[yt-users] yt-users Digest, Vol 89, Issue 7
rahul kashyap
rahulkashyap411 at gmail.com
Mon Jul 6 11:28:40 PDT 2015
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 ?
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> wrote:
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> Today's Topics:
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> 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>
> To: yt-users at lists.spacepope.org
> Subject: [yt-users] Problem in running parallel yt on stampede
> Message-ID:
> <
> 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>
> To: Discussion of the yt analysis package
> <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>
> 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> 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>
> To: Discussion of the yt analysis package
> <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>
> 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>
> 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>
> 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
> >>
> >>
> >>
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
> >
>
>
> --
> Gregory Meece
> Michigan State University
> Department of Physics and Astronomy
> http://galactica.pa.msu.edu/~gmeece
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