Hi,
Am 13.12.2014 um 02:43 schrieb Alex A. Schmidt:
> MPI_comm_disconnect seem to work but not quite.
> The call to it returns almost immediatly while
> the spawn processes keep piling up in the background
> until they are all done...
>
> I think system('env -i qsub...') to launch the third party apps
> would take the execution of every call back to the scheduler
> queue. How would I track each one for their completion?
So your goal is to implement some kind of workflow supervisor by submitting
jobs to the queuing system and act after their completion depending on the
results of the QC software? Does this workflow software need MPI to do this?
Nevertheless, submitting from an application can be done by DRMAA instead of
plain system calls. There you can also check the states of the job in the
queuing system and/or wait for them and control them more easily (i.e.
terminate, suspend,...).
-- Reuti
http://www.drmaa.org/
https://arc.liv.ac.uk/SGE/howto/howto.html#DRMAA
> Alex
>
> 2014-12-12 22:35 GMT-02:00 Gilles Gouaillardet
> <gilles.gouaillar...@gmail.com>:
> Alex,
>
> You need MPI_Comm_disconnect at least.
> I am not sure if this is 100% correct nor working.
>
> If you are using third party apps, why dont you do something like
> system("env -i qsub ...")
> with the right options to make qsub blocking or you manually wait for the end
> of the job ?
>
> That looks like a much cleaner and simpler approach to me.
>
> Cheers,
>
> Gilles
>
> "Alex A. Schmidt" <a...@ufsm.br> wrote:
> Hello Gilles,
>
> Ok, I believe I have a simple toy app running as I think it should:
> 'n' parent processes running under mpi_comm_world, each one
> spawning its own 'm' child processes (each child group work
> together nicely, returning the expected result for an mpi_allreduce call).
>
> Now, as I mentioned before, the apps I want to run in the spawned
> processes are third party mpi apps and I don't think it will be possible
> to exchange messages with them from my app. So, I do I tell
> when the spawned processes have finnished running? All I have to work
> with is the intercommunicator returned from the mpi_comm_spawn call...
>
> Alex
>
>
>
>
> 2014-12-12 2:42 GMT-02:00 Alex A. Schmidt <a...@ufsm.br>:
> Gilles,
>
> Well, yes, I guess....
>
> I'll do tests with the real third party apps and let you know.
> These are huge quantum chemistry codes (dftb+, siesta and Gaussian)
> which greatly benefits from a parallel environment. My code is just
> a front end to use those, but since we have a lot of data to process
> it also benefits from a parallel environment.
>
> Alex
>
>
> 2014-12-12 2:30 GMT-02:00 Gilles Gouaillardet <gilles.gouaillar...@iferc.org>:
> Alex,
>
> just to make sure ...
> this is the behavior you expected, right ?
>
> Cheers,
>
> Gilles
>
>
> On 2014/12/12 13:27, Alex A. Schmidt wrote:
>> Gilles,
>>
>> Ok, very nice!
>>
>> When I excute
>>
>> do rank=1,3
>> call MPI_Comm_spawn('hello_world','
>> ',5,MPI_INFO_NULL,rank,MPI_COMM_WORLD,my_intercomm,MPI_ERRCODES_IGNORE,status)
>> enddo
>>
>> I do get 15 instances of the 'hello_world' app running: 5 for each parent
>> rank 1, 2 and 3.
>>
>> Thanks a lot, Gilles.
>>
>> Best regargs,
>>
>> Alex
>>
>>
>>
>>
>> 2014-12-12 1:32 GMT-02:00 Gilles Gouaillardet <gilles.gouaillar...@iferc.org
>>> :
>>>
>>> Alex,
>>>
>>> just ask MPI_Comm_spawn to start (up to) 5 tasks via the maxprocs
>>> parameter :
>>>
>>> int MPI_Comm_spawn(char *command, char *argv[], int maxprocs,
>>> MPI_Info info,
>>> int root, MPI_Comm comm, MPI_Comm *intercomm,
>>> int array_of_errcodes[])
>>>
>>> INPUT PARAMETERS
>>> maxprocs
>>> - maximum number of processes to start (integer, significant
>>> only at root)
>>>
>>> Cheers,
>>>
>>> Gilles
>>>
>>>
>>> On 2014/12/12 12:23, Alex A. Schmidt wrote:
>>>
>>> Hello Gilles,
>>>
>>> Thanks for your reply. The "env -i PATH=..." stuff seems to work!!!
>>>
>>> call system("sh -c 'env -i PATH=/usr/lib64/openmpi/bin:/bin mpirun -n 2
>>> hello_world' ")
>>>
>>> did produce the expected result with a simple openmi "hello_world" code I
>>> wrote.
>>>
>>> I might be harder though with the real third party app I have in mind. And
>>> I realize
>>> getting passed over a job scheduler with this approach might not work at
>>> all...
>>>
>>> I have looked at the MPI_Comm_spawn call but I failed to understand how it
>>> could help here. For instance, can I use it to launch an mpi app with the
>>> option "-n 5" ?
>>>
>>> Alex
>>>
>>> 2014-12-12 0:36 GMT-02:00 Gilles Gouaillardet <gilles.gouaillar...@iferc.org
>>>
>>>
>>> :
>>>
>>> Alex,
>>>
>>> can you try something like
>>> call system(sh -c 'env -i /.../mpirun -np 2 /.../app_name')
>>>
>>> -i start with an empty environment
>>> that being said, you might need to set a few environment variables
>>> manually :
>>> env -i PATH=/bin ...
>>>
>>> and that being also said, this "trick" could be just a bad idea :
>>> you might be using a scheduler, and if you empty the environment, the
>>> scheduler
>>> will not be aware of the "inside" run.
>>>
>>> on top of that, invoking system might fail depending on the interconnect
>>> you use.
>>>
>>> Bottom line, i believe Ralph's reply is still valid, even if five years
>>> have passed :
>>> changing your workflow, or using MPI_Comm_spawn is a much better approach.
>>>
>>> Cheers,
>>>
>>> Gilles
>>>
>>> On 2014/12/12 11:22, Alex A. Schmidt wrote:
>>>
>>> Dear OpenMPI users,
>>>
>>> Regarding to this previous
>>> post<http://www.open-mpi.org/community/lists/users/2009/06/9560.php>
>>> <http://www.open-mpi.org/community/lists/users/2009/06/9560.php>
>>> <http://www.open-mpi.org/community/lists/users/2009/06/9560.php>
>>> <http://www.open-mpi.org/community/lists/users/2009/06/9560.php> from 2009,
>>> I wonder if the reply
>>> from Ralph Castain is still valid. My need is similar but quite simpler:
>>> to make a system call from an openmpi fortran application to run a
>>> third party openmpi application. I don't need to exchange mpi messages
>>> with the application. I just need to read the resulting output file
>>> generated
>>> by it. I have tried to do the following system call from my fortran openmpi
>>> code:
>>>
>>> call system("sh -c 'mpirun -n 2 app_name")
>>>
>>> but I get
>>>
>>> **********************************************************
>>>
>>> Open MPI does not support recursive calls of mpirun
>>>
>>> **********************************************************
>>>
>>> Is there a way to make this work?
>>>
>>> Best regards,
>>>
>>> Alex
>>>
>>>
>>>
>>>
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>>
>>
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