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Francois Tessier
TAPIOCA
Commits
ab7405a1
Commit
ab7405a1
authored
Sep 28, 2017
by
Francois Tessier
Browse files
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Write-only and read-only version of HACC-IO
parent
3f45ef14
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2 changed files
with
428 additions
and
0 deletions
+428
-0
examples/HACC-IO/miniHACC-AoS-R.cpp
examples/HACC-IO/miniHACC-AoS-R.cpp
+232
-0
examples/HACC-IO/miniHACC-AoS-W.cpp
examples/HACC-IO/miniHACC-AoS-W.cpp
+196
-0
No files found.
examples/HACC-IO/miniHACC-AoS-R.cpp
0 → 100644
View file @
ab7405a1
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <stdint.h>
#include <mpi.h>
#include "tapioca.hpp"
#define RED "\x1b[31m"
#define GREEN "\x1b[32m"
#define BLUE "\x1b[34m"
#define RESET "\x1b[0m"
int
main
(
int
argc
,
char
*
argv
[])
{
int
world_numtasks
,
world_myrank
,
mycolor
,
mykey
,
sub_numtasks
,
sub_myrank
,
i
,
file_id
;
int64_t
num_particles
;
int64_t
sub_particles
,
tot_particles
,
particle_size
,
file_size
,
tot_size
;
int64_t
scan_size
=
0
,
offset
,
hdr
=
0
;
double
start_time
,
end_time
,
tot_time
,
max_time
;
double
io_bw
;
MPI_Comm
sub_comm
;
MPI_Status
status
;
char
output
[
100
];
Tapioca
tp
;
int64_t
chunkCount
[
9
],
chunkOffset
[
9
];
int
chunkSize
[
9
];
MPI_Init
(
&
argc
,
&
argv
);
MPI_Comm_size
(
MPI_COMM_WORLD
,
&
world_numtasks
);
MPI_Comm_rank
(
MPI_COMM_WORLD
,
&
world_myrank
);
mycolor
=
tp
.
topology
.
BridgeNodeId
();
//mycolor = 42;
mykey
=
world_myrank
;
MPI_Comm_split
(
MPI_COMM_WORLD
,
mycolor
,
mykey
,
&
sub_comm
);
MPI_Comm_size
(
sub_comm
,
&
sub_numtasks
);
MPI_Comm_rank
(
sub_comm
,
&
sub_myrank
);
num_particles
=
atoi
(
argv
[
1
]
);
file_id
=
0
;
if
(
argv
[
2
]
!=
NULL
)
file_id
=
atoi
(
argv
[
2
]
);
#ifdef BGQ
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-SOA-%08d-%d.dat"
,
mycolor
,
file_id
);
#elif XC40
snprintf
(
output
,
100
,
"/lus/theta-fs0/projects/Performance/ftessier/HACC/HACC-AOS-%08d-%d.dat"
,
mycolor
,
file_id
);
#else
snprintf
(
output
,
100
,
"./HACC-SOA-%08d-%d.dat"
,
mycolor
,
file_id
);
#endif
/*****************/
/* WRITE */
/*****************/
float
*
xx
,
*
yy
,
*
zz
,
*
vx
,
*
vy
,
*
vz
,
*
phi
;
int64_t
*
pid
;
uint16_t
*
mask
;
xx
=
new
float
[
num_particles
];
yy
=
new
float
[
num_particles
];
zz
=
new
float
[
num_particles
];
vx
=
new
float
[
num_particles
];
vy
=
new
float
[
num_particles
];
vz
=
new
float
[
num_particles
];
phi
=
new
float
[
num_particles
];
pid
=
new
int64_t
[
num_particles
];
mask
=
new
uint16_t
[
num_particles
];
for
(
uint64_t
i
=
0
;
i
<
num_particles
;
i
++
)
{
xx
[
i
]
=
(
float
)
i
;
yy
[
i
]
=
(
float
)
i
;
zz
[
i
]
=
(
float
)
i
;
vx
[
i
]
=
(
float
)
i
;
vy
[
i
]
=
(
float
)
i
;
vz
[
i
]
=
(
float
)
i
;
phi
[
i
]
=
(
float
)
i
;
pid
[
i
]
=
(
int64_t
)
i
;
mask
[
i
]
=
(
uint16_t
)
world_myrank
;
}
MPI_Allreduce
(
&
num_particles
,
&
sub_particles
,
1
,
MPI_LONG_LONG
,
MPI_SUM
,
sub_comm
);
MPI_Allreduce
(
&
num_particles
,
&
tot_particles
,
1
,
MPI_LONG_LONG
,
MPI_SUM
,
MPI_COMM_WORLD
);
particle_size
=
(
7
*
sizeof
(
float
))
+
sizeof
(
int64_t
)
+
sizeof
(
uint16_t
);
file_size
=
particle_size
*
sub_particles
;
tot_size
=
particle_size
*
tot_particles
;
MPI_Exscan
(
&
num_particles
,
&
scan_size
,
1
,
MPI_LONG_LONG
,
MPI_SUM
,
sub_comm
);
if
(
0
==
sub_myrank
)
{
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] miniHACC-AoS
\n
"
,
mycolor
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] Read output file (AoS data layout)
\n
"
,
mycolor
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] --> %lld particles per rank
\n
"
,
mycolor
,
num_particles
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] --> File size: %.2f MB (%lld particles)
\n
"
,
mycolor
,
(
double
)
file_size
/
(
1024
*
1024
),
sub_particles
);
}
/*****************/
/* READ */
/*****************/
float
*
xx_r
,
*
yy_r
,
*
zz_r
,
*
vx_r
,
*
vy_r
,
*
vz_r
,
*
phi_r
;
int64_t
*
pid_r
;
uint16_t
*
mask_r
;
xx_r
=
new
float
[
num_particles
];
yy_r
=
new
float
[
num_particles
];
zz_r
=
new
float
[
num_particles
];
vx_r
=
new
float
[
num_particles
];
vy_r
=
new
float
[
num_particles
];
vz_r
=
new
float
[
num_particles
];
phi_r
=
new
float
[
num_particles
];
pid_r
=
new
int64_t
[
num_particles
];
mask_r
=
new
uint16_t
[
num_particles
];
/*****************/
/* INIT TAPIOCA */
/*****************/
for
(
i
=
0
;
i
<
9
;
i
++
)
{
chunkCount
[
i
]
=
num_particles
;
}
chunkSize
[
0
]
=
sizeof
(
float
);
chunkSize
[
1
]
=
sizeof
(
float
);
chunkSize
[
2
]
=
sizeof
(
float
);
chunkSize
[
3
]
=
sizeof
(
float
);
chunkSize
[
4
]
=
sizeof
(
float
);
chunkSize
[
5
]
=
sizeof
(
float
);
chunkSize
[
6
]
=
sizeof
(
float
);
chunkSize
[
7
]
=
sizeof
(
int64_t
);
chunkSize
[
8
]
=
sizeof
(
uint16_t
);
chunkOffset
[
0
]
=
hdr
+
scan_size
*
particle_size
;
for
(
i
=
1
;
i
<
9
;
i
++
)
{
chunkOffset
[
i
]
=
chunkOffset
[
i
-
1
]
+
chunkCount
[
i
-
1
]
*
chunkSize
[
i
-
1
];
}
tp
.
Init
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
sub_comm
);
tp
.
setAggregationTier
(
NVR
,
"/scratch/tmp"
);
tp
.
setTargetTier
(
HDD
,
file_size
,
output
);
/*****************/
start_time
=
MPI_Wtime
();
if
(
0
==
sub_myrank
)
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] Read output file
\n
"
,
mycolor
);
offset
=
scan_size
*
particle_size
;
tp
.
Read
(
offset
,
xx_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
yy_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
zz_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
vx_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
vy_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
vz_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
phi_r
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Read
(
offset
,
pid_r
,
num_particles
,
MPI_LONG_LONG
,
&
status
);
offset
+=
num_particles
*
sizeof
(
int64_t
);
tp
.
Read
(
offset
,
mask_r
,
num_particles
,
MPI_UNSIGNED_SHORT
,
&
status
);
tp
.
Finalize
();
end_time
=
MPI_Wtime
();
tot_time
=
end_time
-
start_time
;
MPI_Reduce
(
&
tot_time
,
&
max_time
,
1
,
MPI_DOUBLE
,
MPI_MAX
,
0
,
MPI_COMM_WORLD
);
if
(
0
==
world_myrank
)
{
io_bw
=
(
double
)
tot_size
/
max_time
/
(
1024
*
1024
);
fprintf
(
stdout
,
BLUE
"[TIMING]"
RESET
" Read I/O bandwidth: %.2f MBps (%.2f MB in %.2f ms)
\n
"
,
io_bw
,
(
double
)
tot_size
/
(
1024
*
1024
),
max_time
*
1000
);
}
/*****************/
/* VERIFICATION */
/*****************/
for
(
uint64_t
i
=
0
;
i
<
num_particles
;
i
++
)
{
if
((
xx
[
i
]
!=
xx_r
[
i
])
||
(
yy
[
i
]
!=
yy_r
[
i
])
||
(
zz
[
i
]
!=
zz_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
]))
{
fprintf
(
stdout
,
RED
"[ERROR]"
RESET
" Wrong value for particle %d
\n
"
,
i
);
MPI_Abort
(
MPI_COMM_WORLD
,
-
1
);
}
}
if
(
0
==
sub_myrank
)
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] Content verified and consistent
\n
"
,
mycolor
);
/*****************/
/* FREE */
/*****************/
delete
[]
xx
;
delete
[]
xx_r
;
delete
[]
yy
;
delete
[]
yy_r
;
delete
[]
zz
;
delete
[]
zz_r
;
delete
[]
vx
;
delete
[]
vx_r
;
delete
[]
vy
;
delete
[]
vy_r
;
delete
[]
vz
;
delete
[]
vz_r
;
delete
[]
phi
;
delete
[]
phi_r
;
delete
[]
pid
;
delete
[]
pid_r
;
delete
[]
mask
;
delete
[]
mask_r
;
MPI_Finalize
();
}
examples/HACC-IO/miniHACC-AoS-W.cpp
0 → 100644
View file @
ab7405a1
#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
#include <stdint.h>
#include <mpi.h>
#include "tapioca.hpp"
#define RED "\x1b[31m"
#define GREEN "\x1b[32m"
#define BLUE "\x1b[34m"
#define RESET "\x1b[0m"
int
main
(
int
argc
,
char
*
argv
[])
{
int
world_numtasks
,
world_myrank
,
mycolor
,
mykey
,
sub_numtasks
,
sub_myrank
,
i
,
file_id
;
int64_t
num_particles
;
int64_t
sub_particles
,
tot_particles
,
particle_size
,
file_size
,
tot_size
;
int64_t
scan_size
=
0
,
offset
,
hdr
=
0
;
double
start_time
,
end_time
,
tot_time
,
max_time
;
double
io_bw
;
MPI_Comm
sub_comm
;
MPI_Status
status
;
char
output
[
100
];
Tapioca
tp
,
tp2
;
int64_t
chunkCount
[
9
],
chunkOffset
[
9
];
int
chunkSize
[
9
];
MPI_Init
(
&
argc
,
&
argv
);
MPI_Comm_size
(
MPI_COMM_WORLD
,
&
world_numtasks
);
MPI_Comm_rank
(
MPI_COMM_WORLD
,
&
world_myrank
);
mycolor
=
tp
.
topology
.
BridgeNodeId
();
//mycolor = 42;
mykey
=
world_myrank
;
MPI_Comm_split
(
MPI_COMM_WORLD
,
mycolor
,
mykey
,
&
sub_comm
);
MPI_Comm_size
(
sub_comm
,
&
sub_numtasks
);
MPI_Comm_rank
(
sub_comm
,
&
sub_myrank
);
num_particles
=
atoi
(
argv
[
1
]
);
file_id
=
0
;
if
(
argv
[
2
]
!=
NULL
)
file_id
=
atoi
(
argv
[
2
]
);
#ifdef BGQ
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-SOA-%08d-%d.dat"
,
mycolor
,
file_id
);
#elif XC40
snprintf
(
output
,
100
,
"/lus/theta-fs0/projects/Performance/ftessier/HACC/HACC-AOS-%08d-%d.dat"
,
mycolor
,
file_id
);
#else
snprintf
(
output
,
100
,
"./HACC-SOA-%08d-%d.dat"
,
mycolor
,
file_id
);
#endif
/*****************/
/* WRITE */
/*****************/
float
*
xx
,
*
yy
,
*
zz
,
*
vx
,
*
vy
,
*
vz
,
*
phi
;
int64_t
*
pid
;
uint16_t
*
mask
;
xx
=
new
float
[
num_particles
];
yy
=
new
float
[
num_particles
];
zz
=
new
float
[
num_particles
];
vx
=
new
float
[
num_particles
];
vy
=
new
float
[
num_particles
];
vz
=
new
float
[
num_particles
];
phi
=
new
float
[
num_particles
];
pid
=
new
int64_t
[
num_particles
];
mask
=
new
uint16_t
[
num_particles
];
for
(
uint64_t
i
=
0
;
i
<
num_particles
;
i
++
)
{
xx
[
i
]
=
(
float
)
i
;
yy
[
i
]
=
(
float
)
i
;
zz
[
i
]
=
(
float
)
i
;
vx
[
i
]
=
(
float
)
i
;
vy
[
i
]
=
(
float
)
i
;
vz
[
i
]
=
(
float
)
i
;
phi
[
i
]
=
(
float
)
i
;
pid
[
i
]
=
(
int64_t
)
i
;
mask
[
i
]
=
(
uint16_t
)
world_myrank
;
}
MPI_Allreduce
(
&
num_particles
,
&
sub_particles
,
1
,
MPI_LONG_LONG
,
MPI_SUM
,
sub_comm
);
MPI_Allreduce
(
&
num_particles
,
&
tot_particles
,
1
,
MPI_LONG_LONG
,
MPI_SUM
,
MPI_COMM_WORLD
);
particle_size
=
(
7
*
sizeof
(
float
))
+
sizeof
(
int64_t
)
+
sizeof
(
uint16_t
);
file_size
=
particle_size
*
sub_particles
;
tot_size
=
particle_size
*
tot_particles
;
// if (sub_myrank == 0) {
// MPI_File_open(MPI_COMM_SELF, output,
// MPI_MODE_WRONLY | MPI_MODE_CREATE, MPI_INFO_NULL, &file_handle);
// MPI_File_set_size(file_handle, file_size);
// MPI_File_close (&file_handle);
// }
MPI_Exscan
(
&
num_particles
,
&
scan_size
,
1
,
MPI_LONG_LONG
,
MPI_SUM
,
sub_comm
);
if
(
0
==
sub_myrank
)
{
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] miniHACC-AoS
\n
"
,
mycolor
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] Write output file (AoS data layout)
\n
"
,
mycolor
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] --> %lld particles per rank
\n
"
,
mycolor
,
num_particles
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] --> File size: %.2f MB (%lld particles)
\n
"
,
mycolor
,
(
double
)
file_size
/
(
1024
*
1024
),
sub_particles
);
}
/*****************/
/* INIT TAPIOCA */
/*****************/
for
(
i
=
0
;
i
<
9
;
i
++
)
{
chunkCount
[
i
]
=
num_particles
;
}
chunkSize
[
0
]
=
sizeof
(
float
);
chunkSize
[
1
]
=
sizeof
(
float
);
chunkSize
[
2
]
=
sizeof
(
float
);
chunkSize
[
3
]
=
sizeof
(
float
);
chunkSize
[
4
]
=
sizeof
(
float
);
chunkSize
[
5
]
=
sizeof
(
float
);
chunkSize
[
6
]
=
sizeof
(
float
);
chunkSize
[
7
]
=
sizeof
(
int64_t
);
chunkSize
[
8
]
=
sizeof
(
uint16_t
);
chunkOffset
[
0
]
=
hdr
+
scan_size
*
particle_size
;
for
(
i
=
1
;
i
<
9
;
i
++
)
{
chunkOffset
[
i
]
=
chunkOffset
[
i
-
1
]
+
chunkCount
[
i
-
1
]
*
chunkSize
[
i
-
1
];
}
tp
.
Init
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
sub_comm
);
tp
.
setAggregationTier
(
NVR
,
"/scratch/tmp"
);
tp
.
setTargetTier
(
HDD
,
file_size
,
output
);
/*****************/
start_time
=
MPI_Wtime
();
offset
=
scan_size
*
particle_size
;
tp
.
Write
(
offset
,
xx
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Write
(
offset
,
yy
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Write
(
offset
,
zz
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Write
(
offset
,
vx
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Write
(
offset
,
vy
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Write
(
offset
,
vz
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Write
(
offset
,
phi
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Write
(
offset
,
pid
,
num_particles
,
MPI_LONG_LONG
,
&
status
);
offset
+=
num_particles
*
sizeof
(
int64_t
);
tp
.
Write
(
offset
,
mask
,
num_particles
,
MPI_UNSIGNED_SHORT
,
&
status
);
tp
.
Finalize
();
end_time
=
MPI_Wtime
();
tot_time
=
end_time
-
start_time
;
MPI_Reduce
(
&
tot_time
,
&
max_time
,
1
,
MPI_DOUBLE
,
MPI_MAX
,
0
,
MPI_COMM_WORLD
);
if
(
0
==
world_myrank
)
{
io_bw
=
(
double
)
tot_size
/
max_time
/
(
1024
*
1024
);
fprintf
(
stdout
,
BLUE
"[TIMING]"
RESET
" Write I/O bandwidth: %.2f MBps (%.2f MB in %.2f ms)
\n
"
,
io_bw
,
(
double
)
tot_size
/
(
1024
*
1024
),
max_time
*
1000
);
}
MPI_Barrier
(
MPI_COMM_WORLD
);
/*****************/
/* FREE */
/*****************/
delete
[]
xx
;
delete
[]
yy
;
delete
[]
zz
;
delete
[]
vx
;
delete
[]
vy
;
delete
[]
vz
;
delete
[]
phi
;
delete
[]
pid
;
delete
[]
mask
;
MPI_Finalize
();
}
Write
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