github.com/westpa/westpa commits | Ecosyste.ms: OpenCollective

Imported MPI work manager courtesy of Kim Wong ([email protected])

9055c2a92650a124148135ee4e6c88f5f6c75596 authored almost 12 years ago by Matt Zwier <[email protected]>

imported patch mdpfix

d648c077a5264d435b0aa20d3330d7e27911d415 authored almost 12 years ago by Matt Zwier <[email protected]>

Merged upstream (d15db6db5f57)

7eabe0f3da23a02a15ab5079926b102763604dc4 authored almost 12 years ago by Matt Zwier <[email protected]>

Kinetics assignment prototype complete. westpa.assign now uses the buffer

interface instead of the numpy interface where possible.

3dc843aecac228109d09ba2f1335c0411b059f61 authored almost 12 years ago by Matt Zwier <[email protected]>

Update west_tools subrepo

37f17aa35605877bb01b1ba0ba937cc623193011 authored almost 12 years ago by joshua.adelman <[email protected]>

Fixed bug in rate_averaging for recycling simulations. Resolves issue #21

5f7cd114e7afec627b444e4c495764f3f3da6071 authored almost 12 years ago by joshua.adelman <[email protected]>

Update west_tools subrepo

58ea1c479d6b18f5a42ad272f4a03a6335fc9f61 authored almost 12 years ago by joshua.adelman <[email protected]>

Updated setup.py to compile extensions from source if cython is not available and started tracking .c files in repo. Resolves WESTPA issue #18

bacd0e6c7a40a114948c15fbf37d15327051d474 authored almost 12 years ago by joshua.adelman <[email protected]>

Updated working kinetics analysis code to relocated binning extension

d3a61015948fb9dec4e5044f5b5bd798eb5c2dc9 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging in dcf0bdd3f498 (transplant of binning/assign extensions)

f1f6c054fd97b662f18a0ca14d70587fc71e5271 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated .hgignore to ignore more files generated by examples

91e97b833ff27dec009a3e9d60eedf0ec60b1728 authored almost 12 years ago by Matt Zwier <[email protected]>

Moved binning and kinetics extensions to west_tools

806570b6be06c241002358581941612493274597 authored almost 12 years ago by Matt Zwier <[email protected]>

Moved binning and kinetics extensions to west_tools

8fbc883df04a7e9805d1ed76e04c2d0f23e3d9b5 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging dcf0bdd3f498 (transplant of west.binning/west.assign history)

945286414d5881f529918897f92cc5d52f4b5ed4 authored almost 12 years ago by Matt Zwier <[email protected]>

Relocated files prior to import into west_tools

e6b3714ca062ce4c3e943b1d18cb35bba85bc808 authored almost 12 years ago by Matt Zwier <[email protected]>

Merged in f4c809a9d9c4

48617e7ccc9a22f648e4d2e950a259b32bcf2967 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated assignment code and prototype flux accumulator.

a0cd65177bd762393f18d428b8265f707b5475e3 authored almost 12 years ago by Matt Zwier <[email protected]>

Fixed occasional crash due to dtype oddity.

449422ca4d27b25ec5fb6b5845b3f86a05a350e8 authored almost 12 years ago by Matt Zwier <[email protected]>

Changed all west.rc references to westpa.rc

d59d1150b436a6fbfa90b4caa11103c8bde7e5a7 authored almost 12 years ago by Matt Zwier <[email protected]>

Changed all west.rc references to westpa.rc

9fc5f1a42b477799d292bc77381dd7df8dff1ca0 authored almost 12 years ago by Matt Zwier <[email protected]>

Changed all west.rc references to westpa.rc

6c8e2db48a8ef6c08bcc27be45063dfa9701307e authored almost 12 years ago by Matt Zwier <[email protected]>

Merging b90ad753864f and 2a88258c58db

3d5106c0d253dc7719faf237e01b64a14d60f760 authored almost 12 years ago by Matt Zwier <[email protected]>

Merging b90ad753864f and 2a88258c58db

1c3fc92f53cebfbf3a304e36fd8c66f6d84b48e5 authored almost 12 years ago by Matt Zwier <[email protected]>

Possibly spurious subrepo update

28d6eab78b22c9d04862586480d1aa21bc1fcdf2 authored almost 12 years ago by Matt Zwier <[email protected]>

Allowed bin/west to pass arguments to scripts invoked by filename, added

"unknown bin" flag to assign.py, optimized application of numpy.require in
assign.py for a ~2x sp...

aab185cd20386c8ae6f4c67dd01d0c53263903ba authored almost 12 years ago by Matt Zwier <[email protected]>

Allowed bin/west to pass arguments to scripts invoked by filename, added

"unknown bin" flag to assign.py, optimized application of numpy.require in
assign.py for a ~2x sp...

e655877b3b23b7f8dcc8893cd1bb50ef759189e6 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated west_tools subrepo upstream location

899ed3948c2833173f60652806dc4b6718c913fd authored almost 12 years ago by Matt Zwier <[email protected]>

Merging b90397d3082c and 908e2f9b2629

7d4ed98c0753e9a5d61df40b8dd3a2ac2ed899ba authored almost 12 years ago by Matt Zwier <[email protected]>

Removed local cluster dependence in methane_gmx example, updated wwmgr

b7cb299cc42a5a7d72d1f47f27011b06aa654f43 authored almost 12 years ago by Matt Zwier <[email protected]>

Removed old (and generally unreachable) lib/cmds/w_pcpdist.py

6386d6deb8dd683a5a698d5d564437f9ed117207 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated string method plugin to accept positional and keyword args assoc. with the dfunc method

0ed99bcd0360773920e206683fa4774b24974571 authored almost 12 years ago by joshua.adelman <[email protected]>

Added ZMQ Router class for use with ZMQ work manager. Added relevant unit tests for router. Split up zeromq unit tests to test core functionality and environment initialization separately.

3b10e136be8c1d07b50a02185902abbdab281296 authored almost 12 years ago by Nick Rego <[email protected]>

DMZ algorithm refinements

1bac1e1ee9ed1b5ac6a988bf010277f5b6a54fdd authored almost 12 years ago by Matt Zwier <[email protected]>

First pass at DMZ algorithm

d0afa13582258983a994aa6406d47c1b6472ae9d authored almost 12 years ago by Matt Zwier <[email protected]>

w_kinetics gets an overall flux and event durations, but reverse rates could be trouble

db6d8109ba926a6a51ef79032af1f59b664f2e56 authored almost 12 years ago by Matt Zwier <[email protected]>

Skeleton of required bits of w_kinetics

4e6ab3073a4e36b21516b832eeeb31054112c8d8 authored almost 12 years ago by Matt Zwier <[email protected]>

Created w_assign for generalized assignments. Axed crazy generalized dataset

access in data_reader.py. Moved some things about.

22a0e5d7442496c279515d7c0c8f438b19c16c1e authored almost 12 years ago by Matt Zwier <[email protected]>

Working commit for kinetics analysis

fb3ff7c4839308e94cf2713c56dd1a7f30132df7 authored almost 12 years ago by Matt Zwier <[email protected]>

Fixed UnboundLocal error in rate averager.

563bf18b58e4c581032da2c76bcf22f7cd985658 authored almost 12 years ago by Matt Zwier <[email protected]>

Fixed UnboundLocal error in rate averager.

90aa18f0413fb38d5a6da82f107bc502f5af52d9 authored almost 12 years ago by Matt Zwier <[email protected]>

Added tag legacy-branch-close for changeset 3fbccfd4e1fe

374c787584d0185b3836e22b6086838b52fe4b62 authored almost 12 years ago by Matt Zwier <[email protected]>

Added tag legacy-branch-open for changeset aa49cd7d8777

871646e1f941699642c382a966fe58bdfa2a0ec2 authored almost 12 years ago by Matt Zwier <[email protected]>

Merged changesets b363007b8086 and 66531a16a51c

09b293be678abfdfcee4c4c6cd26e3956ae559c1 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated to latest wwmgr

001e3eb4a684e499e8338ec3ea5e957765ec4253 authored almost 12 years ago by Matt Zwier <[email protected]>

Merged changesets 8dd6f0369366 and 576e40485177

56869e4294389444d1c44cb5a17a0e17a207cd50 authored almost 12 years ago by Matt Zwier <[email protected]>

Properly removed tasks from "pending" list when results received. Resolves wwmgr issue #10.

58f8ac2a93ba8f766a328434760c3c30a193b1a7 authored almost 12 years ago by Matt Zwier <[email protected]>

Parallelized rate averaging calculation and updated wwmgr to newest version

f28d47cad9706825da145f426a65cf139e7286c2 authored almost 12 years ago by joshua.adelman <[email protected]>

Parallelized rate averaging calculation and updated wwmgr to newest version

455e77e875032db3bf80cd497a51f76f07c01fa7 authored almost 12 years ago by joshua.adelman <[email protected]>

Added submit_as_completed() method to core and add() method to FutureWatcher

c30eb173971e0cef14c1b4377a6c6d109d1a97b9 authored almost 12 years ago by joshua.adelman <[email protected]>

Updated to latest h5py upstream

1da265ccf595f71e6092b322346b0138b4cab8cb authored almost 12 years ago by Matt Zwier <[email protected]>

Updated h5py subrepository path to h5py upstream

249d7b208d678144a5344147da364154ffced669 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated to newest version of wwmgr.

9c3c30e3c79d145a4dcb1a80dc35fb5b02a8352b authored almost 12 years ago by Matt Zwier <[email protected]>

Split ZMQ work manager into multiple files, added command-line/environment options for all tunables. NB that constructor argument lists have changed for ZMQClient, ZMQServer, and ZMQWorkManager

580c76ab7836ef66e755bc5777293f8ed75febe5 authored almost 12 years ago by Matt Zwier <[email protected]>

Merge with 11e9e6de2cad8b5b491095a9f2ffa77bc6ad2a12

6bb50e343f521f1b9efd436d4407cf23a76e88d3 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated data manager to use appropriate scaleoffset syntax for git version of

h5py.

448a8793d2f3bcf8d8c7c0b8fcaf3f5cb8906d50 authored almost 12 years ago by Matt Zwier <[email protected]>

Updated h5py subrepo to use git (as upstream does)

5830385856600c4c06d148aebebca89293cfefb3 authored almost 12 years ago by Matt Zwier <[email protected]>

Tweaked setup.sh to delete .so files from all directories, including h5py's.

39fe4116469a52288bd77e41983aeff064ae45a7 authored almost 12 years ago by Matt Zwier <[email protected]>

Changed submit() interface to (eventually) support keyword options separate from those passed along to the task function to execute. Rewrote ZMQ wire protocol to use REQ/REP instead of PUSH/PULL for tasks and results, to provide an opportunity for keepalive pulses so that long-idle connections do not result in lost messages and hangs when those connections are forcefully terminated (presumably by a switch).

682009925d213b1319101f68924d92813139b49d authored almost 12 years ago by Matt Zwier <[email protected]>

Added a function to close cached inproc sockets to prevent ZMQ aborts during unit tests.

1b446726f7777944a2dc9a15c019964c78d0fe66 authored almost 12 years ago by Matt Zwier <[email protected]>

Fixed method for target states to work for both files and for --tstates

argument.

7a917a24d1d74b80f3f86438253bd019e1dfbe13 authored about 12 years ago by Ali Sinan Saglam <[email protected]>

Fixed small bug in states.py when parsing target states from file.

ff155fb0ed9abb9b00620cb8f4269fba84406d34 authored about 12 years ago by Ali Sinan Saglam <[email protected]>

Minor updates to w_init and setup.sh

8581556f8cce35effbc1688efbf1ef7be5d4e840 authored about 12 years ago by Matt Zwier <[email protected]>

(WE) Fix bug in initial state tracking where initial state walkers first split and then merged could trigger a KeyError. Resolves WESTPA issue #8.

f365b5870e4e0a916a9db86879c996e3ed981c9d authored about 12 years ago by Matt Zwier <[email protected]>

Cleaned up some import trouble.

928b3b515add9cd4c9566091353661f192bccdc0 authored about 12 years ago by Matt Zwier <[email protected]>

Added patched h5py subrepo, modified setup.sh to build and bin/west to use

included h5py.

8a56a931e35a8614ec28aa1ac70b8125f2882621 authored about 12 years ago by Matt Zwier <[email protected]>

Merge with 765122d4dbb269ef656293771fad2414b3b7e379

6f0cb38c4a91cdcf0e0e81d6a026b15f36763b24 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed bug in data manager wherein pcoord dataset was always compressed if sufficiently large and not expressly prohibited in west.cfg.

0f975f8f70bf0bc7e80231d8c809a954d87b3b8f authored about 12 years ago by Matt Zwier <[email protected]>

Updated weed plugin for new yaml-based config files

6b0ce7001315ec91d364215610d48295336f7ded authored about 12 years ago by joshua.adelman <[email protected]>

Updated string method plugin for new yaml-based config files; Updated sim_manager tests

066db452f73dcfa3fd34a202b122a324a9789139 authored about 12 years ago by joshua.adelman <[email protected]>

Do not fail if a build of h5py without scaleoffset is used.

22742647e5ca833554b666798700fcdee21f847e authored about 12 years ago by Matt Zwier <[email protected]>

Updated to latest WWMGR revision.

6228d6aa45f213ade82c044991b484cade7d4233 authored about 12 years ago by Matt Zwier <[email protected]>

Minor change to ODLD run script.

35385acab8fe00905f5514304fec4962b306c338 authored about 12 years ago by Matt Zwier <[email protected]>

Added command-line option and environment variable for ZMQ server timeout. Removed remarkably useless zmq_comm_mode (which should have been client-specific anyway).

7502a31cd0fb1c4cb097a6559cb3f984b6cdfc0f authored about 12 years ago by Matt Zwier <[email protected]>

Completed YAML-based config file with support for per-dataset HDF5 storage

options.

3a4d7ad3ca0fcdb1b0af693c41613278cad77881 authored about 12 years ago by Matt Zwier <[email protected]>

Completed YAML-based config file with support for per-dataset HDF5 storage

options.

b7dc3ccfee9d1ac01b896338572ab72add357d5e authored about 12 years ago by Matt Zwier <[email protected]>

Working commit of transition to YAML-based config files and some source

reorganization.

1891d119252624200ab1013c8c8f6f5ad27d4161 authored about 12 years ago by Matt Zwier <[email protected]>

Working commit of transition to YAML-based config files and some source

reorganization.

b6b7175fa52d0b98386401db8b023c77ddbb3414 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed bug in sim manager resulting in per-iteration CPU times being recorded as zero (the individual segment values were not affected).

a3fc50375357d1f329ff42dbcec01b1590003bc8 authored about 12 years ago by Matt Zwier <[email protected]>

Greatly increased HDF5 write speed by modifying data manager to use low-level HDF5 routines in update_segments().

b9b3bce1aa802a75597dfda02a29f976889d7fe1 authored about 12 years ago by Matt Zwier <[email protected]>

ZMQ: Fixed "too many open files" error triggered by submitting many tasks using submit() instead of submit_many(), by keeping an open control socket for each thread using _signal_thread.

ZMQ: Made server task dispatch thread dispatch one task per submit()-generated task announcement ...

2f653e34dad6485e197ae5df885306e7d8a8a00e authored about 12 years ago by Matt Zwier <[email protected]>

Added link for plothist

53b8345f2c2f5b6f3f909976bbbba5c17575754b authored about 12 years ago by Matt Zwier <[email protected]>

Updated comments and docstrings in plothist.py

b47d40fd9a790a4f12e8d63f9b81e4199d9dd169 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed bug in pre/post iter template formatting, made "do_reweighting" a valid switch for the WEED plugin (though no effort is made to make sure that only one of "do_reweighting" and "do_equilibrium_reweighting" is used; if one is true, then reweighting is done).

01e6c287909b6cdb092bc8e0562e18e661c7be26 authored about 12 years ago by Matt Zwier <[email protected]>

Added a new configuration file option "system.save_transition_matrices" (defaulting to False) for whether to save per-iteration transition count and flux matrices (perhaps necessary for some third-party analysis tools, but expensive in space and not currently used by any in-package analysis tools).

cd2e2d41e7808ca3bd9e2f029a4175e5add2dcc5 authored about 12 years ago by Matt Zwier <[email protected]>

plothist.py has working evolution blocked by iteration

d9276f4ed966099b4d6df69b4a2a162c94ba82e8 authored about 12 years ago by Matt Zwier <[email protected]>

Added initial plotting tool for histogram output (plothist.py), which works

except for blocking evolution by iteration (not implemented yet).

8148461254f24b36ae235a46ac2660d6f9c91778 authored about 12 years ago by Matt Zwier <[email protected]>

Added preliminary unit tests for sim_manager and expanded we_driver tests

81436b8f2ac1da8fc6acb7382acbded6a9a194cf authored about 12 years ago by joshua.adelman <[email protected]>

Updated west_tools subrepo, removed warning about WEST_SIM_ROOT being set to current dir.

588fa2e2a4b617dee8ffbfd7d23a9afec42f1cd5 authored about 12 years ago by Matt Zwier <[email protected]>

Resurrected w_dumpsegs.

ae9c272f50413ee1010eea301a3065d5d70b74a1 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed small bug in InitialState pcoord initialization

35d631f7ed120df0d3ede3329fe46d8904c3e754 authored about 12 years ago by joshua.adelman <[email protected]>

Added updated w_pcpdist, optimized for speed. Rewrote fasthist to work on

N-dimensional histograms of any core numpy non-complex numeric type.

0f8d46cce21e3f0539b67c0cb960190e669094c7 authored about 12 years ago by Matt Zwier <[email protected]>

Added .hgignore from westpa

a903e511ac8948fec921fae06c9ab5c4ba4e28b6 authored about 12 years ago by Matt Zwier <[email protected]>

Merge with 3c45db2555cf

dff79bd8168d1c7ab6471ab3502989fde0c950e3 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed bug in WESS driver related to reworking of WE driver.

Worked around memory leak in h5py related to enums.

258ea7da5408ed76525753d225c9fd73f1741321 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed coordinate reading in the propagator script and system.py in methane

example.

bf630e883ce3b799de45515cc1bb367e65a0787c authored about 12 years ago by Ali Sinan Saglam <[email protected]>

Updated to latest west_tools

a628be462706be8ec94612547c3fd815e325c7a4 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed serious bug in recycling tracking which would mis-label final state IDs.

6768c9c8a4d27b4d573b8b4cbddd7357b3b20d3d authored about 12 years ago by Matt Zwier <[email protected]>

Updated w_fluxanl to new HDF5 format

fabfc2db623542aff48da22447c6eeac44e9c324 authored about 12 years ago by Matt Zwier <[email protected]>

Added reflecting boundary for ODLD test system, on by default and deactivated by setting self.reflect_at=None in the propagator.

86bde639d70dd93ca336736d002355cdfea97a65 authored about 12 years ago by Matt Zwier <[email protected]>

Fixed broken "enabled" flag for auxiliary data sets in executable propagator.

710bdbe4247ca70134292c29ee3b6e0277549d4c authored about 12 years ago by Matt Zwier <[email protected]>