On Oct 1, 2014, at 6:48 AM, Gilles Gouaillardet <gilles.gouaillar...@iferc.org>
wrote:
> oops, i missed graph and dist graph :-(
>
> the attached patch fixes this
> /* it was straightforward for graph and a bit more challenging for dist
> graph */
>
> i am fine for Nathan's patch for v1.8
> /* v1.8 and trunk have already a different way to handle a memory leak */
> /* the attached patch is vs v1.8 but it is for review only, i will port
> it to the trunk */
>
> imho, there is no ABI break with this patch.
> out of curiosity, what is the ABI break that is/will be introduced with
> the "real" fix ?
I haven't looked at the code at all, but Nathan said it changed the topo
framework interface. That's the ABI I was referring to -- not the MPI ABI.
Sorry for the confusions.
> FYI, i also enhanced the collective/neighbor_allgather_self from the ibm
> test suite in order to test
> graph and dist_graph
>
> Cheers,
>
> Gilles
>
>
> On 2014/10/01 0:58, Jeff Squyres (jsquyres) wrote:
>> On the call today, we decided that Nathan's v1.8 patch is sufficient for the
>> v1.8 series, and the "real" fix will be applied to the trunk and carried
>> forward to the v1.9 series (since it introduces an ABI break for the topo
>> framework, which we try not to do in the middle of a release series).
>>
>> On Sep 30, 2014, at 10:40 AM, Nathan Hjelm <hje...@lanl.gov> wrote:
>>
>>> Not quite right. There still is no topology information at collective
>>> selection time for either graph or dist graph.
>>>
>>> -Nathan
>>>
>>> On Tue, Sep 30, 2014 at 02:03:27PM +0900, Gilles Gouaillardet wrote:
>>>> Nathan,
>>>>
>>>> here is a revision of the previously attached patch, and that supports
>>>> graph and dist graph.
>>>>
>>>> Cheers,
>>>>
>>>> Gilles
>>>>
>>>> On 2014/09/30 0:05, Nathan Hjelm wrote:
>>>>
>>>> An equivalent change would need to be made for graph and dist graph as
>>>> well. That will take a little more work. Also, I was avoiding changing
>>>> anything in topo for 1.8.
>>>>
>>>> -Nathan
>>>>
>>>> On Mon, Sep 29, 2014 at 08:02:41PM +0900, Gilles Gouaillardet wrote:
>>>>
>>>> Nathan,
>>>>
>>>> why not just make the topology information available at that point as you
>>>> described it ?
>>>>
>>>> the attached patch does this, could you please review it ?
>>>>
>>>> Cheers,
>>>>
>>>> Gilles
>>>>
>>>> On 2014/09/26 2:50, Nathan Hjelm wrote:
>>>>
>>>> On Tue, Aug 26, 2014 at 07:03:24PM +0300, Lisandro Dalcin wrote:
>>>>
>>>> I finally managed to track down some issues in mpi4py's test suite
>>>> using Open MPI 1.8+. The code below should be enough to reproduce the
>>>> problem. Run it under valgrind to make sense of my following
>>>> diagnostics.
>>>>
>>>> In this code I'm creating a 2D, periodic Cartesian topology out of
>>>> COMM_SELF. In this case, the process in COMM_SELF has 4 logical in/out
>>>> links to itself. So we have size=1 but indegree=outdegree=4. However,
>>>> in ompi/mca/coll/basic/coll_basic_module.c, "size * 2" request are
>>>> being allocated to manage communication:
>>>>
>>>> if (OMPI_COMM_IS_INTER(comm)) {
>>>> size = ompi_comm_remote_size(comm);
>>>> } else {
>>>> size = ompi_comm_size(comm);
>>>> }
>>>> basic_module->mccb_num_reqs = size * 2;
>>>> basic_module->mccb_reqs = (ompi_request_t**)
>>>> malloc(sizeof(ompi_request_t *) * basic_module->mccb_num_reqs);
>>>>
>>>> I guess you have to also special-case for topologies and allocate
>>>> indegree+outdegree requests (not sure about this number, just
>>>> guessing).
>>>>
>>>>
>>>> I wish this was possible but the topology information is not available
>>>> at that point. We may be able to change that but I don't see the work
>>>> completing anytime soon. I committed an alternative fix as r32796 and
>>>> CMR'd it to 1.8.3. I can confirm that the attached reproducer no longer
>>>> produces a SEGV. Let me know if you run into any more issues.
>>>>
>>>>
>>>> -Nathan
>>>>
>>>> _______________________________________________
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>>>> Link to this post:
>>>> http://www.open-mpi.org/community/lists/devel/2014/09/15915.php
>>>>
>>>> Index: ompi/mca/topo/base/topo_base_cart_create.c
>>>> ===================================================================
>>>> --- ompi/mca/topo/base/topo_base_cart_create.c (revision 32807)
>>>> +++ ompi/mca/topo/base/topo_base_cart_create.c (working copy)
>>>> @@ -163,10 +163,18 @@
>>>> return MPI_ERR_INTERN;
>>>> }
>>>>
>>>> + assert(NULL == new_comm->c_topo);
>>>> + assert(!(new_comm->c_flags & OMPI_COMM_CART));
>>>> + new_comm->c_topo = topo;
>>>> + new_comm->c_topo->mtc.cart = cart;
>>>> + new_comm->c_topo->reorder = reorder;
>>>> + new_comm->c_flags |= OMPI_COMM_CART;
>>>> ret = ompi_comm_enable(old_comm, new_comm,
>>>> new_rank, num_procs, topo_procs);
>>>> if (OMPI_SUCCESS != ret) {
>>>> /* something wrong happened during setting the communicator */
>>>> + new_comm->c_topo = NULL;
>>>> + new_comm->c_flags &= ~OMPI_COMM_CART;
>>>> ompi_comm_free (&new_comm);
>>>> free(topo_procs);
>>>> if(NULL != cart->periods) free(cart->periods);
>>>> @@ -176,10 +184,6 @@
>>>> return ret;
>>>> }
>>>>
>>>> - new_comm->c_topo = topo;
>>>> - new_comm->c_topo->mtc.cart = cart;
>>>> - new_comm->c_topo->reorder = reorder;
>>>> - new_comm->c_flags |= OMPI_COMM_CART;
>>>> *comm_topo = new_comm;
>>>>
>>>> if( MPI_UNDEFINED == new_rank ) {
>>>> Index: ompi/mca/coll/basic/coll_basic_module.c
>>>> ===================================================================
>>>> --- ompi/mca/coll/basic/coll_basic_module.c (revision 32807)
>>>> +++ ompi/mca/coll/basic/coll_basic_module.c (working copy)
>>>> @@ -13,6 +13,8 @@
>>>> * Copyright (c) 2012 Sandia National Laboratories. All rights
>>>> reserved.
>>>> * Copyright (c) 2013 Los Alamos National Security, LLC. All rights
>>>> * reserved.
>>>> + * Copyright (c) 2014 Research Organization for Information Science
>>>> + * and Technology (RIST). All rights reserved.
>>>> * $COPYRIGHT$
>>>> *
>>>> * Additional copyrights may follow
>>>> @@ -28,6 +30,7 @@
>>>> #include "mpi.h"
>>>> #include "ompi/mca/coll/coll.h"
>>>> #include "ompi/mca/coll/base/base.h"
>>>> +#include "ompi/mca/topo/topo.h"
>>>> #include "coll_basic.h"
>>>>
>>>>
>>>> @@ -70,6 +73,15 @@
>>>> } else {
>>>> size = ompi_comm_size(comm);
>>>> }
>>>> + if (comm->c_flags & OMPI_COMM_CART) {
>>>> + int cart_size;
>>>> + assert (NULL != comm->c_topo);
>>>> + comm->c_topo->topo.cart.cartdim_get(comm, &cart_size);
>>>> + cart_size *= 2;
>>>> + if (cart_size > size) {
>>>> + size = cart_size;
>>>> + }
>>>> + }
>>>> basic_module->mccb_num_reqs = size * 2;
>>>> basic_module->mccb_reqs = (ompi_request_t**)
>>>> malloc(sizeof(ompi_request_t *) * basic_module->mccb_num_reqs);
>>>>
>>>> _______________________________________________
>>>> devel mailing list
>>>> de...@open-mpi.org
>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>>> Link to this post:
>>>> http://www.open-mpi.org/community/lists/devel/2014/09/15929.php
>>>>
>>>> _______________________________________________
>>>> devel mailing list
>>>> de...@open-mpi.org
>>>> Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>>> Link to this post:
>>>> http://www.open-mpi.org/community/lists/devel/2014/09/15930.php
>>>> Index: ompi/mca/topo/base/topo_base_cart_create.c
>>>> ===================================================================
>>>> --- ompi/mca/topo/base/topo_base_cart_create.c (revision 32815)
>>>> +++ ompi/mca/topo/base/topo_base_cart_create.c (working copy)
>>>> @@ -163,10 +163,18 @@
>>>> return MPI_ERR_INTERN;
>>>> }
>>>>
>>>> + assert(NULL == new_comm->c_topo);
>>>> + assert(!(new_comm->c_flags & OMPI_COMM_CART));
>>>> + new_comm->c_topo = topo;
>>>> + new_comm->c_topo->mtc.cart = cart;
>>>> + new_comm->c_topo->reorder = reorder;
>>>> + new_comm->c_flags |= OMPI_COMM_CART;
>>>> ret = ompi_comm_enable(old_comm, new_comm,
>>>> new_rank, num_procs, topo_procs);
>>>> if (OMPI_SUCCESS != ret) {
>>>> /* something wrong happened during setting the communicator */
>>>> + new_comm->c_topo = NULL;
>>>> + new_comm->c_flags &= ~OMPI_COMM_CART;
>>>> ompi_comm_free (&new_comm);
>>>> free(topo_procs);
>>>> if(NULL != cart->periods) free(cart->periods);
>>>> @@ -176,10 +184,6 @@
>>>> return ret;
>>>> }
>>>>
>>>> - new_comm->c_topo = topo;
>>>> - new_comm->c_topo->mtc.cart = cart;
>>>> - new_comm->c_topo->reorder = reorder;
>>>> - new_comm->c_flags |= OMPI_COMM_CART;
>>>> *comm_topo = new_comm;
>>>>
>>>> if( MPI_UNDEFINED == new_rank ) {
>>>> Index: ompi/mca/coll/basic/coll_basic_module.c
>>>> ===================================================================
>>>> --- ompi/mca/coll/basic/coll_basic_module.c (revision 32815)
>>>> +++ ompi/mca/coll/basic/coll_basic_module.c (working copy)
>>>> @@ -13,6 +13,8 @@
>>>> * Copyright (c) 2012 Sandia National Laboratories. All rights
>>>> reserved.
>>>> * Copyright (c) 2013 Los Alamos National Security, LLC. All rights
>>>> * reserved.
>>>> + * Copyright (c) 2014 Research Organization for Information Science
>>>> + * and Technology (RIST). All rights reserved.
>>>> * $COPYRIGHT$
>>>> *
>>>> * Additional copyrights may follow
>>>> @@ -28,6 +30,8 @@
>>>> #include "mpi.h"
>>>> #include "ompi/mca/coll/coll.h"
>>>> #include "ompi/mca/coll/base/base.h"
>>>> +#include "ompi/mca/topo/topo.h"
>>>> +#include "ompi/mca/topo/base/base.h"
>>>> #include "coll_basic.h"
>>>>
>>>>
>>>> @@ -70,7 +74,36 @@
>>>> } else {
>>>> size = ompi_comm_size(comm);
>>>> }
>>>> - basic_module->mccb_num_reqs = size * 2;
>>>> + size *= 2;
>>>> + if (OMPI_COMM_IS_CART(comm)) {
>>>> + int cart_size;
>>>> + mca_topo_base_comm_cart_2_1_0_t *cart;
>>>> + assert (NULL != comm->c_topo);
>>>> + cart = comm->c_topo->mtc.cart;
>>>> + cart_size = cart->ndims * 4;
>>>> + if (cart_size > size) {
>>>> + size = cart_size;
>>>> + }
>>>> + } else if (OMPI_COMM_IS_GRAPH(comm)) {
>>>> + int rank, degree;
>>>> + assert (NULL != comm->c_topo);
>>>> + rank = ompi_comm_rank (comm);
>>>> + mca_topo_base_graph_neighbors_count (comm, rank, °ree);
>>>> + degree *= 2;
>>>> + if (degree > size) {
>>>> + size = degree;
>>>> + }
>>>> + } else if (OMPI_COMM_IS_DIST_GRAPH(comm)) {
>>>> + int dist_graph_size;
>>>> + mca_topo_base_comm_dist_graph_2_1_0_t *dist_graph;
>>>> + assert (NULL != comm->c_topo);
>>>> + dist_graph = comm->c_topo->mtc.dist_graph;
>>>> + dist_graph_size = dist_graph->indegree + dist_graph->outdegree;
>>>> + if (dist_graph_size > size) {
>>>> + size = dist_graph_size;
>>>> + }
>>>> + }
>>>> + basic_module->mccb_num_reqs = size;
>>>> basic_module->mccb_reqs = (ompi_request_t**)
>>>> malloc(sizeof(ompi_request_t *) * basic_module->mccb_num_reqs);
>>>>
>>>> _______________________________________________
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>>>> Link to this post:
>>>> http://www.open-mpi.org/community/lists/devel/2014/09/15941.php
>>> _______________________________________________
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>>> http://www.open-mpi.org/community/lists/devel/2014/09/15945.php
>>
>
> <mmcb.v3.patch>_______________________________________________
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--
Jeff Squyres
jsquy...@cisco.com
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