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Francois Tessier
TAPIOCA
Commits
69b6efc9
Commit
69b6efc9
authored
Apr 24, 2017
by
Francois Tessier
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Merge branch 'master' of xgitlab.cels.anl.gov:ftessier/TAPIOCA
parents
4f113485
326c774e
Changes
3
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3 changed files
with
419 additions
and
274 deletions
+419
-274
tapioca.cpp
tapioca.cpp
+2
-274
tp_read.cpp
tp_read.cpp
+206
-0
tp_write.cpp
tp_write.cpp
+211
-0
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tapioca.cpp
View file @
69b6efc9
...
...
@@ -12,137 +12,6 @@ Tapioca::~Tapioca ()
}
void
Tapioca
::
WriteInitialize
(
char
*
filename
,
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
->
filename_
=
filename
;
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
();
if
(
this
->
writeDevNull_
)
MPI_File_open
(
MPI_COMM_SELF
,
"/dev/null"
,
MPI_MODE_WRONLY
|
MPI_MODE_CREATE
,
MPI_INFO_NULL
,
&
this
->
devNullFileHandle_
);
#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
::
ReadInitialize
(
char
*
filename
,
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
->
filename_
=
filename
;
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
();
...
...
@@ -151,6 +20,8 @@ void Tapioca::Finalize ()
free
(
this
->
chunkOffset_
);
this
->
excludedNode
.
clear
();
this
->
commDataSize_
=
0
;
MPI_Win_free
(
&
this
->
RMAWin1
);
MPI_Win_free
(
&
this
->
RMAWin2
);
...
...
@@ -161,149 +32,6 @@ void Tapioca::Finalize ()
}
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
;
bool
multipleRounds
=
false
;
int64_t
chunkDataSize
,
subChunkDataSize
,
cumulDataSize
=
0
,
cumulDataSizeInRound
;
int64_t
winOffset
=
0
,
rankDataOffset
,
offsetInAggrData
;
MPI_Request
request
=
NULL
;
MPI_Type_size
(
datatype
,
&
typeSize
);
c
=
this
->
nCommit_
;
chunkDataSize
=
count
*
typeSize
;
subChunkDataSize
=
chunkDataSize
;
offsetInAggrData
=
offset
-
this
->
offsetInFile_
;
winOffset
=
offsetInAggrData
%
this
->
bufferSize_
;
targetRoundIdx
=
(
*
this
->
chunksIndexMatching
[
c
].
begin
());
targetAggrIdx
=
(
*
this
->
chunksIndexMatching
[
c
].
begin
());
if
(
this
->
chunksIndexMatching
[
c
].
size
()
>
1
)
{
multipleRounds
=
true
;
subChunkDataSize
=
this
->
dataSize
[
targetRoundIdx
];
this
->
chunksIndexMatching
[
c
].
erase
(
this
->
chunksIndexMatching
[
c
].
begin
()
);
}
/*
* Wait if it's not the appropriate round
*/
while
(
this
->
roundsIds
[
targetRoundIdx
]
>
this
->
currentRound_
)
{
this
->
GlobalFence
();
if
(
this
->
amAnAggr_
)
{
if
(
request
!=
NULL
)
MPI_Wait
(
&
request
,
status
);
this
->
Push
(
fileHandle
,
&
request
);
}
this
->
currentRound_
++
;
}
#ifdef TIMING
this
->
startAggrTime
=
MPI_Wtime
();
#endif
buffer
=
this
->
currentRound_
%
NBUFFERS
;
targetGlobAggr
=
this
->
globalAggregatorsRanks
[
targetAggrIdx
];
targetAggr
=
this
->
aggregatorsRanks
[
targetAggrIdx
];
switch
(
buffer
)
{
case
0
:
retval
=
MPI_Put
(
static_cast
<
char
*>
(
buf
)
+
bufOffset
,
subChunkDataSize
,
MPI_BYTE
,
targetAggr
,
winOffset
,
subChunkDataSize
,
MPI_BYTE
,
this
->
RMAWin1
);
this
->
HandleMPIError
(
retval
);
break
;
case
1
:
retval
=
MPI_Put
(
static_cast
<
char
*>
(
buf
)
+
bufOffset
,
subChunkDataSize
,
MPI_BYTE
,
targetAggr
,
winOffset
,
subChunkDataSize
,
MPI_BYTE
,
this
->
RMAWin2
);
this
->
HandleMPIError
(
retval
);
break
;
}
this
->
currentDataSize_
+=
subChunkDataSize
;
/*
* If all the data have been written, wait
*/
if
(
this
->
currentDataSize_
==
this
->
rankDataSize_
)
{
while
(
this
->
currentRound_
<
this
->
totalRounds_
)
{
this
->
GlobalFence
();
if
(
this
->
amAnAggr_
)
{
if
(
request
!=
NULL
)
MPI_Wait
(
&
request
,
status
);
this
->
Push
(
fileHandle
,
&
request
);
}
this
->
currentRound_
++
;
}
}
if
(
multipleRounds
)
{
retval
=
this
->
Write
(
fileHandle
,
offset
+
subChunkDataSize
,
buf
,
chunkDataSize
-
subChunkDataSize
,
MPI_BYTE
,
status
,
subChunkDataSize
);
}
else
{
this
->
nCommit_
++
;
}
if
(
request
!=
NULL
)
MPI_Wait
(
&
request
,
status
);
return
retval
;
}
void
Tapioca
::
Push
(
MPI_File
fileHandle
,
MPI_Request
*
request
)
{
int64_t
offset
,
dataSize
;
int
win
,
buffer
;
buffer
=
this
->
currentRound_
%
NBUFFERS
;
if
(
this
->
amAnAggr_
)
{
#ifdef TIMING
this
->
startIOTime
=
MPI_Wtime
();
#endif
offset
=
(
this
->
nAggr_
*
this
->
currentRound_
+
this
->
globalAggrRank_
)
*
this
->
bufferSize_
;
offset
+=
this
->
offsetInFile_
;
dataSize
=
this
->
bufferSize_
;
if
(
this
->
aggrDataSize_
<
this
->
bufferSize_
)
dataSize
=
this
->
aggrDataSize_
;
switch
(
buffer
)
{
case
0
:
if
(
this
->
writeDevNull_
)
MPI_File_iwrite_at
(
this
->
devNullFileHandle_
,
0
,
buffer1
,
dataSize
,
MPI_BYTE
,
request
);
else
MPI_File_iwrite_at
(
fileHandle
,
offset
,
buffer1
,
dataSize
,
MPI_BYTE
,
request
);
break
;
case
1
:
if
(
this
->
writeDevNull_
)
MPI_File_iwrite_at
(
this
->
devNullFileHandle_
,
0
,
buffer2
,
dataSize
,
MPI_BYTE
,
request
);
else
MPI_File_iwrite_at
(
fileHandle
,
offset
,
buffer2
,
dataSize
,
MPI_BYTE
,
request
);
break
;
}
this
->
aggrDataSize_
-=
dataSize
;
#ifdef TIMING
this
->
endIOTime
=
MPI_Wtime
();
this
->
totIOTime
=
this
->
endIOTime
-
this
->
startIOTime
;
if
(
dataSize
>
0
)
fprintf
(
stdout
,
"[TIMING][AGG][IO] Agg. %d, Rnd %d - %.2f ms
\n
"
,
this
->
commRank_
,
this
->
currentRound_
,
this
->
totIOTime
*
1000
);
#endif
}
}
void
Tapioca
::
GlobalFence
()
{
int
buffer
;
...
...
tp_read.cpp
0 → 100644
View file @
69b6efc9
#include "tapioca.hpp"
void
Tapioca
::
ReadInitialize
(
char
*
filename
,
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
->
filename_
=
filename
;
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
}
int
Tapioca
::
Read
(
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
;
bool
multipleRounds
=
false
;
int64_t
chunkDataSize
,
subChunkDataSize
,
cumulDataSize
=
0
,
cumulDataSizeInRound
;
int64_t
winOffset
=
0
,
rankDataOffset
,
offsetInAggrData
;
MPI_Request
request
=
NULL
;
MPI_Type_size
(
datatype
,
&
typeSize
);
c
=
this
->
nCommit_
;
chunkDataSize
=
count
*
typeSize
;
subChunkDataSize
=
chunkDataSize
;
offsetInAggrData
=
offset
-
this
->
offsetInFile_
;
winOffset
=
offsetInAggrData
%
this
->
bufferSize_
;
targetRoundIdx
=
(
*
this
->
chunksIndexMatching
[
c
].
begin
());
targetAggrIdx
=
(
*
this
->
chunksIndexMatching
[
c
].
begin
());
if
(
this
->
chunksIndexMatching
[
c
].
size
()
>
1
)
{
multipleRounds
=
true
;
subChunkDataSize
=
this
->
dataSize
[
targetRoundIdx
];
this
->
chunksIndexMatching
[
c
].
erase
(
this
->
chunksIndexMatching
[
c
].
begin
()
);
}
/*
* Wait if it's not the appropriate round
*/
while
(
this
->
roundsIds
[
targetRoundIdx
]
>
this
->
currentRound_
)
{
this
->
GlobalFence
();
if
(
this
->
amAnAggr_
)
{
if
(
request
!=
NULL
)
MPI_Wait
(
&
request
,
status
);
this
->
Push
(
fileHandle
,
&
request
);
}
this
->
currentRound_
++
;
}
#ifdef TIMING
this
->
startAggrTime
=
MPI_Wtime
();
#endif
buffer
=
this
->
currentRound_
%
NBUFFERS
;
targetGlobAggr
=
this
->
globalAggregatorsRanks
[
targetAggrIdx
];
targetAggr
=
this
->
aggregatorsRanks
[
targetAggrIdx
];
switch
(
buffer
)
{
case
0
:
retval
=
MPI_Put
(
static_cast
<
char
*>
(
buf
)
+
bufOffset
,
subChunkDataSize
,
MPI_BYTE
,
targetAggr
,
winOffset
,
subChunkDataSize
,
MPI_BYTE
,
this
->
RMAWin1
);
this
->
HandleMPIError
(
retval
);
break
;
case
1
:
retval
=
MPI_Put
(
static_cast
<
char
*>
(
buf
)
+
bufOffset
,
subChunkDataSize
,
MPI_BYTE
,
targetAggr
,
winOffset
,
subChunkDataSize
,
MPI_BYTE
,
this
->
RMAWin2
);
this
->
HandleMPIError
(
retval
);
break
;
}
this
->
currentDataSize_
+=
subChunkDataSize
;
/*
* If all the data have been written, wait
*/
if
(
this
->
currentDataSize_
==
this
->
rankDataSize_
)
{
while
(
this
->
currentRound_
<
this
->
totalRounds_
)
{
this
->
GlobalFence
();
if
(
this
->
amAnAggr_
)
{
if
(
request
!=
NULL
)
MPI_Wait
(
&
request
,
status
);
this
->
Push
(
fileHandle
,
&
request
);
}
this
->
currentRound_
++
;
}
}
if
(
multipleRounds
)
{
retval
=
this
->
Write
(
fileHandle
,
offset
+
subChunkDataSize
,
buf
,
chunkDataSize
-
subChunkDataSize
,
MPI_BYTE
,
status
,
subChunkDataSize
);
}
else
{
this
->
nCommit_
++
;
}
if
(
request
!=
NULL
)
MPI_Wait
(
&
request
,
status
);
return
retval
;
}
void
Tapioca
::
Push
(
MPI_File
fileHandle
,
MPI_Request
*
request
)
{
int64_t
offset
,
dataSize
;
int
win
,
buffer
;
buffer
=
this
->
currentRound_
%
NBUFFERS
;
if
(
this
->
amAnAggr_
)
{
#ifdef TIMING
this
->
startIOTime
=
MPI_Wtime
();
#endif
offset
=
(
this
->
nAggr_
*
this
->
currentRound_
+
this
->
globalAggrRank_
)
*
this
->
bufferSize_
;
offset
+=
this
->
offsetInFile_
;
dataSize
=
this
->
bufferSize_
;
if
(
this
->
aggrDataSize_
<
this
->
bufferSize_
)
dataSize
=
this
->
aggrDataSize_
;
switch
(
buffer
)
{
case
0
:
if
(
this
->
writeDevNull_
)
MPI_File_iwrite_at
(
this
->
devNullFileHandle_
,
0
,
buffer1
,
dataSize
,
MPI_BYTE
,
request
);
else
MPI_File_iwrite_at
(
fileHandle
,
offset
,
buffer1
,
dataSize
,
MPI_BYTE
,
request
);
break
;
case
1
:
if
(
this
->
writeDevNull_
)
MPI_File_iwrite_at
(
this
->
devNullFileHandle_
,
0
,
buffer2
,
dataSize
,
MPI_BYTE
,
request
);
else
MPI_File_iwrite_at
(
fileHandle
,
offset
,
buffer2
,
dataSize
,
MPI_BYTE
,
request
);
break
;
}
this
->
aggrDataSize_
-=
dataSize
;
#ifdef TIMING
this
->
endIOTime
=
MPI_Wtime
();
this
->
totIOTime
=
this
->
endIOTime
-
this
->
startIOTime
;
if
(
dataSize
>
0
)
fprintf
(
stdout
,
"[TIMING][AGG][IO] Agg. %d, Rnd %d - %.2f ms
\n
"
,
this
->
commRank_
,
this
->
currentRound_
,
this
->
totIOTime
*
1000
);
#endif
}
}
tp_write.cpp
0 → 100644
View file @
69b6efc9
#include "tapioca.hpp"
void
Tapioca
::
WriteInitialize
(
char
*
filename
,
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
->
filename_
=
filename
;
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
();
if
(
this
->
writeDevNull_
)
MPI_File_open
(
MPI_COMM_SELF
,
"/dev/null"
,
MPI_MODE_WRONLY
|
MPI_MODE_CREATE
,
MPI_INFO_NULL
,
&
this
->
devNullFileHandle_
);
#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
}
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
;
bool
multipleRounds
=
false
;
int64_t
chunkDataSize
,
subChunkDataSize
,
cumulDataSize
=
0
,
cumulDataSizeInRound
;
int64_t
winOffset
=
0
,
rankDataOffset
,
offsetInAggrData
;
MPI_Request
request
=
NULL
;
MPI_Type_size
(
datatype
,
&
typeSize
);
c
=
this
->
nCommit_
;
chunkDataSize
=
count
*
typeSize
;
subChunkDataSize
=
chunkDataSize
;
offsetInAggrData
=
offset
-
this
->
offsetInFile_
;
winOffset
=
offsetInAggrData
%
this
->
bufferSize_
;
targetRoundIdx
=
(
*
this
->
chunksIndexMatching
[
c
].
begin
());
targetAggrIdx
=
(
*
this
->
chunksIndexMatching
[
c
].
begin
());
if
(
this
->
chunksIndexMatching
[
c
].
size
()
>
1
)
{
multipleRounds
=
true
;
subChunkDataSize
=
this
->
dataSize
[
targetRoundIdx
];
this
->
chunksIndexMatching
[
c
].
erase
(
this
->
chunksIndexMatching
[
c
].
begin
()
);
}
/*
* Wait if it's not the appropriate round
*/
while
(
this
->
roundsIds
[
targetRoundIdx
]
>
this
->
currentRound_
)
{
this
->
GlobalFence
();
if
(
this
->
amAnAggr_
)
{
if
(
request
!=
NULL
)
MPI_Wait
(
&
request
,
status
);
this
->
Push
(
fileHandle
,
&
request
);
}
this
->
currentRound_
++
;
}
#ifdef TIMING
this
->
startAggrTime
=
MPI_Wtime
();
#endif
buffer
=
this
->
currentRound_
%
NBUFFERS
;
targetGlobAggr
=
this
->
globalAggregatorsRanks
[
targetAggrIdx
];
targetAggr
=
this
->
aggregatorsRanks
[
targetAggrIdx
];
switch
(
buffer
)
{
case
0
:
retval
=
MPI_Put
(
static_cast
<
char
*>
(
buf
)
+
bufOffset
,
subChunkDataSize
,
MPI_BYTE
,
targetAggr
,
winOffset
,
subChunkDataSize
,
MPI_BYTE
,
this
->
RMAWin1
);
this
->
HandleMPIError
(
retval
);
break
;
case
1
:
retval
=
MPI_Put
(
static_cast
<
char
*>
(
buf
)
+
bufOffset
,
subChunkDataSize
,
MPI_BYTE
,
targetAggr
,
winOffset
,
subChunkDataSize
,
MPI_BYTE
,
this
->
RMAWin2
);
this
->
HandleMPIError
(
retval
);
break
;
}
this
->
currentDataSize_
+=
subChunkDataSize
;
/*
* If all the data have been written, wait
*/
if
(
this
->
currentDataSize_
==
this
->
rankDataSize_
)
{
while
(
this
->
currentRound_
<
this
->
totalRounds_
)
{
this
->
GlobalFence
();
if
(
this
->
amAnAggr_
)
{
if
(
request
!=
NULL
)
MPI_Wait
(
&
request
,
status
);
this
->
Push
(
fileHandle
,
&
request
);
}
this
->
currentRound_
++
;
}
}
if
(
multipleRounds
)
{
retval
=
this
->
Write
(
fileHandle
,
offset
+
subChunkDataSize
,
buf
,
chunkDataSize
-
subChunkDataSize
,
MPI_BYTE
,
status
,
subChunkDataSize
);
}
else
{
this
->
nCommit_
++
;
}
if
(
request
!=
NULL
)
MPI_Wait
(
&
request
,
status
);
return
retval
;
}
void
Tapioca
::
Push
(
MPI_File
fileHandle
,
MPI_Request
*
request
)
{
int64_t
offset
,
dataSize
;
int
win
,
buffer
;
buffer
=
this
->
currentRound_
%
NBUFFERS
;
if
(
this
->
amAnAggr_
)
{
#ifdef TIMING
this
->
startIOTime
=
MPI_Wtime
();
#endif
offset
=
(
this
->
nAggr_
*
this
->
currentRound_
+
this
->
globalAggrRank_
)
*
this
->
bufferSize_
;
offset
+=
this
->
offsetInFile_
;
dataSize
=
this
->
bufferSize_
;
if
(
this
->
aggrDataSize_
<
this
->
bufferSize_
)
dataSize
=
this
->
aggrDataSize_
;
switch
(
buffer
)
{
case
0
:
if
(
this
->
writeDevNull_
)
MPI_File_iwrite_at
(
this
->
devNullFileHandle_
,
0
,
buffer1
,
dataSize
,
MPI_BYTE
,
request
);
else
MPI_File_iwrite_at
(
fileHandle
,
offset
,
buffer1
,
dataSize
,
MPI_BYTE
,
request
);
break
;
case
1
:
if
(
this
->
writeDevNull_
)
MPI_File_iwrite_at
(
this
->
devNullFileHandle_
,
0
,
buffer2
,
dataSize
,
MPI_BYTE
,
request
);
else
MPI_File_iwrite_at
(
fileHandle
,
offset
,
buffer2
,
dataSize
,
MPI_BYTE
,
request
);
break
;
}
this
->
aggrDataSize_
-=
dataSize
;
#ifdef TIMING
this
->
endIOTime
=
MPI_Wtime
();
this
->
totIOTime
=
this
->
endIOTime
-
this
->
startIOTime
;
if
(
dataSize
>
0
)
fprintf
(
stdout
,
"[TIMING][AGG][IO] Agg. %d, Rnd %d - %.2f ms
\n
"
,
this
->
commRank_
,
this
->
currentRound_
,
this
->
totIOTime
*
1000
);
#endif
}
}
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