<div dir="ltr"><div>Andrew,</div><div><br></div>Just to be clear, in the new script that Yadu posted, you will need to add one entry in your tc.data as follows:<div><br></div><div>persistent-coasters bash /bin/bash</div><div><br></div><div>Thanks,</div><div>Ketan<br><div><br></div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Sep 10, 2014 at 11:03 PM, Yadu Nand <span dir="ltr"><<a href="mailto:yadudoc1729@gmail.com" target="_blank">yadudoc1729@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class=""><div dir="ltr"><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Hi Andrew, </div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">If you would like to have swift move the executable for you, you could try the method used in the following example :</div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif">type file;<br></div><div class="gmail_default"><div class="gmail_default"><font face="arial, helvetica, sans-serif"><br></font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">/* App definition calls bash which in-turn executes the bash script defined as an argument here</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif"> Every file in the input parameter list is staged by swift to the worker nodes</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif"> Every file in the return list is staged back to the client node by swift</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">*/</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">app (file out, file err) foo (file script, file input)</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">{</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif"> bash @script @input stdout=@out stderr=@err;</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">}</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif"><br></font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">// Script to be executed</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">file wrapper <"wrapper.sh">;</font></div><div class="gmail_default"><span style="font-family:arial,helvetica,sans-serif">file hello <"hello.txt">;</span></div><div class="gmail_default"><span style="font-family:arial,helvetica,sans-serif"><br></span></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">file out <"foo.out">;</font></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">file err <"foo.err">;</font></div><div class="gmail_default"><br></div><div class="gmail_default"><font face="arial, helvetica, sans-serif">(out, err) = foo (wrapper, hello);</font></div></div><div class="gmail_default"><div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif">Thanks,</font></div><div><font face="arial, helvetica, sans-serif">Yadu</font></div><div><font face="arial, helvetica, sans-serif"><br></font></div></div></div><div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br></div></div></span><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Wed, Sep 10, 2014 at 8:45 PM, Andrew Stocker <span dir="ltr"><<a href="mailto:amstocker@dons.usfca.edu" target="_blank">amstocker@dons.usfca.edu</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Ketan,<div><br></div><div>I copied the catnap executable to the same directory on each of the computers and now the swift script is working perfectly without error. Thanks for your help! What are the next steps we can take to set up our cluster to not require the script to be on all the computers? Since we are fairly new to parallel computing with a cluster, could you point us towards any resources regarding the technical configuration for Swift? I've looked at the documentation for tc.data but I am still a bit confused by it.</div><div><br></div><div>Thanks,</div><div><br></div><div>Andrew</div></div><div><div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Sep 9, 2014 at 7:49 AM, Ketan Maheshwari <span dir="ltr"><<a href="mailto:ketan@mcs.anl.gov" target="_blank">ketan@mcs.anl.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><br><div class="gmail_quote"><span>On Mon, Sep 8, 2014 at 6:28 PM, Andrew Stocker <span dir="ltr"><<a href="mailto:amstocker@dons.usfca.edu" target="_blank">amstocker@dons.usfca.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div dir="ltr">Thanks for your response!
<div><br>
</div>
<div>Since we're just in the stages of experimentation, our preliminary cluster is just four iMacs connected to a switch. I set up password-less ssh communication between the four and I'm able to start the coaster service (in the folder with coaster-service.conf)
without any errors. I am running Swift from the computer which has the <font face="courier new, monospace">
catnap.sh</font><font face="arial, helvetica, sans-serif"> installed at the correct path, and I'm pretty sure it has the executable bit set ( </font><font face="courier new, monospace">#!/bin/sh
</font><font face="arial, helvetica, sans-serif">is the first line of the program). None of the other three computers have Swift installed, nor do they have </font><font face="courier new, monospace">catnap.sh</font><font face="arial, helvetica, sans-serif"> at
the location specified in tc.data, is this a problem?</font></div></div></div></blockquote><div><br></div></span><div>Yes, that seems to be the issue. The executable--catnap.sh in this case must be available on all compute nodes in the location specified in the tc. </div><div><br></div><div>An alternative in this case is to use catnap.sh as data and move it along with data to target compute nodes. However, we can do that later. For now, could you try to put catnap.sh in a common location on each of the compute nodes and try again.</div><div><br></div><div>No, Swift is not needed to be installed on compute nodes. Swift just needs to be on the submit node.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><span><div dir="ltr">
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">Attached is the log file from the run when I got the error I copy+pasted above. Interestingly, when I run the catnap swift script with only 3 concurrent instances, it seems to run fine since we allow
3 jobs per node and so it is probably only running locally.</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">Regards,</font></div>
<div><font face="arial, helvetica, sans-serif">Andrew</font></div>
</div></span><div><div>
<div class="gmail_extra"><br>
<div class="gmail_quote"><span>On Fri, Sep 5, 2014 at 6:03 PM, Ketan Maheshwari <span dir="ltr">
<<a href="mailto:ketan@mcs.anl.gov" target="_blank">ketan@mcs.anl.gov</a>></span> wrote:<br>
</span><div><div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Andrew,
<div><br>
</div>
<div>Yes, I remember: thanks for getting back on this.</div>
<div><br>
</div>
<div>From the error message and tc.data, indeed it looks like the executable is provided as absolute path but somehow Swift is looking into system path and not finding it. One possibility is that the node on which catnap.sh is running does not have it installed
on the path specified in the tc.data. Can you also check if catnap.sh has the executable bit set. Less likely that this is causing the issue though.</div>
<div><br>
</div>
<div>Also, from the tc.data line it looks like you are using persistent coasters. Have started the coaster service beforehand and made sure the service started correctly without any error messages. Could you indicate more about your cluster. Depending on the
type of cluster, it is possible that we can run Swift in a non-persistent, implicit coasters mode.</div>
<div><br>
</div>
<div>Can you also send the Swift generated log for this run.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Ketan</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote"><span>On Fri, Sep 5, 2014 at 7:16 PM, Andrew Stocker
<span dir="ltr"><<a href="mailto:amstocker@dons.usfca.edu" target="_blank">amstocker@dons.usfca.edu</a>></span> wrote:<br>
</span>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><span>
<div dir="ltr">Hi Ketan,
<div><br>
</div>
<div>I'm not sure if you remember, but myself and my research advisor Xiaosheng spoke to you at LBL in Oakland at the beginning of the summer about starting to use Swift at our school. We have been working hard on setting it up, and I am trying to get your
demo to run but I'm having a problem. For some reason I keep getting the following error when I try to run your catsnsleep demo:</div>
<div><br>
</div>
<div>
<div><font face="courier new, monospace">Execution failed:</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"></span>Exception in catnap:</font></div>
<div><font face="courier new, monospace"> Arguments: [5, data.txt]</font></div>
<div><font face="courier new, monospace"> Host: persistent-coasters</font></div>
<div><font face="courier new, monospace"> Directory: catsnsleep-20140905-1702-mihcat06/jobs/u/catnap-utx080xl</font></div>
<div><font face="courier new, monospace"><br>
</font></div>
<div><font face="courier new, monospace">Caused by:</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"></span>Cannot find executable catnap.sh on site system path</font></div>
<div><font face="courier new, monospace"><span style="white-space:pre-wrap"></span>catnap, catsnsleep.swift, line 13</font></div>
<div><font face="courier new, monospace"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">However I'm not sure why. In our tc.data file we have the line:</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="courier new, monospace">persistent-coasters catnap /usr/local/swift-0.94.1/oakland-demo/catnap.sh</font><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><br>
</div>
<div>which I think should work but obviously something is going wrong. I have been browsing the documentation articles but I can't find anything about why this might be happening. We would greatly appreciate your advice!</div>
<div><br>
</div>
<div>Regards,</div>
<div><br>
</div>
<div>Andrew Stocker</div>
</div>
</div>
</span>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote"><span>On Fri, Jun 20, 2014 at 12:00 PM, Xiaosheng Huang
<span dir="ltr"><<a href="mailto:xhuang22@usfca.edu" target="_blank">xhuang22@usfca.edu</a>></span> wrote:<br>
</span>
<div>
<div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><span><br>
<div class="gmail_quote">---------- Forwarded message ----------<br>
From: <b class="gmail_sendername">Ketan Maheshwari</b> <span dir="ltr"><<a href="mailto:ketan@mcs.anl.gov" target="_blank">ketan@mcs.anl.gov</a>></span><br>
Date: Fri, Jun 20, 2014 at 11:45 AM<br>
Subject: Re: Pointer to Swift tutorials for computational science education and research<br>
To: Xiaosheng Huang <<a href="mailto:xhuang22@usfca.edu" target="_blank">xhuang22@usfca.edu</a>><br>
Cc: Wilde <<a href="mailto:wilde@mcs.anl.gov" target="_blank">wilde@mcs.anl.gov</a>><br>
<br>
<br>
<div dir="ltr">Hi Xiaosheng,
<div><br>
</div>
<div>The tarball is: <a href="http://www.mcs.anl.gov/~ketan/oakland-demo.tgz" target="_blank">http://www.mcs.anl.gov/~ketan/oakland-demo.tgz</a></div>
<div><br>
</div>
<div>There is a small README in there which outlines the steps.</div>
<div><br>
</div>
<div>Best,</div>
<div>Ketan</div>
<div><br>
</div>
</div>
</div>
</span><span><span>
<div style="background-color:rgb(255,255,255)"><font face="garamond, serif">************************************************************</font></div>
<font face="garamond, serif"><span style="background-color:rgb(255,255,255)">Xiaosheng Huang, Assistant Professor</span><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">Department of Physics and Astronomy</span><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">University of San Francisco</span><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">2130 Fulton Street, San Francisco, CA 94117-1080</span><br style="background-color:rgb(255,255,255)">
<br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">Phone: </span><a href="tel:%28415%29%20422-6281" value="+14154226281" target="_blank">(415) 422-6281</a><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">E-mail: </span><a href="mailto:xhuang22@usfca.edu" target="_blank">xhuang22@usfca.edu</a><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255)">******************************</span><span style="background-color:rgb(255,255,255)">******************************</span></font>
</span></span></div>
</blockquote>
</div>
</div>
</div>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</blockquote>
</div></div></div>
<br>
</div>
</div></div></div>
</blockquote></div><br></div></div>
</blockquote></div><br></div>
</div></div><br></div></div><span class="">_______________________________________________<br>
Swift-user mailing list<br>
<a href="mailto:Swift-user@ci.uchicago.edu" target="_blank">Swift-user@ci.uchicago.edu</a><br>
<a href="https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user" target="_blank">https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user</a><br></span></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Yadu Nand B<div><br></div></div>
</font></span></div>
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