Closed mattwthompson closed 2 years ago
jchodera
commented
2 years ago Thanks for reporting this, @mattwthompson! I'll investigate.
I suspect this may be related to https://github.com/openmm/openmm/issues/3310 --- can you try the nightly dev build with
conda install -c omnia-dev openmmand see if that eliminates the issue?
If so, we might need a bugfix release of 7.6 or a warning not to use 7.6, though 7.7 is due imminently.
mattwthompson
commented
2 years ago Running into something else, which surprised me. Do I need to pull down something else for the nightly build?
jchodera
commented
2 years ago @ijpulidos encountered this too. The omnia-dev package is built slightly differently, and will cause this issue if you use a nonstandard CUDA install path: https://github.com/openmm/openmm/issues/3302
You have to set OPENMM_CUDA_COMPILER to your nvcc path.
mattwthompson
commented
2 years ago Thanks for continuing to iterate on this. I managed to get some version of the CUDA toolkit and NVIDIA compiler installed via apt, but ran into
openmm.OpenMMException: Error initializing CUDA: CUDA_ERROR_NO_DEVICE (100) at /home/conda/build_artifacts/openmm_1638768148661/work/platforms/cuda/src/CudaContext.cpp:139This card is Kepler, which seems to be too old to play nicely with CUDA 10.x. I have an Turing card that I can use instead, although this requires setting everything up again so it won't be as quick.
jchodera
commented
2 years ago Shoot, sorry about this---you can grab whichever CUDA version you want with
conda install -c omnia-dev/label/cudaXY openmmwhere cudaXY is cuda92 for CUDA 9.2, for example. That should support your card if you can install CUDA 9.2.
ijpulidos
commented
2 years ago I can confirm this issue does NOT show with the nightly build openmm 7.7 py39_cuda102_debug_1 omnia-dev
mattwthompson
commented
2 years ago Thanks @ijpulidos! That's reassuring. I'll keep working on to verify - it'd be great to be sure this only affects one released version. I should have an update tomorrow.
mattwthompson
commented
2 years ago Okay, I've also been able to verify that that it's fixed in 7.7 (py39_cuda102_debug_1) - or at least looks fixed, I didn't dig deeper than the third digit.
It took a decent amount of coaxing (old hardware, old CUDA, old drivers, kinda-old OS, all with a future OpenMM) to actually access the GPU and a CUDA compiler. I don't know if it's relevant that the system and conda env have different versions of CUDA.
I'd like to hear from @simonboothroyd before closing this, but I think it's resolved. Thanks all!
jchodera
commented
2 years ago This should be resolved now with the release of OpenMM 7.7.
We are finding that using
openmmtoolsto read data fromyankreports wildly different energies with OpenMM 7.6 and the CUDA platform compared to either the OpenMM 7.6 with OpenCL or OpenMM 7.5.1 with either platform.It's not clear if this issue lies with Yank, OpenMMTools, OpenMM, or some combination thereof. A full, extremely verbose reproduction is below, based on attached files.
The short summary of the reproduction is that reported energies for a small solvent system are ~-13000 on BOTH platforms with OpenMM 7.5.1. With 7.6, OpenCL energies are ~-13000 but CUDA energies are wildly deviant around -20000. Or visually:
I didn't find this behavior or write the reproduction (credit to @lilyminium and @simonboothroyd) - just ran it and wrote this issue.
yank-repro.tar.gz
Click to expand!
This is on Ubuntu 18.04 LTS with an Intel CPU and NVIDIA GPU (Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz, Quadro K420). Environments created with ``` $ conda create --name yank-old "yank ==0.25.2" "openmmtools =0.20.0" "openmm <7.6" "pyyaml <6" "cudatoolkit =10.1" ``` ``` $ conda create --name yank-new "yank ==0.25.2" "openmmtools =0.20.0" "openmm >=7.6" "pyyaml <6" "cudatoolkit =10.1" ``` Reproduction script ```python3 import shutil import yaml from openmmtools.multistate import MultiStateReporter from yank.experiment import ExperimentBuilder def main(): for platform in ["CUDA", "OpenCL"]: with open("yank-template.yaml") as file: yank_yaml = yaml.load(file) yank_yaml["options"]["platform"] = platform with open(f"yank-{platform}.yaml", "w") as file: yaml.dump(yank_yaml, file) exp_builder = ExperimentBuilder(f"yank-{platform}.yaml") exp_builder.run_experiments() reporter_solvent_1 = MultiStateReporter("experiments/solvent1.nc", "r") print(f"{platform} ENERGIES", reporter_solvent_1.read_energies()) shutil.move("experiments", f"experiments-{platform}") shutil.move("setup", f"setup-{platform}") if __name__ == "__main__": main() ``` Full reproduction: ``` $ conda activate yank-old (yank-old) [crestone] ~/yank-repro $ python run-yank.py /home/mattthompson/yank-repro/run-yank.py:13: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. yank_yaml = yaml.load(file) 2021-12-06 09:56:50,262: Setting CUDA platform to use precision model 'mixed'. 2021-12-06 09:56:50,331: Reading phase solvent1 2021-12-06 09:56:50,604: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases 2021-12-06 09:56:50,604: Reading phase solvent2 2021-12-06 09:56:50,611: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases 2021-12-06 09:56:50,614: WARNING - yank.experiment - WARNING! You have specified both a solute-only trajectory AND a checkpoint interval of 1! You are about write the trajectory of the solute twice! This can be okay if you are running explicit solvent and want faster retrieval of the solute atoms, but in implicit solvent, this is redundant. 2021-12-06 09:56:50,614: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases Please cite the following: Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209 Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27 Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413 Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669 2021-12-06 09:56:53,995: WARNING - yank.experiment - WARNING! You have specified both a solute-only trajectory AND a checkpoint interval of 1! You are about write the trajectory of the solute twice! This can be okay if you are running explicit solvent and want faster retrieval of the solute atoms, but in implicit solvent, this is redundant. 2021-12-06 09:56:53,995: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases Please cite the following: Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209 Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27 Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413 Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669 2021-12-06 09:56:54,336: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases CUDA ENERGIES (array([[[-13884.00289057, -13878.96598885, -13872.70037222, -13865.20603373, -13856.48297512, -13856.67530188, -13856.77702686, -13856.76343154, -13856.52936344, -13856.13537541, -13855.62442012, -13855.02752858, -13854.70422031, -13854.36746235, -13854.01920529, -13853.6611416 , -13853.29473971, -13852.92128224, -13852.54188764, -13852.15753415], [-13884.00289057, -13878.96598885, -13872.70037222, -13865.20603373, -13856.48297512, -13856.67530188, -13856.77702686, -13856.76343154, -13856.52936344, -13856.13537541, -13855.62442012, -13855.02752858, -13854.70422031, -13854.36746235, -13854.01920529, -13853.6611416 , -13853.29473971, -13852.92128224, -13852.54188764, -13852.15753415], [-13884.00289057, -13878.96598885, -13872.70037222, -13865.20603373, -13856.48297512, -13856.67530188, 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array([[[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], 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1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]]], dtype=int8), array([], shape=(2, 20, 0), dtype=float64)) 2021-12-06 09:56:54,437: Setting OpenCL platform to use precision model 'mixed'. 2021-12-06 09:56:54,584: Reading phase solvent1 2021-12-06 09:56:54,822: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases 2021-12-06 09:56:54,822: Reading phase solvent2 2021-12-06 09:56:54,829: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases 2021-12-06 09:56:54,832: WARNING - yank.experiment - WARNING! You have specified both a solute-only trajectory AND a checkpoint interval of 1! You are about write the trajectory of the solute twice! This can be okay if you are running explicit solvent and want faster retrieval of the solute atoms, but in implicit solvent, this is redundant. 2021-12-06 09:56:54,832: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases Please cite the following: Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209 Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27 Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413 Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669 2021-12-06 09:56:59,035: WARNING - yank.experiment - WARNING! You have specified both a solute-only trajectory AND a checkpoint interval of 1! You are about write the trajectory of the solute twice! This can be okay if you are running explicit solvent and want faster retrieval of the solute atoms, but in implicit solvent, this is redundant. 2021-12-06 09:56:59,036: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases Please cite the following: Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209 Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27 Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413 Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669 2021-12-06 09:56:59,342: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases OpenCL ENERGIES (array([[[-13884.00223714, -13878.96534618, -13872.69975522, -13865.20539949, -13856.48233419, -13856.67466006, -13856.77638992, -13856.76279366, -13856.52872561, -13856.13473747, -13855.62378281, -13855.02689127, -13854.7035832 , -13854.36682592, -13854.01856857, -13853.66050465, -13853.29410314, -13852.92064546, -13852.54125075, -13852.15689734], [-13884.00223714, -13878.96534618, -13872.69975522, -13865.20539949, -13856.48233419, -13856.67466006, -13856.77638992, -13856.76279366, -13856.52872561, -13856.13473747, -13855.62378281, -13855.02689127, -13854.7035832 , -13854.36682592, -13854.01856857, -13853.66050465, -13853.29410314, -13852.92064546, -13852.54125075, -13852.15689734], [-13884.00223714, -13878.96534618, -13872.69975522, -13865.20539949, -13856.48233419, 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1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]]], dtype=int8), array([], shape=(2, 20, 0), dtype=float64)) $ conda deactivate (base) [crestone] ~/yank-repro $ conda activate yank-new (yank-new) [crestone] ~/yank-repro $ python run-yank.py Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. /home/mattthompson/yank-repro/run-yank.py:13: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details. yank_yaml = yaml.load(file) 2021-12-06 10:01:46,610: Setting CUDA platform to use precision model 'mixed'. 2021-12-06 10:01:46,679: Reading phase solvent1 2021-12-06 10:01:46,962: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases 2021-12-06 10:01:46,962: Reading phase solvent2 2021-12-06 10:01:46,969: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases 2021-12-06 10:01:46,971: WARNING - yank.experiment - WARNING! You have specified both a solute-only trajectory AND a checkpoint interval of 1! You are about write the trajectory of the solute twice! This can be okay if you are running explicit solvent and want faster retrieval of the solute atoms, but in implicit solvent, this is redundant. 2021-12-06 10:01:46,971: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases Please cite the following: Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209 Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27 Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413 Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669 2021-12-06 10:01:50,222: WARNING - yank.experiment - WARNING! You have specified both a solute-only trajectory AND a checkpoint interval of 1! You are about write the trajectory of the solute twice! This can be okay if you are running explicit solvent and want faster retrieval of the solute atoms, but in implicit solvent, this is redundant. 2021-12-06 10:01:50,223: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases Please cite the following: Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209 Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27 Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413 Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669 2021-12-06 10:01:50,539: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases CUDA ENERGIES (array([[[-205491.1756646 , -205486.13876289, -205479.87314625, -205472.37880776, -205463.65574915, -205406.40826599, -205406.50999097, -205406.49639565, -205406.26232755, -205405.86833952, -205405.35738423, -205404.76049269, -205404.43718442, -205404.10042646, -205403.7521694 , -205403.39410571, -205403.02770382, -205402.65424635, -205402.27485175, -205401.89049826], [-205491.1756646 , -205486.13876289, -205479.87314625, -205472.37880776, -205463.65574915, -205406.40826599, -205406.50999097, -205406.49639565, -205406.26232755, -205405.86833952, -205405.35738423, -205404.76049269, -205404.43718442, -205404.10042646, -205403.7521694 , -205403.39410571, -205403.02770382, -205402.65424635, -205402.27485175, -205401.89049826], [-205491.1756646 , -205486.13876289, -205479.87314625, 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1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]]], dtype=int8), array([], shape=(2, 20, 0), dtype=float64)) 2021-12-06 10:01:50,640: Setting OpenCL platform to use precision model 'mixed'. 2021-12-06 10:01:50,814: Reading phase solvent1 2021-12-06 10:01:51,064: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases 2021-12-06 10:01:51,064: Reading phase solvent2 2021-12-06 10:01:51,071: WARNING - openmmtools.multistate.multistatesampler - Warning: The openmmtools.multistate API is experimental and may change in future releases 2021-12-06 10:01:51,074: WARNING - yank.experiment - WARNING! You have specified both a solute-only trajectory AND a checkpoint interval of 1! You are about write the trajectory of the solute twice! This can be okay if you are running explicit solvent and want faster retrieval of the solute atoms, but in implicit solvent, this is redundant. 2021-12-06 10:01:51,074: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases Please cite the following: Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209 Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27 Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413 Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669 2021-12-06 10:01:55,234: WARNING - yank.experiment - WARNING! You have specified both a solute-only trajectory AND a checkpoint interval of 1! You are about write the trajectory of the solute twice! This can be okay if you are running explicit solvent and want faster retrieval of the solute atoms, but in implicit solvent, this is redundant. 2021-12-06 10:01:55,235: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases Please cite the following: Friedrichs MS, Eastman P, Vaidyanathan V, Houston M, LeGrand S, Beberg AL, Ensign DL, Bruns CM, and Pande VS. Accelerating molecular dynamic simulations on graphics processing unit. J. Comput. Chem. 30:864, 2009. DOI: 10.1002/jcc.21209 Eastman P and Pande VS. OpenMM: A hardware-independent framework for molecular simulations. Comput. Sci. Eng. 12:34, 2010. DOI: 10.1109/MCSE.2010.27 Eastman P and Pande VS. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 31:1268, 2010. DOI: 10.1002/jcc.21413 Eastman P and Pande VS. Constant constraint matrix approximation: A robust, parallelizable constraint method for molecular simulations. J. Chem. Theor. Comput. 6:434, 2010. DOI: 10.1021/ct900463w Chodera JD and Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs multistate: Simple improvements for enhanced mixing. J. Chem. Phys., 135:194110, 2011. DOI:10.1063/1.3660669 2021-12-06 10:01:55,517: WARNING - openmmtools.multistate.multistatereporter - Warning: The openmmtools.multistate API is experimental and may change in future releases OpenCL ENERGIES (array([[[-13884.00223714, -13878.96534618, -13872.69975522, -13865.20539949, -13856.48233419, -13856.67466006, -13856.77638992, -13856.76279366, -13856.52872561, -13856.13473747, -13855.62378281, -13855.02689127, -13854.7035832 , -13854.36682592, -13854.01856857, -13853.66050465, -13853.29410314, -13852.92064546, -13852.54125075, -13852.15689734], [-13884.00223714, -13878.96534618, -13872.69975522, -13865.20539949, -13856.48233419, -13856.67466006, -13856.77638992, -13856.76279366, -13856.52872561, -13856.13473747, -13855.62378281, -13855.02689127, -13854.7035832 , -13854.36682592, -13854.01856857, -13853.66050465, -13853.29410314, -13852.92064546, -13852.54125075, -13852.15689734], [-13884.00223714, -13878.96534618, -13872.69975522, -13865.20539949, -13856.48233419, 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