WESTPA commits | Ecosyste.ms: OpenCollective

Added back support for '--node' for minimizing number of sockets (now two per node for the master, and two per process per worker node).

github.com/westpa/westpa - 0ba0bfd566ffa9789b67512a42cc2cf272580f14 authored almost 13 years ago

Added gratuitous flushes to help with actually seeing output in logs.

github.com/westpa/westpa - 545d401a2a42cf09807b0f4f7cfbedff40fff472 authored almost 13 years ago

Fixed duplicate random number sequences in subprocesses for processes and zmq work managers.

github.com/westpa/westpa - cd4685b7f90b70b182ae4d41e8ae445c53d46b3a authored almost 13 years ago

Merge with 882dbe63e5710d0a324f53ea8e021653aa5f1024

github.com/westpa/westpa - ee2f928aab07d38070002db5defdb55aa1cfb23b authored almost 13 years ago

More work on graceful Ctrl-C shutdowns.

github.com/westpa/westpa - a0e3fc2ef73c7d5b2ca21aa28a9193fe1f2203d5 authored almost 13 years ago

Fixed typo in WEED affecting simulations with window_size = 0.

github.com/westpa/westpa - 83d6f6cf8e05e5a5735104ddb40d4c2a10d7e20f authored almost 13 years ago

Attempted to address probability leak in restarting simulations with particles in target states; began modifying work managers to support more sane Ctrl-C handling.

github.com/westpa/westpa - a8517dd98355c415dc7d556000f892fd3be96e2f authored almost 13 years ago

Merge with b6afedc0810c95a71f6055d55f903651f262d8d9

github.com/westpa/westpa - 915279325ad0d9df469f66960d9b26d73ca33ba7 authored almost 13 years ago

Minor changes to support new wemdtools (the repo, not the folder); reordered zmq work manager startup and added delay to mitigate "connection refused".

github.com/westpa/westpa - 77547888a2a82be364dafc3e8daed54d7753caaa authored almost 13 years ago

Updated weed extension to refactored version that uses numpy

github.com/westpa/westpa - fcd2fb65c2ed821ca481656e08269a60a4d87ca1 authored almost 13 years ago

Added method to update region set in wemdtools binning mixin

github.com/westpa/westpa - 1d0bd060381340f4172da1291b4faffe268688b3 authored almost 13 years ago

Working w_trace.

github.com/westpa/westpa - 204294ae15829460cc6377c30139f2f77027cb2f authored almost 13 years ago

Working commit, including skeleton of a generalized w_trace.

github.com/westpa/westpa - 2c81fd93909ae736f532ea26e04901b9d8ef49c5 authored almost 13 years ago

Bin hash digests are now stored as hex strings (as in wemdtools) instead of raw byte strings. This avoids a "embedded NULs not permitted in VLEN strings" error.

github.com/westpa/westpa - 9ea21cd66f393d629f5fb6277aef95d02ca65b70 authored almost 13 years ago

Merge with 0a896abdbef70d5f2b7bc674a6fb6884fc9537e0

github.com/westpa/westpa - bf8dfde0e6f1fe07bc316dbcc4227ff77a66ccd9 authored almost 13 years ago

Working commit

github.com/westpa/westpa - 856fea10fc083eb5cfdd5d42da46a2a29cd8a66a authored almost 13 years ago

Fixed bug in sim_manager which prevented storage of segment endpoint type; fixed w_steady_state

github.com/westpa/westpa - c77bd126b76557cbfba840cee8fc6e8553d1bbfd authored almost 13 years ago

Merge with 989e0d2011b1590a4ef22d66d8033c85fa8bd043

github.com/westpa/westpa - 8110f6d2bd97bd1c9b983c12785bdffd8d6bbe42 authored almost 13 years ago

Modified data manager to support omitting progress coordinates when retrieving segments.

github.com/westpa/westpa - 9820c54e761e6907afcbbba8d11b8ded6bd195e2 authored almost 13 years ago

Fixed bug where 'data_ref' was used instead of 'auxref' in reading basis states from a file.

github.com/westpa/westpa - d3fff35d7da716745cb3f547eaec093fb3488897 authored almost 13 years ago

Fixed bug where executable propagator didn't have all the states necessary for successful initial state generation.

github.com/westpa/westpa - 389fcf1ef8577ba6c7ded9f831f3d911f1cebcfa authored almost 13 years ago

Fixed bstate-file reading error

github.com/westpa/westpa - d8b063368f465516885e7dba1e650ac18f238b95 authored almost 13 years ago

Updated data manager to transparently read old file versions, fixed off-by-one in termination condition in sim manager, added doc/config_entries.rst.

With the update to read old HDF5 versions, there are currently no checks to prevent attempts to ...

github.com/westpa/westpa - 5977fa234c723555009f610b5a1217f8830b5de5 authored almost 13 years ago

Fixed bug in target state file parsing.

github.com/westpa/westpa - 2ab7c450549e237cf33e0d88b6f2eae65116d5f5 authored almost 13 years ago

Initial import, including copying (or copying and slight modification) from wemd_feat wemdtools package.

github.com/westpa/westpa - ccdd37f35beeef6b5aa8be0a5c78bd47f3a0b4fb authored almost 13 years ago

Added lib/examples/methane_gmx, updated CHANGELOG

github.com/westpa/westpa - 95663edba90cff6bd62ba544a3f06e3cc3e80b22 authored almost 13 years ago

Merge with aa49cd7d87771080b9ee95696c393bc3daa7b5d1

github.com/westpa/westpa - 6f7e3eaa57247accd4563a5a4985919fcb937b97 authored almost 13 years ago

Restored prepare_new_segments() callback in sim manager, updated old WEED driver to use it.

github.com/westpa/westpa - 31661403ba0cc8b22d73f2f264bf45353d44f5a0 authored almost 13 years ago

Updated state definition tracking for greater internal consistency (mid-iteration restarts can no longer use the wrong ibstate table).

github.com/westpa/westpa - b23ec549f09a09f23a6a06379115c7b3d28f2f0a authored almost 13 years ago

Added fractional windowing to WEED plugin.

github.com/westpa/westpa - cb1556d2e7785748ed7e1504baf755f74869eb58 authored almost 13 years ago

Added w_states tool to manipulated stored lists of basis and target states.

github.com/westpa/westpa - 373f47a6b5706ae3eff4dc1436e7ca655ab2841d authored almost 13 years ago

Updated w_pcpdist for new analysis framework.

github.com/westpa/westpa - ebedf89ad84ff4bc8466e31a804b6735f40fd573 authored almost 13 years ago

Improved error reporting for system module loading (backported from feature branch).

github.com/westpa/westpa - 3d1d6392fc667df7e9af1da7af571e6542971b4b authored almost 13 years ago

Removed ancient and no-longer-working w_sqlite2hdf5

github.com/westpa/westpa - 3ca4d709f8542bffab5bea19e8bc4a5e7fd48625 authored almost 13 years ago

Bring analysis tools partially up-to-date with new data manager internals.

github.com/westpa/westpa - 7fbd8fa8cfbf7f3ea53b31e6e76351134769a141 authored almost 13 years ago

Back to pre-hacking w_run functionality (save the WEED plugin).

github.com/westpa/westpa - f85dafb5ee91118f4e6a5d6f76732409280094cd authored almost 13 years ago

Added WEMD_PROCESS_INDEX environment variable to ZeroMQ, fixed broken post-iter handling.

github.com/westpa/westpa - b61f295055b661ef7db227c7a040120c8a5fcc80 authored almost 13 years ago

Merge with 38c8b43d22ebda35a6b81ea6870c13c3aa68b1cc

github.com/westpa/westpa - 3bef948169ef50a0a3b8f4d1356a1958faa64c92 authored almost 13 years ago

Recycling works again.

github.com/westpa/westpa - 3d0ec43961a31311e572082d305dcb0ddf0fa958 authored almost 13 years ago

w_run runs

github.com/westpa/westpa - 036da0fce8aa0bc62a39e3fcf93d906ec2ed3ae6 authored almost 13 years ago

Progress toward working w_run

github.com/westpa/westpa - 0dfb3504e480d350440ff8f14e9010b6b70b3dc8 authored almost 13 years ago

Fixed critical data corruption problem apparently related once again to h5py.

github.com/westpa/westpa - fc3ed5976bbb93a60ad84038187c570892c4b95c authored almost 13 years ago

Working commit of data restructuring.

Initial state IDs are now negative again. Fixed bug in we_driver where merge_by_weight only merg...

github.com/westpa/westpa - 39f1499a4172506351bb3b8426d79e691eff4182 authored almost 13 years ago

Added tags for v0.5 (the last version of the code using the "old" analysis

framework) and v0.7 (the "production" version of the code as of 2/2012).

github.com/westpa/westpa - 5eea769d37b2f44fe9a28065699abb5eabbd2d0e authored almost 13 years ago

Work managers now provide a proper stack trace when an exception occurs running a task.

Threads/serial provide a real traceback (using the 3-argument form of ``raise``), and processes/...

github.com/westpa/westpa - dd4e5fc4dae65a578566b99f5cda3a52384855a6 authored almost 13 years ago

Initial state preparation in w_init is parallelized with work manager.

github.com/westpa/westpa - 92beb57152c5663711c3080e8a59740329ec7709 authored almost 13 years ago

Working commit of executable propagator/w_init refactoring

github.com/westpa/westpa - fe05f663e8329405e925a2fa02549353fe4559d2 authored almost 13 years ago

Working commit of expanded initial state/pcoord handling framework.

w_init runs. w_run doesn't.

github.com/westpa/westpa - cc6341074431b682588453ff8d512b42121b2462 authored almost 13 years ago

Fixed a few broken things from previous merge

github.com/westpa/westpa - ad60bc8d507c1006af196582ca854eb8747c30cb authored almost 13 years ago

Merge with f99ba64775fb79082b3911552ba9604f7cfaec74

github.com/westpa/westpa - 8248d88cdb2ecd855428c2e0d60242e3548b2358 authored almost 13 years ago

Cleanup in data_manager.py, sim_manager.py, zeromq.py

github.com/westpa/westpa - 2c76733b1ca40b0032c33cb6e37d9d7f747c208d authored almost 13 years ago

Merge with 3cdb3808753c137ede2babaf25ac8adf598a21de

github.com/westpa/westpa - a65807c6d42be678040b3808d3112c0e87c50e9f authored almost 13 years ago

Added support for storing (and then loading) auxiliary data sets in the WEMD HDF5 file.

github.com/westpa/westpa - 4bd3ca1a30da17794c5d9f81a11bb7bef7219416 authored almost 13 years ago

Added manual handling of zmq-received data to address issue #11.

A zero-copy receive, followed by a manual copy of the message contents, followed by unpickling s...

github.com/westpa/westpa - 8c1b7d9bbcfd9c3d951374b0c3a5541366237eec authored almost 13 years ago

Updated changelog.

github.com/westpa/westpa - e9d1eb351d0d3cad1f074bf552fb3e131568e435 authored almost 13 years ago

Merge with 0bedd05ec30ebbadb476560aa1a53b3dac842738

github.com/westpa/westpa - 7bc58c2484a04778ae9367ff77a553402ed64d41 authored almost 13 years ago

Merge with 1d57a981ae330476aa85532c79b68877a35179ed

github.com/westpa/westpa - 2cf0de35b43e9f613d6a364805df792056ce1240 authored almost 13 years ago

Updated w_truncate to new wemd.rc functions, began same for w_steady_state, and removed remarkably obsolete w_sanity and w_segstats.

github.com/westpa/westpa - 5a44547afa8f95b8bb0ab9294c63ade522749ea7 authored almost 13 years ago

Bugfix for issue #10 to fix registering multiple callbacks to the same hook

github.com/westpa/westpa - 866bd7e9ce88350e8109580b4d822868959a7842 authored almost 13 years ago

Slightly more careful use of deepcopy() and del in the dispatch/recieve loop of the ZMQ master, again to mitigate ZMQ-triggered segfaults.

github.com/westpa/westpa - ca0a52971a517d04fef24692813a72370f12c11b authored almost 13 years ago

Restructured internal zmq work driver signaling to re-use connected sockets, hopefully to avoid the dreaded "too many open files" error.

github.com/westpa/westpa - 0c3582b37c95bd5f76b1222abc9d9b081dc0f40c authored about 13 years ago

Modified w_succ and w_trace to use new analysis framework, and emit more data.

github.com/westpa/westpa - 1a88bf107cbb2f7f90d5dd36e95e3e2446183b63 authored about 13 years ago

Bugfix for issue #5 in which plugins did not intialize properly due to worker mode not set

github.com/westpa/westpa - b9047ef505e47ddc376594c63859a83c569c400b authored about 13 years ago

Reworked per-segment generic data storage complete and partially tested. Retrieval is still not written. Numerous changes to config file syntax for added sanity and generality. Replaced superfluous calls to list(sorted(...)) with sorted(...). Added first bits to support generalized recycle-to-generated-states.

github.com/westpa/westpa - 7a1f486ce64be8927c4e2bae8cde1c6af3666fdd authored about 13 years ago

Updated WEED probability adjustment to latest version.

github.com/westpa/westpa - 15ab32af9e0d7e6d50e8f4a9973641ddc9504e50 authored about 13 years ago

Made processes work manager throw exceptions properly, fixed a bug where errors in pre-iteration and post-iteration hooks in the propagator were silently ignored.

github.com/westpa/westpa - c7f7abcc3607fee943d733c4ab69113232ae4096 authored about 13 years ago

A few bugfixes, including restarting stopped simulations. Now, the environment WEMD_SIM_ROOT is set instead of SIM_ROOT if it is not previously defined.

github.com/westpa/westpa - 271a5a41af812d8f1c0d4d3eaa8944d96143273f authored about 13 years ago

Merge with 16eccdf58e5df38c996e3bab53480364fa6c5914

github.com/westpa/westpa - 4ec38cd4f30745819e1dd10c83b88fbf1a3fc3ae authored about 13 years ago

Updated changelog.

github.com/westpa/westpa - 98b0c5ed5f6d65909c1a9f3da14a518aaaa07126 authored about 13 years ago

Added workaround for apparent reference counting bug in pyzmq, which manifests as segfaults in h5py.

github.com/westpa/westpa - 06f95405b174ed743a69d99c5174d7716e564588 authored about 13 years ago

Removed invalid references to processes/threads work managers

github.com/westpa/westpa - 3c15398b0172c0bbfad109f2ebaaf1df3a242b0d authored about 13 years ago

Merge with d11be051b940f08d4956a45c6ac8c8ab786e2036

github.com/westpa/westpa - 5081f9d7a16e64e086ea819f570e58f21f424664 authored about 13 years ago

Updated changelog to reflect addition of WEED code.

github.com/westpa/westpa - d51dacd59c0df04816d5fde4ce56c725e784a128 authored about 13 years ago

Added up-to-date version of WEED code.

github.com/westpa/westpa - 2ffc0628cb9588a2c3439d7bf7ad56d10d953b13 authored about 13 years ago

Working commit of code cleanup.

github.com/westpa/westpa - eea6bf7ffec9182e512f01d76082a0b2c6069912 authored about 13 years ago

Changed all ``(*)_dir`` config file options for the executable propagator to corresponding ``$1_data_ref`` options, to better reflect their use. Other general cleanup.

github.com/westpa/westpa - ae9dc2910567f17b43f762c4484738a4bf35fbca authored about 13 years ago

Slightly optimized handling of "work available" in the ZMQ work manager.

github.com/westpa/westpa - 230fe594cc808ae0216bb0c742a0199e1e1d5a17 authored about 13 years ago

Preliminary working version of new ZMQ work manager

github.com/westpa/westpa - 53757700f2527d4a7b8318d44507f1f38e039135 authored about 13 years ago

Working reincarnated threads and processes work managers.

github.com/westpa/westpa - c90928973e94c0a82521a7e5bb62906956effbe3 authored about 13 years ago

Working version of generalized work manager; efficiency appears approximately the same as before.

github.com/westpa/westpa - 2cab7c4e873e563f0063f37b853c5bb455cc3704 authored about 13 years ago

Working commit of generalized work manager, with re-introduced processes work manager.

github.com/westpa/westpa - f1e74089a2b6a8e4cfca147116a99d5b332cb316 authored about 13 years ago

Merged

github.com/westpa/westpa - e438ebb6d375b3557ab927f6cd7a1fcb680fd30f authored about 13 years ago

Added missing wbf_import, w_bfttimes symlinks

github.com/westpa/westpa - a5070d1370214c82deebecfc735626eab58ccf40 authored about 13 years ago

Fixed uncommented '----' in w_binprobs, optimized some Numpy operations in w_ttimes.

github.com/westpa/westpa - 7aaf2fad1fb95208f3bd4d4a1dd967644c4847db authored about 13 years ago

Changed executable backend to use subprocess.Popen; removed risky threads and processes work managers until they can be fixed.

github.com/westpa/westpa - ac2e584ea4dd484f7f528f54258dfca41c8d72aa authored about 13 years ago

ttimes tweak

github.com/westpa/westpa - 8589e11a1948b3ddf9f55b8037590ad969211e1f authored over 13 years ago

Finalized brute force transition time analysis; fixed error in FPT calculation (introduced recently).

github.com/westpa/westpa - 9233ee35779d934e09043bc155ce85a84c75860a authored over 13 years ago

Continued unifying brute force and weighted ensemble analysis.

github.com/westpa/westpa - fd6b2c61a75a8460cf9cf9d0d3a50919d37e5dfd authored over 13 years ago

Moved w_ttimes and w_ttimes_bf into wemdtools.cmds

github.com/westpa/westpa - 981c6aa24ed883324bffa26c205af059c180f1b1 authored over 13 years ago

Preparation for moving lib/cmds into the wemdtools.cmds package.

github.com/westpa/westpa - 69b6bce547b793968d63fabf99aee2610fe5fc18 authored over 13 years ago

Visual tweaks to w_edpdist

github.com/westpa/westpa - 52c283a95b82be4dbdb3913bf600db6222c3eb7f authored over 13 years ago

Fixed bug in zmq work driver (task may be None here and there), duration probability convergence plotting done.

github.com/westpa/westpa - ac8ebf4846c90c29c7fc96a4ab93a641ce19650e authored over 13 years ago

Working w_ttimes (yet again)

github.com/westpa/westpa - aa430ba89d4298f607bd12f921fbec46204b76bb authored over 13 years ago

Working commit of analysis framework rewrite; fixed bug in w_ttimes.

github.com/westpa/westpa - 57b3087b5179261d6a2c19afdf2b8dc5ebd611f1 authored over 13 years ago

removed w_ttimes_bf.py to replace it with a version based on w_ttimes

github.com/westpa/westpa - eebff9ef055f2b49a66740aa0849146cac9b16d8 authored over 13 years ago

Working commit of analysis framework rewrite, including first bits of EDF evolution script.

github.com/westpa/westpa - 4537799ca418b5f0a18943f62ea853466e7537c8 authored over 13 years ago

w_ttimes adapted to new analysis framework, with support for selection of which bin pairs to generate statistics for.

github.com/westpa/westpa - ace0d27d8517165db78ac4d8ffd0c3753b044438 authored over 13 years ago

Working commit of move of w_ttimes to new analysis framework. IterRangeMixin is generalized to support storage of iteration ranges and strides in HDF5 attributes and to return slices of other data sets based on that information.

github.com/westpa/westpa - e3e1923c5d6d63ef72b0b83ba2e298f680923d46 authored over 13 years ago

Working commit of move of w_ttimes to new analysis framework.

github.com/westpa/westpa - 69d66c3a554607c7b16051c6142a5babefac1c21 authored over 13 years ago

Removed lingering references to unused multiprocessing.Queue and multiprocessing.Pool, after discovering that Kraken doesn't support shared semaphores.

github.com/westpa/westpa - 32a1d461c4c25eb2f0f80eaeecec4330a9a8a2b2 authored over 13 years ago