On Feb 28, 2012, at 9:24 AM, Louise-Amélie Schmitt wrote:
> We're currently trying to switch to a big cluster but we have a lot of doubts
> and questions, especially since the I/O is a serious issue for our NFS.
> - 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)
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.
> - 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.
> - 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.
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and other Galaxy lists, please use the interface at: