Gus Correa wrote:
jody wrote:
Hi
I have noticed on my machine that a struct which i have defined as
typedef struct {
short iSpeciesID;
char sCapacityFile[SHORT_INPUT];
double adGParams[NUM_GPARAMS];
} tVStruct;
(where SHORT_INPUT=64 and NUM_GPARAMS=4)
has size 104 (instead of 98) whereas the corresponding MPI Datatype i
created
int aiLengthsT5[3] = {1, SHORT_INPUT, NUM_GPARAMS};
MPI_Aint aiDispsT5[3] = {0, iShortSize, iShortSize+SHORT_INPUT};
MPI_Datatype aTypesT5[3] = {MPI_UNSIGNED_SHORT, MPI_CHAR,
MPI_DOUBLE};
MPI_Type_create_struct(3, aiLengthsT5, aiDispsT5, aTypesT5,
&m_dtVegetationData3);
MPI_Type_commit(&m_dtVegetationData3);
only has length 98 (as expected). The size differences resulted in an
error when doing
tVegetationData3 VD;
MPI_Send(&VD, 1, m_dtVegetationData3, 1, TAG_STEP_CMD,
MPI_COMM_WORLD);
and the corresponding
tVegetationData3 VD;
MPI_Recv(&VD, 1, m_dtVegetationData3, MPI_ANY_SOURCE,
TAG_STEP_CMD, MPI_COMM_WORLD, &st);
(in fact, the last double in my array was not transmitted correctly)
It seems that on my machine the struct was padded to a multiple of 8.
By manually adding some padding bytes to my MPI Datatype in order
to fill it up to the next multiple of 8 i could work around this problem.
(not very nice, and very probably not portable)
My question: is there a way to tell MPI to automatically use the
required padding?
Thank You
Jody
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Hi Jody
My naive guesses:
I think when you create the MPI structure you can pass the
byte displacement of each structure component.
You would need to modify your aiDispsT5[3], to match the
actual memory alignment, I guess.
Yes, indeed portability may be sacrificed.
There is some clarification in "MPI, The Complete Reference, Vol 1,
2nd Ed, Marc Snir et al.".
Section 3.2 and 3.3 (general on type map & type signature).
Section 3.4.8 MPI_Type_create_struct (examples, specially 3.13).
Section 3.10, on portability, doesn't seem to guarantee portability of
MPI_Type_Struct.
I hope this helps,
Gus Correa
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Hi Jody
How about compiling the program with -fpack-struct ?
This is assuming you're using gcc.
Or use an equivalent flag if using another compiler.
I think in icc it is -noalign,
and pgcc may be -Mnodalign -Mnollalign.
See man gcc/icc/pgcc.
Code won't be optimal, compatible, etc,
which may be a price too high to pay to squeeze a
structure in smallest amount of memory possible.
Also, check if the 8-byte alignment you see
is hidden behind other general optimization flags.
**
How about this 'alignment-aware-memory-wasteful' alternative:
typedef struct {
short iSpeciesID;
short[3] dummy; /* just padding */
char sCapacityFile[SHORT_INPUT];
double adGParams[NUM_GPARAMS];
} tVStruct;
int aiLengthsT5[4] = {1, 3, SHORT_INPUT, NUM_GPARAMS};
MPI_Aint aiDispsT5[4] = {0, iShortSize, 4*iShortSize,
4*iShortSize+SHORT_INPUT};
MPI_Datatype aTypesT5[4] = {MPI_UNSIGNED_SHORT,
MPI_UNSIGNED_SHORT, MPI_CHAR, MPI_DOUBLE};
MPI_Type_create_struct(4, aiLengthsT5, aiDispsT5, aTypesT5,
&m_dtVegetationData3);
MPI_Type_commit(&m_dtVegetationData3);
Maybe replacing some of the 3s and 4s above by a preprocessor macro,
say PAD_SIZE (=3), and (PAD_SIZE+1), to be able to adjust for other
choices of SHORT_INPUT.
Would it be viable?
My two cents,
Gus Correa
