Compiling
---------
-Check out the source:
+Check out the source::
$ git clone http://www.physics.drexel.edu/~wking/code/git/sawsim.git sawsim
$ cd sawsim
-Sawsim is written in noweb_. Extract the `Makefile` and compile with:
+Sawsim is written in noweb_. Extract the `Makefile` and compile with::
$ notangle -Rmakefile src/sawsim.nw | sed 's/ /\t/' > Makefile
$ make
-Run the unit tests with:
+Run the unit tests with::
$ make check
If you're using the Python bindings (`pysawsim` or `bin/*.py`), you
-should run the `pysawsim` unit tests with:
+should run the `pysawsim` unit tests with::
$ ./misc/hooks/pre-commit-pysawsim-check
Upgrading
~~~~~~~~~
-Upgrade to the most recent version:
+Upgrade to the most recent version::
sawsim$ git pull
sawsim$ make && make check && ./misc/hooks/pre-commit-pysawsim-check
.. _pbs-python: http://subtrac.sara.nl/oss/pbs_python
.. [1] mpi4py has no Debian package, but you can install it with
- setuputils` (Debian: python-setuptools) via:
+ distribute_ (a `setuptools` fork) (Debian: python-distribute,
+ Gentoo: setuptools/setuptools) via::
- easy_install --user mpi4py
+ $ easy_install --user mpi4py
+
+ For systems with earlier versions of `distribute`/`setuptools`,
+ which lack the `--user` option, try something along the lines of::
+
+ $ easy_install --user mpi4py
+ $ easy_install --prefix $HOME/.local/ mpi4py
.. [2] pbs-python has no Debian or Gentoo packages, but you can
install it from source. See the `pbs-python homepage`_.
+.. _distribute: http://pypi.python.org/pypi/distribute
+
+
PYTHONPATH
~~~~~~~~~~
statistical analysis. To facilitate this, we provide the `pysawsim`
module which provides a higher level interface to `sawsim`.
-Ensure that . is in your PYTHONPATH_, and run the pysawsim tests:
+Ensure that . is in your PYTHONPATH_, and run the pysawsim tests::
sawsim$ ./misc/hooks/pre-commit-pysawsim-check
parameters, you probably want to enable caching (`-C/--use-cache`).
The output of each `sawsim` run will be stored in your cache directory
(`-d/--cache-dir`) and recycled for future runs with the same sawsim
-parameters. For example, if you place 200 runs in the cache:
+parameters. For example, if you place 200 runs in the cache::
$ bin/sawsim_hist.py -s bin/sawsim -N 200 --use-cache
-And then generate another histogram with the same `sawsim` parameters:
+And then generate another histogram with the same `sawsim` parameters::
$ bin/sawsim_hist.py -s bin/sawsim -N 300 --use-cache
The second call will only execute an additional 100 `sawsim` runs.
-If you ask for *fewer* runs than are contained in the cache, e.g.:
+If you ask for *fewer* runs than are contained in the cache, e.g.::
$ bin/sawsim_hist.py -s bin/sawsim -N 100 --use-cache
Help
----
-As always, run
+As always, run::
sawim$ bin/<whatever> --help