Installing development version of OpenMM

[Nicholas Schafer]

This is a follow-up to a question posed here: viewtopicPhpbb.php?f=161&t=9915&p=0&sta ... 26f642dcfe

The topic is unrelated to the original post, so I thought I would follow up in a new thread.

I have tried installing the development version of OpenMM using

Code: Select all

conda install -c omnia fftw3f
conda install -c omnia-dev openmm

on three separate systems in either a new conda environment or a completely clean system (Windows with Linux subsystem, MacOS X, and Ubuntu) and, in every case, the command

Code: Select all

python -m simtk.testInstallation

gives the error

Code: Select all

python: Error while finding module specification for 'simtk.testInstallation' (ModuleNotFoundError: no module named 'simtk')

Can you please advise re: what might be going wrong with the Conda installation of the development version?

Much appreciated,
Nick

[John Chodera]

It appears the dev builds have been failing due to the development recipe not installing cython.
From the travis build logs, https://api.travis-ci.org/v3/job/473543664/log.txt:

Code: Select all

OPENMM_LIB_PATH = /opt/conda/conda-bld/openmm_1546167745162/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib

OPENMM_INCLUDE_PATH = /opt/conda/conda-bld/openmm_1546167745162/work/./include/opt/conda/conda-bld/openmm_1546167745162/work/./include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/./include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/openmmapi/include/opt/conda/conda-bld/openmm_1546167745162/work/openmmapi/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/openmmapi/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/olla/include/opt/conda/conda-bld/openmm_1546167745162/work/olla/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/olla/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/serialization/include/opt/conda/conda-bld/openmm_1546167745162/work/serialization/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/serialization/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/plugins/amoeba/openmmapi/include/opt/conda/conda-bld/openmm_1546167745162/work/plugins/amoeba/openmmapi/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/plugins/amoeba/openmmapi/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/plugins/rpmd/openmmapi/include/opt/conda/conda-bld/openmm_1546167745162/work/plugins/rpmd/openmmapi/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/plugins/rpmd/openmmapi/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/plugins/drude/openmmapi/include/opt/conda/conda-bld/openmm_1546167745162/work/plugins/drude/openmmapi/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/plugins/drude/openmmapi/include/openmm/internal

Traceback (most recent call last):

  File "setup.py", line 11, in <module>

    from Cython.Build import cythonize

ModuleNotFoundError: No module named 'Cython'

[ 46%] Installing OpenMM Python binary module...

OPENMM_LIB_PATH = /opt/conda/conda-bld/openmm_1546167745162/_b_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib

OPENMM_INCLUDE_PATH = /opt/conda/conda-bld/openmm_1546167745162/work/./include/opt/conda/conda-bld/openmm_1546167745162/work/./include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/./include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/openmmapi/include/opt/conda/conda-bld/openmm_1546167745162/work/openmmapi/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/openmmapi/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/olla/include/opt/conda/conda-bld/openmm_1546167745162/work/olla/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/olla/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/serialization/include/opt/conda/conda-bld/openmm_1546167745162/work/serialization/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/serialization/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/plugins/amoeba/openmmapi/include/opt/conda/conda-bld/openmm_1546167745162/work/plugins/amoeba/openmmapi/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/plugins/amoeba/openmmapi/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/plugins/rpmd/openmmapi/include/opt/conda/conda-bld/openmm_1546167745162/work/plugins/rpmd/openmmapi/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/plugins/rpmd/openmmapi/include/openmm/internal/opt/conda/conda-bld/openmm_1546167745162/work/plugins/drude/openmmapi/include/opt/conda/conda-bld/openmm_1546167745162/work/plugins/drude/openmmapi/include/openmm/opt/conda/conda-bld/openmm_1546167745162/work/plugins/drude/openmmapi/include/openmm/internal

Traceback (most recent call last):

  File "setup.py", line 11, in <module>

    from Cython.Build import cythonize

ModuleNotFoundError: No module named 'Cython'

This must have been introduced when https://github.com/pandegroup/openmm/pull/2184 was merged.

I think I can fix this by updating the conda dev recipe to include cython.

More generally, it would be great if all issues could be reported directly in the GitHub Issue Tracker:

http://github.com/pandegroup/openmm/issues

[John Chodera]

Here's the new PR to fix: https://github.com/omnia-md/conda-dev-recipes/pull/158

I'll hopefully have this tested, merged, and new packages pushed tonight.

[John Chodera]

The corrected dev packages are now being pushed.

Code: Select all

[chodera@lilac:chodera]$ python -m simtk.testInstallation

OpenMM Version: 7.3
Git Revision: bd66a7b92df724d59be3330fd23a1450982051c5

There are 4 Platforms available:

1 Reference - Successfully computed forces
2 CPU - Successfully computed forces
3 CUDA - Successfully computed forces
4 OpenCL - Successfully computed forces

Median difference in forces between platforms:

Reference vs. CPU: 6.30075e-06
Reference vs. CUDA: 6.72964e-06
CPU vs. CUDA: 7.81341e-07
Reference vs. OpenCL: 6.75426e-06
CPU vs. OpenCL: 8.2127e-07
CUDA vs. OpenCL: 2.15057e-07

All differences are within tolerance.

[Matthew Chen]

Hi Dr. Chodera,

We have tried, but still met with the same problem...

Could you help look into this matter?

Thanks and Best,