[Swift-user] Montage wrapper error

[Jonathan Monette]

all files used for this run and created (log files and such) are in 
$HOME/Workspace/Swift/Montage/m101_j_4x4/runs on the ci machines.  If 
you would like I can tar up one of the runs.  Not sure which you would 
prefer.

On 8/3/10 11:33 PM, Mihael Hategan wrote:
> It may be useful for quickly reproducing it. You already know what I
> need. Config files, input files, table files, and scripts if they
> changed.
>
> Mihael
>
> On Tue, 2010-08-03 at 23:29 -0500, Jonathan Monette wrote:
>    
>> Ok.  Let me know if you need more of my input files or configurations.
>>
>> On 8/3/10 11:20 PM, Mihael Hategan wrote:
>>      
>>> Ok. I'll need to take a look at these.
>>>
>>> On Tue, 2010-08-03 at 23:15 -0500, Jonathan Monette wrote:
>>>
>>>        
>>>> with use.provider.staging=true i get
>>>> Execution failed:
>>>>        Exception in mProjectPP:
>>>> Arguments: [-X, raw_dir/2mass-atlas-990214n-j1210091.fits,
>>>> proj_dir/proj_2mass-atlas-990214n-j1210091.fits, template.hdr]
>>>> Host: teraport
>>>> Directory:
>>>> m101_montage-20100803-2312-ex8oc5ff/jobs/y/mProjectPP-yt0gtrvjTODO: outs
>>>> ----
>>>>
>>>> Caused by:
>>>>        Job failed with an exit code of 254
>>>>
>>>> and with that line commented out i get a script printed to the screen
>>>> saying it doesn't know what #!/BIN?BASH
>>>>
>>>> Execution failed:
>>>>        Could not initialize shared directory on teraport
>>>> Caused by:
>>>>        org.globus.cog.abstraction.impl.file.FileResourceException:
>>>> org.globus.cog.karajan.workflow.service.ProtocolException: Unknown
>>>> command: #!/BIN/BASH
>>>>
>>>>
>>>> On 8/3/10 11:04 PM, Mihael Hategan wrote:
>>>>
>>>>          
>>>>> Eh. I'll see if I can fix those.
>>>>>
>>>>> Though if you are using coasters, and given that I do think I fixed the
>>>>> existing issues, there is one more thing you could try:
>>>>> in swift.properties, at the end, say use.provider.staging=true
>>>>>
>>>>> Mihael
>>>>>
>>>>> On Tue, 2010-08-03 at 22:59 -0500, Jonathan Monette wrote:
>>>>>
>>>>>
>>>>>            
>>>>>> <pool handle="teraport">
>>>>>> <execution provider="coaster" url="tp-login2.ci.uchicago.edu"
>>>>>> jobmanager="ssh:pbs" />
>>>>>> <filesystem provider="coaster" url="ssh://tp-login2.ci.uchicago.edu" />
>>>>>> <profile namespace="globus" key="maxtime">3000</profile>
>>>>>> <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">10</profile>
>>>>>> <profile namespace="globus" key="queue">short</profile>
>>>>>> <profile namespace="karajan" key="jobThrottle">0.7</profile>
>>>>>> <profile namespace="karajan" key="initialScore">10000</profile>
>>>>>> <filesystem provider="ssh" url="tp-login2.ci.uchicago.edu"/>
>>>>>> <workdirectory>/home/jonmon/Library/swift/work/teraport</workdirectory>
>>>>>> </pool>
>>>>>>
>>>>>> here is the new sites entry.  I tried running my code and got this error.
>>>>>>
>>>>>> class
>>>>>> org.globus.cog.abstraction.impl.file.coaster.buffers.NIOChannelReadBuffer throws
>>>>>> exception in doStuff. Fix it!
>>>>>> java.lang.NullPointerException
>>>>>>         at
>>>>>> org.globus.cog.abstraction.impl.file.coaster.commands.PutFileCommand.dataRead(PutFileCommand.java:79)
>>>>>>         at
>>>>>> org.globus.cog.abstraction.impl.file.coaster.buffers.ReadBuffer.bufferRead(ReadBuffer.java:77)
>>>>>>         at
>>>>>> org.globus.cog.abstraction.impl.file.coaster.buffers.NIOChannelReadBuffer.doStuff(NIOChannelReadBuffer.java:36)
>>>>>>         at
>>>>>> org.globus.cog.abstraction.impl.file.coaster.buffers.Buffers.run(Buffers.java:122)
>>>>>>
>>>>>>
>>>>>> On 8/3/10 10:55 PM, Mihael Hategan wrote:
>>>>>>
>>>>>>
>>>>>>              
>>>>>>> <filesystem provider="coaster" url="ssh://tp-login2.ci.uchicago.edu"  />
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>                
>>>>>>
>>>>>>              
>>>>>
>>>>>            
>>>>
>>>>          
>>>
>>>        
>>      
>
>    

-- 
Jon

Computers are incredibly fast, accurate, and stupid. Human beings are incredibly slow, inaccurate, and brilliant. Together they are powerful beyond imagination.
- Albert Einstein