Installation
Requirements
atools
requires at least Python 2.7.x, but only uses the standard
library.
Supported queue systems and schedulers:
- PBS torque,
- Moab (Adaptive Computing),
- SUN Grid Engine,
- Slurm workload manager.
Installation
After downloading a release from GitHub and unpacking, simply run
$ ./configure --prefix=<install-path>
$ make install
Note: atools will be configured to use the Python that is in your PATH
when installing. If you change your mind afterwards, edit
conf/atools_python.sh
to your liking.
Depending on the batch system you use, the --with-batchsystem
configure
option should be set appropriately, i.e.,
torque
for PBS torque,moab
for Adaptive Computing Moab,sge
for SUN Grid Engine,slurm
for Slurm workload manager.
The default is torque
One can also specify the default shell atools
will assume for job scripts
at installation time by using the --with-shell
configure option. It
defaults to bash
, but sh
, csh
, and tcsh
are also accepted. Note
that all relevant atools
commands have a --shell
option which overrides
the installation default.
In addition, one can set the default reduce mode as either text
or csv
using the --with-reducemode
configure option. Again, areduce
has a
--mode
option to override this at any time.
Note that a reinstall is not required to change these installation default,
you can simply edit the conf/atools.conf
file to modify atools
behavior after installation.
Usage
Ensure that the bin
directory is in your path when executing atools
commands, i.e., by adding it to the PATH
environment variable.
Note that the Python run time dependency is "hidden" within atools
configuration, and is only required from within the bash wrapper scripts,
so using atools
will not pollute any environment variables except PATH
.