[yt-users] yt-users Digest, Vol 89, Issue 7

Nathan Goldbaum nathan12343 at gmail.com
Mon Jul 6 11:32:20 PDT 2015


On Monday, July 6, 2015, rahul kashyap <rahulkashyap411 at gmail.com> wrote:

> Thanks for the reply.
>
> I came to see your replies just now in the daily digest. Is there
> something I should do to get the replies instantly forwarded to my email ?
>
You'll need to edit your mailing list settings. See the footer at the
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> As Greg suggested, it seems that this problem occurs only on login nodes.
> Using yt-3.1 and submission through job script solves the problem.
>
> Thanks again,
> r
>
> Rahul
>
> On Mon, 6 Jul 2015 1:53 pm  <yt-users-request at lists.spacepope.org
> <javascript:_e(%7B%7D,'cvml','yt-users-request at lists.spacepope.org');>>
> wrote:
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>> Today's Topics:
>>
>>    1. Problem in running parallel yt on stampede (rahul kashyap)
>>    2. Re: Problem in running parallel yt on stampede (Nathan Goldbaum)
>>    3. Re: Problem in running parallel yt on stampede (Greg Meece)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Sun, 05 Jul 2015 22:43:29 +0000
>> From: rahul kashyap <rahulkashyap411 at gmail.com
>> <javascript:_e(%7B%7D,'cvml','rahulkashyap411 at gmail.com');>>
>> To: yt-users at lists.spacepope.org
>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>
>> Subject: [yt-users] Problem in running parallel yt on stampede
>> Message-ID:
>>         <
>> CAMt8yfjzKDr50Nk0tYuiqPFDyr_wCTyMq4KaUwTwR3bS3MMG4A at mail.gmail.com
>> <javascript:_e(%7B%7D,'cvml','CAMt8yfjzKDr50Nk0tYuiqPFDyr_wCTyMq4KaUwTwR3bS3MMG4A at mail.gmail.com');>
>> >
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear yt-users,
>>
>> I'm trying to use parallel yt on stampede and got this error --
>> LiMIC: (limic_open) file open fail
>> [unset]: aborting job:
>> Fatal error in PMPI_Init_thread:
>> Other MPI error, error stack:
>> MPIR_Init_thread(436)....:
>> MPID_Init(371)...........: channel initialization failed
>> MPIDI_CH3_Init(335)......:
>> MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or
>> directory
>>
>> In the interactive ipython, import yt and import mpi4py works ok but,
>> yt.enable_parallelism() gives the same error.
>> Serial scripts runs perfectly fine. I've also tried building mpi4py by
>> specifying mpicc path; itdoesn't work.
>>
>> Any help would be highly appreciated. Thanks in advance.
>>
>> rahul
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>> ------------------------------
>>
>> Message: 2
>> Date: Sun, 5 Jul 2015 16:02:55 -0700
>> From: Nathan Goldbaum <nathan12343 at gmail.com
>> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org
>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>>
>> Subject: Re: [yt-users] Problem in running parallel yt on stampede
>> Message-ID:
>>         <CAJXewOmJbGaAwvHJx4DxLmg2F6U_+bgqE8vFHKf_NXmDX=
>> Rfmg at mail.gmail.com <javascript:_e(%7B%7D,'cvml','Rfmg at mail.gmail.com');>
>> >
>> Content-Type: text/plain; charset="utf-8"
>>
>> How did mpi4py get installed?
>>
>> You may need to troubleshoot this with the Stampede sysadmins, since the
>> error is being raised by the MPI library you're using.
>>
>> On Sunday, July 5, 2015, rahul kashyap <rahulkashyap411 at gmail.com
>> <javascript:_e(%7B%7D,'cvml','rahulkashyap411 at gmail.com');>> wrote:
>>
>> > Dear yt-users,
>> >
>> > I'm trying to use parallel yt on stampede and got this error --
>> > LiMIC: (limic_open) file open fail
>> > [unset]: aborting job:
>> > Fatal error in PMPI_Init_thread:
>> > Other MPI error, error stack:
>> > MPIR_Init_thread(436)....:
>> > MPID_Init(371)...........: channel initialization failed
>> > MPIDI_CH3_Init(335)......:
>> > MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or
>> > directory
>> >
>> > In the interactive ipython, import yt and import mpi4py works ok but,
>> > yt.enable_parallelism() gives the same error.
>> > Serial scripts runs perfectly fine. I've also tried building mpi4py by
>> > specifying mpicc path; itdoesn't work.
>> >
>> > Any help would be highly appreciated. Thanks in advance.
>> >
>> > rahul
>> >
>> >
>> >
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>> ------------------------------
>>
>> Message: 3
>> Date: Sun, 5 Jul 2015 22:56:42 -0400
>> From: Greg Meece <meecegre at msu.edu
>> <javascript:_e(%7B%7D,'cvml','meecegre at msu.edu');>>
>> To: Discussion of the yt analysis package
>>         <yt-users at lists.spacepope.org
>> <javascript:_e(%7B%7D,'cvml','yt-users at lists.spacepope.org');>>
>> Subject: Re: [yt-users] Problem in running parallel yt on stampede
>> Message-ID:
>>         <CADDDyPC334pZ0H_bAe5F9uFj+SWF=
>> hVtCLHhuCSshQUqxO+Evg at mail.gmail.com
>> <javascript:_e(%7B%7D,'cvml','hVtCLHhuCSshQUqxO%2BEvg at mail.gmail.com');>>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Are you running on the login node?
>>
>> I've seen this too when I try to use mpi4py in a script on the Stampede
>> login ode. Specifically, it fails in the 'from mpi4py import MPI' step.
>> This happens even if I am not using yt or not running in parallel.
>>
>> mpi4py works fine (for me at least) in an interactive compute node. I
>> wonder if they have the login nodes set up  to discourage parallel jobs.
>>
>> -- Greg
>>
>> On Sun, Jul 5, 2015 at 7:02 PM, Nathan Goldbaum <nathan12343 at gmail.com
>> <javascript:_e(%7B%7D,'cvml','nathan12343 at gmail.com');>>
>> wrote:
>>
>> > How did mpi4py get installed?
>> >
>> > You may need to troubleshoot this with the Stampede sysadmins, since the
>> > error is being raised by the MPI library you're using.
>> >
>> > On Sunday, July 5, 2015, rahul kashyap <rahulkashyap411 at gmail.com
>> <javascript:_e(%7B%7D,'cvml','rahulkashyap411 at gmail.com');>> wrote:
>> >
>> >> Dear yt-users,
>> >>
>> >> I'm trying to use parallel yt on stampede and got this error --
>> >> LiMIC: (limic_open) file open fail
>> >> [unset]: aborting job:
>> >> Fatal error in PMPI_Init_thread:
>> >> Other MPI error, error stack:
>> >> MPIR_Init_thread(436)....:
>> >> MPID_Init(371)...........: channel initialization failed
>> >> MPIDI_CH3_Init(335)......:
>> >> MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file
>> or
>> >> directory
>> >>
>> >> In the interactive ipython, import yt and import mpi4py works ok but,
>> >> yt.enable_parallelism() gives the same error.
>> >> Serial scripts runs perfectly fine. I've also tried building mpi4py by
>> >> specifying mpicc path; itdoesn't work.
>> >>
>> >> Any help would be highly appreciated. Thanks in advance.
>> >>
>> >> rahul
>> >>
>> >>
>> >>
>> > _______________________________________________
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>> >
>>
>>
>> --
>> Gregory Meece
>> Michigan State University
>> Department of Physics and Astronomy
>> http://galactica.pa.msu.edu/~gmeece
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>> End of yt-users Digest, Vol 89, Issue 7
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