Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

TKY2 Result failure with gather #141

Open
mikemhenry opened this issue May 2, 2024 · 0 comments
Open

TKY2 Result failure with gather #141

mikemhenry opened this issue May 2, 2024 · 0 comments

Comments

@mikemhenry
Copy link
Contributor 

/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:207: RuntimeWarning: divide by zero encountered in scalar power
  F_matrix[i, j] = -df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:208: RuntimeWarning: divide by zero encountered in scalar power
  F_matrix[j, i] = -df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:228: RuntimeWarning: divide by zero encountered in scalar power
  z[i] += f_ij[i, j] * df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:229: RuntimeWarning: divide by zero encountered in scalar power
  z[j] += f_ij[j, i] * df_ij[j, i] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:228: RuntimeWarning: invalid value encountered in scalar add
  z[i] += f_ij[i, j] * df_ij[i, j] ** (-2)
/usr/local/lib/python3.10/site-packages/cinnabar/stats.py:229: RuntimeWarning: invalid value encountered in scalar add
  z[j] += f_ij[j, i] * df_ij[j, i] ** (-2)
Traceback (most recent call last):
  File "/usr/local/bin/openfe", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python3.10/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/openfecli/commands/gather.py", line 376, in gather
    writing_func(legs, writer, allow_partial)
  File "/usr/local/lib/python3.10/site-packages/openfecli/commands/gather.py", line 259, in _write_dg_mle
    f_i, df_i = mle(g, factor='calc_DDG')
  File "/usr/local/lib/python3.10/site-packages/cinnabar/stats.py", line 232, in mle
    Finv = np.linalg.pinv(F_matrix)
  File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 2022, in pinv
    u, s, vt = svd(a, full_matrices=False, hermitian=hermitian)
  File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 1681, in svd
    u, s, vh = gufunc(a, signature=signature, extobj=extobj)
  File "/usr/local/lib/python3.10/site-packages/numpy/linalg/linalg.py", line 121, in _raise_linalgerror_svd_nonconvergence
    raise LinAlgError("SVD did not converge")
numpy.linalg.LinAlgError: SVD did not converge

This is with https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2024/results_tyk2_transformations_openfe_1.0.0rc0_uc_2.tar.gz
mikemhenry added a commit that referenced this issue May 2, 2024
@mikemhenry
updated with results, see issue #141
59e6060
mikemhenry added a commit that referenced this issue May 2, 2024
@mikemhenry @hannahbaumann
@richardjgowers @IAlibay
Test openfe 1.0.0rc0 + refresh showcase (#99)
b70d432 
* spruce up CI

* now test the rc

* Fix choose_protocol.ipynb

* Duplicate openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb history in showcase/openfe_showcase.ipynb history.

* shave and a haircut - 2 bits

* Fix showcase tutorial (#101)

* fix showcase notebook

* small fixes

* added some stuff from hannah pr

* update ligand_networks_for_developers.ipynb for 1.0rc0

* update benchmark_demo.ipynb for 1.0rc0

* first stab at changing examples to tyk2

* more switches to tyk2

* Add TYK2 image, remove T4L references

* Remove output

* Remove atom mapping CLI stuff

* show options atom mappers and ligand networks

* more notebook changes

* Add tyk2 figure and logo

* more changes showcase notebook

* Adress review comments

* Addressing review comments

* fix mapping

* transformation inputs as bullet points

* see if python 3.10 works

* lets see which python versions will work

* rerun ci

* update url for showcase installer

* unpin python version in env

* remove cell merged in by mistake

* see issue #138

* some small fixes for google colab

* just test on python 3.10

* pull down inputs for showcase

* drop osx for now

* put inputs in correct location

* updated with results, see issue #141

* skip running nbval on openfe gather cells at the end

* fix url for download

* update manual spec of default settings for openff bump

this is now 2.1.1 in 1.0 of openfe

* use fetch results for demoing gather

* use fetch to pull in inputs

* we can run more cells in CI, also added a note about it being a single edige

* fix Analysis typo

* pulled down wrong inputs

* Added a hack for google colab

---------

Co-authored-by: hannahbaumann <hbaumann@uci.edu>
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
Co-authored-by: richard gowers <richardjgowers@gmail.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@mikemhenry