS 15000
#mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS 15000
# ls -l $TARGET/
# ls -l $TARGET/
# sleep 5
# sleep 5
#mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS-R $PARTICLES
rm
$TARGET
/
*
rm
$TARGET
/
*
mpirun
-f
$COBALT_NODEFILE
-n
$NPROCS
./miniHACC-AoS
100000
mpirun
-f
$COBALT_NODEFILE
-n
$NPROCS
./miniHACC-AoS
-MPIIO
$PARTICLES
sleep
3
sleep
3
#ls -l /projects/visualization/ftessier/debug/
ls
-l
/projects/visualization/ftessier/debug/
#md5sum /projects/visualization/ftessier/debug/HACC-AOS-00000000-0.dat
md5sum
/projects/visualization/ftessier/debug/HACC-AOS-00000000-0.dat
# sleep 60
echo
# rm $TARGET/*
echo
"---------------------------------------------"
# mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS-MPIIO 60000
echo
# sleep 3
rm
$TARGET
/
*
# ls -l /projects/visualization/ftessier/debug/
mpirun
-f
$COBALT_NODEFILE
-n
$NPROCS
./miniHACC-AoS-W
$PARTICLES
# md5sum /projects/visualization/ftessier/debug/HACC-AOS-00000000-0.dat
sleep
3
ls
-l
/projects/visualization/ftessier/debug/
md5sum
/projects/visualization/ftessier/debug/HACC-AOS-00000000-0.dat
echo
echo
"---------------------------------------------"
echo
sleep
3
mpirun
-f
$COBALT_NODEFILE
-n
$NPROCS
./miniHACC-AoS-R
$PARTICLES
echo
echo
"---------------------------------------------"
echo
sleep
3
rm
$TARGET
/
*
mpirun
-f
$COBALT_NODEFILE
-n
$NPROCS
./miniHACC-AoS
$PARTICLES
ls
-l
/projects/visualization/ftessier/debug/
md5sum
/projects/visualization/ftessier/debug/HACC-AOS-00000000-0.dat
# echo
# echo "---------------------------------------------"
# echo
# sleep 3
# mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS $PARTICLES
# sleep 1
#mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-SoA-R 15000
#mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-SoA-R 15000
# sleep 5
# sleep 5
echo
echo
"---------------------------------------------"
echo
#mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS-R 15000
#mpirun -f $COBALT_NODEFILE -n $NPROCS ./miniHACC-AoS-R 15000
# for run in {0..9}
# for run in {0..9}
...
...
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