<br><br>On Monday, July 6, 2015, rahul kashyap <<a href="mailto:rahulkashyap411@gmail.com">rahulkashyap411@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><p dir="ltr">Thanks for the reply. </p>
<p dir="ltr">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 ?</p></blockquote><div>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<span></span>. You should have gotten a password to edit your settings when you signed up to the mailing list.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<p dir="ltr">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.</p>
<p dir="ltr">Thanks again,<br>
r</p>
<p dir="ltr">Rahul</p>
<br><div class="gmail_quote"><div dir="ltr">On Mon, 6 Jul 2015 1:53 pm <<a href="javascript:_e(%7B%7D,'cvml','yt-users-request@lists.spacepope.org');" target="_blank">yt-users-request@lists.spacepope.org</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send yt-users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Problem in running parallel yt on stampede (rahul kashyap)<br>
2. Re: Problem in running parallel yt on stampede (Nathan Goldbaum)<br>
3. Re: Problem in running parallel yt on stampede (Greg Meece)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sun, 05 Jul 2015 22:43:29 +0000<br>
From: rahul kashyap <<a href="javascript:_e(%7B%7D,'cvml','rahulkashyap411@gmail.com');" target="_blank">rahulkashyap411@gmail.com</a>><br>
To: <a href="javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');" target="_blank">yt-users@lists.spacepope.org</a><br>
Subject: [yt-users] Problem in running parallel yt on stampede<br>
Message-ID:<br>
<<a href="javascript:_e(%7B%7D,'cvml','CAMt8yfjzKDr50Nk0tYuiqPFDyr_wCTyMq4KaUwTwR3bS3MMG4A@mail.gmail.com');" target="_blank">CAMt8yfjzKDr50Nk0tYuiqPFDyr_wCTyMq4KaUwTwR3bS3MMG4A@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear yt-users,<br>
<br>
I'm trying to use parallel yt on stampede and got this error --<br>
LiMIC: (limic_open) file open fail<br>
[unset]: aborting job:<br>
Fatal error in PMPI_Init_thread:<br>
Other MPI error, error stack:<br>
MPIR_Init_thread(436)....:<br>
MPID_Init(371)...........: channel initialization failed<br>
MPIDI_CH3_Init(335)......:<br>
MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or<br>
directory<br>
<br>
In the interactive ipython, import yt and import mpi4py works ok but,<br>
yt.enable_parallelism() gives the same error.<br>
Serial scripts runs perfectly fine. I've also tried building mpi4py by<br>
specifying mpicc path; itdoesn't work.<br>
<br>
Any help would be highly appreciated. Thanks in advance.<br>
<br>
rahul<br>
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Message: 2<br>
Date: Sun, 5 Jul 2015 16:02:55 -0700<br>
From: Nathan Goldbaum <<a href="javascript:_e(%7B%7D,'cvml','nathan12343@gmail.com');" target="_blank">nathan12343@gmail.com</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');" target="_blank">yt-users@lists.spacepope.org</a>><br>
Subject: Re: [yt-users] Problem in running parallel yt on stampede<br>
Message-ID:<br>
<CAJXewOmJbGaAwvHJx4DxLmg2F6U_+bgqE8vFHKf_NXmDX=<a href="javascript:_e(%7B%7D,'cvml','Rfmg@mail.gmail.com');" target="_blank">Rfmg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
How did mpi4py get installed?<br>
<br>
You may need to troubleshoot this with the Stampede sysadmins, since the<br>
error is being raised by the MPI library you're using.<br>
<br>
On Sunday, July 5, 2015, rahul kashyap <<a href="javascript:_e(%7B%7D,'cvml','rahulkashyap411@gmail.com');" target="_blank">rahulkashyap411@gmail.com</a>> wrote:<br>
<br>
> Dear yt-users,<br>
><br>
> I'm trying to use parallel yt on stampede and got this error --<br>
> LiMIC: (limic_open) file open fail<br>
> [unset]: aborting job:<br>
> Fatal error in PMPI_Init_thread:<br>
> Other MPI error, error stack:<br>
> MPIR_Init_thread(436)....:<br>
> MPID_Init(371)...........: channel initialization failed<br>
> MPIDI_CH3_Init(335)......:<br>
> MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or<br>
> directory<br>
><br>
> In the interactive ipython, import yt and import mpi4py works ok but,<br>
> yt.enable_parallelism() gives the same error.<br>
> Serial scripts runs perfectly fine. I've also tried building mpi4py by<br>
> specifying mpicc path; itdoesn't work.<br>
><br>
> Any help would be highly appreciated. Thanks in advance.<br>
><br>
> rahul<br>
><br>
><br>
><br>
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<br>
Message: 3<br>
Date: Sun, 5 Jul 2015 22:56:42 -0400<br>
From: Greg Meece <<a href="javascript:_e(%7B%7D,'cvml','meecegre@msu.edu');" target="_blank">meecegre@msu.edu</a>><br>
To: Discussion of the yt analysis package<br>
<<a href="javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');" target="_blank">yt-users@lists.spacepope.org</a>><br>
Subject: Re: [yt-users] Problem in running parallel yt on stampede<br>
Message-ID:<br>
<CADDDyPC334pZ0H_bAe5F9uFj+SWF=<a href="javascript:_e(%7B%7D,'cvml','hVtCLHhuCSshQUqxO%2BEvg@mail.gmail.com');" target="_blank">hVtCLHhuCSshQUqxO+Evg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Are you running on the login node?<br>
<br>
I've seen this too when I try to use mpi4py in a script on the Stampede<br>
login ode. Specifically, it fails in the 'from mpi4py import MPI' step.<br>
This happens even if I am not using yt or not running in parallel.<br>
<br>
mpi4py works fine (for me at least) in an interactive compute node. I<br>
wonder if they have the login nodes set up to discourage parallel jobs.<br>
<br>
-- Greg<br>
<br>
On Sun, Jul 5, 2015 at 7:02 PM, Nathan Goldbaum <<a href="javascript:_e(%7B%7D,'cvml','nathan12343@gmail.com');" target="_blank">nathan12343@gmail.com</a>><br>
wrote:<br>
<br>
> How did mpi4py get installed?<br>
><br>
> You may need to troubleshoot this with the Stampede sysadmins, since the<br>
> error is being raised by the MPI library you're using.<br>
><br>
> On Sunday, July 5, 2015, rahul kashyap <<a href="javascript:_e(%7B%7D,'cvml','rahulkashyap411@gmail.com');" target="_blank">rahulkashyap411@gmail.com</a>> wrote:<br>
><br>
>> Dear yt-users,<br>
>><br>
>> I'm trying to use parallel yt on stampede and got this error --<br>
>> LiMIC: (limic_open) file open fail<br>
>> [unset]: aborting job:<br>
>> Fatal error in PMPI_Init_thread:<br>
>> Other MPI error, error stack:<br>
>> MPIR_Init_thread(436)....:<br>
>> MPID_Init(371)...........: channel initialization failed<br>
>> MPIDI_CH3_Init(335)......:<br>
>> MPIDI_CH3I_SMP_Init(1723): LiMIC2 device does not exist: No such file or<br>
>> directory<br>
>><br>
>> In the interactive ipython, import yt and import mpi4py works ok but,<br>
>> yt.enable_parallelism() gives the same error.<br>
>> Serial scripts runs perfectly fine. I've also tried building mpi4py by<br>
>> specifying mpicc path; itdoesn't work.<br>
>><br>
>> Any help would be highly appreciated. Thanks in advance.<br>
>><br>
>> rahul<br>
>><br>
>><br>
>><br>
> _______________________________________________<br>
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><br>
><br>
<br>
<br>
--<br>
Gregory Meece<br>
Michigan State University<br>
Department of Physics and Astronomy<br>
<a href="http://galactica.pa.msu.edu/~gmeece" rel="noreferrer" target="_blank">http://galactica.pa.msu.edu/~gmeece</a><br>
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</blockquote></div>
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