Python framework for the sawsim force spectroscopy simulator.
Sawsim is a force-spectroscopy simulator. See the manual for more details.
# emerge -av app-portage/layman # layman --add wtk # emerge -av sci-physics/sawsim
Check out the source:
$ git clone git://tremily.us/sawsim.git $ cd sawsim
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:
$ make check
If you’re using the Python bindings (pysawsim or bin/*.py), you should run the pysawsim unit tests with:
Upgrade to the most recent version:
sawsim$ git pull sawsim$ make && make check && ./misc/hooks/pre-commit-pysawsim-check
|noweb||source code framework||noweb||app-text/noweb|
|check||sawsim unit tests||check||dev-libs/check|
|python 2.5+||pysawsim execution||python||dev-lang/python|
|mpi4py||pysawsim mpi manager||||dev-python/mpi4py|
|pbs-python||pysawsim pbs manager||||sys-cluster/pbs-python|
mpi4py has no Debian package, but you can install it with distribute (a setuptools fork) (Debian: python-distribute, Gentoo: setuptools/setuptools) via:
$ 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
|||pbs-python has no Debian package, but you can install it from source. See the pbs-python homepage.|
If you install Python packages at the user level (vs. system-wide installs) you may need to setup a PYTHONPATH environmental variable so Python can find the packages. You’ll probably want to add a line along the lines of:
to your ~/.bashrc file to ensure that the new PYTHONPATH is setup for all future logins.
The sawsim binary only runs a single pull, but you’ll probably want to run many repetitions to generate enough data for significant 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:
Several pysawsim submodules have scripts (bin/*.py) providing command-line access to their functionality. Many users will probably only need a single call to bin/sawsim_hist_scan.py to fit their unfolding force histograms to a particular model.
For the –manager option, use whatever job scheduling system is most appropriate for your host. For example:
|SMP machine with many processors||subproc|
|Cluster with the Torque/Maui portable batch queue system||pbs|
|Bunch of machines which can host message-passing daemons||mpi|
|My wimpy single-processor, single-core netbook||thread|
By default, the python wrappers do not cache the results of previous runs. However, if you are repeatedly running sawsim with the same 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:
$ bin/sawsim_hist.py -s bin/sawsim -N 200 --use-cache
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.:
$ bin/sawsim_hist.py -s bin/sawsim -N 100 --use-cache
You will not run any new sawsim runs. All 100 runs will be drawn at random from the cache.
As always, run:
sawim$ bin/<whatever> --help
for more details.
Saswim is released under the GNU GPLv3+. See COPYING for details.