On Nov 7, 2013, at 2:45 PM, Jean-Francois Payotte wrote:

> Dear Galaxy developers, 
> 
> I know I am not the only one with this issue, as over time I've stumbled on a 
> few mailing-list threads with other users having the same problem. 
> And I know the recommended solution is to use the -noac mount option. 
> (http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#Unified_Method%29)
>  
> 
> However, it is said that using this -noac mount option comes with a 
> performance trade-off, so when we first ran into this issue (datasets showing 
> "Empty" and "No peek", even though the file on the hard drive is full of 
> content), we implemented the hack found in this thread: 
> http://dev.list.galaxyproject.org/What-s-causing-this-error-td4141958.html#a4141963
>  
> 
> In this thread, John suggested to add a "sleep()" in the "finish_job" method 
> of the "galaxy_dist/lib/galaxy/jobs/runnersdrmaa.py" file. 
> It worked very well for us. Adding a sleep(30) made all the jobs waiting 30 
> seconds before finishing, but the "No peek" issue had at least disappear). 
> 
> However, since the latest Galaxy updates, this file (drmaa.py) has been 
> dramastically changed and the "finish_job" method doesn't exist anymore. 
> Hence, I had to remove this hack, hoping that this issue would have 
> disappeared as well.  Unfortunaley, this "No peek" issue is still there and 
> causing many headaches to some of our workflows users. 
> 
> My question is then: Can I put this "sleep(30)" in some other place (method 
> and/or file) in order to achieve the same result? 
> I would really like to solve this "No peek" issue without resorting to the 
> "-noac" mount option.  Actually, I am not even sure our system administrator 
> would allow it. 

Hi Jean-Fran├žois,

The job runners have been largely refactored into 
lib/galaxy/jobs/runners/__init__.py, which is where you'll find finish_job().  
However, we also recently added some tricks to work around this issue that has 
solved the problem (for usegalaxy.org, at least) without needing -noac.  This 
is available in Monday's distribution release.  Here's the commit:

  
https://bitbucket.org/galaxy/galaxy-central/commits/384240b8cd29963f302a0349476cf83734cfb5df?at=default

To use, set retry_job_output_collection > 0 in the Galaxy config.

--nate

> 
> Thanks again for your help! 
> Jean-Fran├žois 
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