Hi George
It is still not clear to me how to deal with strides in
MPI_Create_type_subarray.
The function/subroutine interface doesn't mention strides at all.
It is a pity that there is little literature (books) about MPI,
and the existing books are lagging behind the new MPI developments and
standards (MPI-2, MPI-3).
My most reliable sources so far were the "MPI - The complete reference"
books, vol-1 (2nd ed.) and vol-2 (which presumably covers MPI-2).
However, they do not even mention MPI_Create_type_subarray,
which is part of the MPI-2 standard.
I found it in the MPI-2 standard on the web, but it is not clear to me
how to achieve the same effect of strides that are available in
MPI_Type_vector.
MPI_Create_type_subarray is in section 4.1.3.
The OMPI MPI_Create_type_subarray man page says there is an example in
section 9.9.2 of the MPI-2 standard.
However, there is no section 9.9.2.
Chapter 9 is about something else ("The info object"), not derived types.
No good example of MPI_Create_type_subarray in section 4.1.3 either,
which is written in the typical terse and hermetic style in which
standards are.
So, how can one handle strides in MPI_Create_type_subarray?
Would one have to first create several MPI_Type_vector for the various
dimensions, then use them as "oldtype" in MPI_Create_type_subarray?
That sounds awkward, because there is only one "oldtype" in
MPI_Create_type_subarray, not one for each dimension.
Is there any simple example of how to achieve stride effect with
MPI_Create_type_subarray in a multi-dimensional array?
BTW, when are you gentlemen going to write an updated version of the
"MPI - The Complete Reference"? :)
Thank you,
Gus Correa
(Hijacking Diego Avesani's thread, apologies to Diego.)
(Also, I know this question is not about Open MPI, but about MPI in
general. But the lack of examples may warrant asking the question here.)
On 01/16/2015 01:39 AM, George Bosilca wrote:
The subarray creation is an multi-dimension extension of the vector type.
You can see it as a vector of vector of vector and so on, one vector per
dimension.
The stride array is used to declare on each dimension what is the
relative displacement
(in number of elements) from the beginning of the dimension array.
It is important to use regular type creation when you can take advantage of such
regularity instead of resorting to use of struct or h*. This insure better
packing/unpacking performance, as well as possible future support for
one-sided
communications.
George.
On Jan 15, 2015, at 19:31, Gus Correa <g...@ldeo.columbia.edu> wrote:
I never used MPI_Type_create_subarray, only MPI_Type_Vector.
What I like about MPI_Type_Vector is that you can define a stride,
hence you can address any regular pattern in memory.
However, it envisages the array layout in memory as a big 1-D array,
with a linear index progressing in either Fortran or C order.
Somebody correct me please if I am wrong, but at first sight MPI_Type_Vector
sounds more flexible to me than MPI_Type_create_subarray, exactly because the
latter doesn't have strides.
The downside is that you need to do some index arithmetic to figure
the right strides, etc, to match the corresponding
Fortran90 array sections.
There are good examples in the "MPI - The complete reference" books I suggested
to you before (actually in vol 1).
Online I could find the two man pages (good information, but no example):
http://www.open-mpi.org/doc/v1.8/man3/MPI_Type_vector.3.php
http://www.open-mpi.org/doc/v1.8/man3/MPI_Type_create_subarray.3.php
There is a very simple 2D example of MPI_Type_vector using strides here:
https://computing.llnl.gov/tutorials/mpi/#Derived_Data_Types
and a similar one here:
http://static.msi.umn.edu/tutorial/scicomp/general/MPI/content6.html
Gus Correa
On 01/15/2015 06:53 PM, Diego Avesani wrote:
dear George, dear Gus, dear all,
Could you please tell me where I can find a good example?
I am sorry but I can not understand the 3D array.
Really Thanks
Diego
On 15 January 2015 at 20:13, George Bosilca <bosi...@icl.utk.edu
<mailto:bosi...@icl.utk.edu>> wrote:
On Jan 15, 2015, at 06:02 , Diego Avesani <diego.aves...@gmail.com
<mailto:diego.aves...@gmail.com>> wrote:
Dear Gus, Dear all,
Thanks a lot.
MPI_Type_Struct works well for the first part of my problem, so I
am very happy to be able to use it.
Regarding MPI_TYPE_VECTOR.
I have studied it and for simple case it is clear to me what id
does (at least I believe). Foe example if I have a matrix define as:
REAL, ALLOCATABLE (AA(:,:))
ALLOCATE AA(100,5)
I could send part of it defining
CALL MPI_TYPE_VECTOR(5,1,5,MPI_DOUBLE_PRECISION,/MY_NEW_TYPE/)
after that I can send part of it with
CALL MPI_SEND( AA(1:/10/,:), /10/, /MY_NEW_TYPE/, 1, 0,
MPI_COMM_WORLD );
Have I understood correctly?
What I can do in case of three dimensional array? for example
AA(:,:,:), I am looking to MPI_TYPE_CREATE_SUBARRAY.
Is that the correct way?
Thanks again
Indeed, using the subarray is the right approach independent on the
number of dimensions of the data (you can use it instead of
MPI_TYPE_VECTOR as well).
George.
Diego
On 13 January 2015 at 19:04, Gus Correa <g...@ldeo.columbia.edu
<mailto:g...@ldeo.columbia.edu>> wrote:
Hi Diego
I guess MPI_Type_Vector is the natural way to send and receive
Fortran90 array sections (e.g. your QQMLS(:,50:100,:)).
I used that before and it works just fine.
I think that is pretty standard MPI programming style.
I guess MPI_Type_Struct tries to emulate Fortran90 and C
structures
(as you did in your previous code, with all the surprises
regarding alignment, etc), not array sections.
Also, MPI type vector should be more easy going (and probably
more efficient) than MPI type struct, with less memory
alignment problems.
I hope this helps,
Gus Correa
PS - These books have a quite complete description and several
examples
of all MPI objects and functions, including MPI types (native
and user defined):
http://mitpress.mit.edu/books/__mpi-complete-reference-0
<http://mitpress.mit.edu/books/mpi-complete-reference-0>
http://mitpress.mit.edu/books/__mpi-complete-reference-1
<http://mitpress.mit.edu/books/mpi-complete-reference-1>
[They cover MPI 1 and 2. I guess there is a new/upcoming book
with MPI 3, but for what you're doing 1 and 2 are more than
enough.]
On 01/13/2015 09:22 AM, Diego Avesani wrote:
Dear all,
I had some wonderful talking about MPI_type_create_struct adn
isend\irecv with
Gilles, Gustavo, George, Gus, Tom and Jeff. Now all is
more clear and my
program works.
Now I have another question. In may program I have matrix:
/QQMLS(:,:,:) /that is allocate as
/ALLOCATE(QQMLS(9,npt,18)/), where npt is the number of
particles
QQMLS is double precision.
I would like to sent form a CPU to another part of it, for
example,
sending QQMLS(:,50:100,:). I mean sending the QQMLS of the
particles
between 50 to 100.
I suppose that i could use MPI_Type_vector but I am not
sure. The
particle that I want to sent could be from 25 to 50 ecc..
ecc..so
blocklength changes everytime.
Do I have to use MPI_type_create_struct?
Do I have correctly understood MPI_Type_vector?
Thanks a lot
Diego
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