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Subject: Re: [OMPI users] [openib] segfault when using openib btl
From: Eloi Gaudry (eg_at_[hidden])
Date: 2010-09-25 06:13:40


  Hi Terry,

I'm sorry to say that I might have missed a point here.

I've lately been relaunching all previously failing computations with
the message coalescing feature being switched off, and I saw the same
hdr->tag=0 error several times, always during a collective call
(MPI_Comm_create, MPI_Allreduce and MPI_Broadcast, so far). And as soon
as I switched to the peer queue option I was previously using (--mca
btl_openib_receive_queues P,65536,256,192,128 instead of using --mca
btl_openib_use_message_coalescing 0), all computations ran flawlessly.

As for the reproducer, I've already tried to write something but I
haven't succeeded so far at reproducing the hdr->tag=0 issue with it.

Eloi

On 24/09/2010 18:37, Terry Dontje wrote:
> Eloi Gaudry wrote:
>> Terry,
>>
>> You were right, the error indeed seems to come from the message coalescing feature.
>> If I turn it off using the "--mca btl_openib_use_message_coalescing 0", I'm not able to observe the "hdr->tag=0" error.
>>
>> There are some trac requests associated to very similar error (https://svn.open-mpi.org/trac/ompi/search?q=coalescing) but they are all closed (excepthttps://svn.open-mpi.org/trac/ompi/ticket/2352
>> that might be related), aren't they ? What would you suggest Terry ?
>>
>>
> Interesting, though it looks to me like the segv in ticket 2352 would
> have happened on the send side instead of the receive side like you
> have. As to what to do next it would be really nice to have some sort
> of reproducer that we can try and debug what is really going on. The
> only other thing to do without a reproducer is to inspect the code on
> the send side to figure out what might make it generate at 0
> hdr->tag. Or maybe instrument the send side to stop when it is about
> ready to send a 0 hdr->tag and see if we can see how the code got there.
>
> I might have some cycles to look at this Monday.
>
> --td
>> Eloi
>>
>>
>> On Friday 24 September 2010 16:00:26 Terry Dontje wrote:
>>
>>> Eloi Gaudry wrote:
>>>
>>>> Terry,
>>>>
>>>> No, I haven't tried any other values than P,65536,256,192,128 yet.
>>>>
>>>> The reason why is quite simple. I've been reading and reading again this
>>>> thread to understand the btl_openib_receive_queues meaning and I can't
>>>> figure out why the default values seem to induce the hdr-
>>>>
>>>>
>>>>> tag=0 issue
>>>>> (http://www.open-mpi.org/community/lists/users/2009/01/7808.php).
>>>>>
>>> Yeah, the size of the fragments and number of them really should not
>>> cause this issue. So I too am a little perplexed about it.
>>>
>>>
>>>> Do you think that the default shared received queue parameters are
>>>> erroneous for this specific Mellanox card ? Any help on finding the
>>>> proper parameters would actually be much appreciated.
>>>>
>>> I don't necessarily think it is the queue size for a specific card but
>>> more so the handling of the queues by the BTL when using certain sizes.
>>> At least that is one gut feel I have.
>>>
>>> In my mind the tag being 0 is either something below OMPI is polluting
>>> the data fragment or OMPI's internal protocol is some how getting messed
>>> up. I can imagine (no empirical data here) the queue sizes could change
>>> how the OMPI protocol sets things up. Another thing may be the
>>> coalescing feature in the openib BTL which tries to gang multiple
>>> messages into one packet when resources are running low. I can see
>>> where changing the queue sizes might affect the coalescing. So, it
>>> might be interesting to turn off the coalescing. You can do that by
>>> setting "--mca btl_openib_use_message_coalescing 0" in your mpirun line.
>>>
>>> If that doesn't solve the issue then obviously there must be something
>>> else going on :-).
>>>
>>> Note, the reason I am interested in this is I am seeing a similar error
>>> condition (hdr->tag == 0) on a development system. Though my failing
>>> case fails with np=8 using the connectivity test program which is mainly
>>> point to point and there are not a significant amount of data transfers
>>> going on either.
>>>
>>> --td
>>>
>>>
>>>> Eloi
>>>>
>>>> On Friday 24 September 2010 14:27:07 you wrote:
>>>>
>>>>> That is interesting. So does the number of processes affect your runs
>>>>> any. The times I've seen hdr->tag be 0 usually has been due to protocol
>>>>> issues. The tag should never be 0. Have you tried to do other
>>>>> receive_queue settings other than the default and the one you mention.
>>>>>
>>>>> I wonder if you did a combination of the two receive queues causes a
>>>>> failure or not. Something like
>>>>>
>>>>> P,128,256,192,128:P,65536,256,192,128
>>>>>
>>>>> I am wondering if it is the first queuing definition causing the issue
>>>>> or possibly the SRQ defined in the default.
>>>>>
>>>>> --td
>>>>>
>>>>> Eloi Gaudry wrote:
>>>>>
>>>>>> Hi Terry,
>>>>>>
>>>>>> The messages being send/received can be of any size, but the error
>>>>>> seems to happen more often with small messages (as an int being
>>>>>> broadcasted or allreduced). The failing communication differs from one
>>>>>> run to another, but some spots are more likely to be failing than
>>>>>> another. And as far as I know, there are always located next to a
>>>>>> small message (an int being broadcasted for instance) communication.
>>>>>> Other typical messages size are
>>>>>>
>>>>>>
>>>>>>> 10k but can be very much larger.
>>>>>>>
>>>>>> I've been checking the hca being used, its' from mellanox (with
>>>>>> vendor_part_id=26428). There is no receive_queues parameters associated
>>>>>> to it.
>>>>>>
>>>>>> $ cat share/openmpi/mca-btl-openib-device-params.ini as well:
>>>>>> [...]
>>>>>>
>>>>>> # A.k.a. ConnectX
>>>>>> [Mellanox Hermon]
>>>>>> vendor_id = 0x2c9,0x5ad,0x66a,0x8f1,0x1708,0x03ba,0x15b3
>>>>>> vendor_part_id =
>>>>>> 25408,25418,25428,26418,26428,25448,26438,26448,26468,26478,26488
>>>>>> use_eager_rdma = 1
>>>>>> mtu = 2048
>>>>>> max_inline_data = 128
>>>>>>
>>>>>> [..]
>>>>>>
>>>>>> $ ompi_info --param btl openib --parsable | grep receive_queues
>>>>>>
>>>>>> mca:btl:openib:param:btl_openib_receive_queues:value:P,128,256,192,128
>>>>>> :S ,2048,256,128,32:S,12288,256,128,32:S,65536,256,128,32
>>>>>> mca:btl:openib:param:btl_openib_receive_queues:data_source:default
>>>>>> value mca:btl:openib:param:btl_openib_receive_queues:status:writable
>>>>>> mca:btl:openib:param:btl_openib_receive_queues:help:Colon-delimited,
>>>>>> comma delimited list of receive queues: P,4096,8,6,4:P,32768,8,6,4
>>>>>> mca:btl:openib:param:btl_openib_receive_queues:deprecated:no
>>>>>>
>>>>>> I was wondering if these parameters (automatically computed at openib
>>>>>> btl init for what I understood) were not incorrect in some way and I
>>>>>> plugged some others values: "P,65536,256,192,128" (someone on the list
>>>>>> used that values when encountering a different issue) . Since that, I
>>>>>> haven't been able to observe the segfault (occuring as hrd->tag = 0 in
>>>>>> btl_openib_component.c:2881) yet.
>>>>>>
>>>>>> Eloi
>>>>>>
>>>>>>
>>>>>> /home/pp_fr/st03230/EG/Softs/openmpi-custom-1.4.2/bin/
>>>>>>
>>>>>> On Thursday 23 September 2010 23:33:48 Terry Dontje wrote:
>>>>>>
>>>>>>> Eloi, I am curious about your problem. Can you tell me what size of
>>>>>>> job it is? Does it always fail on the same bcast, or same process?
>>>>>>>
>>>>>>> Eloi Gaudry wrote:
>>>>>>>
>>>>>>>> Hi Nysal,
>>>>>>>>
>>>>>>>> Thanks for your suggestions.
>>>>>>>>
>>>>>>>> I'm now able to get the checksum computed and redirected to stdout,
>>>>>>>> thanks (I forgot the "-mca pml_base_verbose 5" option, you were
>>>>>>>> right). I haven't been able to observe the segmentation fault (with
>>>>>>>> hdr->tag=0) so far (when using pml csum) but I 'll let you know when
>>>>>>>> I am.
>>>>>>>>
>>>>>>>> I've got two others question, which may be related to the error
>>>>>>>> observed:
>>>>>>>>
>>>>>>>> 1/ does the maximum number of MPI_Comm that can be handled by OpenMPI
>>>>>>>> somehow depends on the btl being used (i.e. if I'm using openib, may
>>>>>>>> I use the same number of MPI_Comm object as with tcp) ? Is there
>>>>>>>> something as MPI_COMM_MAX in OpenMPI ?
>>>>>>>>
>>>>>>>> 2/ the segfaults only appears during a mpi collective call, with very
>>>>>>>> small message (one int is being broadcast, for instance) ; i followed
>>>>>>>> the guidelines given athttp://icl.cs.utk.edu/open-
>>>>>>>> mpi/faq/?category=openfabrics#ib-small-message-rdma but the
>>>>>>>> debug-build of OpenMPI asserts if I use a different min-size that
>>>>>>>> 255. Anyway, if I deactivate eager_rdma, the segfaults remains. Does
>>>>>>>> the openib btl handle very small message differently (even with
>>>>>>>> eager_rdma
>>>>>>>> deactivated) than tcp ?
>>>>>>>>
>>>>>>> Others on the list does coalescing happen with non-eager_rdma? If so
>>>>>>> then that would possibly be one difference between the openib btl and
>>>>>>> tcp aside from the actual protocol used.
>>>>>>>
>>>>>>>
>>>>>>>> is there a way to make sure that large messages and small messages
>>>>>>>> are handled the same way ?
>>>>>>>>
>>>>>>> Do you mean so they all look like eager messages? How large of
>>>>>>> messages are we talking about here 1K, 1M or 10M?
>>>>>>>
>>>>>>> --td
>>>>>>>
>>>>>>>
>>>>>>>> Regards,
>>>>>>>> Eloi
>>>>>>>>
>>>>>>>> On Friday 17 September 2010 17:57:17 Nysal Jan wrote:
>>>>>>>>
>>>>>>>>> Hi Eloi,
>>>>>>>>> Create a debug build of OpenMPI (--enable-debug) and while running
>>>>>>>>> with the csum PML add "-mca pml_base_verbose 5" to the command line.
>>>>>>>>> This will print the checksum details for each fragment sent over the
>>>>>>>>> wire. I'm guessing it didnt catch anything because the BTL failed.
>>>>>>>>> The checksum verification is done in the PML, which the BTL calls
>>>>>>>>> via a callback function. In your case the PML callback is never
>>>>>>>>> called because the hdr->tag is invalid. So enabling checksum
>>>>>>>>> tracing also might not be of much use. Is it the first Bcast that
>>>>>>>>> fails or the nth Bcast and what is the message size? I'm not sure
>>>>>>>>> what could be the problem at this moment. I'm afraid you will have
>>>>>>>>> to debug the BTL to find out more.
>>>>>>>>>
>>>>>>>>> --Nysal
>>>>>>>>>
>>>>>>>>> On Fri, Sep 17, 2010 at 4:39 PM, Eloi Gaudry<eg_at_[hidden]> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Nysal,
>>>>>>>>>>
>>>>>>>>>> thanks for your response.
>>>>>>>>>>
>>>>>>>>>> I've been unable so far to write a test case that could illustrate
>>>>>>>>>> the hdr->tag=0 error.
>>>>>>>>>> Actually, I'm only observing this issue when running an internode
>>>>>>>>>> computation involving infiniband hardware from Mellanox (MT25418,
>>>>>>>>>> ConnectX IB DDR, PCIe 2.0
>>>>>>>>>> 2.5GT/s, rev a0) with our time-domain software.
>>>>>>>>>>
>>>>>>>>>> I checked, double-checked, and rechecked again every MPI use
>>>>>>>>>> performed during a parallel computation and I couldn't find any
>>>>>>>>>> error so far. The fact that the very
>>>>>>>>>> same parallel computation run flawlessly when using tcp (and
>>>>>>>>>> disabling openib support) might seem to indicate that the issue is
>>>>>>>>>> somewhere located inside the
>>>>>>>>>> openib btl or at the hardware/driver level.
>>>>>>>>>>
>>>>>>>>>> I've just used the "-mca pml csum" option and I haven't seen any
>>>>>>>>>> related messages (when hdr->tag=0 and the segfaults occurs).
>>>>>>>>>> Any suggestion ?
>>>>>>>>>>
>>>>>>>>>> Regards,
>>>>>>>>>> Eloi
>>>>>>>>>>
>>>>>>>>>> On Friday 17 September 2010 16:03:34 Nysal Jan wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Eloi,
>>>>>>>>>>> Sorry for the delay in response. I haven't read the entire email
>>>>>>>>>>> thread, but do you have a test case which can reproduce this
>>>>>>>>>>> error? Without that it will be difficult to nail down the cause.
>>>>>>>>>>> Just to clarify, I do not work for an iwarp vendor. I can
>>>>>>>>>>> certainly try to reproduce it on an IB system. There is also a
>>>>>>>>>>> PML called csum, you can use it via "-mca pml csum", which will
>>>>>>>>>>> checksum the MPI messages and verify it at the receiver side for
>>>>>>>>>>> any data
>>>>>>>>>>> corruption. You can try using it to see if it is able
>>>>>>>>>>>
>>>>>>>>>> to
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> catch anything.
>>>>>>>>>>>
>>>>>>>>>>> Regards
>>>>>>>>>>> --Nysal
>>>>>>>>>>>
>>>>>>>>>>> On Thu, Sep 16, 2010 at 3:48 PM, Eloi Gaudry<eg_at_[hidden]> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Nysal,
>>>>>>>>>>>>
>>>>>>>>>>>> I'm sorry to intrrupt, but I was wondering if you had a chance to
>>>>>>>>>>>> look
>>>>>>>>>>>>
>>>>>>>>>> at
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> this error.
>>>>>>>>>>>>
>>>>>>>>>>>> Regards,
>>>>>>>>>>>> Eloi
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Eloi Gaudry
>>>>>>>>>>>>
>>>>>>>>>>>> Free Field Technologies
>>>>>>>>>>>> Company Website:http://www.fft.be
>>>>>>>>>>>> Company Phone: +32 10 487 959
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> ---------- Forwarded message ----------
>>>>>>>>>>>> From: Eloi Gaudry<eg_at_[hidden]>
>>>>>>>>>>>> To: Open MPI Users<users_at_[hidden]>
>>>>>>>>>>>> Date: Wed, 15 Sep 2010 16:27:43 +0200
>>>>>>>>>>>> Subject: Re: [OMPI users] [openib] segfault when using openib btl
>>>>>>>>>>>> Hi,
>>>>>>>>>>>>
>>>>>>>>>>>> I was wondering if anybody got a chance to have a look at this
>>>>>>>>>>>> issue.
>>>>>>>>>>>>
>>>>>>>>>>>> Regards,
>>>>>>>>>>>> Eloi
>>>>>>>>>>>>
>>>>>>>>>>>> On Wednesday 18 August 2010 09:16:26 Eloi Gaudry wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Jeff,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Please find enclosed the output (valgrind.out.gz) from
>>>>>>>>>>>>> /opt/openmpi-debug-1.4.2/bin/orterun -np 2 --host pbn11,pbn10
>>>>>>>>>>>>> --mca
>>>>>>>>>>>>>
>>>>>>>>>> btl
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>> openib,self --display-map --verbose --mca mpi_warn_on_fork 0
>>>>>>>>>>>>> --mca btl_openib_want_fork_support 0 -tag-output
>>>>>>>>>>>>> /opt/valgrind-3.5.0/bin/valgrind --tool=memcheck
>>>>>>>>>>>>> --suppressions=/opt/openmpi-debug-1.4.2/share/openmpi/openmpi-
>>>>>>>>>>>>> valgrind.supp --suppressions=./suppressions.python.supp
>>>>>>>>>>>>> /opt/actran/bin/actranpy_mp ...
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tuesday 17 August 2010 09:32:53 Eloi Gaudry wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Monday 16 August 2010 19:14:47 Jeff Squyres wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Aug 16, 2010, at 10:05 AM, Eloi Gaudry wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> I did run our application through valgrind but it couldn't
>>>>>>>>>>>>>>>> find any "Invalid write": there is a bunch of "Invalid read"
>>>>>>>>>>>>>>>> (I'm using
>>>>>>>>>>>>>>>>
>>>>>>>>>>>> 1.4.2
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>> with the suppression file), "Use of uninitialized bytes" and
>>>>>>>>>>>>>>>> "Conditional jump depending on uninitialized bytes" in
>>>>>>>>>>>>>>>>
>>>>>>>>>> different
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> ompi
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>> routines. Some of them are located in btl_openib_component.c.
>>>>>>>>>>>>>>>> I'll send you an output of valgrind shortly.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> A lot of them in btl_openib_* are to be expected --
>>>>>>>>>>>>>>> OpenFabrics uses OS-bypass methods for some of its memory,
>>>>>>>>>>>>>>> and therefore valgrind is unaware of them (and therefore
>>>>>>>>>>>>>>> incorrectly marks them as
>>>>>>>>>>>>>>> uninitialized).
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> would it help if i use the upcoming 1.5 version of openmpi ? i
>>>>>>>>>>>>>>
>>>>>>>>>> read
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> that
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>> a huge effort has been done to clean-up the valgrind output ?
>>>>>>>>>>>>>> but maybe that this doesn't concern this btl (for the reasons
>>>>>>>>>>>>>> you mentionned).
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Another question, you said that the callback function pointer
>>>>>>>>>>>>>>>>
>>>>>>>>>>>> should
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>> never be 0. But can the tag be null (hdr->tag) ?
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> The tag is not a pointer -- it's just an integer.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I was worrying that its value could not be null.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I'll send a valgrind output soon (i need to build libpython
>>>>>>>>>>>>>> without pymalloc first).
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks for your help,
>>>>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> On 16/08/2010 18:22, Jeff Squyres wrote:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Sorry for the delay in replying.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Odd; the values of the callback function pointer should
>>>>>>>>>>>>>>>>> never
>>>>>>>>>>>>>>>>>
>>>>>>>>>> be
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> 0.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> This seems to suggest some kind of memory corruption is
>>>>>>>>>>>>>>>>> occurring.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> I don't know if it's possible, because the stack trace looks
>>>>>>>>>>>>>>>>> like you're calling through python, but can you run this
>>>>>>>>>>>>>>>>> application through valgrind, or some other memory-checking
>>>>>>>>>>>>>>>>> debugger?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Aug 10, 2010, at 7:15 AM, Eloi Gaudry wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> sorry, i just forgot to add the values of the function
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> parameters:
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> (gdb) print reg->cbdata
>>>>>>>>>>>>>>>>>> $1 = (void *) 0x0
>>>>>>>>>>>>>>>>>> (gdb) print openib_btl->super
>>>>>>>>>>>>>>>>>> $2 = {btl_component = 0x2b341edd7380, btl_eager_limit =
>>>>>>>>>>>>>>>>>>
>>>>>>>>>> 12288,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>> btl_rndv_eager_limit = 12288, btl_max_send_size = 65536,
>>>>>>>>>>>>>>>>>> btl_rdma_pipeline_send_length = 1048576,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> btl_rdma_pipeline_frag_size = 1048576,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> btl_min_rdma_pipeline_size
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> = 1060864, btl_exclusivity = 1024, btl_latency = 10,
>>>>>>>>>>>>>>>>>> btl_bandwidth = 800, btl_flags = 310, btl_add_procs =
>>>>>>>>>>>>>>>>>> 0x2b341eb8ee47<mca_btl_openib_add_procs>, btl_del_procs =
>>>>>>>>>>>>>>>>>> 0x2b341eb90156<mca_btl_openib_del_procs>, btl_register =
>>>>>>>>>>>>>>>>>> 0, btl_finalize =
>>>>>>>>>>>>>>>>>> 0x2b341eb93186<mca_btl_openib_finalize>,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> btl_alloc
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> = 0x2b341eb90a3e<mca_btl_openib_alloc>, btl_free =
>>>>>>>>>>>>>>>>>> 0x2b341eb91400<mca_btl_openib_free>, btl_prepare_src =
>>>>>>>>>>>>>>>>>> 0x2b341eb91813<mca_btl_openib_prepare_src>,
>>>>>>>>>>>>>>>>>> btl_prepare_dst
>>>>>>>>>>>>>>>>>>
>>>>>>>>>> =
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 0x2b341eb91f2e<mca_btl_openib_prepare_dst>, btl_send =
>>>>>>>>>>>>>>>>>> 0x2b341eb94517<mca_btl_openib_send>, btl_sendi =
>>>>>>>>>>>>>>>>>> 0x2b341eb9340d<mca_btl_openib_sendi>, btl_put =
>>>>>>>>>>>>>>>>>> 0x2b341eb94660<mca_btl_openib_put>, btl_get =
>>>>>>>>>>>>>>>>>> 0x2b341eb94c4e<mca_btl_openib_get>, btl_dump =
>>>>>>>>>>>>>>>>>> 0x2b341acd45cb<mca_btl_base_dump>, btl_mpool = 0xf3f4110,
>>>>>>>>>>>>>>>>>> btl_register_error =
>>>>>>>>>>>>>>>>>> 0x2b341eb90565<mca_btl_openib_register_error_cb>,
>>>>>>>>>>>>>>>>>> btl_ft_event
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> =
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 0x2b341eb952e7<mca_btl_openib_ft_event>}
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> (gdb) print hdr->tag
>>>>>>>>>>>>>>>>>> $3 = 0 '\0'
>>>>>>>>>>>>>>>>>> (gdb) print des
>>>>>>>>>>>>>>>>>> $4 = (mca_btl_base_descriptor_t *) 0xf4a6700
>>>>>>>>>>>>>>>>>> (gdb) print reg->cbfunc
>>>>>>>>>>>>>>>>>> $5 = (mca_btl_base_module_recv_cb_fn_t) 0
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Tuesday 10 August 2010 16:04:08 Eloi Gaudry wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Here is the output of a core file generated during a
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> segmentation
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> fault observed during a collective call (using openib):
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> #0 0x0000000000000000 in ?? ()
>>>>>>>>>>>>>>>>>>> (gdb) where
>>>>>>>>>>>>>>>>>>> #0 0x0000000000000000 in ?? ()
>>>>>>>>>>>>>>>>>>> #1 0x00002aedbc4e05f4 in btl_openib_handle_incoming
>>>>>>>>>>>>>>>>>>> (openib_btl=0x1902f9b0, ep=0x1908a1c0, frag=0x190d9700,
>>>>>>>>>>>>>>>>>>> byte_len=18) at btl_openib_component.c:2881 #2
>>>>>>>>>>>>>>>>>>> 0x00002aedbc4e25e2 in handle_wc (device=0x19024ac0, cq=0,
>>>>>>>>>>>>>>>>>>> wc=0x7ffff279ce90) at
>>>>>>>>>>>>>>>>>>> btl_openib_component.c:3178 #3 0x00002aedbc4e2e9d in
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> poll_device
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> (device=0x19024ac0, count=2) at
>>>>>>>>>>>>>>>>>>> btl_openib_component.c:3318
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> #4
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> 0x00002aedbc4e34b8 in progress_one_device
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> (device=0x19024ac0)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> at btl_openib_component.c:3426 #5 0x00002aedbc4e3561 in
>>>>>>>>>>>>>>>>>>> btl_openib_component_progress () at
>>>>>>>>>>>>>>>>>>> btl_openib_component.c:3451
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> #6
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> 0x00002aedb8b22ab8 in opal_progress () at
>>>>>>>>>>>>>>>>>>> runtime/opal_progress.c:207 #7 0x00002aedb859f497 in
>>>>>>>>>>>>>>>>>>> opal_condition_wait (c=0x2aedb888ccc0, m=0x2aedb888cd20)
>>>>>>>>>>>>>>>>>>> at ../opal/threads/condition.h:99 #8
>>>>>>>>>>>>>>>>>>> 0x00002aedb859fa31 in ompi_request_default_wait_all
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> (count=2,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> requests=0x7ffff279d0e0, statuses=0x0) at
>>>>>>>>>>>>>>>>>>> request/req_wait.c:262 #9 0x00002aedbd7559ad in
>>>>>>>>>>>>>>>>>>> ompi_coll_tuned_allreduce_intra_recursivedoubling
>>>>>>>>>>>>>>>>>>> (sbuf=0x7ffff279d444, rbuf=0x7ffff279d440, count=1,
>>>>>>>>>>>>>>>>>>> dtype=0x6788220, op=0x6787a20,
>>>>>>>>>>>>>>>>>>> comm=0x19d81ff0, module=0x19d82b20) at
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> coll_tuned_allreduce.c:223
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> #10 0x00002aedbd7514f7 in
>>>>>>>>>>>>>>>>>>> ompi_coll_tuned_allreduce_intra_dec_fixed
>>>>>>>>>>>>>>>>>>> (sbuf=0x7ffff279d444, rbuf=0x7ffff279d440, count=1,
>>>>>>>>>>>>>>>>>>> dtype=0x6788220, op=0x6787a20, comm=0x19d81ff0,
>>>>>>>>>>>>>>>>>>> module=0x19d82b20) at
>>>>>>>>>>>>>>>>>>> coll_tuned_decision_fixed.c:63
>>>>>>>>>>>>>>>>>>> #11 0x00002aedb85c7792 in PMPI_Allreduce
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> (sendbuf=0x7ffff279d444,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> recvbuf=0x7ffff279d440, count=1, datatype=0x6788220,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> op=0x6787a20,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> comm=0x19d81ff0) at pallreduce.c:102 #12
>>>>>>>>>>>>>>>>>>> 0x0000000004387dbf
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> in
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> FEMTown::MPI::Allreduce (sendbuf=0x7ffff279d444,
>>>>>>>>>>>>>>>>>>> recvbuf=0x7ffff279d440, count=1, datatype=0x6788220,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> op=0x6787a20,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> comm=0x19d81ff0) at stubs.cpp:626 #13 0x0000000004058be8
>>>>>>>>>>>>>>>>>>> in FEMTown::Domain::align (itf=
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> {<FEMTown::Boost::shared_base_ptr<FEMTown::Domain::Int
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> er fa ce>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> = {_vptr.shared_base_ptr = 0x7ffff279d620, ptr_ = {px =
>>>>>>>>>>>>>>>>>>> 0x199942a4, pn = {pi_ = 0x6}}},<No data fields>}) at
>>>>>>>>>>>>>>>>>>> interface.cpp:371 #14 0x00000000040cb858 in
>>>>>>>>>>>>>>>>>>> FEMTown::Field::detail::align_itfs_and_neighbhors (dim=2,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> set={px
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> = 0x7ffff279d780, pn = {pi_ = 0x2f279d640}},
>>>>>>>>>>>>>>>>>>> check_info=@0x7ffff279d7f0) at check.cpp:63 #15
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> 0x00000000040cbfa8
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> in FEMTown::Field::align_elements (set={px =
>>>>>>>>>>>>>>>>>>> 0x7ffff279d950, pn
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> =
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> {pi_ = 0x66e08d0}}, check_info=@0x7ffff279d7f0) at
>>>>>>>>>>>>>>>>>>> check.cpp:159 #16 0x00000000039acdd4 in
>>>>>>>>>>>>>>>>>>> PyField_align_elements (self=0x0, args=0x2aaab0765050,
>>>>>>>>>>>>>>>>>>> kwds=0x19d2e950) at check.cpp:31 #17 0x0000000001fbf76d in
>>>>>>>>>>>>>>>>>>> FEMTown::Main::ExErrCatch<_object* (*)(_object*, _object*,
>>>>>>>>>>>>>>>>>>> _object*)>::exec<_object>
>>>>>>>>>>>>>>>>>>> (this=0x7ffff279dc20, s=0x0, po1=0x2aaab0765050,
>>>>>>>>>>>>>>>>>>> po2=0x19d2e950) at
>>>>>>>>>>>>>>>>>>> /home/qa/svntop/femtown/modules/main/py/exception.hpp:463
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> #18
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> 0x00000000039acc82 in PyField_align_elements_ewrap
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> (self=0x0,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> args=0x2aaab0765050, kwds=0x19d2e950) at check.cpp:39 #19
>>>>>>>>>>>>>>>>>>> 0x00000000044093a0 in PyEval_EvalFrameEx (f=0x19b52e90,
>>>>>>>>>>>>>>>>>>> throwflag=<value optimized out>) at Python/ceval.c:3921
>>>>>>>>>>>>>>>>>>> #20 0x000000000440aae9 in PyEval_EvalCodeEx
>>>>>>>>>>>>>>>>>>> (co=0x2aaab754ad50, globals=<value optimized out>,
>>>>>>>>>>>>>>>>>>> locals=<value optimized out>, args=0x3, argcount=1,
>>>>>>>>>>>>>>>>>>> kws=0x19ace4a0, kwcount=2,
>>>>>>>>>>>>>>>>>>> defs=0x2aaab75e4800, defcount=2, closure=0x0) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:2968
>>>>>>>>>>>>>>>>>>> #21 0x0000000004408f58 in PyEval_EvalFrameEx
>>>>>>>>>>>>>>>>>>> (f=0x19ace2d0, throwflag=<value optimized out>) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:3802 #22 0x000000000440aae9 in
>>>>>>>>>>>>>>>>>>> PyEval_EvalCodeEx (co=0x2aaab7550120, globals=<value
>>>>>>>>>>>>>>>>>>> optimized out>, locals=<value optimized out>, args=0x7,
>>>>>>>>>>>>>>>>>>> argcount=1, kws=0x19acc418, kwcount=3,
>>>>>>>>>>>>>>>>>>> defs=0x2aaab759e958, defcount=6, closure=0x0) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:2968
>>>>>>>>>>>>>>>>>>> #23 0x0000000004408f58 in PyEval_EvalFrameEx
>>>>>>>>>>>>>>>>>>> (f=0x19acc1c0, throwflag=<value optimized out>) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:3802 #24 0x000000000440aae9 in
>>>>>>>>>>>>>>>>>>> PyEval_EvalCodeEx (co=0x2aaab8b5e738, globals=<value
>>>>>>>>>>>>>>>>>>> optimized out>, locals=<value optimized out>, args=0x6,
>>>>>>>>>>>>>>>>>>> argcount=1, kws=0x19abd328, kwcount=5,
>>>>>>>>>>>>>>>>>>> defs=0x2aaab891b7e8, defcount=3, closure=0x0) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:2968
>>>>>>>>>>>>>>>>>>> #25 0x0000000004408f58 in PyEval_EvalFrameEx
>>>>>>>>>>>>>>>>>>> (f=0x19abcea0, throwflag=<value optimized out>) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:3802 #26 0x000000000440aae9 in
>>>>>>>>>>>>>>>>>>> PyEval_EvalCodeEx (co=0x2aaab3eb4198, globals=<value
>>>>>>>>>>>>>>>>>>> optimized out>, locals=<value optimized out>, args=0xb,
>>>>>>>>>>>>>>>>>>> argcount=1, kws=0x19a89df0, kwcount=10, defs=0x0,
>>>>>>>>>>>>>>>>>>> defcount=0, closure=0x0) at Python/ceval.c:2968
>>>>>>>>>>>>>>>>>>> #27 0x0000000004408f58 in PyEval_EvalFrameEx
>>>>>>>>>>>>>>>>>>> (f=0x19a89c40, throwflag=<value optimized out>) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:3802 #28 0x000000000440aae9 in
>>>>>>>>>>>>>>>>>>> PyEval_EvalCodeEx (co=0x2aaab3eb4288, globals=<value
>>>>>>>>>>>>>>>>>>> optimized out>, locals=<value optimized out>, args=0x1,
>>>>>>>>>>>>>>>>>>> argcount=0, kws=0x19a89330, kwcount=0,
>>>>>>>>>>>>>>>>>>> defs=0x2aaab8b66668, defcount=1, closure=0x0) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:2968
>>>>>>>>>>>>>>>>>>> #29 0x0000000004408f58 in PyEval_EvalFrameEx
>>>>>>>>>>>>>>>>>>> (f=0x19a891b0, throwflag=<value optimized out>) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:3802 #30 0x000000000440aae9 in
>>>>>>>>>>>>>>>>>>> PyEval_EvalCodeEx (co=0x2aaab8b6a738, globals=<value
>>>>>>>>>>>>>>>>>>> optimized out>, locals=<value optimized out>, args=0x0,
>>>>>>>>>>>>>>>>>>> argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0,
>>>>>>>>>>>>>>>>>>> closure=0x0) at
>>>>>>>>>>>>>>>>>>> Python/ceval.c:2968
>>>>>>>>>>>>>>>>>>> #31 0x000000000440ac02 in PyEval_EvalCode (co=0x1902f9b0,
>>>>>>>>>>>>>>>>>>> globals=0x0, locals=0x190d9700) at Python/ceval.c:522 #32
>>>>>>>>>>>>>>>>>>> 0x000000000442853c in PyRun_StringFlags (str=0x192fd3d8
>>>>>>>>>>>>>>>>>>> "DIRECT.Actran.main()", start=<value optimized out>,
>>>>>>>>>>>>>>>>>>> globals=0x192213d0, locals=0x192213d0, flags=0x0) at
>>>>>>>>>>>>>>>>>>> Python/pythonrun.c:1335 #33 0x0000000004429690 in
>>>>>>>>>>>>>>>>>>> PyRun_SimpleStringFlags (command=0x192fd3d8
>>>>>>>>>>>>>>>>>>> "DIRECT.Actran.main()", flags=0x0) at
>>>>>>>>>>>>>>>>>>> Python/pythonrun.c:957 #34 0x0000000001fa1cf9 in
>>>>>>>>>>>>>>>>>>> FEMTown::Python::FEMPy::run_application
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> (this=0x7ffff279f650)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> at fempy.cpp:873 #35 0x000000000434ce99 in
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> FEMTown::Main::Batch::run
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> (this=0x7ffff279f650) at batch.cpp:374 #36
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> 0x0000000001f9aa25
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> in main (argc=8, argv=0x7ffff279fa48) at main.cpp:10 (gdb)
>>>>>>>>>>>>>>>>>>> f 1 #1 0x00002aedbc4e05f4 in btl_openib_handle_incoming
>>>>>>>>>>>>>>>>>>> (openib_btl=0x1902f9b0, ep=0x1908a1c0, frag=0x190d9700,
>>>>>>>>>>>>>>>>>>> byte_len=18) at btl_openib_component.c:2881 2881
>>>>>>>>>>>>>>>>>>> reg->cbfunc(&openib_btl->super, hdr->tag, des,
>>>>>>>>>>>>>>>>>>> reg->cbdata
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> );
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Current language: auto; currently c
>>>>>>>>>>>>>>>>>>> (gdb)
>>>>>>>>>>>>>>>>>>> #1 0x00002aedbc4e05f4 in btl_openib_handle_incoming
>>>>>>>>>>>>>>>>>>> (openib_btl=0x1902f9b0, ep=0x1908a1c0, frag=0x190d9700,
>>>>>>>>>>>>>>>>>>> byte_len=18) at btl_openib_component.c:2881 2881
>>>>>>>>>>>>>>>>>>> reg->cbfunc(&openib_btl->super, hdr->tag, des,
>>>>>>>>>>>>>>>>>>> reg->cbdata
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> );
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> (gdb) l 2876
>>>>>>>>>>>>>>>>>>> 2877 if(OPAL_LIKELY(!(is_credit_msg =
>>>>>>>>>>>>>>>>>>> is_credit_message(frag)))) { 2878 /* call
>>>>>>>>>>>>>>>>>>> registered callback */
>>>>>>>>>>>>>>>>>>> 2879 mca_btl_active_message_callback_t* reg;
>>>>>>>>>>>>>>>>>>> 2880 reg = mca_btl_base_active_message_trigger
>>>>>>>>>>>>>>>>>>> + hdr->tag; 2881
>>>>>>>>>>>>>>>>>>> reg->cbfunc(&openib_btl->super, hdr->tag, des,
>>>>>>>>>>>>>>>>>>> reg->cbdata ); 2882
>>>>>>>>>>>>>>>>>>> if(MCA_BTL_OPENIB_RDMA_FRAG(frag)) { 2883
>>>>>>>>>>>>>>>>>>> cqp
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> =
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> (hdr->credits>> 11)& 0x0f;
>>>>>>>>>>>>>>>>>>> 2884 hdr->credits&= 0x87ff;
>>>>>>>>>>>>>>>>>>> 2885 } else {
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Friday 16 July 2010 16:01:02 Eloi Gaudry wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Edgar,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The only difference I could observed was that the
>>>>>>>>>>>>>>>>>>>> segmentation fault appeared sometimes later during the
>>>>>>>>>>>>>>>>>>>> parallel computation.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I'm running out of idea here. I wish I could use the
>>>>>>>>>>>>>>>>>>>> "--mca
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> coll
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> tuned" with "--mca self,sm,tcp" so that I could check
>>>>>>>>>>>>>>>>>>>> that the issue is not somehow limited to the tuned
>>>>>>>>>>>>>>>>>>>> collective routines.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Thursday 15 July 2010 17:24:24 Edgar Gabriel wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On 7/15/2010 10:18 AM, Eloi Gaudry wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> hi edgar,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> thanks for the tips, I'm gonna try this option as well.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> the
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> segmentation fault i'm observing always happened during
>>>>>>>>>>>>>>>>>>>>>> a collective communication indeed... does it basically
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> switch
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> all
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> collective communication to basic mode, right ?
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> sorry for my ignorance, but what's a NCA ?
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> sorry, I meant to type HCA (InifinBand networking card)
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>> Edgar
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> thanks,
>>>>>>>>>>>>>>>>>>>>>> éloi
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Thursday 15 July 2010 16:20:54 Edgar Gabriel wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> you could try first to use the algorithms in the basic
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> module,
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> e.g.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> mpirun -np x --mca coll basic ./mytest
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> and see whether this makes a difference. I used to
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> observe
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> sometimes a (similar ?) problem in the openib btl
>>>>>>>>>>>>>>>>>>>>>>> triggered from the tuned collective component, in
>>>>>>>>>>>>>>>>>>>>>>> cases where the ofed libraries were installed but no
>>>>>>>>>>>>>>>>>>>>>>> NCA was found on a node. It used to work however with
>>>>>>>>>>>>>>>>>>>>>>> the basic component.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>> Edgar
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On 7/15/2010 3:08 AM, Eloi Gaudry wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> hi Rolf,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> unfortunately, i couldn't get rid of that annoying
>>>>>>>>>>>>>>>>>>>>>>>> segmentation fault when selecting another bcast
>>>>>>>>>>>>>>>>>>>>>>>> algorithm. i'm now going to replace MPI_Bcast with a
>>>>>>>>>>>>>>>>>>>>>>>> naive
>>>>>>>>>>>>>>>>>>>>>>>> implementation (using MPI_Send and MPI_Recv) and see
>>>>>>>>>>>>>>>>>>>>>>>> if
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> that
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> helps.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> regards,
>>>>>>>>>>>>>>>>>>>>>>>> éloi
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Wednesday 14 July 2010 10:59:53 Eloi Gaudry wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi Rolf,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> thanks for your input. You're right, I miss the
>>>>>>>>>>>>>>>>>>>>>>>>> coll_tuned_use_dynamic_rules option.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> I'll check if I the segmentation fault disappears
>>>>>>>>>>>>>>>>>>>>>>>>> when
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> using
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> the basic bcast linear algorithm using the proper
>>>>>>>>>>>>>>>>>>>>>>>>> command line you provided.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Tuesday 13 July 2010 20:39:59 Rolf vandeVaart
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Eloi:
>>>>>>>>>>>>>>>>>>>>>>>>>> To select the different bcast algorithms, you need
>>>>>>>>>>>>>>>>>>>>>>>>>> to add an extra mca parameter that tells the
>>>>>>>>>>>>>>>>>>>>>>>>>> library to use dynamic selection. --mca
>>>>>>>>>>>>>>>>>>>>>>>>>> coll_tuned_use_dynamic_rules 1
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> One way to make sure you are typing this in
>>>>>>>>>>>>>>>>>>>>>>>>>> correctly is
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> to
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> use it with ompi_info. Do the following:
>>>>>>>>>>>>>>>>>>>>>>>>>> ompi_info -mca coll_tuned_use_dynamic_rules 1
>>>>>>>>>>>>>>>>>>>>>>>>>> --param
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> coll
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> You should see lots of output with all the
>>>>>>>>>>>>>>>>>>>>>>>>>> different algorithms that can be selected for the
>>>>>>>>>>>>>>>>>>>>>>>>>> various collectives. Therefore, you need this:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> --mca coll_tuned_use_dynamic_rules 1 --mca
>>>>>>>>>>>>>>>>>>>>>>>>>> coll_tuned_bcast_algorithm 1
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Rolf
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> On 07/13/10 11:28, Eloi Gaudry wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> I've found that "--mca coll_tuned_bcast_algorithm
>>>>>>>>>>>>>>>>>>>>>>>>>>> 1" allowed to switch to the basic linear
>>>>>>>>>>>>>>>>>>>>>>>>>>> algorithm. Anyway whatever the algorithm used,
>>>>>>>>>>>>>>>>>>>>>>>>>>> the segmentation fault remains.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Does anyone could give some advice on ways to
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> diagnose
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> the
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> issue I'm facing ?
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Regards,
>>>>>>>>>>>>>>>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> On Monday 12 July 2010 10:53:58 Eloi Gaudry wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> I'm focusing on the MPI_Bcast routine that seems
>>>>>>>>>>>>>>>>>>>>>>>>>>>> to randomly segfault when using the openib btl.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> I'd
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> like
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> to
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> know if there is any way to make OpenMPI switch
>>>>>>>>>>>>>>>>>>>>>>>>>>>> to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> a
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> different algorithm than the default one being
>>>>>>>>>>>>>>>>>>>>>>>>>>>> selected for MPI_Bcast.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks for your help,
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Friday 02 July 2010 11:06:52 Eloi Gaudry wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I'm observing a random segmentation fault during
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> an
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> internode parallel computation involving the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> openib
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>> btl
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and OpenMPI-1.4.2 (the same issue can be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> observed with OpenMPI-1.3.3).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mpirun (Open MPI) 1.4.2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Report bugs to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://www.open-mpi.org/community/help/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [pbn08:02624] *** Process received signal ***
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [pbn08:02624] Signal: Segmentation fault (11)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [pbn08:02624] Signal code: Address not mapped
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>> (1)
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [pbn08:02624] Failing at address: (nil)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [pbn08:02624] [ 0] /lib64/libpthread.so.0
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [0x349540e4c0] [pbn08:02624] *** End of error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> message
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ***
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sh: line 1: 2624 Segmentation fault
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> \/share\/hpc3\/actran_suite\/Actran_11\.0\.rc2\.41872\/R
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ed Ha tE L\ -5 \/ x 86 _6 4\ /bin\/actranpy_mp
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> '--apl=/share/hpc3/actran_suite/Actran_11.0.rc2.41872/Re
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dH at EL -5 /x 86 _ 64 /A c tran_11.0.rc2.41872'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> '--inputfile=/work/st25652/LSF_130073_0_47696_0/Case1_3D
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> re al _m 4_ n2 .d a t'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> '--scratch=/scratch/st25652/LSF_130073_0_47696_0/scratch
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ' '--mem=3200' '--threads=1'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> '--errorlevel=FATAL' '--t_max=0.1'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> '--parallel=domain'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If I choose not to use the openib btl (by using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --mca btl self,sm,tcp on the command line, for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> instance), I don't encounter any problem and the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> parallel computation runs flawlessly.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I would like to get some help to be able:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - to diagnose the issue I'm facing with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> openib btl - understand why this issue is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> observed only when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> using
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the openib btl and not when using self,sm,tcp
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Any help would be very much appreciated.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The outputs of ompi_info and the configure
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts of OpenMPI are enclosed to this email,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and some
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> information
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on the infiniband drivers as well.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Here is the command line used when launching a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> parallel
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> computation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using infiniband:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path_to_openmpi/bin/mpirun -np $NPROCESS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --hostfile host.list --mca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> btl openib,sm,self,tcp --display-map --verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --version --mca mpi_warn_on_fork 0 --mca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> btl_openib_want_fork_support 0 [...]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the command line used if not using infiniband:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> path_to_openmpi/bin/mpirun -np $NPROCESS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --hostfile host.list --mca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> btl self,sm,tcp --display-map --verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --version
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> --mca
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mpi_warn_on_fork 0 --mca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> btl_openib_want_fork_support
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>> 0
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [...]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Eloi
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> users mailing list
>>>>>>>> users_at_[hidden]
>>>>>>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>>>>>>
>>
>>