The Configuration Object¶
The config dictionary passed to the top level functions controls how Sheepdog behaves. These are the available options:
The hostname to submit GridEngine jobs to. This is the server you normally SSH into to run qsub etc.
This must be specified and has no default value.
The SSH port to connect to. Defaults to 22.
The username to connect with. Defaults to the current system user.
The path to the SSH key that should be used. The key must be passphraseless. Defaults to seeing if any key from an SSH agent or .ssh/id_rsa or .ssh/id_dsa may be used. Use of an SSH agent is recommended.
The remote directory to place job scripts in. Relative paths will be relative to the user’s home directory. Defaults to .sheepdog.
Local Server Options¶
The file (or path) to store the sqlite database in. Since results are kept between requests in case you want to get them later, it might be nice to have database per set of related projects. Or per project. Or per request, whatever.
Defaults to ./sheepdog.sqlite.
The port that the local HTTP server will listen on. The GridEngine clients must be able to connect to the local computer on this port.
Defaults to None, which will cause Sheepdog to find an available high-numbered port and use that. Specify a particular port number if you wish to run on a specific port.
The hostname by which GridEngine workers may contact the local server. Defaults to the local FQDN (which really should work!)
A string containing the Python interpreter to use to execute the script. This is passed to the GridEngine -S option and placed on the script shebang.
Should be a Python binary which the GridEngine worker can execute.
Defaults to /usr/bin/python.
A list of strings containing GridEngine options. This is used to specify additional GridEngine related arguments, for example -l ubuntu=1 to specify a resource requirement or -r y to specify that the job may be re-run.
If unspecified, the defaults are:
["-wd $HOME/.sheepdog/", "-o $HOME/.sheepdog/", "-e $HOME/.sheepdog/"]
Note that -S /path/to/shell is always specified by the shell option detailed above, and -t 1-N is always specified with N equal to the number of arguments being evaluated.
If the resource specification -l mem_grab=2G (2G for example) is present, the sheepdog client will automatically call resource.setrlimit to restrict the process to that amount of memory.
All these options are written to the top of the job file which is copied to the GridEngine server, so may be inspected manually too.