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Francois Tessier
TAPIOCA
Commits
e179f1a6
Commit
e179f1a6
authored
Mar 01, 2017
by
Francois Tessier
Browse files
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Resolve conflict
parents
dcf8cf1b
b4b1015a
Changes
5
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Showing
5 changed files
with
113 additions
and
33 deletions
+113
-33
miniHACC-AoS.cpp
examples/miniHACC-AoS.cpp
+11
-11
miniHACC-SoA.cpp
examples/miniHACC-SoA.cpp
+14
-12
tapioca.cpp
tapioca.cpp
+77
-6
tapioca.hpp
tapioca.hpp
+10
-3
topology.hpp
topology/topology.hpp
+1
-1
No files found.
examples/miniHACC-AoS.cpp
View file @
e179f1a6
...
...
@@ -38,7 +38,7 @@ int main (int argc, char * argv[])
MPI_Comm_size
(
sub_comm
,
&
sub_numtasks
);
MPI_Comm_rank
(
sub_comm
,
&
sub_myrank
);
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-AOS-%08d
.dat"
,
mycolor
);
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-AOS-%08d
-%d.dat"
,
mycolor
,
atoi
(
argv
[
1
])
);
/*****************/
/* WRITE */
...
...
@@ -116,7 +116,7 @@ int main (int argc, char * argv[])
chunkOffset
[
i
]
=
chunkOffset
[
i
-
1
]
+
chunkCount
[
i
-
1
]
*
chunkSize
[
i
-
1
];
}
tp
.
Initialize
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
ARRAY_OF_STRUCTURES
,
sub_comm
);
tp
.
Write
Initialize
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
ARRAY_OF_STRUCTURES
,
sub_comm
);
/*****************/
start_time
=
MPI_Wtime
();
...
...
@@ -126,31 +126,31 @@ int main (int argc, char * argv[])
offset
=
scan_size
*
particle_size
;
tp
.
Commit
(
file_handle
,
offset
,
xx
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
xx
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
yy
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
yy
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
zz
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
zz
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
vx
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
vx
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
vy
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
vy
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
vz
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
vz
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
phi
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
phi
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
num_particles
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
pid
,
num_particles
,
MPI_LONG_LONG
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
pid
,
num_particles
,
MPI_LONG_LONG
,
&
status
);
offset
+=
num_particles
*
sizeof
(
int64_t
);
tp
.
Commit
(
file_handle
,
offset
,
mask
,
num_particles
,
MPI_UNSIGNED_SHORT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
mask
,
num_particles
,
MPI_UNSIGNED_SHORT
,
&
status
);
MPI_File_close
(
&
file_handle
);
...
...
examples/miniHACC-SoA.cpp
View file @
e179f1a6
...
...
@@ -14,7 +14,7 @@
int
main
(
int
argc
,
char
*
argv
[])
{
int
world_numtasks
,
world_myrank
,
mycolor
,
mykey
,
sub_numtasks
,
sub_myrank
,
i
;
int64_t
num_particles
=
25000
;
int64_t
num_particles
=
atoi
(
argv
[
2
])
;
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
;
...
...
@@ -32,13 +32,14 @@ int main (int argc, char * argv[])
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
);
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-SOA-%08d
.dat"
,
mycolor
);
snprintf
(
output
,
100
,
"/projects/visualization/ftessier/debug/HACC-SOA-%08d
-%d.dat"
,
mycolor
,
atoi
(
argv
[
1
])
);
/*****************/
/* WRITE */
...
...
@@ -90,6 +91,7 @@ int main (int argc, char * argv[])
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] miniHACC-SoA
\n
"
,
mycolor
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] Write output file (SoA data layout)
\n
"
,
mycolor
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] --> %lld particles per rank
\n
"
,
mycolor
,
num_particles
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] --> %d ranks, %d nodes
\n
"
,
mycolor
,
sub_numtasks
,
sub_numtasks
/
16
);
fprintf
(
stdout
,
GREEN
"[INFO]"
RESET
" [%08d] --> File size: %.2f MB (%lld particles)
\n
"
,
mycolor
,
(
double
)
file_size
/
(
1024
*
1024
),
sub_particles
);
}
...
...
@@ -118,7 +120,7 @@ int main (int argc, char * argv[])
chunkOffset
[
i
]
+=
scan_size
*
chunkSize
[
i
];
}
tp
.
Initialize
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
STRUCTURE_OF_ARRAYS
,
sub_comm
);
tp
.
Write
Initialize
(
chunkCount
,
chunkSize
,
chunkOffset
,
9
,
hdr
,
STRUCTURE_OF_ARRAYS
,
sub_comm
);
/*****************/
start_time
=
MPI_Wtime
();
...
...
@@ -128,31 +130,31 @@ int main (int argc, char * argv[])
offset
=
scan_size
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
xx
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
xx
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
(
sub_particles
-
scan_size
)
*
sizeof
(
float
)
+
scan_size
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
yy
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
yy
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
(
sub_particles
-
scan_size
)
*
sizeof
(
float
)
+
scan_size
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
zz
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
zz
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
(
sub_particles
-
scan_size
)
*
sizeof
(
float
)
+
scan_size
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
vx
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
vx
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
(
sub_particles
-
scan_size
)
*
sizeof
(
float
)
+
scan_size
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
vy
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
vy
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
(
sub_particles
-
scan_size
)
*
sizeof
(
float
)
+
scan_size
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
vz
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
vz
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
(
sub_particles
-
scan_size
)
*
sizeof
(
float
)
+
scan_size
*
sizeof
(
float
);
tp
.
Commit
(
file_handle
,
offset
,
phi
,
num_particles
,
MPI_FLOAT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
phi
,
num_particles
,
MPI_FLOAT
,
&
status
);
offset
+=
(
sub_particles
-
scan_size
)
*
sizeof
(
float
)
+
scan_size
*
sizeof
(
int64_t
);
tp
.
Commit
(
file_handle
,
offset
,
pid
,
num_particles
,
MPI_LONG_LONG
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
pid
,
num_particles
,
MPI_LONG_LONG
,
&
status
);
offset
+=
(
sub_particles
-
scan_size
)
*
sizeof
(
int64_t
)
+
scan_size
*
sizeof
(
uint16_t
);
tp
.
Commit
(
file_handle
,
offset
,
mask
,
num_particles
,
MPI_UNSIGNED_SHORT
,
&
status
);
tp
.
Write
(
file_handle
,
offset
,
mask
,
num_particles
,
MPI_UNSIGNED_SHORT
,
&
status
);
MPI_File_close
(
&
file_handle
);
...
...
tapioca.cpp
View file @
e179f1a6
...
...
@@ -12,7 +12,7 @@ Tapioca::~Tapioca ()
}
void
Tapioca
::
Initialize
(
int64_t
*
chunkCount
,
int
*
chunkSize
,
int64_t
*
chunkOffset
,
void
Tapioca
::
Write
Initialize
(
int64_t
*
chunkCount
,
int
*
chunkSize
,
int64_t
*
chunkOffset
,
int
nChunks
,
int64_t
offset
,
MEMORY_LAYOUT
layout
,
MPI_Comm
comm
)
{
int
chunk
;
...
...
@@ -79,20 +79,88 @@ void Tapioca::Initialize (int64_t *chunkCount, int *chunkSize, int64_t *chunkOff
}
void
Tapioca
::
Finalize
()
void
Tapioca
::
ReadInitialize
(
int64_t
*
chunkCount
,
int
*
chunkSize
,
int64_t
*
chunkOffset
,
int
nChunks
,
int64_t
offset
,
MEMORY_LAYOUT
layout
,
MPI_Comm
comm
)
{
int
chunk
;
#ifdef TIMING
double
startInitTime
,
endInitTime
,
startElectTime
,
endElectTime
;
startInitTime
=
MPI_Wtime
();
#endif
this
->
nChunks_
=
nChunks
;
this
->
chunksIndexMatching
.
resize
(
this
->
nChunks_
);
this
->
chunkCount_
=
(
int64_t
*
)
malloc
(
this
->
nChunks_
*
sizeof
(
int64_t
));
this
->
chunkSize_
=
(
int
*
)
malloc
(
this
->
nChunks_
*
sizeof
(
int
));
this
->
chunkOffset_
=
(
int64_t
*
)
malloc
(
this
->
nChunks_
*
sizeof
(
int64_t
));
memcpy
(
this
->
chunkCount_
,
chunkCount
,
this
->
nChunks_
*
sizeof
(
int64_t
));
memcpy
(
this
->
chunkSize_
,
chunkSize
,
this
->
nChunks_
*
sizeof
(
int
));
memcpy
(
this
->
chunkOffset_
,
chunkOffset
,
this
->
nChunks_
*
sizeof
(
int64_t
));
for
(
chunk
=
0
;
chunk
<
this
->
nChunks_
;
chunk
++
)
this
->
rankDataSize_
+=
this
->
chunkCount_
[
chunk
]
*
this
->
chunkSize_
[
chunk
];
this
->
offsetInFile_
=
offset
;
this
->
layout_
=
layout
;
MPI_Comm_dup
(
comm
,
&
this
->
subComm_
);
this
->
SetCommValues
();
this
->
SetOffsets
();
#ifdef DEBUG
if
(
this
->
commRank_
==
MASTER
)
{
fprintf
(
stdout
,
"[DEBUG] #Aggr = %d
\n
"
,
this
->
nAggr_
);
fprintf
(
stdout
,
"[DEBUG] bufferSize = %lld
\n
"
,
this
->
bufferSize_
);
fprintf
(
stdout
,
"[DEBUG] commDataSize = %lld
\n
"
,
this
->
commDataSize_
);
fprintf
(
stdout
,
"[DEBUG] strategy = %s
\n
"
,
this
->
getStrategyName
());
}
#endif
this
->
SetNodesList
();
//this->IdentifyMyAggregators ();
#ifdef TIMING
startElectTime
=
MPI_Wtime
();
#endif
//this->ElectAggregators ();
#ifdef TIMING
endElectTime
=
MPI_Wtime
();
#endif
this
->
InitAggregators
();
#ifdef TIMING
endInitTime
=
MPI_Wtime
();
this
->
PrintTime
(
startInitTime
,
endInitTime
,
"Initialize"
);
this
->
PrintTime
(
startElectTime
,
endElectTime
,
" |-> Elect aggregators"
);
#endif
}
void
Tapioca
::
Finalize
()
{
this
->
chunksIndexMatching
.
clear
();
free
(
this
->
chunkCount_
);
free
(
this
->
chunkSize_
);
free
(
this
->
chunkOffset_
);
this
->
excludedNode
.
clear
();
MPI_Win_free
(
&
this
->
RMAWin1
);
MPI_Win_free
(
&
this
->
RMAWin2
);
MPI_Comm_free
(
&
this
->
subComm_
);
free
(
this
->
buffer1
);
free
(
this
->
buffer2
);
}
int
Tapioca
::
Commit
(
MPI_File
fileHandle
,
MPI_Offset
offset
,
void
*
buf
,
int
count
,
MPI_Datatype
datatype
,
MPI_Status
*
status
,
int64_t
bufOffset
)
int
Tapioca
::
Write
(
MPI_File
fileHandle
,
MPI_Offset
offset
,
void
*
buf
,
int
count
,
MPI_Datatype
datatype
,
MPI_Status
*
status
,
int64_t
bufOffset
)
{
int
retval
,
i
,
c
,
targetRoundIdx
,
targetAggrIdx
,
targetGlobAggr
;
int
typeSize
,
targetAggr
,
win
,
buffer
;
...
...
@@ -184,8 +252,8 @@ int Tapioca::Commit (MPI_File fileHandle, MPI_Offset offset, void *buf,
}
if
(
multipleRounds
)
{
retval
=
this
->
Commit
(
fileHandle
,
offset
+
subChunkDataSize
,
buf
,
chunkDataSize
-
subChunkDataSize
,
MPI_BYTE
,
status
,
subChunkDataSize
);
retval
=
this
->
Write
(
fileHandle
,
offset
+
subChunkDataSize
,
buf
,
chunkDataSize
-
subChunkDataSize
,
MPI_BYTE
,
status
,
subChunkDataSize
);
}
else
{
this
->
nCommit_
++
;
...
...
@@ -411,6 +479,9 @@ void Tapioca::SetNodesList ()
for
(
i
=
0
;
i
<
worldSize
;
i
++
)
this
->
excludedNode
[
coords
[
i
]]
=
false
;
free
(
coords
);
free
(
myCoords
);
}
...
...
tapioca.hpp
View file @
e179f1a6
...
...
@@ -52,11 +52,18 @@ class Tapioca
Tapioca
();
~
Tapioca
();
void
Initialize
(
int64_t
*
chunkCount
,
int
*
chunkSize
,
int64_t
*
chunkOffset
,
int
nChunks
,
int64_t
offset
,
MEMORY_LAYOUT
layout
,
MPI_Comm
comm
);
int
Commit
(
MPI_File
fileHandle
,
MPI_Offset
offset
,
void
Write
Initialize
(
int64_t
*
chunkCount
,
int
*
chunkSize
,
int64_t
*
chunkOffset
,
int
nChunks
,
int64_t
offset
,
MEMORY_LAYOUT
layout
,
MPI_Comm
comm
);
int
Write
(
MPI_File
fileHandle
,
MPI_Offset
offset
,
void
*
buf
,
int
count
,
MPI_Datatype
datatype
,
MPI_Status
*
status
,
int64_t
bufOffset
=
0
);
void
ReadInitialize
(
int64_t
*
chunkCount
,
int
*
chunkSize
,
int64_t
*
chunkOffset
,
int
nChunks
,
int64_t
offset
,
MEMORY_LAYOUT
layout
,
MPI_Comm
comm
);
int
Read
(
MPI_File
fileHandle
,
MPI_Offset
offset
,
void
*
buf
,
int
count
,
MPI_Datatype
datatype
,
MPI_Status
*
status
,
int64_t
bufOffset
=
0
);
void
Finalize
();
void
MPIIOInfo
(
MPI_File
fileHandle
);
...
...
topology/topology.hpp
View file @
e179f1a6
...
...
@@ -11,7 +11,7 @@ class iTopology {
/**********************/
virtual
int
IONodeId
()
=
0
;
virtual
int
BridgeNodeId
()
=
0
;
virtual
int
ComputeNodeId
()
=
0
;
//
virtual int ComputeNodeId () = 0;
virtual
int
ProcessPerNode
()
=
0
;
/**********************/
...
...
Write
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