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choderalab / openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
http://openmmtools.readthedocs.io
MIT License
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FIREMinimizationIntegrator fails on explicitly solvated system using CPU platform #686

Open IAlibay opened 1 year ago

IAlibay commented 1 year ago

Context

This is related to why #684 needed fixing, and hopefully some of the alchemical pains here will go away with #672

Bug report

We noticed that the FIREMinimizationIntegrator applied to an explicitly solvated system will yield NaNs when using a CPU platform, but will run fine on CUDA, OpenCL, and Reference.

Minimum reproducible code:

from openmmtools.integrators import FIREMinimizationIntegrator
from openmmtools import testsystems
import openmm

t = testsystems.AlanineDipeptideExplicit()
system, positions = t.system, t.positions
integrator = FIREMinimizationIntegrator()
platform = openmm.Platform.getPlatformByName('CPU')
context = openmm.Context(system, integrator, platform)
context.setPositions(positions)
integrator.step(10000)
state = context.getState(getEnergy=True)
state.getPotentialEnergy()

Error output:

OpenMMException                           Traceback (most recent call last)
Cell In[1], line 11
      9 context = openmm.Context(system, integrator, platform)
     10 context.setPositions(positions)
---> 11 integrator.step(10000)
     12 state = context.getState(getEnergy=True)
     13 state.getPotentialEnergy()

File ~/software/mambaforge/install/envs/openfe-latest/lib/python3.10/site-packages/openmm/openmm.py:13583, in CustomIntegrator.step(self, steps)
  13573 def step(self, steps):
  13574     r"""
  13575     step(self, steps)
  13576     Advance a simulation through time by taking a series of time steps.
   (...)
  13581         the number of time steps to take
  13582     """
> 13583     return _openmm.CustomIntegrator_step(self, steps)

OpenMMException: Particle coordinate is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan

mamba list output:

```bash # packages in environment at /home/ialibay/software/mambaforge/install/envs/openfe-latest: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge amberlite 22.0 pypi_0 pypi ambertools 22.0 py310h206695f_3 conda-forge amberutils 21.0 pypi_0 pypi anyio 3.6.2 pyhd8ed1ab_0 conda-forge argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h5764c6d_3 conda-forge arpack 3.7.0 hdefa2d7_2 conda-forge asttokens 2.2.1 pyhd8ed1ab_0 conda-forge astunparse 1.6.3 pyhd8ed1ab_0 conda-forge attrs 22.2.0 pyh71513ae_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge beautifulsoup4 4.12.2 pyha770c72_0 conda-forge bleach 6.0.0 pyhd8ed1ab_0 conda-forge blosc 1.21.3 hafa529b_0 conda-forge boost 1.74.0 py310h7c3ba0c_5 conda-forge boost-cpp 1.74.0 h75c5d50_8 conda-forge brotli 1.0.9 h166bdaf_8 conda-forge brotli-bin 1.0.9 h166bdaf_8 conda-forge brotlipy 0.7.0 py310h5764c6d_1005 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 5.3.0 pyhd8ed1ab_0 conda-forge cairo 1.16.0 ha61ee94_1014 conda-forge certifi 2022.12.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_3 conda-forge cftime 1.6.2 py310hde88566_1 conda-forge charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge click 8.1.3 unix_pyhd8ed1ab_2 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge comm 0.1.3 pyhd8ed1ab_0 conda-forge contourpy 1.0.7 py310hdf3cbec_0 conda-forge coverage 7.2.3 py310h1fa729e_0 conda-forge cryptography 40.0.2 py310h34c0648_0 conda-forge cudatoolkit 11.8.0 h37601d7_11 conda-forge curl 8.0.1 h588be90_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge cython 0.29.34 py310heca2aa9_0 conda-forge debugpy 1.6.7 py310heca2aa9_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge entrypoints 0.4 pyhd8ed1ab_0 conda-forge executing 1.2.0 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge fftw 3.3.10 nompi_hc118613_107 conda-forge flit-core 3.8.0 pyhd8ed1ab_0 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 hab24e00_0 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 4.39.3 py310h1fa729e_0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge gettext 0.21.1 h27087fc_0 conda-forge greenlet 2.0.2 py310heca2aa9_0 conda-forge gufe 0.7.2 pyhd8ed1ab_0 conda-forge hdf4 4.2.15 h9772cbc_5 conda-forge hdf5 1.12.2 nompi_h4df4325_101 conda-forge icu 70.1 h27087fc_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib-metadata 6.5.0 pyha770c72_0 conda-forge importlib_metadata 6.5.0 hd8ed1ab_0 conda-forge importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge ipykernel 6.22.0 pyh210e3f2_0 conda-forge ipython 8.12.0 pyh41d4057_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.7.5 pyhd8ed1ab_0 conda-forge jedi 0.18.2 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jpeg 9e h0b41bf4_3 conda-forge jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge jupyter_core 5.3.0 py310hff52083_0 conda-forge jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge jupyter_server 2.5.0 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge jupyterlab_widgets 1.1.4 pyhd8ed1ab_0 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py310hbf28c38_1 conda-forge krb5 1.20.1 h81ceb04_0 conda-forge lcms2 2.15 hfd0df8a_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.0.6 hcb278e6_1 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_8 conda-forge libbrotlidec 1.0.9 h166bdaf_8 conda-forge libbrotlienc 1.0.9 h166bdaf_8 conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcurl 8.0.1 h588be90_0 conda-forge libdeflate 1.17 h0b41bf4_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libglib 2.76.1 ha491796_0 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libiconv 1.17 h166bdaf_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge libllvm11 11.1.0 he0ac6c6_5 conda-forge libnetcdf 4.8.1 nompi_h261ec11_106 conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libpng 1.6.39 h753d276_0 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 hf14f497_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libtiff 4.5.0 h6adf6a1_2 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.0 h0b41bf4_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxml2 2.10.3 hca2bb57_4 conda-forge libxslt 1.1.37 h873f0b0_0 conda-forge libzip 1.9.2 hc929e4a_1 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge llvmlite 0.39.1 py310h58363a5_1 conda-forge lomap2 2.3.0 pyhd8ed1ab_0 conda-forge lxml 4.9.2 py310hbdc0903_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge markupsafe 2.1.2 py310h1fa729e_0 conda-forge matplotlib-base 3.7.1 py310he60537e_0 conda-forge matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge mdtraj 1.9.7 py310h902c554_4 conda-forge mistune 2.0.5 pyhd8ed1ab_0 conda-forge mmpbsa-py 16.0 pypi_0 pypi mpiplus v0.0.1 pyhd8ed1ab_1004 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge nbclassic 0.5.5 pyhb4ecaf3_1 conda-forge nbclient 0.7.3 pyhd8ed1ab_0 conda-forge nbconvert 7.3.1 pyhd8ed1ab_0 conda-forge nbconvert-core 7.3.1 pyhd8ed1ab_0 conda-forge nbconvert-pandoc 7.3.1 pyhd8ed1ab_0 conda-forge nbformat 5.8.0 pyhd8ed1ab_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge netcdf-fortran 4.6.0 nompi_he1eeb6f_102 conda-forge netcdf4 1.6.2 nompi_py310h55e1e36_100 conda-forge networkx 3.1 pyhd8ed1ab_0 conda-forge nomkl 1.0 h5ca1d4c_0 conda-forge nose 1.3.7 py_1006 conda-forge notebook 6.5.4 pyha770c72_0 conda-forge notebook-shim 0.2.2 pyhd8ed1ab_0 conda-forge numba 0.56.4 py310h0e39c9b_1 conda-forge numexpr 2.8.4 py310h690d005_100 conda-forge numpy 1.23.5 py310h53a5b5f_0 conda-forge ocl-icd 2.3.1 h7f98852_0 conda-forge ocl-icd-system 1.0.0 1 conda-forge openfe 0.7.2 pyhd8ed1ab_0 conda-forge openfe-benchmarks 0.0.0 pypi_0 pypi openff-amber-ff-ports 0.0.3 pyh6c4a22f_0 conda-forge openff-forcefields 2023.04.1 pyh1a96a4e_0 conda-forge openff-interchange 0.2.3 pyhd8ed1ab_1 conda-forge openff-interchange-base 0.2.3 pyhd8ed1ab_1 conda-forge openff-models 0.0.4 pyh1a96a4e_0 conda-forge openff-toolkit 0.12.1 pyhd8ed1ab_2 conda-forge openff-toolkit-base 0.12.1 pyhd8ed1ab_2 conda-forge openff-units 0.2.0 pyh1a96a4e_0 conda-forge openff-utilities 0.1.8 pyh1a96a4e_0 conda-forge openjpeg 2.5.0 hfec8fc6_2 conda-forge openmm 8.0.0 py310h5728c26_0 conda-forge openmmforcefields 0.11.2 pyhd8ed1ab_1 conda-forge openmmtools 0.22.0 pyhd8ed1ab_0 conda-forge openssl 3.1.0 h0b41bf4_0 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge packmol 20.010 h86c2bf4_0 conda-forge packmol-memgen 1.2.3rc0 pypi_0 pypi pandas 2.0.0 py310h9b08913_0 conda-forge pandoc 2.19.2 h32600fe_2 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge panedr 0.7.1 pyhd8ed1ab_0 conda-forge parmed 3.4.4 py310heca2aa9_0 conda-forge parso 0.8.3 pyhd8ed1ab_0 conda-forge pbr 5.11.1 pyhd8ed1ab_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge pdb4amber 22.0 pypi_0 pypi pdbfixer 1.8.1 pyh6c4a22f_0 conda-forge perl 5.32.1 2_h7f98852_perl5 conda-forge pexpect 4.8.0 pyh1a96a4e_2 conda-forge pickleshare 0.7.5 py_1003 conda-forge pillow 9.4.0 py310h023d228_1 conda-forge pint 0.20.1 pyhd8ed1ab_0 conda-forge pip 23.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge platformdirs 3.2.0 pyhd8ed1ab_0 conda-forge plugcli 0.1.0 pyhd8ed1ab_0 conda-forge pooch 1.7.0 pyha770c72_3 conda-forge prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge prompt-toolkit 3.0.38 pyha770c72_0 conda-forge prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge psutil 5.9.5 py310h1fa729e_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge py3dmol 2.0.1.post1 pypi_0 pypi pycairo 1.23.0 py310hb8a676c_0 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pydantic 1.10.7 py310h1fa729e_0 conda-forge pyedr 0.7.1 pyhd8ed1ab_0 conda-forge pygments 2.15.0 pyhd8ed1ab_0 conda-forge pymbar 3.1.1 py310hde88566_2 conda-forge pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pyrsistent 0.19.3 py310h1fa729e_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytables 3.7.0 py310hb60b9b2_3 conda-forge python 3.10.10 he550d4f_0_cpython conda-forge python-constraint 1.4.0 py_0 conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 3_cp310 conda-forge pytraj 2.0.6 pypi_0 pypi pytz 2023.3 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py310h5764c6d_5 conda-forge pyzmq 25.0.2 py310h059b190_0 conda-forge rdkit 2022.09.1 py310h10c98a6_0 conda-forge readline 8.2 h8228510_1 conda-forge reportlab 3.6.12 py310h46e8714_2 conda-forge requests 2.28.2 pyhd8ed1ab_1 conda-forge rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge sander 22.0 pypi_0 pypi scipy 1.10.1 py310h8deb116_0 conda-forge send2trash 1.8.0 pyhd8ed1ab_0 conda-forge setuptools 67.6.1 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge smirnoff99frosst 1.1.0 pyh44b312d_0 conda-forge snappy 1.1.10 h9fff704_0 conda-forge sniffio 1.3.0 pyhd8ed1ab_0 conda-forge soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge sqlalchemy 2.0.9 py310h1fa729e_0 conda-forge stack_data 0.6.2 pyhd8ed1ab_0 conda-forge terminado 0.17.1 pyh41d4057_0 conda-forge tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge tinydb 4.7.1 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tornado 6.3 py310h1fa729e_0 conda-forge tqdm 4.65.0 pyhd8ed1ab_1 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge typing-extensions 4.5.0 hd8ed1ab_0 conda-forge typing_extensions 4.5.0 pyha770c72_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge unicodedata2 15.0.0 py310h5764c6d_0 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge validators 0.20.0 pyhd8ed1ab_0 conda-forge wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 py_1 conda-forge websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge widgetsnbextension 3.6.4 pyhd8ed1ab_0 conda-forge xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.4 h0b41bf4_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.2.1 h7f98852_2 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 4.3.4 h9c3ff4c_1 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge ```
ijpulidos commented 1 year ago

Oh, I've been trying to get an example on how to reproduce this error because other users have also encountered it. Can you please share the scripts and data to reproduce this? It should help us test and debug behavior when we work on #672 . Thanks for reporting!

ijpulidos commented 1 year ago

Oh, haha, I am blind, i see the code now. Sorry!

IAlibay commented 1 year ago

As per a slack conversation with @ijpulidos, I tested also this on OpenMM 7.7 and it also fails there (i.e. it fails on both 8 and 7.7)