On Wed, Jun 20, 2012 at 2:57 PM, Hongfeng Yang <span dir="ltr"><<a href="mailto:hyang@whoi.edu" target="_blank">hyang@whoi.edu</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Jonathan,<br>
<br>
Then I need to turn on the debugger in the code. How should I set xterm<br>
display in order to attach gdp?<br></blockquote><div><br></div><div>Just to clarify:</div><div><br></div><div> The situation is that we have run successfully on a single node (12 processes), but</div><div>at 24 processes we get a SEGV. It appears to be during file access, but the best way</div>
<div>to debug this error would be to use the debugger.</div><div><br></div><div>PETSc has the ability to spawn and attach gdb to make this possible in parallel. On other</div><div>clusters, we have just set the DISPLAY env var to enable the xterm to spawn on the user</div>
<div>machine. Hopefully this is possible on this cluster.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thanks,<br>
<br>
Hongfeng<br>
<br>
On 6/20/12 2:32 PM, Jonathan Murray wrote:<br>
> we use nfs to access the filesystem<br>
> the filesystem is either xfs or ext4<br>
><br>
> how are you submitting your jobs? is there a shell script?<br>
><br>
> thanks<br>
><br>
> On 06/20/2012 04:18 PM, Hongfeng Yang wrote:<br>
>> Hi Jonathan,<br>
>><br>
>> I am running a software on the cluster scylla. So far I can run the code<br>
>> on ONE compute node, but could not get it proceed on two or more nodes.<br>
>><br>
>> The code developers suspect that it could be related to the filesystem<br>
>> on our cluster as the code gets stuck in reading the mesh. Do you know<br>
>> what kind of filesystems are on the master and compute nodes on scylla?<br>
>><br>
>> Thanks,<br>
>><br>
>> Hongfeng<br>
>><br>
>><br>
>> -------- Original Message --------<br>
>> Subject: Re: Error message from running on cluster<br>
>> Date: Wed, 20 Jun 2012 08:01:18 -0600<br>
>> From: Matthew Knepley<<a href="mailto:knepley@mcs.anl.gov">knepley@mcs.anl.gov</a>><br>
>> To: Hongfeng Yang<<a href="mailto:hyang@whoi.edu">hyang@whoi.edu</a>><br>
>> CC: <a href="mailto:cig-short@geodynamics.org">cig-short@geodynamics.org</a><br>
>><br>
>><br>
>><br>
>> On Wed, Jun 20, 2012 at 7:18 AM, Hongfeng Yang<<a href="mailto:hyang@whoi.edu">hyang@whoi.edu</a><br>
>> <mailto:<a href="mailto:hyang@whoi.edu">hyang@whoi.edu</a>>> wrote:<br>
>><br>
>> Hi Matt,<br>
>><br>
>> Last night I did not send the error message of running pylith on our<br>
>> cluster at WHOI. Sorry for that. Here it is.<br>
>><br>
>> Could you help figure out what the problem might be?<br>
>><br>
>><br>
>> So it looks like there is a problem when trying to read in the mesh,<br>
>> although it is hard to tell since<br>
>> we get an SEGV. My guess is that the filesystem is not exactly what you<br>
>> think it is.I recommend<br>
>> going through the cluster documentation to understand exactly how the<br>
>> filesystem is accessed from<br>
>> nodes other than the head node.<br>
>><br>
>> Matt<br>
>><br>
>><br>
>> Thanks,<br>
>><br>
>> Hongfeng<br>
>><br>
>> --<br>
>> Postdoctoral Investigator<br>
>> Department of Geology and Geophysics<br>
>> Woods Hole Oceanographic Institution<br>
>> 360 Woods Hole Rd, MS 24<br>
>> Woods Hole, MA 02543<br>
>><br>
>><br>
>><br>
<span class="HOEnZb"><font color="#888888">>><br>
>> --<br>
>> What most experimenters take for granted before they begin their<br>
>> experiments is infinitely more interesting than any results to which<br>
>> their experiments lead.<br>
>> -- Norbert Wiener<br>
>><br>
><br>
<br>
<br>
--<br>
Postdoctoral Investigator<br>
Department of Geology and Geophysics<br>
Woods Hole Oceanographic Institution<br>
360 Woods Hole Rd, MS 24<br>
Woods Hole, MA 02543<br>
<br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<br>