Not sure if this helps, but I once had a problem with .bashrc not being sourced on a machine so I just did something like<div><br></div><div>run.sh:</div><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
#!/bin/bash</blockquote><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
source ~/.basrhc</blockquote><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
"$*"</blockquote><div><br></div><div>and then you can do something like </div><div>globus-job-run ... run.sh COMMAND </div><div><br><div class="gmail_quote">On Wed, Jun 30, 2010 at 2:07 PM, Sarah Kenny <span dir="ltr"><<a href="mailto:skenny@uchicago.edu">skenny@uchicago.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">one thing i can tell currently is that it's NOT running my .bashrc<br>
using that port.<br>
<div><div></div><div class="h5"><br>
On Wed, Jun 30, 2010 at 12:39 PM, Michael Wilde <<a href="mailto:wilde@mcs.anl.gov">wilde@mcs.anl.gov</a>> wrote:<br>
> Hmm. Note that the ports below get you to the GT5 GRAM service at QueenBee.<br>
><br>
> One possibility is that perhaps the services differ in whether they run softenv, .bashrc, etc? Needs more experimentation to understand the discrepancies we are seeing.<br>
><br>
> Maybe you can try the different URIs manually and see what PATH gets set up, if it seems that the discrepancy is related to that.<br>
><br>
> - Mike<br>
><br>
><br>
><br>
> ----- "Sarah Kenny" <<a href="mailto:skenny@uchicago.edu">skenny@uchicago.edu</a>> wrote:<br>
><br>
>> awesome, using your sites file it's working...although, weird thing<br>
>> is<br>
>> it wasn't the java line at all. it looks like it has to do with<br>
>> specifying the port on the coaster line. i usually don't specify port<br>
>> for other sites (e.g. abe) but i tried that and it worked. in fact,<br>
>> even if i remove the PATHPREFIX setting in your sties file it still<br>
>> works as long as port is specified, if i remove the port<br>
>> specification<br>
>> it fails as before...not sure how/why the port affects the java<br>
>> version but that seems to be the case:<br>
>><br>
>> <execution provider="coaster" url="<a href="http://grid-qb.loni-lsu.teragrid.org" target="_blank">grid-qb.loni-lsu.teragrid.org</a>"<br>
>> jobManager="gt2:gt2:PBS"/><br>
>><br>
>> <execution provider="coaster"<br>
>> url="<a href="http://grid-qb.loni-lsu.teragrid.org:2120" target="_blank">grid-qb.loni-lsu.teragrid.org:2120</a>"<br>
>> jobmanager="gt2:gt2:pbs"/><br>
>><br>
>> anyway, it's running...thanks!<br>
>><br>
>> ~sk<br>
>><br>
>> On Wed, Jun 30, 2010 at 11:51 AM, <<a href="mailto:wilde@mcs.anl.gov">wilde@mcs.anl.gov</a>> wrote:<br>
>> > Yup, job finished, so seems to have basic sanity.<br>
>> ><br>
>> > Sites entry is below. I used the SIDGrid TG DBS acct, and my Swift<br>
>> build:<br>
>> > /home/wilde/swift/src/stable/cog/modules/swift/dist/swift-svn/bin<br>
>> ><br>
>> > - Mike<br>
>> ><br>
>> ><br>
>> > <pool handle="pbs"><br>
>> ><br>
>> > <execution provider="coaster"<br>
>> url="<a href="http://grid-qb.loni-lsu.teragrid.org:2120" target="_blank">grid-qb.loni-lsu.teragrid.org:2120</a>" jobmanager="gt2:gt2:pbs"/><br>
>> ><br>
>> > <profile namespace="globus" key="workersPerNode">8</profile><br>
>> > <profile namespace="globus" key="slots">1</profile><br>
>> > <profile namespace="globus" key="nodeGranularity">1</profile><br>
>> > <profile namespace="globus" key="maxNodes">1</profile><br>
>> > <profile namespace="karajan" key="jobThrottle">.15</profile><br>
>> > <profile namespace="karajan" key="initialScore">10000</profile><br>
>> > <profile namespace="env"<br>
>> key="PATHPPREFIX">/usr/local/compilers/jdk/bin</profile><br>
>> ><br>
>> > <profile namespace="globus"<br>
>> key="project">TG-DBSACCTHERE</profile><br>
>> ><br>
>> > <gridftp url="<a href="http://gridftp-qb.loni-lsu.teragrid.org:2811" target="_blank">gridftp-qb.loni-lsu.teragrid.org:2811</a>" /><br>
>> > <workdirectory>/home/ux454325/swiftwork</workdirectory><br>
>> ><br>
>> > </pool><br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
>> > ----- "Sarah Kenny" <<a href="mailto:skenny@uchicago.edu">skenny@uchicago.edu</a>> wrote:<br>
>> ><br>
>> >> yeah, you definitely got further than me if you're in the<br>
>> queue...but<br>
>> >> i can't replicate this (even when i update to the latest swift)<br>
>> can<br>
>> >> you post your whole sites and tc files?<br>
>> >><br>
>> >> thanks<br>
>> >> ~sk<br>
>> >><br>
>> >> On Tue, Jun 29, 2010 at 3:45 PM, Michael Wilde <<a href="mailto:wilde@mcs.anl.gov">wilde@mcs.anl.gov</a>><br>
>> >> wrote:<br>
>> >> > I added this line to sites.xml, and now I see a PBS job queued<br>
>> on<br>
>> >> QueenBee, which I *think* means that the coaster service was able<br>
>> to<br>
>> >> start:<br>
>> >> ><br>
>> >> > <profile namespace="env"<br>
>> >> key="PATHPPREFIX">/usr/local/compilers/jdk/bin</profile><br>
>> >> ><br>
>> >> > - Mike<br>
>> >> ><br>
>> >> ><br>
>> >> > ----- "Mihael Hategan" <<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:<br>
>> >> ><br>
>> >> >> On Tue, 2010-06-29 at 12:32 -0500, <a href="mailto:wilde@mcs.anl.gov">wilde@mcs.anl.gov</a> wrote:<br>
>> >> >> > With my login, globus-job-run gets gcj (see below). When I<br>
>> login<br>
>> >> to<br>
>> >> >> QueenBee, my default .soft entries give me Sun Java 1.6.<br>
>> >> >> ><br>
>> >> >> > When I use globus-job-run, neither .profile nor .bashrc seems<br>
>> to<br>
>> >> be<br>
>> >> >> run (as I placed PATH= statements in both).<br>
>> >> >> ><br>
>> >> >> > Mihael, is there any other provision to find the right Java<br>
>> for<br>
>> >> >> coaster service startup?<br>
>> >> >><br>
>> >> >> The addition of it to PATH should be sufficient as far as I can<br>
>> >> tell.<br>
>> >> >><br>
>> >> >> I can try to debug it.<br>
>> >> >><br>
>> >> >> Skenny, can you pass me your sites file?<br>
>> >> >><br>
>> >> >> Mihael<br>
>> >> ><br>
>> >> > --<br>
>> >> > Michael Wilde<br>
>> >> > Computation Institute, University of Chicago<br>
>> >> > Mathematics and Computer Science Division<br>
>> >> > Argonne National Laboratory<br>
>> >> ><br>
>> >> ><br>
>> ><br>
>> > --<br>
>> > Michael Wilde<br>
>> > Computation Institute, University of Chicago<br>
>> > Mathematics and Computer Science Division<br>
>> > Argonne National Laboratory<br>
>> ><br>
>> ><br>
><br>
> --<br>
> Michael Wilde<br>
> Computation Institute, University of Chicago<br>
> Mathematics and Computer Science Division<br>
> Argonne National Laboratory<br>
><br>
><br>
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