FIREMinimizationIntegrator fails on explicitly solvated system using CPU platform
IAlibay opened this issue · 3 comments
IAlibay commented
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:
# 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-forgeijpulidos commented
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
Oh, haha, I am blind, i see the code now. Sorry!
IAlibay commented
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)