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Subject: Re: [OMPI users] Dynamic processes connection and segfault on MPI_Comm_accept
From: Grzegorz Maj (maju3_at_[hidden])
Date: 2010-07-12 14:13:37


2010/7/12 Ralph Castain <rhc_at_[hidden]>:
> Dug around a bit and found the problem!!
>
> I have no idea who or why this was done, but somebody set a limit of 64 separate jobids in the dynamic init called by ompi_comm_set, which builds the intercommunicator. Unfortunately, they hard-wired the array size, but never check that size before adding to it.
>
> So after 64 calls to connect_accept, you are overwriting other areas of the code. As you found, hitting 66 causes it to segfault.
>
> I'll fix this on the developer's trunk (I'll also add that original patch to it). Rather than my searching this thread in detail, can you remind me what version you are using so I can patch it too?

I'm using 1.4.2
Thanks a lot and I'm looking forward for the patch.

>
> Thanks for your patience with this!
> Ralph
>
>
> On Jul 12, 2010, at 7:20 AM, Grzegorz Maj wrote:
>
>> 1024 is not the problem: changing it to 2048 hasn't change anything.
>> Following your advice I've run my process using gdb. Unfortunately I
>> didn't get anything more than:
>>
>> Program received signal SIGSEGV, Segmentation fault.
>> [Switching to Thread 0xf7e4c6c0 (LWP 20246)]
>> 0xf7f39905 in ompi_comm_set () from /home/gmaj/openmpi/lib/libmpi.so.0
>>
>> (gdb) bt
>> #0  0xf7f39905 in ompi_comm_set () from /home/gmaj/openmpi/lib/libmpi.so.0
>> #1  0xf7e3ba95 in connect_accept () from
>> /home/gmaj/openmpi/lib/openmpi/mca_dpm_orte.so
>> #2  0xf7f62013 in PMPI_Comm_connect () from /home/gmaj/openmpi/lib/libmpi.so.0
>> #3  0x080489ed in main (argc=825832753, argv=0x34393638) at client.c:43
>>
>> What's more: when I've added a breakpoint on ompi_comm_set in 66th
>> process and stepped a couple of instructions, one of the other
>> processes crashed (as usualy on ompi_comm_set) earlier than 66th did.
>>
>> Finally I decided to recompile openmpi using -g flag for gcc. In this
>> case the 66 processes issue has gone! I was running my applications
>> exactly the same way as previously (even without recompilation) and
>> I've run successfully over 130 processes.
>> When switching back to the openmpi compilation without -g it again segfaults.
>>
>> Any ideas? I'm really confused.
>>
>>
>>
>> 2010/7/7 Ralph Castain <rhc_at_[hidden]>:
>>> I would guess the #files limit of 1024. However, if it behaves the same way when spread across multiple machines, I would suspect it is somewhere in your program itself. Given that the segfault is in your process, can you use gdb to look at the core file and see where and why it fails?
>>>
>>> On Jul 7, 2010, at 10:17 AM, Grzegorz Maj wrote:
>>>
>>>> 2010/7/7 Ralph Castain <rhc_at_[hidden]>:
>>>>>
>>>>> On Jul 6, 2010, at 8:48 AM, Grzegorz Maj wrote:
>>>>>
>>>>>> Hi Ralph,
>>>>>> sorry for the late response, but I couldn't find free time to play
>>>>>> with this. Finally I've applied the patch you prepared. I've launched
>>>>>> my processes in the way you've described and I think it's working as
>>>>>> you expected. None of my processes runs the orted daemon and they can
>>>>>> perform MPI operations. Unfortunately I'm still hitting the 65
>>>>>> processes issue :(
>>>>>> Maybe I'm doing something wrong.
>>>>>> I attach my source code. If anybody could have a look on this, I would
>>>>>> be grateful.
>>>>>>
>>>>>> When I run that code with clients_count <= 65 everything works fine:
>>>>>> all the processes create a common grid, exchange some information and
>>>>>> disconnect.
>>>>>> When I set clients_count > 65 the 66th process crashes on
>>>>>> MPI_Comm_connect (segmentation fault).
>>>>>
>>>>> I didn't have time to check the code, but my guess is that you are still hitting some kind of file descriptor or other limit. Check to see what your limits are - usually "ulimit" will tell you.
>>>>
>>>> My limitations are:
>>>> time(seconds)        unlimited
>>>> file(blocks)         unlimited
>>>> data(kb)             unlimited
>>>> stack(kb)            10240
>>>> coredump(blocks)     0
>>>> memory(kb)           unlimited
>>>> locked memory(kb)    64
>>>> process              200704
>>>> nofiles              1024
>>>> vmemory(kb)          unlimited
>>>> locks                unlimited
>>>>
>>>> Which one do you think could be responsible for that?
>>>>
>>>> I was trying to run all the 66 processes on one machine or spread them
>>>> across several machines and it always crashes the same way on the 66th
>>>> process.
>>>>
>>>>>
>>>>>>
>>>>>> Another thing I would like to know is if it's normal that any of my
>>>>>> processes when calling MPI_Comm_connect or MPI_Comm_accept when the
>>>>>> other side is not ready, is eating up a full CPU available.
>>>>>
>>>>> Yes - the waiting process is polling in a tight loop waiting for the connection to be made.
>>>>>
>>>>>>
>>>>>> Any help would be appreciated,
>>>>>> Grzegorz Maj
>>>>>>
>>>>>>
>>>>>> 2010/4/24 Ralph Castain <rhc_at_[hidden]>:
>>>>>>> Actually, OMPI is distributed with a daemon that does pretty much what you
>>>>>>> want. Checkout "man ompi-server". I originally wrote that code to support
>>>>>>> cross-application MPI publish/subscribe operations, but we can utilize it
>>>>>>> here too. Have to blame me for not making it more publicly known.
>>>>>>> The attached patch upgrades ompi-server and modifies the singleton startup
>>>>>>> to provide your desired support. This solution works in the following
>>>>>>> manner:
>>>>>>> 1. launch "ompi-server -report-uri <filename>". This starts a persistent
>>>>>>> daemon called "ompi-server" that acts as a rendezvous point for
>>>>>>> independently started applications.  The problem with starting different
>>>>>>> applications and wanting them to MPI connect/accept lies in the need to have
>>>>>>> the applications find each other. If they can't discover contact info for
>>>>>>> the other app, then they can't wire up their interconnects. The
>>>>>>> "ompi-server" tool provides that rendezvous point. I don't like that
>>>>>>> comm_accept segfaulted - should have just error'd out.
>>>>>>> 2. set OMPI_MCA_orte_server=file:<filename>" in the environment where you
>>>>>>> will start your processes. This will allow your singleton processes to find
>>>>>>> the ompi-server. I automatically also set the envar to connect the MPI
>>>>>>> publish/subscribe system for you.
>>>>>>> 3. run your processes. As they think they are singletons, they will detect
>>>>>>> the presence of the above envar and automatically connect themselves to the
>>>>>>> "ompi-server" daemon. This provides each process with the ability to perform
>>>>>>> any MPI-2 operation.
>>>>>>> I tested this on my machines and it worked, so hopefully it will meet your
>>>>>>> needs. You only need to run one "ompi-server" period, so long as you locate
>>>>>>> it where all of the processes can find the contact file and can open a TCP
>>>>>>> socket to the daemon. There is a way to knit multiple ompi-servers into a
>>>>>>> broader network (e.g., to connect processes that cannot directly access a
>>>>>>> server due to network segmentation), but it's a tad tricky - let me know if
>>>>>>> you require it and I'll try to help.
>>>>>>> If you have trouble wiring them all into a single communicator, you might
>>>>>>> ask separately about that and see if one of our MPI experts can provide
>>>>>>> advice (I'm just the RTE grunt).
>>>>>>> HTH - let me know how this works for you and I'll incorporate it into future
>>>>>>> OMPI releases.
>>>>>>> Ralph
>>>>>>>
>>>>>>>
>>>>>>> On Apr 24, 2010, at 1:49 AM, Krzysztof Zarzycki wrote:
>>>>>>>
>>>>>>> Hi Ralph,
>>>>>>> I'm Krzysztof and I'm working with Grzegorz Maj on this our small
>>>>>>> project/experiment.
>>>>>>> We definitely would like to give your patch a try. But could you please
>>>>>>> explain your solution a little more?
>>>>>>> You still would like to start one mpirun per mpi grid, and then have
>>>>>>> processes started by us to join the MPI comm?
>>>>>>> It is a good solution of course.
>>>>>>> But it would be especially preferable to have one daemon running
>>>>>>> persistently on our "entry" machine that can handle several mpi grid starts.
>>>>>>> Can your patch help us this way too?
>>>>>>> Thanks for your help!
>>>>>>> Krzysztof
>>>>>>>
>>>>>>> On 24 April 2010 03:51, Ralph Castain <rhc_at_[hidden]> wrote:
>>>>>>>>
>>>>>>>> In thinking about this, my proposed solution won't entirely fix the
>>>>>>>> problem - you'll still wind up with all those daemons. I believe I can
>>>>>>>> resolve that one as well, but it would require a patch.
>>>>>>>>
>>>>>>>> Would you like me to send you something you could try? Might take a couple
>>>>>>>> of iterations to get it right...
>>>>>>>>
>>>>>>>> On Apr 23, 2010, at 12:12 PM, Ralph Castain wrote:
>>>>>>>>
>>>>>>>>> Hmmm....I -think- this will work, but I cannot guarantee it:
>>>>>>>>>
>>>>>>>>> 1. launch one process (can just be a spinner) using mpirun that includes
>>>>>>>>> the following option:
>>>>>>>>>
>>>>>>>>> mpirun -report-uri file
>>>>>>>>>
>>>>>>>>> where file is some filename that mpirun can create and insert its
>>>>>>>>> contact info into it. This can be a relative or absolute path. This process
>>>>>>>>> must remain alive throughout your application - doesn't matter what it does.
>>>>>>>>> It's purpose is solely to keep mpirun alive.
>>>>>>>>>
>>>>>>>>> 2. set OMPI_MCA_dpm_orte_server=FILE:file in your environment, where
>>>>>>>>> "file" is the filename given above. This will tell your processes how to
>>>>>>>>> find mpirun, which is acting as a meeting place to handle the connect/accept
>>>>>>>>> operations
>>>>>>>>>
>>>>>>>>> Now run your processes, and have them connect/accept to each other.
>>>>>>>>>
>>>>>>>>> The reason I cannot guarantee this will work is that these processes
>>>>>>>>> will all have the same rank && name since they all start as singletons.
>>>>>>>>> Hence, connect/accept is likely to fail.
>>>>>>>>>
>>>>>>>>> But it -might- work, so you might want to give it a try.
>>>>>>>>>
>>>>>>>>> On Apr 23, 2010, at 8:10 AM, Grzegorz Maj wrote:
>>>>>>>>>
>>>>>>>>>> To be more precise: by 'server process' I mean some process that I
>>>>>>>>>> could run once on my system and it could help in creating those
>>>>>>>>>> groups.
>>>>>>>>>> My typical scenario is:
>>>>>>>>>> 1. run N separate processes, each without mpirun
>>>>>>>>>> 2. connect them into MPI group
>>>>>>>>>> 3. do some job
>>>>>>>>>> 4. exit all N processes
>>>>>>>>>> 5. goto 1
>>>>>>>>>>
>>>>>>>>>> 2010/4/23 Grzegorz Maj <maju3_at_[hidden]>:
>>>>>>>>>>> Thank you Ralph for your explanation.
>>>>>>>>>>> And, apart from that descriptors' issue, is there any other way to
>>>>>>>>>>> solve my problem, i.e. to run separately a number of processes,
>>>>>>>>>>> without mpirun and then to collect them into an MPI intracomm group?
>>>>>>>>>>> If I for example would need to run some 'server process' (even using
>>>>>>>>>>> mpirun) for this task, that's OK. Any ideas?
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Grzegorz Maj
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> 2010/4/18 Ralph Castain <rhc_at_[hidden]>:
>>>>>>>>>>>> Okay, but here is the problem. If you don't use mpirun, and are not
>>>>>>>>>>>> operating in an environment we support for "direct" launch (i.e., starting
>>>>>>>>>>>> processes outside of mpirun), then every one of those processes thinks it is
>>>>>>>>>>>> a singleton - yes?
>>>>>>>>>>>>
>>>>>>>>>>>> What you may not realize is that each singleton immediately
>>>>>>>>>>>> fork/exec's an orted daemon that is configured to behave just like mpirun.
>>>>>>>>>>>> This is required in order to support MPI-2 operations such as
>>>>>>>>>>>> MPI_Comm_spawn, MPI_Comm_connect/accept, etc.
>>>>>>>>>>>>
>>>>>>>>>>>> So if you launch 64 processes that think they are singletons, then
>>>>>>>>>>>> you have 64 copies of orted running as well. This eats up a lot of file
>>>>>>>>>>>> descriptors, which is probably why you are hitting this 65 process limit -
>>>>>>>>>>>> your system is probably running out of file descriptors. You might check you
>>>>>>>>>>>> system limits and see if you can get them revised upward.
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Apr 17, 2010, at 4:24 PM, Grzegorz Maj wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Yes, I know. The problem is that I need to use some special way for
>>>>>>>>>>>>> running my processes provided by the environment in which I'm
>>>>>>>>>>>>> working
>>>>>>>>>>>>> and unfortunately I can't use mpirun.
>>>>>>>>>>>>>
>>>>>>>>>>>>> 2010/4/18 Ralph Castain <rhc_at_[hidden]>:
>>>>>>>>>>>>>> Guess I don't understand why you can't use mpirun - all it does is
>>>>>>>>>>>>>> start things, provide a means to forward io, etc. It mainly sits there
>>>>>>>>>>>>>> quietly without using any cpu unless required to support the job.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sounds like it would solve your problem. Otherwise, I know of no
>>>>>>>>>>>>>> way to get all these processes into comm_world.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Apr 17, 2010, at 2:27 PM, Grzegorz Maj wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>> I'd like to dynamically create a group of processes communicating
>>>>>>>>>>>>>>> via
>>>>>>>>>>>>>>> MPI. Those processes need to be run without mpirun and create
>>>>>>>>>>>>>>> intracommunicator after the startup. Any ideas how to do this
>>>>>>>>>>>>>>> efficiently?
>>>>>>>>>>>>>>> I came up with a solution in which the processes are connecting
>>>>>>>>>>>>>>> one by
>>>>>>>>>>>>>>> one using MPI_Comm_connect, but unfortunately all the processes
>>>>>>>>>>>>>>> that
>>>>>>>>>>>>>>> are already in the group need to call MPI_Comm_accept. This means
>>>>>>>>>>>>>>> that
>>>>>>>>>>>>>>> when the n-th process wants to connect I need to collect all the
>>>>>>>>>>>>>>> n-1
>>>>>>>>>>>>>>> processes on the MPI_Comm_accept call. After I run about 40
>>>>>>>>>>>>>>> processes
>>>>>>>>>>>>>>> every subsequent call takes more and more time, which I'd like to
>>>>>>>>>>>>>>> avoid.
>>>>>>>>>>>>>>> Another problem in this solution is that when I try to connect
>>>>>>>>>>>>>>> 66-th
>>>>>>>>>>>>>>> process the root of the existing group segfaults on
>>>>>>>>>>>>>>> MPI_Comm_accept.
>>>>>>>>>>>>>>> Maybe it's my bug, but it's weird as everything works fine for at
>>>>>>>>>>>>>>> most
>>>>>>>>>>>>>>> 65 processes. Is there any limitation I don't know about?
>>>>>>>>>>>>>>> My last question is about MPI_COMM_WORLD. When I run my processes
>>>>>>>>>>>>>>> without mpirun their MPI_COMM_WORLD is the same as MPI_COMM_SELF.
>>>>>>>>>>>>>>> Is
>>>>>>>>>>>>>>> there any way to change MPI_COMM_WORLD and set it to the
>>>>>>>>>>>>>>> intracommunicator that I've created?
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>> Grzegorz Maj
>>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
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