On Mar 12, 2012, at 9:44 AM, Louise-Amélie Schmitt wrote:

> Hi Nate, and thanks for the reply
>>> - We saw the outputs_to_working_directory option in the .ini file, but it 
>>> only concerns output files, is there a way to make a local copy of all the 
>>> input files in the job working directory? (including indices)
>> Hi L-A,
>> 
>> Unfortunately no.  This option was only created so that you could mount the 
>> file_path directory read-only on your cluster nodes for security purposes.
>> 
> In the end it shouldn't be necessary. The guy in charge of the cluster said 
> so.
>>> - Can we set the job working directory as an absolute path so it's local to 
>>> the nodes, like /tmp ?
>> No, things like the external metadata inputs and outputs are written to the 
>> working directory and are expected to be available on both the cluster and 
>> the application server at the same path.
>> 
> Ok, I see. How do you manage that then? Is it actually not an issue I/O-wise?

Most of the things written to the working directory aren't large enough to 
cause performance problems.  The worst culprit, before we split up the load 
across a pool of servers, was tophat.  Ideally, Galaxy needs a mechanism to 
define whether local or network temp space should be used (or perhaps more 
abstractly, a way to estimate the size needed based on the inputs).

--nate

>>> - If it's possible, will the job working directories created for each job 
>>> be cleaned properly at the end?
>> Yes, depending on the value of "cleanup_job" in the config file.
>> 
>> Enhancements that remove this "shared directory" limitation are on our 
>> roadmap for this year.
> Ok, thanks a lot for all this information!
> 
> Best,
> L-A
> 
>> --nate
>> 
>>> Thanks,
>>> L-A
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