Closed MiloszGrabski closed 3 weeks ago
mattwthompson
commented
1 month ago Is this a fresh install or a fresh environment? I don't know why 0.3 is pulled down, you could try installing openff-evaluator =0.4. Everything else I checked for your environment looks good
MiloszGrabski
commented
1 month ago This is fresh install, but rest of the environment was used just for openmm. I tried newer version per suggestion and got a number of dependency issues. I will try completely brand new environment with first evaluator followed by openmm.
warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE Could not solve for environment specs The following packages are incompatible ├─ openff-evaluator 0.4* is installable with the potential options │ ├─ openff-evaluator [0.4.5|0.4.6|0.4.7|0.4.8] would require │ │ └─ openff-evaluator-base [0.4.5 pyhd8ed1ab_1|0.4.6 pyhd8ed1ab_0|0.4.7 pyhd8ed1ab_0|0.4.8 pyhd8ed1ab_0], which requires │ │ ├─ openmmtools 0.21.5. , which requires │ │ │ ├─ hdf5 1.12. with the potential options │ │ │ │ ├─ hdf5 [1.12.2|1.14.0] would require │ │ │ │ │ └─ openssl >=1.1.1s,<1.1.2a , which can be installed; │ │ │ │ ├─ hdf5 1.12.2 would require │ │ │ │ │ └─ openssl >=1.1.1q,<1.1.2a , which can be installed; │ │ │ │ ├─ hdf5 1.12.2, which can be installed; │ │ │ │ ├─ hdf5 1.12.2, which can be installed; │ │ │ │ ├─ hdf5 1.12.2, which can be installed; │ │ │ │ ├─ hdf5 1.12.0 would require │ │ │ │ │ └─ openssl >=1.1.1g,<1.1.2a , which can be installed; │ │ │ │ ├─ hdf5 1.12.0 would require │ │ │ │ │ └─ openssl >=1.1.1h,<1.1.2a , which can be installed; │ │ │ │ ├─ hdf5 1.12.0 would require │ │ │ │ │ └─ openssl >=1.1.1i,<1.1.2a , which can be installed; │ │ │ │ ├─ hdf5 [1.12.0|1.12.1] would require │ │ │ │ │ └─ openssl >=1.1.1k,<1.1.2a , which can be installed; │ │ │ │ ├─ hdf5 1.12.0, which can be installed; │ │ │ │ ├─ hdf5 1.12.1 would require │ │ │ │ │ └─ openssl >=1.1.1l,<1.1.2a , which can be installed; │ │ │ │ ├─ hdf5 1.12.1 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.12.1 conflicts with any installable versions previously reported; │ │ │ │ └─ hdf5 1.12.1 conflicts with any installable versions previously reported; │ │ │ └─ netcdf4 1.5. with the potential options │ │ │ ├─ netcdf4 [1.5.0|1.5.0.1|...|1.5.3] would require │ │ │ │ └─ python >=2.7,<2.8.0a0 , which can be installed; │ │ │ ├─ netcdf4 [1.5.0|1.5.0.1|...|1.5.7] would require │ │ │ │ └─ python >=3.6,<3.7.0a0 , which can be installed; │ │ │ ├─ netcdf4 [1.5.0|1.5.0.1|...|1.5.8] would require │ │ │ │ └─ python >=3.7,<3.8.0a0 , which can be installed; │ │ │ ├─ netcdf4 [1.5.3|1.5.4|...|1.5.8] would require │ │ │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ │ │ ├─ netcdf4 [1.5.4|1.5.5|...|1.5.8] would require │ │ │ │ └─ python >=3.9,<3.10.0a0 , which can be installed; │ │ │ ├─ netcdf4 1.5.8 would require │ │ │ │ └─ hdf5 >=1.12.1,<1.12.2.0a0 mpimpich with the potential options │ │ │ │ ├─ hdf5 [1.12.0|1.12.1], which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.12.1, which can be installed (as previously explained); │ │ │ │ └─ hdf5 1.12.1 conflicts with any installable versions previously reported; │ │ │ ├─ netcdf4 1.5.8 would require │ │ │ │ └─ hdf5 >=1.12.1,<1.12.2.0a0 mpiopenmpi with the potential options │ │ │ │ ├─ hdf5 [1.12.0|1.12.1], which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.12.1, which can be installed (as previously explained); │ │ │ │ └─ hdf5 1.12.1 conflicts with any installable versions previously reported; │ │ │ └─ netcdf4 1.5.8 would require │ │ │ └─ hdf5 >=1.12.1,<1.12.2.0a0 with the potential options │ │ │ ├─ hdf5 [1.12.0|1.12.1], which can be installed (as previously explained); │ │ │ ├─ hdf5 1.12.1, which can be installed (as previously explained); │ │ │ ├─ hdf5 1.12.1 conflicts with any installable versions previously reported; │ │ │ ├─ hdf5 1.12.1 conflicts with any installable versions previously reported; │ │ │ └─ hdf5 1.12.1 conflicts with any installable versions previously reported; │ │ └─ pint 0.20.1 , which can be installed; │ └─ openff-evaluator [0.4.0|0.4.1|...|0.4.5] would require │ ├─ mdtraj >=1.9.3,<=1.9.4 with the potential options │ │ ├─ mdtraj 1.9.3 would require │ │ │ └─ python >=2.7,<2.8.0a0 , which can be installed; │ │ ├─ mdtraj [1.9.3|1.9.4] would require │ │ │ └─ python >=3.6,<3.7.0a0 , which can be installed; │ │ ├─ mdtraj [1.9.3|1.9.4] would require │ │ │ └─ python >=3.7,<3.8.0a0 , which can be installed; │ │ ├─ mdtraj [1.9.3|1.9.4] would require │ │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ │ └─ mdtraj 1.9.4 would require │ │ └─ python >=3.9,<3.10.0a0 , which can be installed; │ └─ openff-evaluator-base 0.4.0 pyhd8ed1ab_0, which requires │ └─ mdtraj >=1.9.3,<=1.9.4 , which can be installed (as previously explained); ├─ openff-toolkit is installable with the potential options │ ├─ openff-toolkit [0.13.0|0.13.1|...|0.16.3] would require │ │ └─ ambertools >=22 with the potential options │ │ ├─ ambertools [22.0|22.4|22.5|23.0] would require │ │ │ ├─ libnetcdf >=4.9.2,<4.9.3.0a0 with the potential options │ │ │ │ ├─ libnetcdf 4.9.2 would require │ │ │ │ │ ├─ hdf5 >=1.14.3,<1.14.4.0a0 but there are no viable options │ │ │ │ │ │ ├─ hdf5 1.14.3 would require │ │ │ │ │ │ │ └─ openssl >=3.3.0,<4.0a0 , which conflicts with any installable versions previously reported; │ │ │ │ │ │ ├─ hdf5 1.14.3 would require │ │ │ │ │ │ │ └─ openssl >=3.3.1,<4.0a0 , which conflicts with any installable versions previously reported; │ │ │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ │ │ └─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ │ └─ openssl >=3.3.1,<4.0a0 , which conflicts with any installable versions previously reported; │ │ │ │ ├─ libnetcdf 4.9.2 would require │ │ │ │ │ └─ hdf5 >=1.14.2,<1.14.4.0a0 mpimpich but there are no viable options │ │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ │ └─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ │ ├─ libnetcdf 4.9.2 would require │ │ │ │ │ └─ hdf5 >=1.14.1,<1.14.2.0a0 mpimpich, which conflicts with any installable versions previously reported; │ │ │ │ ├─ libnetcdf [4.9.1|4.9.2] would require │ │ │ │ │ └─ hdf5 >=1.14.0,<1.14.1.0a0 mpimpich with the potential options │ │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ │ ├─ hdf5 1.14.0 would require │ │ │ │ │ │ └─ openssl >=1.1.1t,<1.1.2a , which can be installed; │ │ │ │ │ └─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ │ ├─ libnetcdf 4.9.2 would require │ │ │ │ │ ├─ hdf5 >=1.14.3,<1.14.4.0a0 mpimpich but there are no viable options │ │ │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ │ │ └─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ │ └─ openssl >=3.3.1,<4.0a0 , which conflicts with any installable versions previously reported; │ │ │ │ ├─ libnetcdf [4.9.1|4.9.2] would require │ │ │ │ │ └─ hdf5 >=1.14.0,<1.14.1.0a0 mpiopenmpi with the potential options │ │ │ │ │ ├─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ │ └─ hdf5 1.14.0, which can be installed (as previously explained); │ │ │ │ ├─ libnetcdf 4.9.2 would require │ │ │ │ │ └─ hdf5 >=1.14.2,<1.14.4.0a0 mpiopenmpi but there are no viable options │ │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ │ └─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ │ ├─ libnetcdf 4.9.2 would require │ │ │ │ │ └─ hdf5 >=1.14.1,<1.14.2.0a0 mpiopenmpi, which conflicts with any installable versions previously reported; │ │ │ │ ├─ libnetcdf 4.9.2 would require │ │ │ │ │ ├─ hdf5 >=1.14.3,<1.14.4.0a0 mpiopenmpi but there are no viable options │ │ │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ │ │ └─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ │ └─ openssl >=3.3.1,<4.0a0 , which conflicts with any installable versions previously reported; │ │ │ │ ├─ libnetcdf [4.9.1|4.9.2] would require │ │ │ │ │ └─ hdf5 >=1.14.0,<1.14.1.0a0 with the potential options │ │ │ │ │ ├─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ │ ├─ hdf5 1.14.0, which can be installed (as previously explained); │ │ │ │ │ ├─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ │ │ └─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ │ ├─ libnetcdf 4.9.2 would require │ │ │ │ │ └─ hdf5 >=1.14.1,<1.14.2.0a0 , which conflicts with any installable versions previously reported; │ │ │ │ └─ libnetcdf 4.9.2 would require │ │ │ │ └─ hdf5 >=1.14.2,<1.14.4.0a0 but there are no viable options │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ │ └─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ └─ netcdf-fortran >=4.6.0,<4.7.0a0 with the potential options │ │ │ ├─ netcdf-fortran 4.6.1 would require │ │ │ │ └─ hdf5 >=1.14.2,<1.14.4.0a0 but there are no viable options │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ │ └─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ ├─ netcdf-fortran 4.6.0 would require │ │ │ │ └─ hdf5 >=1.12.2,<1.12.3.0a0 mpimpich with the potential options │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.12.2, which can be installed (as previously explained); │ │ │ │ └─ hdf5 1.12.2, which can be installed; │ │ │ ├─ netcdf-fortran 4.6.0 would require │ │ │ │ └─ hdf5 >=1.12.2,<1.12.3.0a0 mpiopenmpi with the potential options │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.12.2, which can be installed (as previously explained); │ │ │ │ └─ hdf5 1.12.2, which can be installed; │ │ │ ├─ netcdf-fortran 4.6.0 would require │ │ │ │ └─ hdf5 >=1.12.2,<1.12.3.0a0 with the potential options │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.12.2, which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.12.2, which can be installed; │ │ │ │ ├─ hdf5 1.12.2, which can be installed; │ │ │ │ └─ hdf5 1.12.2, which can be installed; │ │ │ ├─ netcdf-fortran [4.6.0|4.6.1] would require │ │ │ │ └─ hdf5 >=1.14.0,<1.14.1.0a0 mpimpich with the potential options │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.0, which can be installed (as previously explained); │ │ │ │ └─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ ├─ netcdf-fortran [4.6.0|4.6.1] would require │ │ │ │ └─ hdf5 >=1.14.0,<1.14.1.0a0 mpiopenmpi with the potential options │ │ │ │ ├─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ └─ hdf5 1.14.0, which can be installed (as previously explained); │ │ │ ├─ netcdf-fortran [4.6.0|4.6.1] would require │ │ │ │ └─ hdf5 >=1.14.0,<1.14.1.0a0 with the potential options │ │ │ │ ├─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.0, which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ │ └─ hdf5 1.14.0 conflicts with any installable versions previously reported; │ │ │ ├─ netcdf-fortran 4.6.1 would require │ │ │ │ └─ hdf5 >=1.14.1,<1.14.2.0a0 mpimpich, which conflicts with any installable versions previously reported; │ │ │ ├─ netcdf-fortran 4.6.1 would require │ │ │ │ └─ hdf5 >=1.14.3,<1.14.4.0a0 mpimpich but there are no viable options │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ └─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ ├─ netcdf-fortran 4.6.1 would require │ │ │ │ └─ hdf5 >=1.14.2,<1.14.4.0a0 mpimpich but there are no viable options │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ └─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ ├─ netcdf-fortran 4.6.1 would require │ │ │ │ └─ hdf5 >=1.14.3,<1.14.4.0a0 mpiopenmpi but there are no viable options │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ └─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ ├─ netcdf-fortran 4.6.1 would require │ │ │ │ └─ hdf5 >=1.14.2,<1.14.4.0a0 mpiopenmpi but there are no viable options │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ └─ hdf5 1.14.2 conflicts with any installable versions previously reported; │ │ │ ├─ netcdf-fortran 4.6.1 would require │ │ │ │ └─ hdf5 >=1.14.1,<1.14.2.0a0 mpiopenmpi, which conflicts with any installable versions previously reported; │ │ │ ├─ netcdf-fortran 4.6.1 would require │ │ │ │ └─ hdf5 >=1.14.3,<1.14.4.0a0 but there are no viable options │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3, which cannot be installed (as previously explained); │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ ├─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ │ └─ hdf5 1.14.3 conflicts with any installable versions previously reported; │ │ │ └─ netcdf-fortran 4.6.1 would require │ │ │ └─ hdf5 >=1.14.1,<1.14.2.0a0 , which conflicts with any installable versions previously reported; │ │ ├─ ambertools 22.0 would require │ │ │ └─ openssl >=1.1.1q,<1.1.2a , which can be installed; │ │ ├─ ambertools 22.0 would require │ │ │ └─ openssl >=1.1.1o,<1.1.2a , which can be installed; │ │ ├─ ambertools [20.0|20.10|...|22.0] would require │ │ │ └─ python >=3.7,<3.8.0a0 , which can be installed; │ │ ├─ ambertools [20.0|20.10|...|23.6] would require │ │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ │ ├─ ambertools [20.10|20.11|...|23.6] would require │ │ │ └─ python >=3.9,<3.10.0a0 , which can be installed; │ │ ├─ ambertools [22.0|22.1|22.2|22.3|22.4] would require │ │ │ └─ libnetcdf >=4.9.1,<4.9.2.0a0 with the potential options │ │ │ ├─ libnetcdf [4.9.1|4.9.2], which can be installed (as previously explained); │ │ │ ├─ libnetcdf [4.9.1|4.9.2], which can be installed (as previously explained); │ │ │ ├─ libnetcdf [4.9.1|4.9.2], which can be installed (as previously explained); │ │ │ ├─ libnetcdf 4.9.1 would require │ │ │ │ └─ hdf5 >=1.12.2,<1.12.3.0a0 mpimpich with the potential options │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.12.2, which can be installed (as previously explained); │ │ │ │ └─ hdf5 1.12.2, which can be installed; │ │ │ ├─ libnetcdf 4.9.1 would require │ │ │ │ └─ hdf5 >=1.12.2,<1.12.3.0a0 mpiopenmpi with the potential options │ │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ │ ├─ hdf5 1.12.2, which can be installed (as previously explained); │ │ │ │ └─ hdf5 1.12.2, which can be installed; │ │ │ └─ libnetcdf 4.9.1 would require │ │ │ └─ hdf5 >=1.12.2,<1.12.3.0a0 with the potential options │ │ │ ├─ hdf5 [1.12.2|1.14.0], which can be installed (as previously explained); │ │ │ ├─ hdf5 1.12.2, which can be installed (as previously explained); │ │ │ ├─ hdf5 1.12.2, which can be installed; │ │ │ ├─ hdf5 1.12.2, which can be installed; │ │ │ └─ hdf5 1.12.2, which can be installed; │ │ ├─ ambertools [23.0|23.3|23.6] would require │ │ │ ├─ libnetcdf >=4.9.2,<4.9.3.0a0 with the potential options │ │ │ │ ├─ libnetcdf 4.9.2, which cannot be installed (as previously explained); │ │ │ │ ├─ libnetcdf 4.9.2, which cannot be installed (as previously explained); │ │ │ │ ├─ libnetcdf 4.9.2, which cannot be installed (as previously explained); │ │ │ │ ├─ libnetcdf [4.9.1|4.9.2], which can be installed (as previously explained); │ │ │ │ ├─ libnetcdf 4.9.2, which cannot be installed (as previously explained); │ │ │ │ ├─ libnetcdf [4.9.1|4.9.2], which can be installed (as previously explained); │ │ │ │ ├─ libnetcdf 4.9.2, which cannot be installed (as previously explained); │ │ │ │ ├─ libnetcdf 4.9.2, which cannot be installed (as previously explained); │ │ │ │ ├─ libnetcdf 4.9.2, which cannot be installed (as previously explained); │ │ │ │ ├─ libnetcdf [4.9.1|4.9.2], which can be installed (as previously explained); │ │ │ │ ├─ libnetcdf 4.9.2, which cannot be installed (as previously explained); │ │ │ │ └─ libnetcdf 4.9.2, which cannot be installed (as previously explained); │ │ │ └─ openssl [>=3.3.0,<4.0a0 |>=3.3.1,<4.0a0 ], which conflicts with any installable versions previously reported; │ │ ├─ ambertools [23.3|23.6] would require │ │ │ └─ python >=3.11,<3.12.0a0 , which can be installed; │ │ └─ ambertools [23.3|23.6] would require │ │ └─ python >=3.12,<3.13.0a0 , which can be installed; │ ├─ openff-toolkit [0.10.0|0.10.1|...|0.9.2] would require │ │ └─ ambertools >=20 with the potential options │ │ ├─ ambertools [22.0|22.4|22.5|23.0], which can be installed (as previously explained); │ │ ├─ ambertools 22.0, which can be installed (as previously explained); │ │ ├─ ambertools 22.0, which can be installed (as previously explained); │ │ ├─ ambertools [20.0|20.10|...|22.0], which can be installed (as previously explained); │ │ ├─ ambertools [20.0|20.10|...|23.6], which can be installed (as previously explained); │ │ ├─ ambertools [20.10|20.11|...|23.6], which can be installed (as previously explained); │ │ ├─ ambertools [22.0|22.1|22.2|22.3|22.4], which can be installed (as previously explained); │ │ ├─ ambertools [23.0|23.3|23.6], which cannot be installed (as previously explained); │ │ ├─ ambertools [23.3|23.6], which can be installed (as previously explained); │ │ ├─ ambertools [23.3|23.6], which can be installed (as previously explained); │ │ └─ ambertools [20.0|20.10|...|21.9] would require │ │ └─ python >=3.6,<3.7.0a0 , which can be installed; │ ├─ openff-toolkit 0.11.2 would require │ │ └─ openff-toolkit-base 0.11.2 pyhd8ed1ab_2, which requires │ │ └─ pint <0.20 with the potential options │ │ ├─ pint [0.6|0.7.1|...|0.9] would require │ │ │ └─ python [2.7 |>=2.7,<2.8.0a0 ], which can be installed; │ │ ├─ pint [0.6|0.7.1|0.7.2] would require │ │ │ └─ python 3.4 , which can be installed; │ │ ├─ pint [0.6|0.7.1|0.7.2|0.8.0|0.8.1] would require │ │ │ └─ python 3.5 , which can be installed; │ │ ├─ pint [0.7.2|0.8.0|0.8.1] would require │ │ │ └─ python 3.6 , which can be installed; │ │ ├─ pint 0.9 would require │ │ │ └─ python >=3.6,<3.7.0a0 , which can be installed; │ │ ├─ pint 0.9 would require │ │ │ └─ python >=3.7,<3.8.0a0 , which can be installed; │ │ ├─ pint 0.9 would require │ │ │ └─ python >=3.8,<3.9.0a0 , which can be installed; │ │ └─ pint [0.10|0.10.1|...|0.9] conflicts with any installable versions previously reported; │ └─ openff-toolkit [0.14.4|0.14.5|0.15.0] would require │ └─ openff-toolkit-base [0.14.4 pyhd8ed1ab_0|0.14.4 pyhd8ed1ab_1|0.14.5 pyhd8ed1ab_1|0.15.0 pyhd8ed1ab_0], which requires │ └─ openff-units >=0.2.1 but there are no viable options │ ├─ openff-units 0.2.2 would require │ │ └─ pint >=0.21,<=0.23.0 , which conflicts with any installable versions previously reported; │ └─ openff-units 0.2.1 would require │ └─ pint 0.21. , which conflicts with any installable versions previously reported; ├─ pint is installable with the potential options │ ├─ pint 0.20.1 would require │ │ └─ numpy <2.0.0a0 , which can be installed; │ ├─ pint [0.22|0.23] conflicts with any installable versions previously reported; │ ├─ pint [0.6|0.7.1|...|0.9], which can be installed (as previously explained); │ ├─ pint [0.6|0.7.1|0.7.2], which can be installed (as previously explained); │ ├─ pint [0.6|0.7.1|0.7.2|0.8.0|0.8.1], which can be installed (as previously explained); │ ├─ pint [0.7.2|0.8.0|0.8.1], which can be installed (as previously explained); │ ├─ pint 0.9, which can be installed (as previously explained); │ ├─ pint 0.9, which can be installed (as previously explained); │ ├─ pint 0.9, which can be installed (as previously explained); │ ├─ pint [0.10|0.10.1|...|0.9] conflicts with any installable versions previously reported; │ ├─ pint [0.20|0.24|0.24.1|0.24.3] conflicts with any installable versions previously reported; │ └─ pint 0.21 conflicts with any installable versions previously reported; └─ pyarrow-core is installable with the potential options ├─ pyarrow-core [16.0.0|16.1.0] would require │ └─ libarrow [16.0.0. cpu|16.0.0. cuda|16.1.0. cpu|16.1.0. cuda] but there are no viable options │ ├─ libarrow [16.0.0|16.1.0] would require │ │ └─ libgoogle-cloud >=2.23.0,<2.24.0a0 , which requires │ │ └─ openssl >=3.2.1,<4.0a0 , which conflicts with any installable versions previously reported; │ ├─ libarrow 16.1.0 would require │ │ └─ libgoogle-cloud >=2.24.0,<2.25.0a0 , which requires │ │ └─ openssl >=3.3.0,<4.0a0 , which conflicts with any installable versions previously reported; │ └─ libarrow [16.1.0|17.0.0] would require │ ├─ azure-identity-cpp >=1.8.0,<1.8.1.0a0 , which requires │ │ └─ openssl >=3.3.1,<4.0a0 , which conflicts with any installable versions previously reported; │ └─ libgoogle-cloud >=2.25.0,<2.26.0a0 , which requires │ └─ openssl >=3.3.1,<4.0a0 , which conflicts with any installable versions previously reported; ├─ pyarrow-core [16.0.0|16.1.0|17.0.0] would require │ └─ python >=3.11,<3.12.0a0 , which can be installed; ├─ pyarrow-core [16.0.0|16.1.0|17.0.0] would require │ └─ python >=3.12,<3.13.0a0 , which can be installed; ├─ pyarrow-core [16.0.0|16.1.0|17.0.0] would require │ └─ python >=3.8,<3.9.0a0 , which can be installed; ├─ pyarrow-core [16.0.0|16.1.0|17.0.0] would require │ └─ python >=3.9,<3.10.0a0 , which can be installed; ├─ pyarrow-core 16.1.0 would require │ └─ numpy >=2.0.0rc.2,<3.0a0 with the potential options │ ├─ numpy [2.0.0|2.0.1] conflicts with any installable versions previously reported; │ ├─ numpy [2.0.0|2.0.1] would require │ │ └─ python >=3.11,<3.12.0a0 , which can be installed; │ ├─ numpy [2.0.0|2.0.1] would require │ │ └─ python >=3.12,<3.13.0a0 , which can be installed; │ ├─ numpy [2.0.0|2.0.1] would require │ │ └─ python >=3.9,<3.10.0a0 , which can be installed; │ └─ numpy [2.0.0rc1|2.0.0rc2] would require │ └─ _numpy_rc, which does not exist (perhaps a missing channel); └─ pyarrow-core 17.0.0 would require └─ libarrow [17.0.0. cpu|17.0.0. cuda], which cannot be installed (as previously explained).
MiloszGrabski
commented
1 month ago I think I tracked down which package has an issue with the >=4 version of evaluator. I created a brand new environment: python=3.10 Did conda install of openff-evaluator, installed version 4.8 Did conda install openmmforcefields, it downgraded version to 3.11, which results in pint.compat error. It looks that the newest version of evaluator is not compatible with openmmforcefields package. I am using openmmforcefields for SystemGenerator.
The following packages will be downloaded:
package | build
---------------------------|-----------------
ambertools-23.3 | py310h05519df_6 89.3 MB conda-forge
fftw-3.3.10 |nompi_hf1063bd_110 2.0 MB conda-forge
libboost-1.82.0 | h6fcfa73_6 2.5 MB conda-forge
libboost-python-1.82.0 | py310hcb52e73_6 116 KB conda-forge
netcdf-fortran-4.6.1 |nompi_h228c76a_104 422 KB conda-forge
openmmforcefields-0.14.1 | pyhd8ed1ab_0 2.3 MB conda-forge
rdkit-2023.09.6 | py310hb79e901_1 36.0 MB conda-forge
validators-0.33.0 | pyhd8ed1ab_0 37 KB conda-forge
------------------------------------------------------------
Total: 132.7 MBThe following NEW packages will be INSTALLED:
alabaster conda-forge/noarch::alabaster-1.0.0-pyhd8ed1ab_0 ambertools conda-forge/linux-64::ambertools-23.3-py310h05519df_6 arpack conda-forge/linux-64::arpack-3.8.0-nompi_h0baa96a_101 c-blosc2 conda-forge/linux-64::c-blosc2-2.14.4-hb4ffafa_1 cerberus conda-forge/noarch::cerberus-1.3.5-pyhd8ed1ab_0 clusterutils conda-forge/noarch::clusterutils-0.3.1-pyhd8ed1ab_1 cmiles-base conda-forge/noarch::cmiles-base-0.1.6-pyhd8ed1ab_2 docopt conda-forge/noarch::docopt-0.6.2-py_1 docutils conda-forge/noarch::docutils-0.21.2-pyhd8ed1ab_0 fftw conda-forge/linux-64::fftw-3.3.10-nompi_hf1063bd_110 imagesize conda-forge/noarch::imagesize-1.4.1-pyhd8ed1ab_0 libaec conda-forge/linux-64::libaec-1.1.3-h59595ed_0 mpi conda-forge/linux-64::mpi-1.0-mpich mpich conda-forge/linux-64::mpich-4.2.2-h4a7f18d_101 netcdf-fortran conda-forge/linux-64::netcdf-fortran-4.6.1-nompi_h228c76a_104 numpydoc conda-forge/noarch::numpydoc-1.7.0-pyhd8ed1ab_3 openff-interchange conda-forge/noarch::openff-interchange-0.3.29-pyhd8ed1ab_0 openff-toolkit conda-forge/noarch::openff-toolkit-0.16.3-pyhd8ed1ab_0 openmmforcefields conda-forge/noarch::openmmforcefields-0.14.1-pyhd8ed1ab_0 openmoltools conda-forge/noarch::openmoltools-0.8.8-pyhd8ed1ab_1 panedr conda-forge/noarch::panedr-0.8.0-pyhd8ed1ab_0 perl conda-forge/linux-64::perl-5.32.1-7_hd590300_perl5 py-cpuinfo conda-forge/noarch::py-cpuinfo-9.0.0-pyhd8ed1ab_0 snowballstemmer conda-forge/noarch::snowballstemmer-2.2.0-pyhd8ed1ab_0 sphinx conda-forge/noarch::sphinx-8.0.2-pyhd8ed1ab_0 sphinxcontrib-app~ conda-forge/noarch::sphinxcontrib-applehelp-2.0.0-pyhd8ed1ab_0 sphinxcontrib-dev~ conda-forge/noarch::sphinxcontrib-devhelp-2.0.0-pyhd8ed1ab_0 sphinxcontrib-htm~ conda-forge/noarch::sphinxcontrib-htmlhelp-2.1.0-pyhd8ed1ab_0 sphinxcontrib-jsm~ conda-forge/noarch::sphinxcontrib-jsmath-1.0.1-pyhd8ed1ab_0 sphinxcontrib-qth~ conda-forge/noarch::sphinxcontrib-qthelp-2.0.0-pyhd8ed1ab_0 sphinxcontrib-ser~ conda-forge/noarch::sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0 tabulate conda-forge/noarch::tabulate-0.9.0-pyhd8ed1ab_1 tinydb conda-forge/noarch::tinydb-4.8.0-pyhd8ed1ab_0 validators conda-forge/noarch::validators-0.33.0-pyhd8ed1ab_0 xorg-libxt conda-forge/linux-64::xorg-libxt-1.3.0-hd590300_1 yank conda-forge/noarch::yank-0.25.2-pyhd8ed1ab_0 zlib-ng conda-forge/linux-64::zlib-ng-2.0.7-h0b41bf4_0
The following packages will be REMOVED:
librdkit-2024.03.5-h79cfef2_3
The following packages will be UPDATED:
h5py 3.7.0-nompi_py310h06dffec_100 --> 3.11.0-nompi_py310hf054cd7_102 hdf5 1.12.1-nompi_h4df4325_104 --> 1.14.3-nompi_hdf9ad27_105 libnetcdf 4.8.1-nompi_h329d8a1_102 --> 4.9.2-nompi_h135f659_114 netcdf4 1.5.8-nompi_py310hd7ca5b8_101 --> 1.6.5-nompi_py310h3aa39b3_102 openmmtools 0.21.5-pyhd8ed1ab_1 --> 0.23.1-pyhd8ed1ab_0 pytables 3.7.0-py310hf5df6ce_0 --> 3.9.2-py310hd76cd5d_2
The following packages will be DOWNGRADED:
libboost 1.84.0-hba137d9_3 --> 1.82.0-h6fcfa73_6 libboost-python 1.84.0-py310ha7c98ff_5 --> 1.82.0-py310hcb52e73_6 openff-evaluator 0.4.8-pyhd8ed1ab_0 --> 0.3.11-pyhd8ed1ab_0 openff-evaluator-~ 0.4.8-pyhd8ed1ab_0 --> 0.3.11-pyhd8ed1ab_0 rdkit 2024.03.5-py310h57e35d3_3 --> 2023.09.6-py310hb79e901_1
Downloading and Extracting Packages:
Preparing transaction: done Verifying transaction: done Executing transaction: done
mattwthompson
commented
1 month ago The change is due to new AmberTools builds now bringing it their own packmol instead of pulling one down: https://github.com/conda-forge/ambertools-feedstock/pull/137
$ CONDA_SUBDIR=linux-64 micromamba create --name evaluator-561 -c conda-forge "openff-evaluator =0.4.8" "openmmforcefields=0.14" "ambertools =23.6"
warning libmamba 'root_prefix' set with default value: /Users/mattthompson/micromamba
conda-forge/noarch Using cache
conda-forge/linux-64 36.8MB @ 24.3MB/s 1.5s
warning libmamba linux version not found, defaulting to '0'
warning libmamba glibc version not found (virtual package skipped)
error libmamba Could not solve for environment specs
The following packages are incompatible
├─ ambertools 23.6** is installable with the potential options
│ ├─ ambertools 23.6 would require
│ │ └─ packmol 9999999999 , which can be installed;
│ ├─ ambertools 23.6 would require
│ │ └─ __cuda, which is missing on the system;
│ └─ ambertools 23.6 would require
│ └─ openmpi >=5.0.3,<6.0a0 , which requires
│ └─ __glibc >=2.17,<3.0.a0 , which is missing on the system;
└─ openff-evaluator 0.4.8** is not installable because it requires
└─ openff-evaluator-base 0.4.8 pyhd8ed1ab_0, which requires
└─ packmol but there are no viable options
├─ packmol [18.169|20.010|...|20.4.1] conflicts with any installable versions previously reported;
└─ packmol 20.15.0 would require
└─ __glibc >=2.17,<3.0.a0 , which is missing on the system.
critical libmamba Could not solve for environment specsIn general you're much better off creating new environments and seeing what the solver brings down. Making sweeping changing to an existing environment brings in changes that are often unrelated to the issue at hand or generally path-dependent/difficult to reproduce.
There are some tensions between a couple of the other upstreams (I'm tempted to vendor the parts of openmmtools we need), however ...
It looks that the newest version of evaluator is not compatible with openmmforcefields package. I am using openmmforcefields for SystemGenerator.
Evaluator does not use SystemGenerator at all, so you may be better off using separate environments.
If you can share more about what you're doing I may be able to provide more useful guidance.
mattwthompson
commented
1 month ago Okay, I found another quirk in packaging that could be nudging downgraded solutions. This potential issue is unfortunately obfuscated by tooling that we're each using to hunt it down.
Unfortunately it may take a couple of hours to isolate and test, but I'll update here when I have clarity and hopefully a solution. Thanks for your patience!
mattwthompson
commented
1 month ago Looping back around, there are two things at play
packmol change I referenced above. New builds won't depend on the standalone packmol and will just hope that AmberTools is available or it's otherwise installed somehowpint =0.20.1 in builds for a while now, which has been updated in #562. This will need a release (0.4.9) for the changes to be liveMiloszGrabski
commented
1 month ago Thanks for looking into this so quickly. "If you can share more about what you're doing I may be able to provide more useful guidance." - looking into mixed solvent systems and chameleonicity, which means I have to deal with non-typical solvent systems. I currently build those using mdapackmol pacakge, but wanted more integrated way to do so. I was looking into this: import mdapackmol Which led me to evaluator, my current system works, just looking for something "cleaner".
This is the bit of code I want to replace with evaluator
fragment = convert_smiles(smiles)
uni = Universe(fragment)
for_packing = list()
side_l = side_length.real/2
for_packing.append(mdp.PackmolStructure(uni, number=count, instructions = [f'inside box {-side_l} {-side_l} {-side_l} {side_l} {side_l} {side_l}', 'chain F']))
solvent_system = mdp.packmol(for_packing)
ag = solvent_system.select_atoms("chainID F")
ag.residues.resnames = ['FRA' for r in ag.residues.resnames]
solvent_system.atoms.write(f'{fragment_id}.pdb')Hmm okay, you might be better off with smaller wrapper or just calling packmol yourself. But this is supported behavior within the public API and should work.
Until #563 is complete, my recommendation is to use the latest version of Evaluator and AmberTools 22. I'm able to get this environment solved with versions of things I think should work:
$ CONDA_SUBDIR=linux-64 micromamba create --name evaluator-561 -c conda-forge "openff-evaluator =0.4.8" openmmforcefields "ambertools =22"Until #563 is complete, my recommendation is to use the latest version of Evaluator and AmberTools 22.
I am not in much of a rush, so I can wait till the release. Again, thanks for looking into this.
mattwthompson
commented
1 month ago Release 0.4.9, online in the next hour, should fix packaging issues you've uncovered
packmol package if the AmberTools version brought down isn't 23.6upcast_ error doesn't bubble up)MiloszGrabski
commented
3 weeks ago Release 0.4.9, online in the next hour, should fix packaging issues you've uncovered
- You might need to install a standalone
packmolpackage if the AmberTools version brought down isn't 23.6- There's an upgrade in the Pint version required; this is not likely visible (so long as the
upcast_error doesn't bubble up)- Please create a new environment if possible and avoid updating an existing one
I will have a look soon and will let you know. I have completely given up on MDAPackmol as it was not transferring residue names for proteins. Worked fine for simple solvent mixtures but not when wanted to include a protein. I have created my own method using OpenFF Molecule, OpenMM modeller.Add() and using Poission Disk Sampling for fragment placement. Work quite well, but as soon as I am able I will move to Evaluator, for simplicity and "cleanness" of the code.
mattwthompson
commented
3 weeks ago If it's just a PACKMOL wrapper you're after, you could also try this one: https://github.com/openforcefield/openff-interchange/blob/v0.3.29/openff/interchange/components/_packmol.py
MiloszGrabski
commented
3 weeks ago I am not particularly attached to packmol; was using MDAPackmol just because it was easy to get going and it was before I learnt that you can do the same thing with evaluator. I will try to create a brand new environment tomorrow and see if changes you have made are compatible with basic openmm I am using. If I can use evaluator I have not need for packmol.
MiloszGrabski
commented
3 weeks ago A different problem came up, did following steps: 1) create environment python=3.10 2) install newest version from setup.py 3) mamba install openmm 4) mamba install openff-toolkit 5) mamba install openforcefields then tested using terminal
>>> from openff.evaluator.protocols.coordinates import BuildCoordinatesPackmol
Traceback (most recent call last):
File "
mamba list #
_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge ambertools 23.6 cuda_None_nompi_py310ha112c55_105 conda-forge amberutils 21.0 pypi_0 pypi annotated-types 0.7.0 pyhd8ed1ab_0 conda-forge anyio 4.4.0 pyhd8ed1ab_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge arpack 3.9.1 nompi_h77f6705_101 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge attrs 24.2.0 pyh71513ae_0 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge blosc 1.21.6 hef167b5_0 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bson 0.5.9 py_0 conda-forge bzip2 1.0.8 h4bc722e_7 conda-forge c-ares 1.33.0 ha66036c_0 conda-forge c-blosc2 2.15.1 hc57e6cf_0 conda-forge ca-certificates 2024.7.4 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.5.0 pyhd8ed1ab_0 conda-forge cairo 1.18.0 hebfffa5_3 conda-forge certifi 2024.7.4 pyhd8ed1ab_0 conda-forge cffi 1.17.0 py310h2fdcea3_0 conda-forge chardet 5.2.0 py310hff52083_1 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.2.2 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 py310hd41b1e2_0 conda-forge cudatoolkit 11.8.0 h4ba93d1_13 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge debugpy 1.8.5 py310hea249c9_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge edgembar 0.2 pypi_0 pypi entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge fftw 3.3.10 nompi_hf1063bd_110 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.1 py310h5b4e0ec_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge freetype-py 2.3.0 pyhd8ed1ab_0 conda-forge greenlet 3.0.3 py310hc6cd4ac_0 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge hdf4 4.2.15 h2a13503_7 conda-forge hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge httpcore 1.0.5 pyhd8ed1ab_0 conda-forge httpx 0.27.0 pyhd8ed1ab_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 75.1 he02047a_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge importlib-metadata 8.4.0 pyha770c72_0 conda-forge importlib_metadata 8.4.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.4 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jupyterlab_widgets 3.0.13 pyhd8ed1ab_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py310hd41b1e2_1 conda-forge krb5 1.21.3 h659f571_0 conda-forge lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.40 hf3520f5_7 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.1.3 h59595ed_0 conda-forge libblas 3.9.0 23_linux64_openblas conda-forge libboost 1.84.0 h0ccab89_5 conda-forge libboost-python 1.84.0 py310ha7c98ff_5 conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 23_linux64_openblas conda-forge libcurl 8.9.1 hdb1bdb2_0 conda-forge libdeflate 1.21 h4bc722e_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 14.1.0 h77fa898_0 conda-forge libgfortran-ng 14.1.0 h69a702a_0 conda-forge libgfortran5 14.1.0 hc5f4f2c_0 conda-forge libglib 2.80.3 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pyhca7485f_0 conda-forge openff-evaluator 0.4.9 pypi_0 pypi openff-forcefields 2024.07.0 pyhff2d567_0 conda-forge openff-interchange 0.3.29 pyhd8ed1ab_0 conda-forge openff-interchange-base 0.3.29 pyhd8ed1ab_0 conda-forge openff-models 0.1.2 pyhca7485f_0 conda-forge openff-toolkit 0.16.4 pyhd8ed1ab_0 conda-forge openff-toolkit-base 0.16.4 pyhd8ed1ab_0 conda-forge openff-units 0.2.2 pyhca7485f_0 conda-forge openff-utilities 0.1.12 pyhd8ed1ab_0 conda-forge openjpeg 2.5.2 h488ebb8_0 conda-forge openmm 8.1.2 py310h6b72300_2 conda-forge openmmforcefields 0.14.1 pyhd8ed1ab_0 conda-forge openssl 3.3.1 h4bc722e_2 conda-forge overrides 7.7.0 pyhd8ed1ab_0 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge packmol-memgen 2024.2.9 pypi_0 pypi pandas 2.2.2 py310hf9f9076_1 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge panedr 0.8.0 pyhd8ed1ab_0 conda-forge parmed 4.2.2 py310hc6cd4ac_1 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge pcre2 10.44 hba22ea6_2 conda-forge pdb4amber 22.0 pypi_0 pypi perl 5.32.1 7_hd590300_perl5 conda-forge pexpect 4.9.0 pyhd8ed1ab_0 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 10.4.0 py310hebfe307_0 conda-forge pint 0.23 pyhd8ed1ab_1 conda-forge pip 24.2 pyhd8ed1ab_0 conda-forge pixman 0.43.2 h59595ed_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.47 pyha770c72_0 conda-forge psutil 6.0.0 py310hc51659f_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge py-cpuinfo 9.0.0 pyhd8ed1ab_0 conda-forge pycairo 1.26.1 py310he029307_0 conda-forge pycparser 2.22 pyhd8ed1ab_0 conda-forge pydantic 2.8.2 pyhd8ed1ab_0 conda-forge pydantic-core 2.20.1 py310h42e942d_0 conda-forge pyedr 0.8.0 pyhd8ed1ab_0 conda-forge pygments 2.18.0 pyhd8ed1ab_0 conda-forge pymsmt 22.0 pypi_0 pypi pyparsing 3.1.2 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytables 3.10.1 py310hbb5d6fa_1 conda-forge python 3.10.14 hd12c33a_0_cpython conda-forge python-constraint 1.4.0 py_0 conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.20.0 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.10 5_cp310 conda-forge pytraj 2.0.6 pypi_0 pypi pytz 2024.1 pyhd8ed1ab_0 conda-forge pyyaml 6.0.2 py310h5b4e0ec_0 conda-forge pyzmq 26.2.0 py310h71f11fc_0 conda-forge qhull 2020.2 h434a139_5 conda-forge rdkit 2024.03.5 py310h57e35d3_3 conda-forge readline 8.2 h8228510_1 conda-forge referencing 0.35.1 pyhd8ed1ab_0 conda-forge reportlab 4.2.2 py310hc51659f_0 conda-forge requests 2.32.3 pyhd8ed1ab_0 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge rlpycairo 0.2.0 pyhd8ed1ab_0 conda-forge rpds-py 0.20.0 py310h42e942d_0 conda-forge sander 22.0 pypi_0 pypi scipy 1.14.1 py310ha3fb0e1_0 conda-forge send2trash 1.8.3 pyh0d859eb_0 conda-forge setuptools 72.2.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge snappy 1.2.1 ha2e4443_0 conda-forge sniffio 1.3.1 pyhd8ed1ab_0 conda-forge soupsieve 2.5 pyhd8ed1ab_1 conda-forge sqlalchemy 2.0.32 py310h5b4e0ec_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge terminado 0.18.1 pyh0d859eb_0 conda-forge tinycss2 1.3.0 pyhd8ed1ab_0 conda-forge tinydb 4.8.0 pyhd8ed1ab_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.4.1 py310hc51659f_0 conda-forge tqdm 4.66.5 pyhd8ed1ab_0 conda-forge traitlets 5.14.3 pyhd8ed1ab_0 conda-forge types-python-dateutil 2.9.0.20240821 pyhd8ed1ab_0 conda-forge typing-extensions 4.12.2 hd8ed1ab_0 conda-forge typing_extensions 4.12.2 pyha770c72_0 conda-forge typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge tzdata 2024a h0c530f3_0 conda-forge unicodedata2 15.1.0 py310h2372a71_0 conda-forge uri-template 1.3.0 pyhd8ed1ab_0 conda-forge urllib3 2.2.2 pyhd8ed1ab_1 conda-forge validators 0.33.0 pyhd8ed1ab_0 conda-forge wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge webcolors 24.8.0 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pyhd8ed1ab_2 conda-forge websocket-client 1.8.0 pyhd8ed1ab_0 conda-forge wheel 0.44.0 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.13 pyhd8ed1ab_0 conda-forge xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 hb711507_1 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxt 1.3.0 hd590300_1 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zeromq 4.3.5 h75354e8_4 conda-forge zipp 3.20.0 pyhd8ed1ab_0 conda-forge zlib 1.3.1 h4ab18f5_1 conda-forge zlib-ng 2.2.1 he02047a_0 conda-forge zstandard 0.18.0 py310h5764c6d_1 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge
mattwthompson
commented
3 weeks ago Does this happen when you use the recommended installation method of downloading the release builds? https://docs.openforcefield.org/projects/evaluator/en/stable/install.html#installation-from-conda
mattwthompson
commented
3 weeks ago I can't reproduce this with a recent environment that has similar packages installed https://gist.github.com/mattwthompson/669a21bf80489f7c8d05070a4b7a18d4
MiloszGrabski
commented
3 weeks ago Ok, I am able to load everything now. For some reason when I tried to install from conda it failed to resolve it. Must have been internal problem. I still did not manage to repeat: this. Thank you for sorting this out. I will create another ticket as there is different issues connected with this code: https://github.com/MobleyLab/drug-computing/blob/f38a4148e9e70238c88fc8110d95b34688f02838/uci-pharmsci/lectures/SMIRNOFF_simulations/mixture_simulations.ipynb
Performed fresh installation of openff-evaluator using conda. When tried importing: from openff.evaluator.protocols.coordinates import BuildCoordinatesPackmol I got following error:
AttributeError: module 'pint.compat' has no attribute 'upcast_types'
which originated from this: pint.compat.upcast_types.append(ParameterGradient)
conda list dump:
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hb0abfc5_7 conda-forge aws-c-s3 0.5.10 h44b787d_4 conda-forge aws-c-sdkutils 0.1.16 he027950_3 conda-forge aws-checksums 0.1.18 he027950_7 conda-forge aws-crt-cpp 0.26.12 he940a02_1 conda-forge aws-sdk-cpp 1.11.329 h0f5bab0_6 conda-forge azure-core-cpp 1.12.0 h830ed8b_0 conda-forge azure-identity-cpp 1.8.0 hdb0d106_1 conda-forge azure-storage-blobs-cpp 12.11.0 ha67cba7_1 conda-forge azure-storage-common-cpp 12.6.0 he3f277c_1 conda-forge azure-storage-files-datalake-cpp 12.10.0 h29b5301_1 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge biopython 1.83 py310h2372a71_0 conda-forge bleach 6.1.0 pyhd8ed1ab_0 conda-forge blosc 1.21.5 hc2324a3_1 conda-forge bokeh 3.5.1 pyhd8ed1ab_0 conda-forge boost 1.78.0 py310hcb52e73_5 conda-forge boost-cpp 1.78.0 h2c5509c_4 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bson 0.5.9 py_0 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.28.1 hd590300_0 conda-forge c-blosc2 2.14.4 hb4ffafa_1 conda-forge ca-certificates 2024.7.4 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.3.3 pyhd8ed1ab_0 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge cerberus 1.3.5 pyhd8ed1ab_0 conda-forge certifi 2024.7.4 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py310h2fee648_0 conda-forge cftime 1.6.3 py310h261611a_1 conda-forge chardet 5.2.0 py310hff52083_1 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge clusterutils 0.3.1 pyhd8ed1ab_1 conda-forge cmiles-base 0.1.6 pyhd8ed1ab_2 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.2.2 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 py310hd41b1e2_0 conda-forge cudatoolkit 11.8.0 h4ba93d1_13 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cython 3.0.10 py310hc6cd4ac_0 conda-forge cytoolz 0.12.3 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