Re: [yt-users] yt-users Digest, Vol 89, Issue 7
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
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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)
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Message: 1 Date: Sun, 05 Jul 2015 22:43:29 +0000 From: rahul kashyap
To: yt-users@lists.spacepope.org Subject: [yt-users] Problem in running parallel yt on stampede Message-ID: < CAMt8yfjzKDr50Nk0tYuiqPFDyr_wCTyMq4KaUwTwR3bS3MMG4A@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 -------------- next part -------------- An HTML attachment was scrubbed... URL: < http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2015...
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Message: 2 Date: Sun, 5 Jul 2015 16:02:55 -0700 From: Nathan Goldbaum
To: Discussion of the yt analysis package Subject: Re: [yt-users] Problem in running parallel yt on stampede Message-ID: 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
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
-------------- next part -------------- An HTML attachment was scrubbed... URL: < http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2015...
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Message: 3 Date: Sun, 5 Jul 2015 22:56:42 -0400 From: Greg Meece
To: Discussion of the yt analysis package Subject: Re: [yt-users] Problem in running parallel yt on stampede Message-ID: 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
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
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 -------------- next part -------------- An HTML attachment was scrubbed... URL: < http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2015...
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End of yt-users Digest, Vol 89, Issue 7 ***************************************
On Monday, July 6, 2015, rahul kashyap
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 bottom of this email for a link to access the mailing list settings. You should have gotten a password to edit your settings when you signed up to the mailing list.
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
javascript:_e(%7B%7D,'cvml','yt-users-request@lists.spacepope.org');> wrote: Send yt-users mailing list submissions to yt-users@lists.spacepope.org javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');
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When replying, please edit your Subject line so it is more specific than "Re: Contents of yt-users digest..."
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
javascript:_e(%7B%7D,'cvml','rahulkashyap411@gmail.com');> To: yt-users@lists.spacepope.org javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org'); Subject: [yt-users] Problem in running parallel yt on stampede Message-ID: < CAMt8yfjzKDr50Nk0tYuiqPFDyr_wCTyMq4KaUwTwR3bS3MMG4A@mail.gmail.com javascript:_e(%7B%7D,'cvml','CAMt8yfjzKDr50Nk0tYuiqPFDyr_wCTyMq4KaUwTwR3bS3MMG4A@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 -------------- next part -------------- An HTML attachment was scrubbed... URL: < http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2015...
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Message: 2 Date: Sun, 5 Jul 2015 16:02:55 -0700 From: Nathan Goldbaum
javascript:_e(%7B%7D,'cvml','nathan12343@gmail.com');> To: Discussion of the yt analysis package javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');> Subject: Re: [yt-users] Problem in running parallel yt on stampede Message-ID: javascript:_e(%7B%7D,'cvml','Rfmg@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
javascript:_e(%7B%7D,'cvml','rahulkashyap411@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
-------------- next part -------------- An HTML attachment was scrubbed... URL: < http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2015...
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Message: 3 Date: Sun, 5 Jul 2015 22:56:42 -0400 From: Greg Meece
javascript:_e(%7B%7D,'cvml','meecegre@msu.edu');> To: Discussion of the yt analysis package javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');> Subject: Re: [yt-users] Problem in running parallel yt on stampede Message-ID: javascript:_e(%7B%7D,'cvml','hVtCLHhuCSshQUqxO%2BEvg@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
javascript:_e(%7B%7D,'cvml','nathan12343@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
javascript:_e(%7B%7D,'cvml','rahulkashyap411@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 -------------- next part -------------- An HTML attachment was scrubbed... URL: < http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/2015...
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participants (2)
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Nathan Goldbaum
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rahul kashyap