Package: pysawsim
Sawsim is a force-spectroscopy simulator.  See the manual for more
details.PackagesGentooI’ve packaged sawsim forGentooas sci-physics/sawsim in mywtk
overlay.  To install, run:# emerge -av app-portage/layman
# layman --add wtk
# emerge -av sci-physics/sawsimTo stay current, follow the sawsimAtomorRSSfeed, and
re-emerge when there are interesting changes.You can skip theCompilingandUpgradingsections of this README ;).CompilingCheck out the source:$ git clone git://tremily.us/sawsim.git
$ cd sawsimSawsim is written innoweb.  Extract theMakefileand compile with:$ notangle -Rmakefile src/sawsim.nw | sed 's/        /\t/' > Makefile
$ makeRun the unit tests with:$ make checkIf you’re using the Python bindings (pysawsimorbin/*.py), you
should run thepysawsimunit tests with:$ ./misc/hooks/pre-commit-pysawsim-checkUpgradingUpgrade to the most recent version:sawsim$ git pull
sawsim$ make && make check && ./misc/hooks/pre-commit-pysawsim-checkDependenciesPackagePurposeDebianGentoogitversion controlgit-coredev-vcs/gitnowebsource code frameworknowebapp-text/nowebGSLsawsim dependencylibgsl0-devsci-libs/gslchecksawsim unit testscheckdev-libs/checkpython2.5+pysawsim executionpythondev-lang/pythonnosepysawsim testingpython-nosedev-python/nosematplotlibpysawsim executionpython-matplotlibdev-python/matplotlibnumpypysawsim executionpython-numpydev-python/numpyscipypysawsim executionpython-scipysci-libs/scipympi4pypysawsim mpi manager[1]dev-python/mpi4pypbs-pythonpysawsim pbs manager[2]sys-cluster/pbs-python[1]mpi4py has no Debian package, but you can install it withdistribute(asetuptoolsfork) (Debian: python-distribute,
Gentoo: setuptools/setuptools) via:$ easy_install --user mpi4pyFor systems with earlier versions ofdistribute/setuptools,
which lack the–useroption, try something along the lines of:$ easy_install --user mpi4py
$ easy_install --prefix $HOME/.local/ mpi4py[2]pbs-python has no Debian package, but you can install it from
source.  See thepbs-python homepage.PYTHONPATHIf you install Python packages at the user level (vs. system-wide
installs) you may need to setup aPYTHONPATHenvironmental variable
so Python can find the packages.  You’ll probably want to add a line
along the lines of:export PYTHONPATH=".:$HOME/.local/lib/python2.6/site-packages"to your~/.bashrcfile to ensure that the newPYTHONPATHis setup
for all future logins.Python wrapperThesawsimbinary 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 thepysawsimmodule which provides a higher level interface tosawsim.Ensure that . is in yourPYTHONPATH, and run the pysawsim tests:sawsim$ ./misc/hooks/pre-commit-pysawsim-checkSeveralpysawsimsubmodules have scripts (bin/*.py) providing
command-line access to their functionality.  Many users will probably
only need a single call tobin/sawsim_hist_scan.pyto fit their
unfolding force histograms to a particular model.Job managersFor the–manageroption, use whatever job scheduling system is most
appropriate for your host.  For example:Host descriptionManagerSMP machine with many processorssubprocCluster with the Torque/Maui portable batch queue systempbsBunch of machines which can host message-passing daemonsmpiMy wimpy single-processor, single-core netbookthreadCachingBy 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 eachsawsimrun 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-cacheAnd then generate another histogram with the samesawsimparameters:$ bin/sawsim_hist.py -s bin/sawsim -N 300 --use-cacheThe second call will only execute an additional 100sawsimruns.If you ask forfewerruns than are contained in the cache, e.g.:$ bin/sawsim_hist.py -s bin/sawsim -N 100 --use-cacheYou will not runanynewsawsimruns.  All 100 runs will be drawn
at random from the cache.HelpAs always, run:sawim$ bin/<whatever> --helpfor more details.LicenseSaswim is released under the GNU GPLv3+.  SeeCOPYINGfor details.