OpenMM 7.7

[Peter Eastman]

OpenMM 7.7 is now released! The release notes are at https://github.com/openmm/openmm/releases/tag/7.7.0. You can install it with the command

Code: Select all

conda install -c conda-forge openmm

Merry Christmas!

[Elsaid Mohamed]

Hi,

I did install that in conda, it gives me "ModuleNotFoundError: No module named 'openmm'"
The version of openmm in conda enviroment is 7.5.1, and I failed to update it!

Thanks in advance

[Peter Eastman]

What output does the following give?

Code: Select all

conda install -c conda-forge openmm=7.7.0

[Elsaid Mohamed]

Hi,
There is no openmm in the installed packages. I just downloaded and installed fresh version of anaconda.
It gives

"UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

- alabaster -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|3.4.*|>=3.7,<3.8.0a0']
- anaconda==2021.11 -> python[version='3.7.11|3.9.7|3.8.12',build='h12debd9_1|h12debd9_0|h12debd9_0']
- appdirs -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.5,<3.6.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0']
- argon2-cffi -> python[version='2.7.*|3.5.*|3.6.*|3.6.12|3.6.12|3.7.10|3.7.10|3.7.12|3.7.9|3.6.9|3.6.9|3.6.9|3.6.9|>=3.5,<3.6.0a0|3.4.*|3.7.*|3.8.*|3.9.*|3.10.*',build='0_73_pypy|3_73_pypy|4_73_pypy|5_73_pypy|5_73_pypy|0_73_pypy|0_73_pypy|1_73_pypy|2_73_pypy|1_73_pypy']
- asn1crypto -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- asn1crypto -> python[version='3.7.*|3.8.*']
- atomicwrites -> python[version='2.7.*|3.5.*|3.6.*|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- backcall -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0']
- backports -> python[version='2.7.*|3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0']
- backports.shutil_get_terminal_size -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0']
- binaryornot -> python[version='2.7.*|3.5.*|3.6.*|3.4.*']
- bkcharts -> python[version='3.4.*|>=3.10,<3.11.0a0|>=3.7.1,<3.8.0a0']
- brotlipy -> python[version='3.10.*|3.4.*|3.6.12|3.6.12|3.7.10|3.7.10|3.7.12|3.7.9|3.6.9|3.6.9|3.6.9|3.6.9|3.9.*|3.8.*|3.7.*',build='0_73_pypy|3_73_pypy|4_73_pypy|5_73_pypy|5_73_pypy|0_73_pypy|0_73_pypy|1_73_pypy|2_73_pypy|1_73_pypy']
- cached-property -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0']
- cffi -> python[version='2.7.*|3.5.*|3.6.*|3.6.12|3.6.12|3.7.10|3.7.10|3.7.12|>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.6,<3.7.0a0|3.7.9|3.6.9|3.6.9|3.6.9|>=2.7,<2.8.0a0|3.6.9|>=3.5,<3.6.0a0|3.4.*',build='0_73_pypy|3_73_pypy|4_73_pypy|5_73_pypy|5_73_pypy|0_73_pypy|0_73_pypy|1_73_pypy|2_73_pypy|1_73_pypy']
- clyent -> python[version='>=3.10,<3.11.0a0']
- colorama -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- conda-env -> python[version='2.7.*|3.4.*|3.5.*']
- conda-pack -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- cryptography -> python[version='3.10.*|3.6.12|3.6.12|3.7.10|3.7.10|3.7.12|3.7.9|3.6.9|3.6.9|3.6.9|3.6.9|3.9.*|3.8.*|3.7.*|3.4.*|>=3.5|<=3.3',build='0_73_pypy|3_73_pypy|4_73_pypy|5_73_pypy|5_73_pypy|0_73_pypy|0_73_pypy|1_73_pypy|2_73_pypy|1_73_pypy']
- diff-match-patch -> python[version='2.7.*|3.4.*|3.5.*|3.6.*']
- get_terminal_size -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0']
- gevent -> python[version='3.10.*|3.6.12|3.6.12|3.7.10|3.7.10|3.7.12|3.7.9|3.6.9|3.6.9|3.6.9|3.6.9|3.4.*|3.7.*|3.9.*|3.8.*',build='0_73_pypy|3_73_pypy|4_73_pypy|5_73_pypy|5_73_pypy|0_73_pypy|0_73_pypy|1_73_pypy|2_73_pypy|1_73_pypy']
- glib -> python[version='2.7.*|3.6.*|3.7.*|3.8.*']
- glob2 -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- heapdict -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0']
- html5lib -> python[version='2.7.*|3.5.*|3.6.*|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0']
- importlib_metadata -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0']
- intervaltree -> python[version='2.7.*|3.5.*|3.6.*']
- ipython_genutils -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=3.8,<3.9.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
- jdcal -> python[version='2.7.*|3.5.*|3.6.*|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.5,<3.6.0a0']
- jinja2-time -> python[version='2.7.*|3.5.*|3.6.*|3.4.*']
- mpmath -> python[version='>=3.10,<3.11.0a0']
- olefile -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0']
- patsy -> python[version='>=3.10,<3.11.0a0']
- pexpect -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|3.4.*']
- pexpect -> python[version='3.7.*|3.8.*']
- poyo -> python[version='2.7.*|3.5.*|3.6.*|3.4.*']
- ptyprocess -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|3.4.*|>=3.8,<3.9.0a0']
- pyls-spyder -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.5,<3.6.0a0']
- singledispatch -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.8,<3.9.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
- sortedcollections -> python[version='>=3.8,<3.9.0a0']
- text-unidecode -> python[version='>=2.7,<2.8.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0']
- three-merge -> python[version='2.7.*|3.4.*|3.5.*|3.6.*']
- wcwidth -> python[version='2.7.*|3.4.*|3.5.*|3.6.*|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0']
- whichcraft -> python[version='2.7.*|3.5.*|3.6.*|3.4.*']
- xmltodict -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.5,<3.6.0a0|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0']
- zict -> python[version='2.7.*|3.5.*|3.6.*|3.4.*|>=3.6,<3.7.0a0|>=2.7,<2.8.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
- zict -> python[version='>=3.8,<3.9.0a0']
- zope.event -> python[version='2.7.*|3.5.*|3.6.*|>=3.10,<3.11.0a0|>=3.5,<3.6.0a0|3.4.*']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package pip conflicts for:
brotlipy -> python[version='>=3.10,<3.11.0a0'] -> pip
tornado -> python[version='>=3.7,<3.8.0a0'] -> pip
jupyter_console -> python[version='>=3.6'] -> pip
wheel -> python[version='!=3.0,!=3.1,!=3.2,!=3.3,!=3.4'] -> pip
python-slugify -> python[version='>=3.6'] -> pip
seaborn -> python[version='>=3.6'] -> pip
certifi -> python[version='>=3.7,<3.8.0a0'] -> pip
backports.tempfile -> python -> pip
ruamel_yaml -> python[version='>=3.7,<3.8.0a0'] -> pip
ply -> python -> pip
sqlalchemy -> python[version='>=3.9,<3.10.0a0'] -> pip
xlrd -> python[version='>=3.6'] -> pip
pexpect -> python -> pip
mistune -> python[version='>=2.7'] -> pip
babel -> python -> pip
black -> python[version='>=3.6'] -> pip
qtconsole -> python[version='>=3.6'] -> pip
soupsieve -> python[version='>=3.6'] -> pip
mypy_extensions -> python[version='>=3.9,<3.10.0a0'] -> pip
navigator-updater -> python[version='>=3.9,<3.10.0a0'] -> pip
ujson -> python[version='>=3.10,<3.11.0a0'] -> pip
parso -> python[version='>=3.6'] -> pip
regex -> python[version='>=3.10,<3.11.0a0'] -> pip
pygments -> python[version='>=3.6'] -> pip
conda-package-handling -> python[version='>=3.7,<3.8.0a0'] -> pip
cloudpickle -> python[version='>=3.6'] -> pip
multipledispatch -> python -> pip
jeepney -> python[version='>=3.5'] -> pip
xlwt -> python -> pip
ipython -> python[version='>=3.10,<3.11.0a0'] -> pip
conda-verify -> python[version='>=3.7,<3.8.0a0'] -> pip
anaconda==2021.11 -> pip[version='21.2.2|21.2.4|21.2.4',build='py39h06a4308_0|py37h06a4308_0|py38h06a4308_0']
sphinx -> python[version='>=3.6'] -> pip
tqdm -> python[version='>=2.7'] -> pip
sphinxcontrib-htmlhelp -> python[version='>=3.5'] -> pip
sniffio -> python[version='>=3.7,<3.8.0a0'] -> pip
mccabe -> python -> pip
jsonschema -> python[version='>=3.7'] -> pip
.......
.........>=9.3.0'] -> __glibc[version='>=2.17']
- libuv -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- libwebp -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- libwebp-base -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- libxcb -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- libxml2 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- libxslt -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- libzopfli -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- llvmlite -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- lxml -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- lz4-c -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- lzo -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- markupsafe -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- matplotlib -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- matplotlib-base -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- mistune -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- mkl-service -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- mkl_fft -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- mkl_random -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- mpc -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- mpfr -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- mpich -> libgfortran-ng -> __glibc[version='>=2.17']
- msgpack-python -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- ncurses -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- numba -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- numexpr -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- numpy -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- numpy-base -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- openjpeg -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- openmm=7.7.0 -> __glibc[version='>=2.17']
- openmm=7.7.0 -> cudatoolkit[version='11.0|11.0.*'] -> __glibc[version='>=2.17,<3.0.a0']
- openssl -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pandas -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pango -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- patchelf -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- pcre -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pillow -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pixman -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- psutil -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- py-lief -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pycosat -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pycurl -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pyerfa -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pyodbc -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pyqt -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- pyrsistent -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pytables -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- python=3.9 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pywavelets -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pyyaml -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- pyzmq -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- qt -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- readline -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- regex -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- ripgrep -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- ruamel_yaml -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- scikit-image -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- scikit-learn -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- scipy -> libgfortran-ng -> __glibc[version='>=2.17']
- sip -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- snappy -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- sqlalchemy -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- sqlite -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- statsmodels -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- tbb -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- tbb4py -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- tifffile -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']
- tk -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- tornado -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- typed-ast -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- ujson -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- unixodbc -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- wrapt -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- xz -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- yaml -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- zeromq -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- zfp -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- zlib -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- zope.interface -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']
- zstd -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.31


"

[Peter Eastman]

You're running into an incompatibility with something else you already have installed in the environment. I suggest creating a new environment to install into:

Code: Select all

conda create --name openmm python=3.9
conda activate openmm
conda install -c conda-forge openmm

[Elsaid Mohamed]

Thanks, it works.

[Josh Buckner]

I would like to report an issue with the file

OpenMMFortranModule.f90

that is generated when building OpenMM from source and is also included in the conda package.

This file contains three lines in which the result of an interface subroutine is declared as
'long long'

This is not a valid fortran type and causes the fortran compiler to error out.

Changing the three lines from 'long long' to 'integer(...)' solves the problem.

Should I submit a formal bug report elsewhere?