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bumps

Data fitting with uncertainty analysis

https://github.com/bumps/bumps

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    8 of 15 committers (53.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Data fitting with uncertainty analysis

Basic Info
  • Host: GitHub
  • Owner: bumps
  • License: other
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 13.1 MB
Statistics
  • Stars: 54
  • Watchers: 9
  • Forks: 35
  • Open Issues: 99
  • Releases: 57
Created over 14 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License

README.amdahl 

For large fits across mutliple nodes you may find that the proposal step is a bottleneck.
The compiled DE stepper can speed this up by a factor of 2 compared to the numba
version that is usually used. This might help on large allocations, but not enough
to support it in the automatic build infrastructure.

Update: MSVC is 6x faster than numba on one machine. Need to check performance with and
without compiled on HPC hardware to know if the compiled version is required.

To use the compiled de stepper and bounds checks, first make sure the "random123" library submodule has been checked out

    git clone --branch v1.14.0 https://github.com/DEShawResearch/random123.git bumps/dream/random123

Then, to compile on unix use:

    (cd bumps/dream && cc compiled.c -I ./random123/include/ -O2 -fopenmp -shared -lm -o _compiled.so -fPIC -DMAX_THREADS=64)

On OS/X clang doesn't support OpenMP:

    (cd bumps/dream && cc compiled.c -I ./random123/include/ -O2 -shared -lm -o _compiled.so -fPIC -DMAX_THREADS=64)

MSVC on windows using Visual Studio build tools (2022):

    % set up compiler environment
    "C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Auxiliary\Build\vcvarsall.bat" x86_amd64
    cd bumps\dream
    cl compiled.c -I .\random123\include /O2 /openmp /LD /GL /Fe_compiled.so

This only works when _compiled.so is in the bumps/dream directory.  If running
from a pip installed version, you will need to fetch the bumps repository:

    $ git clone https://github.com/bumps/bumps.git
    $ cd bumps

Compile as above, then find the bumps install path using the following:

    $ python -c "import bumps.dream; print(bumps.dream.__file__)"
    #dream/path/__init__.py

Copy the compiled module to the install, with the #dream/path printed above:

    $ cp bumps/dream/_compiled.so #dream/path

There is no provision for using _compiled.so in a frozen application.

Run with no more than 64 OMP threads.  If the number of processors is more than 64, then use:

    OMP_NUM_THREADS=64 ./run.py ...

I don't know how OMP_NUM_THREADS behaves if it is larger than the number of processors.

Owner

  • Name: bumps
  • Login: bumps
  • Kind: organization

GitHub Events

Total
  • Create event: 118
  • Commit comment event: 2
  • Issues event: 45
  • Release event: 27
  • Watch event: 1
  • Delete event: 100
  • Issue comment event: 171
  • Push event: 424
  • Pull request review comment event: 94
  • Pull request event: 178
  • Pull request review event: 148
  • Fork event: 1
Last Year
  • Create event: 118
  • Commit comment event: 2
  • Issues event: 45
  • Release event: 27
  • Watch event: 1
  • Delete event: 100
  • Issue comment event: 171
  • Push event: 424
  • Pull request review comment event: 94
  • Pull request event: 178
  • Pull request review event: 148
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 744
  • Total Committers: 15
  • Avg Commits per committer: 49.6
  • Development Distribution Score (DDS): 0.212
Past Year
  • Commits: 18
  • Committers: 3
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.389
Top Committers
Name Email Commits
Paul Kienzle p****e@n****v 586
Paul Kienzle p****e@n****v 46
Brian Ben Maranville b****e@n****v 35
Paul Kienzle p****e@g****m 32
Stuart Prescott s****t@d****g 16
Aaron Schankler a****r@n****v 7
Scott Wu s****x@g****m 5
acaruana2009 5****9 4
edr1 e****s@n****v 4
Mathieu Doucet d****m@o****v 3
Lila l****a@n****l 2
Andrew McCluskey a****y@e****u 1
David P. Hoogerheide d****e@n****v 1
Paul Kienzle p****e@h****v 1
Andrew Nelson a****f@g****m 1
Committer Domains (Top 20 + Academic)
nist.gov: 6 h122044.ncnr.nist.gov: 1 ess.eu: 1 ornl.gov: 1 debian.org: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 122
  • Total pull requests: 278
  • Average time to close issues: 10 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 14
  • Total pull request authors: 17
  • Average comments per issue: 1.52
  • Average comments per pull request: 1.25
  • Merged pull requests: 204
  • Bot issues: 0
  • Bot pull requests: 8
Past Year
  • Issues: 45
  • Pull requests: 226
  • Average time to close issues: 12 days
  • Average time to close pull requests: 11 days
  • Issue authors: 7
  • Pull request authors: 9
  • Average comments per issue: 1.2
  • Average comments per pull request: 1.12
  • Merged pull requests: 168
  • Bot issues: 0
  • Bot pull requests: 8
View more stats
Top Authors
Issue Authors
  • pkienzle (71)
  • bmaranville (21)
  • hoogerheide (7)
  • acaruana2009 (5)
  • glass-ships (4)
  • llimeht (4)
  • XaelShan (2)
  • alexander-grutter (2)
  • jmborr (1)
  • ohcpaull (1)
  • RONNCC (1)
  • backmari (1)
  • krzywon (1)
  • andyyuan78 (1)
Pull Request Authors
  • bmaranville (147)
  • pkienzle (68)
  • glass-ships (24)
  • dependabot[bot] (11)
  • hoogerheide (10)
  • llimeht (7)
  • acaruana2009 (4)
  • backmari (2)
  • krzywon (2)
  • tsole0 (2)
  • e-rus (2)
  • yusufameri (2)
  • a-detiste (2)
  • jmborr (1)
  • cyankaet (1)
Top Labels
Issue Labels
v1.0 (2) v1.1 (1) critical (1)
Pull Request Labels
dependencies (11) v1.0 (10) v1.1 (8) github_actions (3) critical (2) webview (2) bugfix (1)

Packages

  • Total packages: 3
  • Total downloads:
    • npm 225 last-month
    • pypi 53,558 last-month
  • Total dependent packages: 10
    (may contain duplicates)
  • Total dependent repositories: 16
    (may contain duplicates)
  • Total versions: 104
  • Total maintainers: 2
pypi.org: bumps

Data fitting with bayesian uncertainty analysis

  • Documentation: https://bumps.readthedocs.io/
  • License: Bumps is in the public domain. Code in individual files has copyright and license set by individual authors. bumps.gui, bumps.quasinewton ---------------------------- Copyright (C) 2006-2011, University of Maryland Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/ or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. DREAM ----- Copyright (c) 2008, Los Alamos National Security, LLC All rights reserved. Copyright 2008. Los Alamos National Security, LLC. This software was produced under U.S. Government contract DE-AC52-06NA25396 for Los Alamos National Laboratory (LANL), which is operated by Los Alamos National Security, LLC for the U.S. Department of Energy. The U.S. Government has rights to use, reproduce, and distribute this software. NEITHER THE GOVERNMENT NOR LOS ALAMOS NATIONAL SECURITY, LLC MAKES A NY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. If software is modified to produce derivative works, such modified software should be clearly marked, so as not to confuse it with the version available from LANL. Additionally, redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Los Alamos National Security, LLC, Los Alamos National Laboratory, LANL the U.S. Government, nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY LOS ALAMOS NATIONAL SECURITY, LLC AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL LOS ALAMOS NATIONAL SECURITY, LLC OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Random123 --------- Copyright 2010-2012, D. E. Shaw Research. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions, and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions, and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of D. E. Shaw Research nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. MPFit ----- The original version of this software, called LMFIT, was written in FORTRAN as part of the MINPACK-1 package by XXX. Craig Markwardt converted the FORTRAN code to IDL. The information for the IDL version is: Craig B. Markwardt, NASA/GSFC Code 662, Greenbelt, MD 20770 craigm@lheamail.gsfc.nasa.gov UPDATED VERSIONs can be found on my WEB PAGE: http://cow.physics.wisc.edu/~craigm/idl/idl.html Mark Rivers created this Python version from Craig's IDL version. Mark Rivers, University of Chicago Building 434A, Argonne National Laboratory 9700 South Cass Avenue, Argonne, IL 60439 rivers@cars.uchicago.edu Updated versions can be found at http://cars.uchicago.edu/software bumps.simplex ------------- :: # ******NOTICE*************** # From optimize.py module by Travis E. Oliphant # # You may copy and use this module as you see fit with no # guarantee implied provided you keep this notice in all copies. # *****END NOTICE************ bumps.cli.warn_with_traceback ----------------------------- From http://stackoverflow.com/questions/22373927/get-traceback-of-warnings answered by mgab (2014-03-13) edited by Gareth Rees (2015-11-28) bumps.dream.entropy.Timer ------------------------- Based on: Eli Bendersky https://stackoverflow.com/a/5849861 Extended with tic/toc by Paul Kienzle bumps.dream.entropy.MultivariateT.rvs ------------------------------------- From farhawa on stack overflow https://stackoverflow.com/questions/29798795/multivariate-student-t-distribution-with-python bumps.lsqerror.comb ------------------- From dheerosaur https://stackoverflow.com/questions/4941753/is-there-a-math-ncr-function-in-python/4941932#4941932
  • Latest release: 1.0.2
    published 12 months ago
  • Versions: 67
  • Dependent Packages: 7
  • Dependent Repositories: 14
  • Downloads: 53,558 Last month
  • Docker Downloads: 0
Rankings
Dependent packages count: 1.4%
Dependent repos count: 3.9%
Docker downloads count: 4.6%
Average: 5.4%
Downloads: 5.8%
Forks count: 7.5%
Stargazers count: 9.4%
Maintainers (2)
pkienzle bmaranville
Last synced: 10 months ago
conda-forge.org: bumps
  • Versions: 9
  • Dependent Packages: 2
  • Dependent Repositories: 2
Rankings
Dependent packages count: 19.6%
Dependent repos count: 20.3%
Average: 28.1%
Forks count: 32.5%
Stargazers count: 39.9%
Last synced: 10 months ago
npmjs.org: bumps-webview-client

This is the Javascript + HTML client for the webview interface in Bumps

  • Versions: 28
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 225 Last month
Rankings
Dependent repos count: 25.3%
Average: 29.1%
Dependent packages count: 32.9%
Maintainers (1)
bmaranville
Last synced: 10 months ago

Dependencies

setup.py pypi
  • six *
.github/workflows/test.yml actions
  • actions/checkout v1 composite
  • actions/setup-python v4 composite
doc/requirements.txt pypi
  • matplotlib >=1.0
  • numpy >=1.0
  • scipy >=0.7.0
  • setuptools *