[GE globus] Grid Engine and GT4

Melvin Koh melvin at apstc.sun.com.sg
Mon Jun 19 05:00:32 BST 2006


Diego,

The problem is not with the sge-jobmanager dir. The fatal error is in fact
this:

> /opt/globus4/lib/perl/Globus/GRAM/JobManager/sge.pm line 186.Syntax:
> globus-gass-cache [-help] -op [-r resource][-t tag]...[URL]Use -help to
> display full usageERROR: operation requires an URLSyntax: globus-gass-cache
> [-help] -op [-r resource][-t tag]...[URL]Use -help to display full usage


If you look at line 186 of the GT2 sge.pm, there is this line:

system("$cache_pgm -add -t $tag -n $script_url file:/dev/null");

$cache_pgm is referring to globus-gass-cache command, which has changed
it's syntax in GT4. You need to modify this line to the new syntax. I've
not used the command before, so I can't help you much here. Perhaps you
can get more help on the globus mailing lists.

-- 
-----------------------------------------
Melvin Koh Chee Kian
Grid Research Engineer
Asia Pacific Science & Technology Center
Sun Microsystems Inc.
Website: http://apstc.sun.com.sg/
-----------------------------------------

On Fri, 16 Jun 2006, Diego Bello wrote:

> On 6/16/06, David McBride <dwm at doc.ic.ac.uk> wrote:
> >
> > On Thu, 2006-06-15 at 17:53 -0400, Diego Bello wrote:
> > > With the gt4 integration package, I get this when starting container:
> >
> > > java.io.IOException: java.io.IOException:
> > > /opt/globus4/libexec/globus-scheduler-provider-sge: not found
> >
> > Hi,
> >
> > The LeSC GT4-SGE adaptor never shipped with an MDS information provider,
> > which results in the above error.
> >
> > This will only affect you if you're trying to run an MDS service; it
> > doesn't affect GRAM or WS-GRAM.
> >
> > I'm surprised that the GT4 JobManager doesn't work with when invoked by
> > the GRAM backend; I didn't think the changes between the two releases
> > were that significant.
> >
> > The error you're getting corresponds to
> > Globus::GRAM::Error::TEMP_SCRIPT_FILE_FAILED -- which is returned if the
> > JobManager is unable to create the temporary script file for some
> > reason.
> >
> > Unfortunately, by default Globus doesn't seem to write out the logging
> > output generated by the JobManager anywhere.  Rewriting the new()
> > function in the file JobManager.pm to read as follows will force log
> > files to be created in /tmp:
> >
> > $GLOBUS_LOCATION/lib/perl/Globus/GRAM/JobManager.pm:
> >
> > --------8<---------------------8<---------------------8<-------------
> >
> > sub new
> > {
> >     my $class = shift;
> >     my $self = {};
> >     my $description = shift;
> >
> >     $self->{JobDescription} = $description;
> >
> > # [dwm] Begin changes
> > #
> > #    if(defined($description->logfile()))
> > #    {
> >
> >     my $WHOAMI = `whoami`;
> >     chomp $WHOAMI;
> >
> >         local(*FH);
> >         open(FH, '>>'. "/tmp/$WHOAMI-jobmanager.log");
> >         select((select(FH),$|=1)[$[]);
> >         $self->{log} = *FH;
> > #    }
> > # [dwm] End changes
> >
> >     bless $self, $class;
> >
> >     $self->log("New Perl JobManager created.");
> >
> >     return $self;
> > }
> >
> > --------8<---------------------8<---------------------8<-------------
> >
> > If you're still can't work out what's going wrong, the JobManager perl
> > script itself will have been installed in
> > $GLOBUS_LOCATION/lib/perl/Globus/GRAM/JobManager/sge.pm -- if you know
> > any Perl at all, try adding additional logging statements to the
> > submit() function to try to narrow down the problem.
> >
> > I'm afraid I haven't done any work with SGE and GT4 since the adapator
> > was released, so I probably can't be of much more help;  however, it's
> > possible that you might find my latest internal revision (which I've
> > been using with my GT2-based LCG grid work) useful -- see:
> >
> > http://www.doc.ic.ac.uk/~dwm/Code/gnu-arch/2006/sge-jobmanager--main/
> > http://www.doc.ic.ac.uk/~dwm/arch/2006/ (GNU Arch Repository)
> >
> > Best of luck.
> >
> > Cheers,
> > David
> > --
> > David McBride <dwm at doc.ic.ac.uk>
> > Department of Computing, Imperial College, London
> >
> 
> I found something, when trying to submit a test job with a XML descriptor
> with this:
> globusrun-ws -submit -factory localhost -Ft SGE -f test_super_simple.xml
> 
> <!-- test_super_simple.xml -->
> <job>
>     <executable>/bin/echo</executable>
>     <directory>/tmp</directory>
>     <argument>12</argument>
>     <argument>abc</argument>
>     <argument>34</argument>
>     <argument>this is an example_string </argument>
>     <argument>Globus was here</argument>
>     <environment>
>        <name>PI</name>
>        <value>3.141</value>
>     </environment>
>     <stdin>/dev/null</stdin>
>     <stdout>stdout</stdout>
>     <stderr>stderr</stderr>
>     <count>2</count>
> </job>
> 
> 
> The container's error is this:
> 
> 2006-06-16 20:46:41,135 ERROR exec.JobManagerScript [Thread-38,run:307]
> Script stderr:
> Failed to read /etc/sge-jobmanager/jobmanager.conf for reading: No such file
> or directory at /opt/globus4/lib/perl/Globus/GRAM/JobManager/sge.pm line
> 137.Failed to read  for reading: No such file or directory at
> /opt/globus4/lib/perl/Globus/GRAM/JobManager/sge.pm line 137.Failed to read
> for reading: No such file or directory at
> /opt/globus4/lib/perl/Globus/GRAM/JobManager/sge.pm line 137.Unable to read
> configuration file '/etc/sge-jobmanager/vqueues.conf': No such file or
> directoryWill continue without any virtual queue definitions. at
> /opt/globus4/lib/perl/Globus/GRAM/JobManager/sge.pm line 186.Syntax:
> globus-gass-cache [-help] -op [-r resource][-t tag]...[URL]Use -help to
> display full usageERROR: operation requires an URLSyntax: globus-gass-cache
> [-help] -op [-r resource][-t tag]...[URL]Use -help to display full usage
> 2006-06-16 20:46:41,136 WARN
> exec.StateMachine[Thread-28,createFaultFromErrorCode:2936] Unhandled
> fault code 28
> 2006-06-16 20:49:27,776 WARN  usefulrp.GLUEResourceProperty [GLUE refresher
> 0,runScript:314] Script Execution error when executing shell
> /opt/globus4/libexec/globus-scheduler-provider-sge
> 
> 
> 
> It seems it is looking for a /etc/sge-jobmanager directory, wich is
> specified in the sge.pm file, but I have not such directory or the
> jobmanager.conf and vqueues.conf files.
> 
> I think it is looking for queue information, wich is not found, and then the
> error, am I right?, what do you think?.
> 
> Regards.
> 

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