[mpich-devel] MPI_Alltoall fails when called with newly created communicators (Giuseppe Congiu)
Paul Coffman
pcoffman at anl.gov
Wed Oct 21 10:29:20 CDT 2015
Giuseppe -
So if you're creating the separate communicators to address issues with
collective IO aggregation memory and performance, actually in MPICH 3.2rc1
there already exists a one-sided aggregation method that does away with the
alltoall calls with significant performance and memory enhancements,
although currently this is only implemented for GPFS. See
src/mpi/romio/adio/ad_gpfs/ad_gpfs_tuning.c and search for 'one-sided'
essentially it is enabled with the env vars GPFSMPIO_WRITE_AGGMETHOD and
GPFSMPIO_READ_AGGMETHOD with some others for additional tweaking. And
actually if you are using NFS there are a couple of tricks to get it to work
with that also let me know and I can help you.
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1. Re: Argonne Spam Quarantine Notification (Bland, Wesley)
2. Re: Argonne Spam Quarantine Notification (Jeff Hammond)
3. Re: Argonne Spam Quarantine Notification (Kenneth Raffenetti)
4. [PATCH] MPI_Aint_* tests: use MPI_INTEGER datatype in
Fortran (Jeff Squyres)
5. Re: [PATCH] MPI_Aint_* tests: use MPI_INTEGER datatype in
Fortran (Kenneth Raffenetti)
6. MPI_Alltoall fails when called with newly created
communicators (Giuseppe Congiu)
----------------------------------------------------------------------
Message: 1
Date: Thu, 1 Oct 2015 11:41:39 +0000
From: "Bland, Wesley" <wesley.bland at intel.com>
To: "devel at mpich.org" <devel at mpich.org>
Subject: Re: [mpich-devel] Argonne Spam Quarantine Notification
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Looks like it didn't work.
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Message: 2
Date: Thu, 1 Oct 2015 04:53:20 -0700
From: Jeff Hammond <jeff.science at gmail.com>
To: "devel at mpich.org" <devel at mpich.org>
Subject: Re: [mpich-devel] Argonne Spam Quarantine Notification
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If all else fails, individuals can apply the time-tested solution of email
filters...
Jeff
On Thursday, October 1, 2015, Bland, Wesley <wesley.bland at intel.com> wrote:
> Looks like it didn't work.
>
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--
Jeff Hammond
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http://jeffhammond.github.io/
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Message: 3
Date: Thu, 1 Oct 2015 08:47:38 -0500
From: Kenneth Raffenetti <raffenet at mcs.anl.gov>
To: <devel at mpich.org>
Subject: Re: [mpich-devel] Argonne Spam Quarantine Notification
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*sigh* - I spelled "quarantine" wrong in the regex filter. Hopefully I got
it this time.
Ken
On 10/01/2015 06:41 AM, Bland, Wesley wrote:
> Looks like it didn't work.
>
> On Oct 1, 2015, at 6:00 AM, Argonne Anti Spam Quarantine
<spam-quarantine at anl.gov<mailto:spam-quarantine at anl.gov>> wrote:
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> IronPort Spam Quarantine Notification
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>
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> entation_for_Users
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Message: 4
Date: Wed, 14 Oct 2015 18:58:45 -0700
From: Jeff Squyres <jsquyres at cisco.com>
To: devel at mpich.org
Subject: [mpich-devel] [PATCH] MPI_Aint_* tests: use MPI_INTEGER
datatype in Fortran
Message-ID: <1444874325-13804-1-git-send-email-jsquyres at cisco.com>
MPI_INT corresponds to type(C_INT); MPI_INTEGER corresponds to INTEGER.
---
test/mpi/f08/rma/aintf08.f90 | 4 ++--
test/mpi/f77/rma/aintf.f | 6 +++---
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/test/mpi/f08/rma/aintf08.f90 b/test/mpi/f08/rma/aintf08.f90
index cef75eb..b4dce12 100644
--- a/test/mpi/f08/rma/aintf08.f90
+++ b/test/mpi/f08/rma/aintf08.f90
@@ -42,7 +42,7 @@ program main
endif
! Exchange bases
- call MPI_Type_size(MPI_INT, intsize, ierr);
+ call MPI_Type_size(MPI_INTEGER, intsize, ierr);
call MPI_Allgather(MPI_IN_PLACE, 0, MPI_DATATYPE_NULL, bases, 1,
MPI_AINT, MPI_COMM_WORLD, ierr)
call MPI_Win_create_dynamic(MPI_INFO_NULL, MPI_COMM_WORLD, win, ierr)
@@ -60,7 +60,7 @@ program main
! Get value and verify it
call MPI_Win_fence(MPI_MODE_NOPRECEDE, win, ierr)
- call MPI_Get(val, 1, MPI_INT, target_rank, offset, 1, MPI_INT, win,
ierr)
+ call MPI_Get(val, 1, MPI_INTEGER, target_rank, offset, 1,
+ MPI_INTEGER, win, ierr)
call MPI_Win_fence(MPI_MODE_NOSUCCEED, win, ierr)
if (val /= 1234) then
diff --git a/test/mpi/f77/rma/aintf.f b/test/mpi/f77/rma/aintf.f index
87464ba..9df429b 100644
--- a/test/mpi/f77/rma/aintf.f
+++ b/test/mpi/f77/rma/aintf.f
@@ -46,7 +46,7 @@
endif
! Exchange bases
- call MPI_Type_size(MPI_INT, intsize, ierr);
+ call MPI_Type_size(MPI_INTEGER, intsize, ierr);
call MPI_Allgather(MPI_IN_PLACE, 0, MPI_DATATYPE_NULL, bases,
& 1, MPI_AINT, MPI_COMM_WORLD, ierr)
@@ -68,8 +68,8 @@
! Get value and verify it
call MPI_Win_fence(MPI_MODE_NOPRECEDE, win, ierr)
- call MPI_Get(val, 1, MPI_INT, target_rank,
- & offset, 1, MPI_INT, win, ierr)
+ call MPI_Get(val, 1, MPI_INTEGER, target_rank,
+ & offset, 1, MPI_INTEGER, win, ierr)
call MPI_Win_fence(MPI_MODE_NOSUCCEED, win, ierr)
if (val /= 1234) then
--
2.4.3
------------------------------
Message: 5
Date: Thu, 15 Oct 2015 08:45:28 -0500
From: Kenneth Raffenetti <raffenet at mcs.anl.gov>
To: <devel at mpich.org>
Subject: Re: [mpich-devel] [PATCH] MPI_Aint_* tests: use MPI_INTEGER
datatype in Fortran
Message-ID: <561FADF8.2060002 at mcs.anl.gov>
Content-Type: text/plain; charset="utf-8"; format=flowed
Thanks Jeff. The patch looks good. We are in a freeze now leading up to
release, so this probably won't make 3.2. Either way, it will land in
master soon.
Ken
On 10/14/2015 08:58 PM, Jeff Squyres wrote:
> MPI_INT corresponds to type(C_INT); MPI_INTEGER corresponds to INTEGER.
> ---
> test/mpi/f08/rma/aintf08.f90 | 4 ++--
> test/mpi/f77/rma/aintf.f | 6 +++---
> 2 files changed, 5 insertions(+), 5 deletions(-)
>
> diff --git a/test/mpi/f08/rma/aintf08.f90 b/test/mpi/f08/rma/aintf08.f90
> index cef75eb..b4dce12 100644
> --- a/test/mpi/f08/rma/aintf08.f90
> +++ b/test/mpi/f08/rma/aintf08.f90
> @@ -42,7 +42,7 @@ program main
> endif
>
> ! Exchange bases
> - call MPI_Type_size(MPI_INT, intsize, ierr);
> + call MPI_Type_size(MPI_INTEGER, intsize, ierr);
> call MPI_Allgather(MPI_IN_PLACE, 0, MPI_DATATYPE_NULL, bases, 1,
MPI_AINT, MPI_COMM_WORLD, ierr)
> call MPI_Win_create_dynamic(MPI_INFO_NULL, MPI_COMM_WORLD, win,
ierr)
>
> @@ -60,7 +60,7 @@ program main
>
> ! Get value and verify it
> call MPI_Win_fence(MPI_MODE_NOPRECEDE, win, ierr)
> - call MPI_Get(val, 1, MPI_INT, target_rank, offset, 1, MPI_INT, win,
ierr)
> + call MPI_Get(val, 1, MPI_INTEGER, target_rank, offset, 1,
MPI_INTEGER, win, ierr)
> call MPI_Win_fence(MPI_MODE_NOSUCCEED, win, ierr)
>
> if (val /= 1234) then
> diff --git a/test/mpi/f77/rma/aintf.f b/test/mpi/f77/rma/aintf.f
> index 87464ba..9df429b 100644
> --- a/test/mpi/f77/rma/aintf.f
> +++ b/test/mpi/f77/rma/aintf.f
> @@ -46,7 +46,7 @@
> endif
>
> ! Exchange bases
> - call MPI_Type_size(MPI_INT, intsize, ierr);
> + call MPI_Type_size(MPI_INTEGER, intsize, ierr);
>
> call MPI_Allgather(MPI_IN_PLACE, 0, MPI_DATATYPE_NULL, bases,
> & 1, MPI_AINT, MPI_COMM_WORLD, ierr)
> @@ -68,8 +68,8 @@
>
> ! Get value and verify it
> call MPI_Win_fence(MPI_MODE_NOPRECEDE, win, ierr)
> - call MPI_Get(val, 1, MPI_INT, target_rank,
> - & offset, 1, MPI_INT, win, ierr)
> + call MPI_Get(val, 1, MPI_INTEGER, target_rank,
> + & offset, 1, MPI_INTEGER, win, ierr)
> call MPI_Win_fence(MPI_MODE_NOSUCCEED, win, ierr)
>
> if (val /= 1234) then
>
------------------------------
Message: 6
Date: Wed, 21 Oct 2015 08:06:50 +0100
From: Giuseppe Congiu <giuseppe.congiu at seagate.com>
To: devel at mpich.org
Subject: [mpich-devel] MPI_Alltoall fails when called with newly
created communicators
Message-ID:
<CABjftneMXf_gMccMsC8CCrO-bxDTYed_LZZYyUrpRMq47rdnaA at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hello everyone,
I am currently working on a partitioned collective I/O implementation for a
EU project. The idea is to partition the accessed file range into disjoint
access regions (i.e., regions that do not overlap with each other) and
assign processes from these regions to independent communicators created by
splitting the original communicator with MPI_Comm_split. Very much like it
is done in the ParColl paper or in the Memory Conscious Collective I/O
paper.
The code is pretty simple. It just uses the access pattern information to
create the new communicators, assign aggregators to each of them and then
compute file domains and data dependencies for every process using default
functions from ROMIO (i.e. ADIOI_Calc_file_domains, ADIOI_Calc_my_req,
ADIOI_Calc_others_req).
I am currently testing my implementation using coll_perf with 512
processes. Every process writes 64MB of data for a total of 32GBs (no reads
are performed). The ranks belonging to non-overlapping regions (of file
areas) are printed out by the process with rank 0 in the global
communicator:
[romio/adio/common/ad_aggregate.c:0] file_area_count = 8
[romio/adio/common/ad_aggregate.c:0] file_area_ranklist[0] = 0 1 2 3
... 63
[romio/adio/common/ad_aggregate.c:0] file_area_ranklist[1] = 64 65 66 67
... 127
[romio/adio/common/ad_aggregate.c:0] file_area_ranklist[2] = 128 129 130
131 ... 191
[romio/adio/common/ad_aggregate.c:0] file_area_ranklist[3] = 192 193 194
195 ... 255
[romio/adio/common/ad_aggregate.c:0] file_area_ranklist[4] = 256 257 258
259 ... 319
[romio/adio/common/ad_aggregate.c:0] file_area_ranklist[5] = 320 321 322
323 ... 383
[romio/adio/common/ad_aggregate.c:0] file_area_ranklist[6] = 384 385 386
387 ... 447
[romio/adio/common/ad_aggregate.c:0] file_area_ranklist[7] = 448 449 450
451 ... 511
Afterwards, every aggregator in each communication group prints its rank
and aggregator number in ranklist:
[romio/adio/common/ad_aggregate.c:0] my_cb_nodes_index = 0
[romio/adio/common/ad_aggregate.c:0] fd->hints->ranklist[0] = 0
[romio/adio/common/ad_aggregate.c:0] my_cb_nodes_index = 0
[romio/adio/common/ad_aggregate.c:0] fd->hints->ranklist[0] = 0
[romio/adio/common/ad_aggregate.c:0] my_cb_nodes_index = 0
[romio/adio/common/ad_aggregate.c:0] fd->hints->ranklist[0] = 0
[romio/adio/common/ad_aggregate.c:0] my_cb_nodes_index = 0
[romio/adio/common/ad_aggregate.c:0] fd->hints->ranklist[0] = 0
In this particular case I have set fd->hints->cb_nodes to 4. This means
that there are 4 aggregators but 8 non-overlapping regions (file areas).
Thus, I create only 4 communicators and assign to each of them 2 file
areas. In the previous printed messages the only aggregator for each
communicator is printing its information.
Then every process prints its group name, the number of process in the
group, its rank in the old and new communicator:
group-0:128:0:0
group-0:128:1:1
group-0:128:2:2
group-0:128:3:3
---
group-0:128:127:127
group-1:128:128:0
group-1:128:129:1
group-1:128:130:2
group-1:128:131:3
---
group-1:128:255:127
group-2:128:256:0
group-2:128:257:1
group-2:128:258:2
group-2:128:259:3
---
group-2:128:383:127
group-3:128:384:0
group-3:128:385:1
group-3:128:386:2
group-3:128:387:3
---
group-3:128:511:127
So far it looks like the communicators are created properly. After calling
the ADIOI_Calc_* functions every aggregator prints MIN and MAX offsets for
every independent access range:
[romio/adio/common/ad_write_coll.c:0] st_loc = 17179869184, end_loc =
25769803775
[romio/adio/common/ad_write_coll.c:0] st_loc = 8589934592, end_loc =
17179869183
[romio/adio/common/ad_write_coll.c:0] st_loc = 25769803776, end_loc =
34359738367
[romio/adio/common/ad_write_coll.c:0] st_loc = 0, end_loc = 8589934591
Even though the new communicators seems to be created correctly, something
bad happens when two phase I/O starts and the first MPI_Alltoall() is
called to exchange access information among processes. MPI_Alltoall is
called using the new communicators separately and every buffer passed to it
has the new nprocs size for the corresponding communicator. Nevertheless,
for some reason I am getting the following error message:
Fatal error in PMPI_Alltoall: Other MPI error, error stack:
PMPI_Alltoall(888)......: MPI_Alltoall(sbuf=0x2551e98, scount=1, MPI_INT,
rbuf=0x2551be8, rcount=1, MPI_INT, comm=0x84000001) failed
MPIR_Alltoall_impl(760).:
MPIR_Alltoall(725)......:
MPIR_Alltoall_intra(283):
repeated many more times.
This is actually strange because if I look at the file after coll_perf
crashes there is some data in it (~200MB). Like if the problem was caused
by only one communicator among the four.
Does anybody have any idea of what is happening and why?
Thanks,
--
Giuseppe Congiu *?* Research Engineer II
Seagate Technology, LLC
office: +44 (0)23 9249 6082 *?* mobile:
www.seagate.com
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