sawsim.git
6 years agoefbfbf: upgrade to Bugs Everywhere Directory v1.5 master
W. Trevor King [Sat, 27 Oct 2012 16:32:51 +0000 (12:32 -0400)]
efbfbf: upgrade to Bugs Everywhere Directory v1.5

6 years agoAdd --help, --stack, and --output to sawsim_plot_histogram_file.py.
W. Trevor King [Fri, 27 Jul 2012 20:23:41 +0000 (16:23 -0400)]
Add --help, --stack, and --output to sawsim_plot_histogram_file.py.

6 years agoFix $(BUILD) -> $(BUILD_DIR) in k_model_utils.c rule.
W. Trevor King [Thu, 28 Jun 2012 11:48:17 +0000 (07:48 -0400)]
Fix $(BUILD) -> $(BUILD_DIR) in k_model_utils.c rule.

BUILD isn't defined, and the old way gave errors like:

  $ make -j17 all_bin
  mkdir build
  notangle -Rk-model-utils.c src/sawsim.nw > build/k_model_utils.c
  /bin/sh: cannot create build/k_model_utils.c: Directory nonexistent
  make: *** [build/k_model_utils.c] Error 2
  make: *** Waiting for unfinished jobs....

You'd only have seen this error with parallel builds, otherwise
BUILD_DIR would have already have been created as a dependency of
another file by the time k_model_utils.c needed it.

7 years agoAdd testing command line to the README.
W. Trevor King [Fri, 18 May 2012 17:01:51 +0000 (13:01 -0400)]
Add testing command line to the README.

7 years agoEnsure that printed histograms always have at least two bins listed.
W. Trevor King [Fri, 18 May 2012 17:00:54 +0000 (13:00 -0400)]
Ensure that printed histograms always have at least two bins listed.

Otherwise it is impossible to calculate the bin width from the printed
histogram.

7 years agoChange my email address from drexel.edu to tremily.us.
W. Trevor King [Wed, 18 Apr 2012 17:23:39 +0000 (13:23 -0400)]
Change my email address from drexel.edu to tremily.us.

7 years agoUpdate URLs from einstein to tremily.
W. Trevor King [Wed, 22 Feb 2012 18:52:34 +0000 (13:52 -0500)]
Update URLs from einstein to tremily.

7 years agoAdd bin/sawsim_plot_histogram_file.py and Histogram.plot().
W. Trevor King [Thu, 12 Jan 2012 17:18:32 +0000 (12:18 -0500)]
Add bin/sawsim_plot_histogram_file.py and Histogram.plot().

This moves some of the matplotlib initialization into the more basic
pysawsim.histogram module, and provides an easy way to display
histogram files.

7 years agoRelax precision in pysawsim.histogram.Histogram bin_edges doctest.
W. Trevor King [Tue, 6 Dec 2011 19:44:29 +0000 (14:44 -0500)]
Relax precision in pysawsim.histogram.Histogram bin_edges doctest.

7 years agoAdd underscore to PYSAWSIM_LOG_LEVEL_MSG reference in parameter_scan.py.
W. Trevor King [Fri, 16 Sep 2011 16:32:28 +0000 (12:32 -0400)]
Add underscore to PYSAWSIM_LOG_LEVEL_MSG reference in parameter_scan.py.

7 years agoAdd the PYSAWSIM_LOG_LEVEL environmental variable.
W. Trevor King [Fri, 16 Sep 2011 16:30:32 +0000 (12:30 -0400)]
Add the PYSAWSIM_LOG_LEVEL environmental variable.

7 years agoClose parens in gamma calculation in manual's timescale discussion.
W. Trevor King [Tue, 13 Sep 2011 15:16:06 +0000 (11:16 -0400)]
Close parens in gamma calculation in manual's timescale discussion.

7 years agoFix omega -> \omega in manual's timescale discussion.
W. Trevor King [Tue, 13 Sep 2011 15:15:07 +0000 (11:15 -0400)]
Fix omega -> \omega in manual's timescale discussion.

8 years agoAdd download_url to setup.py.
W. Trevor King [Tue, 19 Apr 2011 20:23:40 +0000 (16:23 -0400)]
Add download_url to setup.py.

8 years agoUse README for long_description in setup.py.
W. Trevor King [Tue, 19 Apr 2011 18:39:36 +0000 (14:39 -0400)]
Use README for long_description in setup.py.

8 years agoAdd author information to setup.py.
W. Trevor King [Tue, 19 Apr 2011 18:18:40 +0000 (14:18 -0400)]
Add author information to setup.py.

8 years agoAdd --csv option to pysawsim.parameter_scan.
W. Trevor King [Sat, 9 Apr 2011 17:15:52 +0000 (13:15 -0400)]
Add --csv option to pysawsim.parameter_scan.

8 years agoAdd WORKER_POOL environmental option to facilitate pysawsim.manager benchmarking.
W. Trevor King [Fri, 1 Apr 2011 01:45:43 +0000 (18:45 -0700)]
Add WORKER_POOL environmental option to facilitate pysawsim.manager benchmarking.

8 years agoMerge commit 'origin/master'
W. Trevor King [Fri, 1 Apr 2011 00:16:47 +0000 (17:16 -0700)]
Merge commit 'origin/master'

8 years agoCorrect mpi4py URL.
W. Trevor King [Fri, 1 Apr 2011 00:01:45 +0000 (20:01 -0400)]
Correct mpi4py URL.

8 years agoFix typo in setup.py which produced a 'pysawsim/managerpysawsim/test' error.
W. Trevor King [Fri, 31 Dec 2010 18:39:12 +0000 (13:39 -0500)]
Fix typo in setup.py which produced a 'pysawsim/managerpysawsim/test' error.

8 years agoStandardize max step calculation and fit-parameter requirements in pysawsim.test.
W. Trevor King [Sat, 6 Nov 2010 15:27:44 +0000 (08:27 -0700)]
Standardize max step calculation and fit-parameter requirements in pysawsim.test.

8 years agoWider bins and weaker comparisons allow bell_rate to pass doctests.
W. Trevor King [Sat, 6 Nov 2010 14:30:39 +0000 (07:30 -0700)]
Wider bins and weaker comparisons allow bell_rate to pass doctests.

8 years agoCompare theory vs. sim scaled by bin width (not theory, which may be zero).
W. Trevor King [Sat, 6 Nov 2010 14:21:20 +0000 (07:21 -0700)]
Compare theory vs. sim scaled by bin width (not theory, which may be zero).

8 years agoFix Gumbel normalization in pysawsim.test.bell_rate.probability_distribution.
W. Trevor King [Sat, 6 Nov 2010 14:15:48 +0000 (07:15 -0700)]
Fix Gumbel normalization in pysawsim.test.bell_rate.probability_distribution.

8 years agoEnsure that self.headings exists in Histogram, e.g. in bell_rate.py's theory hist.
W. Trevor King [Sat, 6 Nov 2010 13:59:56 +0000 (06:59 -0700)]
Ensure that self.headings exists in Histogram, e.g. in bell_rate.py's theory hist.

8 years agoFor high K_0, the Bell model's <f> can be negative. Fix pysawsim.test.bell_rate.
W. Trevor King [Sat, 6 Nov 2010 13:36:02 +0000 (06:36 -0700)]
For high K_0, the Bell model's <f> can be negative.  Fix pysawsim.test.bell_rate.

8 years agoMove Bell model unfolding rate test into pysawsim/test/bell_rate.py.
W. Trevor King [Fri, 5 Nov 2010 20:58:45 +0000 (16:58 -0400)]
Move Bell model unfolding rate test into pysawsim/test/bell_rate.py.

Cleaned up model and parameter estimation.  See
  W. Trevor King, Meihong Su, and Guoliang Yang.  Monte Carlo
  simulation of mechanical unfolding of proteins based on a simple
  two-state model. International Journal of Biological Macromolecules
  46 (2010) 159-166.  doi: 10.1016/j.ijbiomac.2009.12.001
  (king10 in src/sawsim.bib)
for details.

8 years agoUse verbose nosetests (to easily ensure tests are being run).
W. Trevor King [Fri, 5 Nov 2010 20:55:04 +0000 (16:55 -0400)]
Use verbose nosetests (to easily ensure tests are being run).

8 years agoBe less specific about fit info in pysawsim.fit.ModelFitter doctest.
W. Trevor King [Fri, 5 Nov 2010 21:00:26 +0000 (14:00 -0700)]
Be less specific about fit info in pysawsim.fit.ModelFitter doctest.

8 years agopysawsim/fit.py should not be executable.
W. Trevor King [Fri, 5 Nov 2010 20:52:33 +0000 (16:52 -0400)]
pysawsim/fit.py should not be executable.

8 years agoEscape LaTeX backslashes in pysawsim.test.constant_rate.
W. Trevor King [Fri, 5 Nov 2010 18:36:58 +0000 (14:36 -0400)]
Escape LaTeX backslashes in pysawsim.test.constant_rate.

8 years agoNo need to give an explicit K in the pysawsim constant-rate analysis.
W. Trevor King [Fri, 5 Nov 2010 18:31:53 +0000 (14:31 -0400)]
No need to give an explicit K in the pysawsim constant-rate analysis.

8 years agoAdd doctest call to pysawsim.test.constant_rate.test() so nosetests will run it.
W. Trevor King [Fri, 5 Nov 2010 18:12:20 +0000 (14:12 -0400)]
Add doctest call to pysawsim.test.constant_rate.test() so nosetests will run it.

8 years agoconstant_rate.py should not be executable.
W. Trevor King [Fri, 5 Nov 2010 17:55:14 +0000 (10:55 -0700)]
constant_rate.py should not be executable.

8 years agoFixup pysawsim.test.constant_rate so it passes.
W. Trevor King [Fri, 5 Nov 2010 17:43:33 +0000 (10:43 -0700)]
Fixup pysawsim.test.constant_rate so it passes.

8 years agoOnly log WARNING level messages (and more urgent ones) in pysawsim.
W. Trevor King [Fri, 5 Nov 2010 17:42:05 +0000 (10:42 -0700)]
Only log WARNING level messages (and more urgent ones) in pysawsim.

8 years agoForce bin_edges and counts to be numy arrays in Histogram.
W. Trevor King [Fri, 5 Nov 2010 17:30:49 +0000 (10:30 -0700)]
Force bin_edges and counts to be numy arrays in Histogram.

8 years agoModelFitter.fit() should always return a list (even for single-parameter fits).
W. Trevor King [Fri, 5 Nov 2010 17:30:08 +0000 (10:30 -0700)]
ModelFitter.fit() should always return a list (even for single-parameter fits).

8 years agoMove constant unfolding rate test into pysawsim/test/constant_rate.py.
W. Trevor King [Fri, 5 Nov 2010 17:03:14 +0000 (13:03 -0400)]
Move constant unfolding rate test into pysawsim/test/constant_rate.py.

8 years agoAccount for binwidth in HistogramModelFitter doctest.
W. Trevor King [Fri, 5 Nov 2010 17:01:32 +0000 (13:01 -0400)]
Account for binwidth in HistogramModelFitter doctest.

Wider bins should increase the bin counts (all else being equal).

Also select a smaller sigma for the doctest, since that will make the
mean estimation less prone to errors large enough to break the test.

8 years agoSplit Histogram.analyze() out of Histogram.from_stream().
W. Trevor King [Fri, 5 Nov 2010 17:00:35 +0000 (13:00 -0400)]
Split Histogram.analyze() out of Histogram.from_stream().

8 years agoAdd pysawsim.test submodule (currently empty).
W. Trevor King [Fri, 5 Nov 2010 11:44:17 +0000 (07:44 -0400)]
Add pysawsim.test submodule (currently empty).

8 years agoMoved testing/common/fit.py to pysawsim/fit.py and cleaned up.
W. Trevor King [Thu, 4 Nov 2010 18:53:50 +0000 (14:53 -0400)]
Moved testing/common/fit.py to pysawsim/fit.py and cleaned up.

8 years agoMerge remote branch 'pub/master'
W. Trevor King [Thu, 4 Nov 2010 18:51:39 +0000 (14:51 -0400)]
Merge remote branch 'pub/master'

8 years agoDisable epilog line wrapping in pysawsim/parameter_error.py.
W. Trevor King [Thu, 4 Nov 2010 17:30:56 +0000 (13:30 -0400)]
Disable epilog line wrapping in pysawsim/parameter_error.py.

8 years agoThere *is* a Gentoo package for pbs_python: sys-cluster/pbs-python ;).
W. Trevor King [Wed, 3 Nov 2010 13:22:03 +0000 (09:22 -0400)]
There *is* a Gentoo package for pbs_python: sys-cluster/pbs-python ;).

8 years agoUpdate Gentoo overlay info in README now that my overlay is in the global list.
W. Trevor King [Wed, 3 Nov 2010 12:18:40 +0000 (08:18 -0400)]
Update Gentoo overlay info in README now that my overlay is in the global list.

8 years agoAdd a Gentoo package section to the README.
W. Trevor King [Tue, 2 Nov 2010 21:14:27 +0000 (17:14 -0400)]
Add a Gentoo package section to the README.

8 years agoBetter pysawsim.sawsim.SAWSIM detection via distutils.spawn.find_executable().
W. Trevor King [Tue, 2 Nov 2010 19:45:00 +0000 (15:45 -0400)]
Better pysawsim.sawsim.SAWSIM detection via distutils.spawn.find_executable().

8 years agoAdd simple setup.py for installing pysawsim.
W. Trevor King [Tue, 2 Nov 2010 19:03:43 +0000 (15:03 -0400)]
Add simple setup.py for installing pysawsim.

8 years agoUse `rm -rf` instead of `rmdir` for `make clean`.
W. Trevor King [Tue, 2 Nov 2010 18:20:04 +0000 (14:20 -0400)]
Use `rm -rf` instead of `rmdir` for `make clean`.

This avoids "No such file or directory" errors if you run `make clean`
without having build the to-be-cleaned directories.

8 years agoCreate new phony Makefile targets all_doc and all_bin.
W. Trevor King [Tue, 2 Nov 2010 18:18:46 +0000 (14:18 -0400)]
Create new phony Makefile targets all_doc and all_bin.

8 years agoFix : -> :: (rst markup) in README; document setupools/distrubute fork.
W. Trevor King [Mon, 1 Nov 2010 14:59:01 +0000 (10:59 -0400)]
Fix : -> :: (rst markup) in README; document setupools/distrubute fork.

8 years agoUse numpy.ndarray.sum() vs. __builtin__.sum() to compute hist bin counts.
W. Trevor King [Fri, 29 Oct 2010 19:19:31 +0000 (15:19 -0400)]
Use numpy.ndarray.sum() vs. __builtin__.sum() to compute hist bin counts.

It's much faster:
  $ time python -c 'import numpy; sum(numpy.arange(int(1e6)))'
  real    0m3.312s
  user    0m3.188s
  sys     0m0.118s
  $ time python -c 'import numpy; numpy.arange(int(1e6)).sum()'
  real    0m0.878s
  user    0m0.753s
  sys     0m0.122s

8 years agoRemove cruft from testing/ in preparation for test migration to pysawsim/test/.
W. Trevor King [Fri, 29 Oct 2010 12:49:59 +0000 (08:49 -0400)]
Remove cruft from testing/ in preparation for test migration to pysawsim/test/.

8 years agoPython FAQ GIL link should point to GIL blurb, not GIL TOC entry.
W. Trevor King [Wed, 27 Oct 2010 19:54:56 +0000 (15:54 -0400)]
Python FAQ GIL link should point to GIL blurb, not GIL TOC entry.

8 years agoMerge remote branch 'borg/master'
W. Trevor King [Wed, 27 Oct 2010 19:19:35 +0000 (15:19 -0400)]
Merge remote branch 'borg/master'

8 years ago-m/--manager now defaults to auto-select.
W. Trevor King [Wed, 27 Oct 2010 19:19:50 +0000 (12:19 -0700)]
-m/--manager now defaults to auto-select.

8 years agoAdd ability to import a default manager with get_manager().
W. Trevor King [Wed, 27 Oct 2010 19:10:58 +0000 (12:10 -0700)]
Add ability to import a default manager with get_manager().

8 years agopysawsim/parameter_error.py should not be executable.
W. Trevor King [Wed, 27 Oct 2010 17:28:51 +0000 (10:28 -0700)]
pysawsim/parameter_error.py should not be executable.

8 years agoAdd support for nosetests multiprocessing plugin.
W. Trevor King [Wed, 27 Oct 2010 16:21:49 +0000 (09:21 -0700)]
Add support for nosetests multiprocessing plugin.

See
  python-nose/doc/doc_tests/test_multiprocess/multiprocess.rst
for an explanation of the plugin and its peculiarities.

On a 16-core SMP machine, the test suite now runs with:
  Ran 27 tests in 58.077s
vs the old:
  Ran 23 tests in 69.325s

The extra tests are repeats, probably having to do with a
split-vs-share issue that I haven't tracked down yet.  The tests could
be faster still if we used the subproc manager by default for Python
>= 2.6.  I'll do that next.

8 years agoConvert tabs to spaces in pre-commit-pysawsim-check.
W. Trevor King [Wed, 27 Oct 2010 15:17:29 +0000 (11:17 -0400)]
Convert tabs to spaces in pre-commit-pysawsim-check.

8 years agoUse single-quote delimited strings when possssible.
W. Trevor King [Wed, 27 Oct 2010 15:07:08 +0000 (08:07 -0700)]
Use single-quote delimited strings when possssible.

8 years agoHistogramMatcher should not plot residual comparisons by default.
W. Trevor King [Wed, 27 Oct 2010 15:01:59 +0000 (08:01 -0700)]
HistogramMatcher should not plot residual comparisons by default.

8 years agoAdded bin/sawsim_param_error.py and pysawsim/parameter_error.py
W. Trevor King [Wed, 27 Oct 2010 14:59:40 +0000 (07:59 -0700)]
Added bin/sawsim_param_error.py and pysawsim/parameter_error.py

8 years agoAssorted minor cleanups to pysawsim/parameter_scan.py.
W. Trevor King [Wed, 27 Oct 2010 00:35:24 +0000 (20:35 -0400)]
Assorted minor cleanups to pysawsim/parameter_scan.py.

8 years agoRemove some more velocity-specific cruft from pysawsim/parameter_scan.py.
W. Trevor King [Tue, 26 Oct 2010 22:00:26 +0000 (18:00 -0400)]
Remove some more velocity-specific cruft from pysawsim/parameter_scan.py.

8 years agoparameter_scan.py no longer needs to import anything from the .manager submod.
W. Trevor King [Tue, 26 Oct 2010 21:23:58 +0000 (17:23 -0400)]
parameter_scan.py no longer needs to import anything from the .manager submod.

8 years agoPrint the CommandError of failed sawsim executions.
W. Trevor King [Sun, 24 Oct 2010 14:19:30 +0000 (10:19 -0400)]
Print the CommandError of failed sawsim executions.

8 years agoSave CommandError in failed InvokeJobs.
W. Trevor King [Sun, 24 Oct 2010 14:16:42 +0000 (10:16 -0400)]
Save CommandError in failed InvokeJobs.

8 years agoAdd pysawsim.invoke.CommandError.__repr__() method and doctest.
W. Trevor King [Sun, 24 Oct 2010 14:15:58 +0000 (10:15 -0400)]
Add pysawsim.invoke.CommandError.__repr__() method and doctest.

8 years agoMake pysawsim.invoke.CommandError picklable, and add doctest proof.
W. Trevor King [Sun, 24 Oct 2010 14:04:24 +0000 (10:04 -0400)]
Make pysawsim.invoke.CommandError picklable, and add doctest proof.

8 years agoFix cache shuffling (random.shuffle() shuffles in place, returns None).
W. Trevor King [Sun, 24 Oct 2010 13:47:53 +0000 (09:47 -0400)]
Fix cache shuffling (random.shuffle() shuffles in place, returns None).

8 years agoMove __version__ import from sawsim_histogram to sawsim (for caching).
W. Trevor King [Sun, 24 Oct 2010 13:45:02 +0000 (09:45 -0400)]
Move __version__ import from sawsim_histogram to sawsim (for caching).

8 years agoStart fleshing out "Related work" section in the manual.
W. Trevor King [Sat, 23 Oct 2010 17:57:16 +0000 (13:57 -0400)]
Start fleshing out "Related work" section in the manual.

To facilitate this, I've added the following new keys to sawsim.bib:
  jollymore09, kellermayer97, king10, marszalek98, oberhauser98, rief97a
I also renamed the old rief97 -> rief97b to avoid confusion with rief97a.

Also, run a second bibtex/pdflatex pass on compilation to handle a
single layer of cross referencing in the `note` field.

8 years agoFix some long URLs that had been wrapped by pybtex.
W. Trevor King [Sat, 23 Oct 2010 15:40:19 +0000 (11:40 -0400)]
Fix some long URLs that had been wrapped by pybtex.

8 years agoUpdate the README with more information about the pysawsim wrappers.
W. Trevor King [Sat, 23 Oct 2010 14:48:16 +0000 (10:48 -0400)]
Update the README with more information about the pysawsim wrappers.

8 years agoAdd namedtuple definition from Python 2.6's collections.py as _collections.py
W. Trevor King [Sat, 23 Oct 2010 14:03:48 +0000 (10:03 -0400)]
Add namedtuple definition from Python 2.6's collections.py as _collections.py

8 years agoMove `import with_statement` from sawsim_histogram to sawsim.
W. Trevor King [Sat, 23 Oct 2010 13:31:47 +0000 (09:31 -0400)]
Move `import with_statement` from sawsim_histogram to sawsim.

8 years agoReplace EXAMPLE_HISTOGRAM_FILE_CONTENTS histograms with N=400 examples.
W. Trevor King [Sat, 23 Oct 2010 13:10:02 +0000 (09:10 -0400)]
Replace EXAMPLE_HISTOGRAM_FILE_CONTENTS histograms with N=400 examples.

8 years agoAdd epilogs to each OptionParser in pysawsim.
W. Trevor King [Sat, 23 Oct 2010 12:38:04 +0000 (08:38 -0400)]
Add epilogs to each OptionParser in pysawsim.

8 years agoMove sawsim running into a new pysawsim.sawsim.SawsimRunner class.
W. Trevor King [Sat, 23 Oct 2010 11:42:02 +0000 (07:42 -0400)]
Move sawsim running into a new pysawsim.sawsim.SawsimRunner class.

8 years agoAdd 'mpi' to pysawsim.manager.MANAGERS.
W. Trevor King [Thu, 21 Oct 2010 01:38:43 +0000 (18:38 -0700)]
Add 'mpi' to pysawsim.manager.MANAGERS.

8 years agoRelax command-not-found doctest messages.
W. Trevor King [Thu, 21 Oct 2010 01:36:25 +0000 (18:36 -0700)]
Relax command-not-found doctest messages.

8 years agoMerge branch 'master' of http://www.physics.drexel.edu/~wking/code/git/sawsim
W. Trevor King [Thu, 21 Oct 2010 01:31:54 +0000 (18:31 -0700)]
Merge branch 'master' of physics.drexel.edu/~wking/code/git/sawsim

8 years agoFix dropped receive during ThreadManager._spawn_jobs.
W. Trevor King [Thu, 21 Oct 2010 01:29:25 +0000 (18:29 -0700)]
Fix dropped receive during ThreadManager._spawn_jobs.

8 years agoAdd autogenerated .be/id-cache to .gitignore.
W. Trevor King [Wed, 20 Oct 2010 23:48:32 +0000 (19:48 -0400)]
Add autogenerated .be/id-cache to .gitignore.

8 years agoMerge branch 'master' of ssh://wking@einstein/~/public_html/code/git/sawsim
W. Trevor King [Wed, 20 Oct 2010 23:42:00 +0000 (19:42 -0400)]
Merge branch 'master' of ssh://wking@einstein/~/public_html/code/git/sawsim

8 years agoUpgrade .be bug cache to Bugs Everywhere Directory v1.4.
W. Trevor King [Wed, 20 Oct 2010 23:35:55 +0000 (19:35 -0400)]
Upgrade .be bug cache to Bugs Everywhere Directory v1.4.

8 years agoDisable pysawsim.manager.subproc is multiprocessing is missing.
W. Trevor King [Wed, 20 Oct 2010 23:20:14 +0000 (19:20 -0400)]
Disable pysawsim.manager.subproc is multiprocessing is missing.

8 years agoWork around namedtuple import for Pythons < 2.6.
W. Trevor King [Wed, 20 Oct 2010 23:09:40 +0000 (19:09 -0400)]
Work around namedtuple import for Pythons < 2.6.

8 years agoAlso cleanup local mpd if the pysawsim nosetests fail.
W. Trevor King [Wed, 20 Oct 2010 19:57:45 +0000 (15:57 -0400)]
Also cleanup local mpd if the pysawsim nosetests fail.

8 years agoAdd CC, CFLAGS, and LDFLAGS to the Makefile for easy customization.
W. Trevor King [Wed, 20 Oct 2010 19:49:02 +0000 (15:49 -0400)]
Add CC, CFLAGS, and LDFLAGS to the Makefile for easy customization.

8 years agoWork around missing MPD with a more elaborate pysawsim nosetest hook.
W. Trevor King [Wed, 20 Oct 2010 19:23:16 +0000 (15:23 -0400)]
Work around missing MPD with a more elaborate pysawsim nosetest hook.

8 years agoKill off worker-node implementations of master code.
W. Trevor King [Wed, 20 Oct 2010 17:57:28 +0000 (13:57 -0400)]
Kill off worker-node implementations of master code.

8 years agoAdd pysawsim.manager.mpi with an mpi4py-based manager.
W. Trevor King [Wed, 20 Oct 2010 17:34:48 +0000 (13:34 -0400)]
Add pysawsim.manager.mpi with an mpi4py-based manager.

Test with:
  mpdboot -1 -n 1 -f <(hostname)
  mpiexec -n 5 nosetests --with-doctest --doctest-tests pysawsim/manager/mpi.py
  mpdallexit

I still need to find a way to turn off the doctests when mpi4py is
installed, but the tests are not being run from an `mpiexec`ed
environment.

8 years agoAdd link to Python wiki's parallel processing page.
W. Trevor King [Wed, 20 Oct 2010 11:41:48 +0000 (07:41 -0400)]
Add link to Python wiki's parallel processing page.

8 years agoAdjust pysawsim.manager.pbs to skip most doctests if pbs mod is missing.
W. Trevor King [Wed, 20 Oct 2010 11:30:45 +0000 (07:30 -0400)]
Adjust pysawsim.manager.pbs to skip most doctests if pbs mod is missing.

8 years agoRemove execute permission from pysawsim/manager/pbs.py.
W. Trevor King [Wed, 20 Oct 2010 10:42:14 +0000 (06:42 -0400)]
Remove execute permission from pysawsim/manager/pbs.py.