[Swift-devel] coasters and java on queen bee

Tue Jun 29 12:32:32 CDT 2010

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?

- Mike

---

Running from PADS:

login1$ globus-job-run grid-qb.loni-lsu.teragrid.org:2120/jobmanager-fork /bin/sh -c 'echo $PATH'
/usr/local/bin:/bin:/usr/bin
login1$ 

login1$ globus-job-run grid-qb.loni-lsu.teragrid.org:2120/jobmanager-fork /bin/sh -c "type java"    
java is /usr/bin/java
login1$

login1$ globus-job-run grid-qb.loni-lsu.teragrid.org:2120/jobmanager-fork /bin/sh -c "java -version"
java version "1.4.2"
gcj (GCC) 3.4.6 20060404 (Red Hat 3.4.6-8)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

---

----- "Michael Wilde" <wilde at mcs.anl.gov> wrote:

> Assuming you are starting coasters via GT2, I would suggest a few
> experiments with globus-job-rub to see how your path is being set up.
> 
> Similarly if you are running locally or via ssh.
> 
> I had similar problems on Abe quite a while ago, which is configured
> much like QueenBee, but much has changed since then both in coasters
> and possibly on the systems.
> 
> I suspect we need to debug a bit more ourselves before we go to the
> sysadmins.
> 
> - Mike
> 
> ----- "Sarah Kenny" <skenny at uchicago.edu> wrote:
> 
> > pre-pending the path via .bashrc,tc.data or sites.xml seems to have
> > no
> > effect...i was under the impression that others were successfully
> > running coasters on queen bee, so thought someone might've dealt
> with
> > this already...but perhaps i should try poking the loni admins to
> see
> > if they can shed some light.
> > 
> > thanks
> > ~sk
> > 
> > On Tue, Jun 29, 2010 at 10:39 AM, Michael Wilde <wilde at mcs.anl.gov>
> > wrote:
> > > It seems like some interaction between coaster bootstrap, softenv
> > (or lack thereof) and site conventions is causing gcj to be used.
> That
> > seems to be in your PATH and you can try to explicitly put the
> correct
> > JAVA in your PATH in .bashrc and/or .profile. Setting JAVA_HOME
> alone
> > wont cause the correct Java to be run.
> > >
> > > - Mike
> > >
> > > ----- "Sarah Kenny" <skenny at uchicago.edu> wrote:
> > >
> > >> nope :(
> > >>
> > >> On Mon, Jun 28, 2010 at 2:40 PM, Mihael Hategan
> > <hategan at mcs.anl.gov>
> > >> wrote:
> > >> > Ok. That might not work either.
> > >> >
> > >> > However, you may try to add the proper java executable to the
> > PATH.
> > >> I
> > >> > think that might work better.
> > >> >
> > >> > On Mon, 2010-06-28 at 14:34 -0500, Sarah Kenny wrote:
> > >> >> tc.data had no effect...will try sites
> > >> >>
> > >> >> On Mon, Jun 28, 2010 at 2:30 PM, Mihael Hategan
> > >> <hategan at mcs.anl.gov> wrote:
> > >> >> > Have you tried setting JAVA_HOME in tc.data or sites.xml? I
> > have
> > >> a
> > >> >> > suspicion that might work.
> > >> >> >
> > >> >> > On Mon, 2010-06-28 at 14:11 -0500, Sarah Kenny wrote:
> > >> >> >> anyone else get this using coasters on queen bee?
> > >> >> >>
> > >> >> >> STDOUT: Warning: -jar not understood. Ignoring.
> > >> >> >> Exception in thread "main" java.lang.NoClassDefFoundError:
> > >> .tmp.bootstrap.Z29712
> > >> >> >>    at gnu.gcj.runtime.FirstThread.run()
> > >> (/usr/lib64/libgcj.so.5.0.0)
> > >> >> >>    at _Jv_ThreadRun(java.lang.Thread)
> > >> (/usr/lib64/libgcj.so.5.0.0)
> > >> >> >>    at _Jv_RunMain(java.lang.Class, byte const, int, byte
> > const,
> > >> >> >> boolean) (/usr/lib64/libgcj.so.5.0.0)
> > >> >> >>    at __gcj_personality_v0
> (/home/skenny/java.version=1.4.2)
> > >> >> >>    at __libc_start_main (/lib64/tls/libc-2.3.4.so)
> > >> >> >>    at _Jv_RegisterClasses
> (/home/skenny/java.version=1.4.2)
> > >> >> >>
> > >> >> >> not sure why it's showing my java version as 1.4.2...when
> > i'm
> > >> logged
> > >> >> >> into the headnode (or a worker node) my java version is
> much
> > >> newer:
> > >> >> >>
> > >> >> >> [skenny at qb1 ~]$ java -version
> > >> >> >> java version "1.6.0_20"
> > >> >> >> Java(TM) SE Runtime Environment (build 1.6.0_20-b02)
> > >> >> >> Java HotSpot(TM) 64-Bit Server VM (build 16.3-b01, mixed
> > mode)
> > >> >> >>
> > >> >> >> i also tried adding JAVA_HOME to my .bashrc on the site
> > which
> > >> had no effect.
> > >> >> >>
> > >> >> >> any idea how i can get swift to use the right java?
> > >> >> >>
> > >> >> >> using a slightly older swift (swift-r3116
> cog-r2482)...don't
> > >> know if
> > >> >> >> this has maybe been fixed in a later version (?)
> > >> >> >>
> > >> >> >>
> > >> >> >> thanks
> > >> >> >> ~sk
> > >> >> >> _______________________________________________
> > >> >> >> Swift-devel mailing list
> > >> >> >> Swift-devel at ci.uchicago.edu
> > >> >> >> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > >> >> >
> > >> >> >
> > >> >> >
> > >> >
> > >> >
> > >> >
> > >> _______________________________________________
> > >> Swift-devel mailing list
> > >> Swift-devel at ci.uchicago.edu
> > >> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
> > >
> > > --
> > > 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