[Swift-devel] coasters and java on queen bee

[Glen Hocky]

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

run.sh:

> #!/bin/bash

source ~/.basrhc

"$*"


and then you can do something like
globus-job-run ...      run.sh COMMAND

On Wed, Jun 30, 2010 at 2:07 PM, Sarah Kenny <skenny at uchicago.edu> wrote:

> one thing i can tell currently is that it's NOT running my .bashrc
> using that port.
>
> On Wed, Jun 30, 2010 at 12:39 PM, Michael Wilde <wilde at mcs.anl.gov> wrote:
> > Hmm. Note that the ports below get you to the GT5 GRAM service at
> QueenBee.
> >
> > 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.
> >
> > 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.
> >
> > - Mike
> >
> >
> >
> > ----- "Sarah Kenny" <skenny at uchicago.edu> wrote:
> >
> >> awesome, using your sites file it's working...although, weird thing
> >> is
> >> it wasn't the java line at all. it looks like it has to do with
> >> specifying the port on the coaster line. i usually don't specify port
> >> for other sites (e.g. abe) but i tried that and it worked. in fact,
> >> even if i remove the PATHPREFIX setting in your sties file it still
> >> works as long as port is specified, if i remove the port
> >> specification
> >> it fails as before...not sure how/why the port affects the java
> >> version but that seems to be the case:
> >>
> >> <execution provider="coaster" url="grid-qb.loni-lsu.teragrid.org"
> >> jobManager="gt2:gt2:PBS"/>
> >>
> >> <execution provider="coaster"
> >> url="grid-qb.loni-lsu.teragrid.org:2120"
> >> jobmanager="gt2:gt2:pbs"/>
> >>
> >> anyway, it's running...thanks!
> >>
> >> ~sk
> >>
> >> On Wed, Jun 30, 2010 at 11:51 AM,  <wilde at mcs.anl.gov> wrote:
> >> > Yup, job finished, so seems to have basic sanity.
> >> >
> >> > Sites entry is below. I used the SIDGrid TG DBS acct, and my Swift
> >> build:
> >> >  /home/wilde/swift/src/stable/cog/modules/swift/dist/swift-svn/bin
> >> >
> >> > - Mike
> >> >
> >> >
> >> >  <pool handle="pbs">
> >> >
> >> >    <execution provider="coaster"
> >> url="grid-qb.loni-lsu.teragrid.org:2120" jobmanager="gt2:gt2:pbs"/>
> >> >
> >> >    <profile namespace="globus" key="workersPerNode">8</profile>
> >> >    <profile namespace="globus" key="slots">1</profile>
> >> >    <profile namespace="globus" key="nodeGranularity">1</profile>
> >> >    <profile namespace="globus" key="maxNodes">1</profile>
> >> >    <profile namespace="karajan" key="jobThrottle">.15</profile>
> >> >    <profile namespace="karajan" key="initialScore">10000</profile>
> >> >    <profile namespace="env"
> >> key="PATHPPREFIX">/usr/local/compilers/jdk/bin</profile>
> >> >
> >> >    <profile namespace="globus"
> >> key="project">TG-DBSACCTHERE</profile>
> >> >
> >> >    <gridftp url="gridftp-qb.loni-lsu.teragrid.org:2811" />
> >> >    <workdirectory>/home/ux454325/swiftwork</workdirectory>
> >> >
> >> >  </pool>
> >> >
> >> >
> >> >
> >> >
> >> > ----- "Sarah Kenny" <skenny at uchicago.edu> wrote:
> >> >
> >> >> yeah, you definitely got further than me if you're in the
> >> queue...but
> >> >> i can't replicate this (even when i update to the latest swift)
> >> can
> >> >> you post your whole sites and tc files?
> >> >>
> >> >> thanks
> >> >> ~sk
> >> >>
> >> >> On Tue, Jun 29, 2010 at 3:45 PM, Michael Wilde <wilde at mcs.anl.gov>
> >> >> wrote:
> >> >> > I added this line to sites.xml, and now I see a PBS job queued
> >> on
> >> >> QueenBee, which I *think* means that the coaster service was able
> >> to
> >> >> start:
> >> >> >
> >> >> > <profile namespace="env"
> >> >> key="PATHPPREFIX">/usr/local/compilers/jdk/bin</profile>
> >> >> >
> >> >> > - Mike
> >> >> >
> >> >> >
> >> >> > ----- "Mihael Hategan" <hategan at mcs.anl.gov> wrote:
> >> >> >
> >> >> >> On Tue, 2010-06-29 at 12:32 -0500, wilde at mcs.anl.gov wrote:
> >> >> >> > With my login, globus-job-run gets gcj (see below). When I
> >> login
> >> >> to
> >> >> >> QueenBee, my default .soft entries give me Sun Java 1.6.
> >> >> >> >
> >> >> >> > When I use globus-job-run, neither .profile nor .bashrc seems
> >> to
> >> >> be
> >> >> >> run (as I placed PATH= statements in both).
> >> >> >> >
> >> >> >> > Mihael, is there any other provision to find the right Java
> >> for
> >> >> >> coaster service startup?
> >> >> >>
> >> >> >> The addition of it to PATH should be sufficient as far as I can
> >> >> tell.
> >> >> >>
> >> >> >> I can try to debug it.
> >> >> >>
> >> >> >> Skenny, can you pass me your sites file?
> >> >> >>
> >> >> >> Mihael
> >> >> >
> >> >> > --
> >> >> > Michael Wilde
> >> >> > Computation Institute, University of Chicago
> >> >> > Mathematics and Computer Science Division
> >> >> > Argonne National Laboratory
> >> >> >
> >> >> >
> >> >
> >> > --
> >> > Michael Wilde
> >> > Computation Institute, University of Chicago
> >> > Mathematics and Computer Science Division
> >> > Argonne National Laboratory
> >> >
> >> >
> >
> > --
> > Michael Wilde
> > Computation Institute, University of Chicago
> > Mathematics and Computer Science Division
> > Argonne National Laboratory
> >
> >
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