Fix spectator support #1233
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Fix spectator support #1233
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The current test takes a considerable amount of time. |
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Can you mark it for GPU or for slow? |
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@ijpulidos have you ran this locally or should I run this PR on our GPU runner? |
The test already ran before on CPU (check my previous comment). And yes, I have run it locally with GPU. Though it shouldn't really use the GPU, it would just set the contexts and such, since it isn't running any iterations. We are just putting it in the GPU CI because it's a slow test, but I guess we could also mark it as |
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By the way, I also made sure that starting an example protein-ligand simulation wasn't affected by this. |
mikemhenry
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Sep 12, 2023
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* run CI on new 0.10.x branch (#1212) * run CI on new 0.10.x branch * Update .github/workflows/CI.yaml Co-authored-by: Iván Pulido <[email protected]> --------- Co-authored-by: Iván Pulido <[email protected]> * print perses version on startup (#1176) * Update comments in `RESTCapableHybridTopologyFactory` (#1189) * update comments * bump ci --------- Co-authored-by: Iván Pulido <[email protected]> Co-authored-by: Mike Henry <[email protected]> * use python executable from env (#1174) * use python executable from env * run tests using the shell * parmed 4 seems to be giving us some issues * actually I think we want the newer parmed * pin pymbar for now * ooof, parmed != pymbar * add some more debugging to figure out how we are getting old parmed * Update devtools/conda-envs/test_env.yaml * see if shell=True fixes it * removed parmed by mistake * Support pymbar 4 (#1173) * switch to using pymbar 3 & 4 support from openmmtools * fix typo on import * fix yaml * switch to using pymbar 4 * missed a pymbar import * missed another one * bump ci * missed a import * go back to how it was * Update devtools/conda-envs/test_env.yaml --------- Co-authored-by: Iván Pulido <[email protected]> * Remove example testing (#1214) * Store initial and final topologies for all phases -- small molecule pipeline (#1210) * Initial and final topologies serialized per phase. * Using properties instead of private attrs. * Fix test * Remove uneeded code/attributes * bump ci * Store phase topologies separately * Fix tests. vacuum topologies expected. * Better docstring. --------- Co-authored-by: Mike Henry <[email protected]> * Improve docker building (#1200) * Added note about example for adding oe license * make docker file much simpler * build images in CI * forgot to add conda-forge * fix permissions on a step * get oe_license file mounted in docker container * mount path must be absolute * setup singulairty to test + fix testing on docker image * add some testing deps to the image * add -v for tests, fix envar * tests are failing, want to test rest of pipeline * use latest openmm version * hardcode perses version for now * bump ci * make sure we can make openeye dir * support a dev build as well * don't hardcode value * fix name clash * forgot to add conda-forge * bump ci * test docker image and fix missing deps * install ps * also push latest tag * don't build on tag since the conda-forge package won't exist yet * don't test the examples * Remove docker deb build, we can do these ourselves * better document container use * build a latest version for apptainer * build with 11.2 to make things more compatable * skip docker test to see if other bits build okay * see if I can get the step to fail if there is an error * skip docker tests to make sure apptainer builds okay * Add mpiplus and mpi4py to docker image * give correct path to oe license * add mpi stuff to docker * clean up diskspace before build * skip tests for singularity now that the only failures come from a package bug * Clean examples -- CLI protein-ligand example for Tyk2 (#1223) * Improving examples dir structure and readme * Adding Tyk2 CLI example * removing new-cli/ripk2 example (deprecated) * fix typo for link * Clarify tyk2 cli example docs * Realtime analysis interval to default to checkpoint interval (#1227) * CI miscellaneous fixes (#1217) * CI minor fixes. Allow codecov to fail. * bump ci --------- Co-authored-by: Mike Henry <[email protected]> * Changing offline freq default to checkpoint interval * Fixing input yaml for example * commenting offline-freq param --------- Co-authored-by: Mike Henry <[email protected]> * MPI example with dipeptide mutation (#1228) * peptide mutation MPI example added * better documentation of motivation * Fix/issue 1194 (#1230) * set cutoff distance in sterics_custom_nonbonded_force * matching cutoff for custom forces. Improving logic. * test for HTF nonbonded cutoff --------- Co-authored-by: Iván Pulido <[email protected]> * Fix/issue 1196 (#1229) * CI miscellaneous fixes (#1217) * CI minor fixes. Allow codecov to fail. * bump ci --------- Co-authored-by: Mike Henry <[email protected]> * added dels to contexts * Update perses/app/setup_relative_calculation.py --------- Co-authored-by: Iván Pulido <[email protected]> * Fix spectator support (#1233) * fix spectator support. Enabling test. * Test to run on GPU CI. * pin <4 for pymbar on GPU --------- Co-authored-by: Iván Pulido <[email protected]> Co-authored-by: Ivy Zhang <[email protected]>
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Description
These changes remove an unnecessary call to
RelativeFEPSetup._setup_complex_phasemethod, fixing the support for spectator molecules.Motivation and context
Resolves #1232
Resolves #1219
How has this been tested?
Re-enabling previously skipped test for setting up bace system with spectator molecule.
Change log