Poor GPU utilisation in toolkit example

[tdudgeon]

Describe the bug When running the toolkit showcase notebook I'm seeing very low GPU utilisation. In contrast, when running a MD simulation using just OpenMM tooling (e.g. SystemGenerator and Modeller) close to 100% utilisation is seen. The force fields used are not the same (OpenMM system using amber/ff14SB.xml, gaff-2.11 and amber/tip3p_standard.xml), but either the force fields or the process of generating the OpenMM System using Interchange seems to result in very sub-optimal performance.

To Reproduce Run the notebook as described.

Output nvidia-smi shows GPU utilisation fluctuating, usually in single figures and never more than 15%

Computing environment (please complete the following information): Ubuntu 23.04 GeoForce RTX 3060 GPU Browser: Chrome 116.0.5845.140 (Official Build) (64-bit) Python 3.11.5 Output of running conda list:

# packages in environment at /home/timbo/miniconda3/envs/openff-toolkit-examples:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
ambertools                23.3            py311hbcc7a2f_2    conda-forge
amberutils                21.0                     pypi_0    pypi
anyio                     4.0.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py311hd4cff14_3    conda-forge
arpack                    3.7.0                hdefa2d7_2    conda-forge
arrow                     1.2.3              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.0              pyhd8ed1ab_0    conda-forge
astunparse                1.6.3              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
aws-c-auth                0.7.3                he2921ad_3    conda-forge
aws-c-cal                 0.6.2                hc309b26_0    conda-forge
aws-c-common              0.9.0                hd590300_0    conda-forge
aws-c-compression         0.2.17               h4d4d85c_2    conda-forge
aws-c-event-stream        0.3.2                h2e3709c_0    conda-forge
aws-c-http                0.7.12               hc865f51_1    conda-forge
aws-c-io                  0.13.32              h1a03231_3    conda-forge
aws-c-mqtt                0.9.5                h3a0376c_1    conda-forge
aws-c-s3                  0.3.17               h1678ad6_0    conda-forge
aws-c-sdkutils            0.1.12               h4d4d85c_1    conda-forge
aws-checksums             0.1.17               h4d4d85c_1    conda-forge
aws-crt-cpp               0.23.1               hffbee3f_1    conda-forge
aws-sdk-cpp               1.11.156             he6c2984_2    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               h0f2a231_0    conda-forge
boost                     1.78.0          py311h59ea3da_4    conda-forge
boost-cpp                 1.78.0               h2c5509c_4    conda-forge
brotli                    1.1.0                hd590300_0    conda-forge
brotli-bin                1.1.0                hd590300_0    conda-forge
brotli-python             1.1.0           py311hb755f60_0    conda-forge
bson                      0.5.9                      py_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.19.1               hd590300_0    conda-forge
c-blosc2                  2.10.2               hb4ffafa_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.3.1              pyhd8ed1ab_0    conda-forge
cairo                     1.16.0            h0c91306_1017    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py311h409f033_3    conda-forge
charset-normalizer        3.2.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.4              pyhd8ed1ab_0    conda-forge
contourpy                 1.1.1           py311h9547e67_0    conda-forge
cudatoolkit               11.8.0              h4ba93d1_12    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
debugpy                   1.8.0           py311hb755f60_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            1.1.3              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_108    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                 4.42.1          py311h459d7ec_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
gettext                   0.21.1               h27087fc_0    conda-forge
gflags                    2.2.2             he1b5a44_1004    conda-forge
glog                      0.6.0                h6f12383_0    conda-forge
greenlet                  2.0.2           py311hb755f60_1    conda-forge
h5py                      3.9.0           nompi_py311h3839ddf_102    conda-forge
hdf4                      4.2.15               h501b40f_6    conda-forge
hdf5                      1.14.2          nompi_h4f84152_100    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
importlib_resources       6.0.1              pyhd8ed1ab_0    conda-forge
ipykernel                 6.25.2             pyh2140261_0    conda-forge
ipython                   8.15.0             pyh0d859eb_0    conda-forge
ipywidgets                8.1.1              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.0             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
json5                     0.9.14             pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py311h38be061_2    conda-forge
jsonschema                4.19.0             pyhd8ed1ab_1    conda-forge
jsonschema-specifications 2023.7.1           pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.19.0             pyhd8ed1ab_1    conda-forge
jupyter-lsp               2.2.0              pyhd8ed1ab_0    conda-forge
jupyter_client            8.3.1              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.1           py311h38be061_0    conda-forge
jupyter_events            0.7.0              pyhd8ed1ab_2    conda-forge
jupyter_server            2.7.3              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab                4.0.6              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.25.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.9              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py311h9547e67_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
lcms2                     2.15                 h7f713cb_2    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20230802.0      cxx17_h59595ed_3    conda-forge
libaec                    1.0.6                hcb278e6_1    conda-forge
libarrow                  13.0.0           h1935d02_4_cpu    conda-forge
libblas                   3.9.0           18_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_0    conda-forge
libbrotlidec              1.1.0                hd590300_0    conda-forge
libbrotlienc              1.1.0                hd590300_0    conda-forge
libcblas                  3.9.0           18_linux64_openblas    conda-forge
libcrc32c                 1.1.2                h9c3ff4c_0    conda-forge
libcurl                   8.3.0                hca28451_0    conda-forge
libdeflate                1.19                 hd590300_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libevent                  2.1.12               hf998b51_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_1    conda-forge
libgfortran-ng            13.2.0               h69a702a_1    conda-forge
libgfortran5              13.2.0               ha4646dd_1    conda-forge
libglib                   2.78.0               hebfc3b9_0    conda-forge
libgomp                   13.2.0               h807b86a_1    conda-forge
libgoogle-cloud           2.12.0               h8d7e28b_2    conda-forge
libgrpc                   1.57.0               ha4d0f93_1    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             2.1.5.1              hd590300_1    conda-forge
liblapack                 3.9.0           18_linux64_openblas    conda-forge
libnetcdf                 4.9.2           nompi_h80fb2b6_112    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libnuma                   2.0.16               h0b41bf4_1    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libprotobuf               4.23.4               hf27288f_6    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.43.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_1    conda-forge
libthrift                 0.19.0               h8fd135c_0    conda-forge
libtiff                   4.6.0                h29866fb_1    conda-forge
libutf8proc               2.8.0                h166bdaf_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libxslt                   1.1.37               h0054252_1    conda-forge
libzip                    1.10.1               h2629f0a_3    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lxml                      4.9.3           py311h1a07684_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.1.3           py311h459d7ec_0    conda-forge
matplotlib-base           3.7.2           py311h54ef318_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mda-xdrlib                0.2.0              pyhd8ed1ab_0    conda-forge
mdtraj                    1.9.9           py311h90fe790_0    conda-forge
mistune                   3.0.1              pyhd8ed1ab_0    conda-forge
mmpbsa-py                 16.0                     pypi_0    pypi
msgpack-python            1.0.5           py311ha3edf6b_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.8.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
netcdf-fortran            4.6.1           nompi_hacb5139_102    conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
nglview                   3.0.8              pyh1da8cd4_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
notebook                  7.0.3              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numexpr                   2.8.4           py311h039bad6_101    conda-forge
numpy                     1.26.0          py311h64a7726_0    conda-forge
ocl-icd                   2.3.1                h7f98852_0    conda-forge
ocl-icd-system            1.0.0                         1    conda-forge
openff-amber-ff-ports     0.0.3              pyh6c4a22f_0    conda-forge
openff-forcefields        2023.08.0          pyh1a96a4e_0    conda-forge
openff-interchange        0.3.14             pyhd8ed1ab_0    conda-forge
openff-interchange-base   0.3.14             pyhd8ed1ab_0    conda-forge
openff-models             0.1.0              pyh1a96a4e_1    conda-forge
openff-toolkit            0.14.3             pyhd8ed1ab_0    conda-forge
openff-toolkit-base       0.14.3             pyhd8ed1ab_0    conda-forge
openff-toolkit-examples   0.14.3               hd8ed1ab_0    conda-forge
openff-units              0.2.1              pyh1a96a4e_0    conda-forge
openff-utilities          0.1.9              pyh1a96a4e_0    conda-forge
openjpeg                  2.5.0                h488ebb8_3    conda-forge
openmm                    8.0.0           py311h59c6c42_1    conda-forge
openmmforcefields         0.11.2             pyhd8ed1ab_1    conda-forge
openssl                   3.1.2                hd590300_0    conda-forge
orc                       1.9.0                h52d3b3c_2    conda-forge
overrides                 7.4.0              pyhd8ed1ab_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h86c2bf4_0    conda-forge
packmol-memgen            2023.2.24                pypi_0    pypi
pandas                    2.1.0           py311h320fe9a_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panedr                    0.7.2              pyhd8ed1ab_0    conda-forge
parmed                    4.1.0           py311hcafe171_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                  1.9                pyh1a96a4e_0    conda-forge
perl                      5.32.1          4_hd590300_perl5    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.0.1          py311h8aef010_0    conda-forge
pint                      0.21               pyhd8ed1ab_0    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              3.10.0             pyhd8ed1ab_0    conda-forge
plotly                    5.17.0             pyhd8ed1ab_0    conda-forge
prometheus_client         0.17.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.39             pyha770c72_0    conda-forge
prompt_toolkit            3.0.39               hd8ed1ab_0    conda-forge
psutil                    5.9.5           py311h2582759_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
py-cpuinfo                9.0.0              pyhd8ed1ab_0    conda-forge
pyarrow                   13.0.0          py311h39c9aba_4_cpu    conda-forge
pycairo                   1.24.0          py311h8feb60e_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pydantic                  1.10.12         py311h459d7ec_1    conda-forge
pyedr                     0.7.2              pyhd8ed1ab_0    conda-forge
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pymsmt                    22.0                     pypi_0    pypi
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.8.0           py311h10c7f7f_3    conda-forge
python                    3.11.5          hab00c5b_0_cpython    conda-forge
python-constraint         1.4.0                      py_0    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.18.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.11                    3_cp311    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py311h459d7ec_0    conda-forge
pyzmq                     25.1.1          py311h75c88c4_0    conda-forge
qcelemental               0.26.0             pyhd8ed1ab_0    conda-forge
qcengine                  0.28.1             pyhd8ed1ab_0    conda-forge
qcportal                  0.15.8             pyhd8ed1ab_0    conda-forge
rdkit                     2023.03.3       py311hc21844d_0    conda-forge
rdma-core                 28.9                 h59595ed_1    conda-forge
re2                       2023.03.02           h8c504da_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.30.2             pyhd8ed1ab_0    conda-forge
reportlab                 4.0.4           py311h459d7ec_0    conda-forge
requests                  2.31.0             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                   0.10.3          py311h46250e7_0    conda-forge
s2n                       1.3.51               h06160fa_0    conda-forge
sander                    22.0                     pypi_0    pypi
scipy                     1.11.2          py311h64a7726_1    conda-forge
send2trash                1.8.2              pyh41d4057_0    conda-forge
setuptools                68.2.2             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                 2.5                pyhd8ed1ab_1    conda-forge
sqlalchemy                2.0.20          py311h459d7ec_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
tenacity                  8.2.3              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tinydb                    4.8.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.3.3           py311h459d7ec_0    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.10.0             pyhd8ed1ab_0    conda-forge
typing-extensions         4.7.1                hd8ed1ab_0    conda-forge
typing_extensions         4.7.1              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
ucx                       1.14.1               h64cca9d_4    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.0.4              pyhd8ed1ab_0    conda-forge
validators                0.22.0             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.6.3              pyhd8ed1ab_0    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.9              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               1.8.6                h8ee46fc_0    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                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.16.2             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zlib-ng                   2.0.7                h0b41bf4_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

[mattwthompson]

I'm not sure efficient hardware usage is really in the scope of that example. I think the

simulation.context.setVelocitiesToTemperature(300 * openmm_unit.kelvin)
simulation.runForClockTime(1.0 * openmm_unit.minute)

cell is just mean to show that it can run and produce sane-looking results to start out a simulation.

That being said, there isn't any fundamental reason why one system maxes GPU utilization and a similar one doesn't. The different code paths should be making objects that only differ in minutiae like the particle parameters. Without CUDA hardware I can't do much more than i.e. guess something is wrong with the platform and OpenMM isn't seeing the GPU at all.

[ijpulidos]

I can reproduce it locally with CUDA hardware. I could detect that the DCDReporter was saving the trajectory too often (every 10 steps). This cripples the performance because it's doing more IO (saving the trajectory) than actually computing stuff, if you just increase the number of steps for writing the trajectory (say to something like 100 or 200), you should be able to see that the usage of the GPU goes up to ~90% (depending on the GPU of course).

I hope this helps answering the question, I don't see a real issue other than we might want to increase the number of steps in the reporter for the showcase.

[tdudgeon]

Confirmed. The reporting interval is much too low.

[mattwthompson]

Thanks Ivan! That definitely makes sense. I think the reason for such frequent writing is to ensure that a minute on a user's laptop produces enough frames to see that something is moving. I suspect your workstations hooked up to a GPU can still get a decent-looking trajectory with a more reasonable frequency. We'd want to run this on low-end hardware to see how many steps of that complex can run in a minute of wall time.

[ijpulidos]

@mattwthompson Yeah, I suspected that's the reason as well. That makes sense.

[mattwthompson]

I think the example could be updated with a brief explanation of why it was set to 10 and a suggestion that the user increase it to 100, 1000, or something like that if they have a GPU hooked up. This could probably be done automatically, I don't feel strongly about either approach.

[mattwthompson]

In #1743 - likely to be merged within 12 hours, and included in a 0.14.5 release - I've made the following changes that should make the toolkit showcase a bit smoother in that cell:

• By default, frames are written every 100 steps. This should push the CPU time away from reporting and towards for calculations, but still provide a decent number of frame (at least double digits) even with older hardware
• An attempt is made to detect whether or not OpenMM is CUDA-enabled (openmm.Platform.getPlatformByName("CUDA") does not raise an exception) in which case the stride is extended to 1000. I don't have an NVIDIA GPU wired up to my development setup, so this is just a guess. It's plausible this is still too low but I expect it should be an improvement over 10, which looks almost comical with the benefit of hindsight and this investigation.

This should better utilize a GPU if one is found - and there should also be a nice improvement when one isn't found. It's pretty cool to find a fix that's wider in scope than the original problem.