This can totally be due to the new ambermini restrictions introduced in https://github.com/conda-forge/ambertools-feedstock/pull/29.

Can you paste the output of conda list?

jaimergp on 13 Apr 2020

Here is the output of conda list:

packages in environment at /home/kael/anaconda3:

#

Kael-the-Mad on 13 Apr 2020

Hm, that output shows v0.6.0?

openforcefield 0.6.0 py37_1

jaimergp on 13 Apr 2020

No, I manually installed the downloaded v0.6.0 from Anaconda Cloud.
The current list is twisted by me ...

Please note that I firstly installed the ambertools via Anaconda (python 3.7.6) binary,
then RDKit,
then OpenMM.
The openforcefield was installed after the above packages.
(There seems to be no "ambermini" in my installation)
I thought the package dependencies could be solved automatically.
*
Here is my solution, and it works for the runing of ethanol and cyclohexane case:
Download version 0.6.0 tar
Download the versioin 0.6.0 openforcefield and install it locally.

Kael-the-Mad on 13 Apr 2020

Here is the output of conda install openforcefield again (just print the solved environment)

$ conda install openforcefield
Collecting package metadata (current_repodata.json): done
Solving environment: | 
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - <unknown>/linux-64::openforcefield==0.6.0=py37_1                                                         done

## Package Plan ##

  environment location: /home/kael/anaconda3

  added / updated specs:
    - openforcefield

The following packages will be SUPERSEDED by a higher-priority channel:

openforcefield ::openforcefield-0.6.0-py37_1 --> omnia::openforcefield-0.0.4-py37_1

Kael-the-Mad on 13 Apr 2020

I see! I am adding tests for this scenario in #577.

In the meantime, I could create a new environment that correctly installs v0.6:

$ conda create -n openff576 openforcefield

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/jaime/.conda/envs/openff576

  added / updated specs:
    - openforcefield


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ambertools-19.11           |   py37h00db77c_5        74.5 MB  conda-forge
    boost-1.72.0               |   py37h9de70de_0         316 KB  conda-forge
    boost-cpp-1.72.0           |       h8e57a91_0        21.8 MB  conda-forge
    cairo-1.16.0               |    hcf35c78_1003         1.5 MB  conda-forge
    glib-2.58.3                |py37he00f558_1004         3.3 MB  conda-forge
    libtiff-4.1.0              |       hc7e4089_6         668 KB  conda-forge
    libwebp-base-1.1.0         |       h516909a_3         845 KB  conda-forge
    llvm-openmp-10.0.0         |       hc9558a2_0         2.8 MB  conda-forge
    lz4-c-1.9.2                |       he1b5a44_0         223 KB  conda-forge
    mistune-0.8.4              |py37h8f50634_1001          53 KB  conda-forge
    nbconvert-5.6.1            |   py37hc8dfbb8_1         487 KB  conda-forge
    netcdf-fortran-4.5.2       |nompi_h45d7149_104         1.2 MB  conda-forge
    pillow-7.1.1               |   py37h718be6c_0         654 KB  conda-forge
    pycairo-1.19.1             |   py37h01af8b0_3          77 KB  conda-forge
    rdkit-2020.03.1            |   py37hdd87690_1        24.7 MB  conda-forge
    scipy-1.4.1                |   py37ha3d9a3c_3        18.8 MB  conda-forge
    urllib3-1.25.8             |   py37hc8dfbb8_1         160 KB  conda-forge
    yaml-0.2.3                 |       h516909a_0          82 KB  conda-forge
    zstd-1.4.4                 |       h6597ccf_3         991 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       153.0 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_llvm
  ambertools         conda-forge/linux-64::ambertools-19.11-py37h00db77c_5
  attrs              conda-forge/noarch::attrs-19.3.0-py_0
  backcall           conda-forge/noarch::backcall-0.1.0-py_0
  bleach             conda-forge/noarch::bleach-3.1.4-pyh9f0ad1d_0
  boost              conda-forge/linux-64::boost-1.72.0-py37h9de70de_0
  boost-cpp          conda-forge/linux-64::boost-cpp-1.72.0-h8e57a91_0
  bson               conda-forge/noarch::bson-0.5.9-py_0
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h516909a_2
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.4.5.1-hecc5488_0
  cairo              conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003
  certifi            conda-forge/linux-64::certifi-2020.4.5.1-py37hc8dfbb8_0
  cffi               conda-forge/linux-64::cffi-1.14.0-py37hd463f26_0
  chardet            conda-forge/linux-64::chardet-3.0.4-py37hc8dfbb8_1006
  cryptography       conda-forge/linux-64::cryptography-2.8-py37hb09aad4_2
  curl               conda-forge/linux-64::curl-7.69.1-h33f0ec9_0
  cycler             conda-forge/noarch::cycler-0.10.0-py_2
  cython             conda-forge/linux-64::cython-0.29.16-py37h3340039_0
  decorator          conda-forge/noarch::decorator-4.4.2-py_0
  defusedxml         conda-forge/noarch::defusedxml-0.6.0-py_0
  entrypoints        conda-forge/linux-64::entrypoints-0.3-py37hc8dfbb8_1001
  fftw               conda-forge/linux-64::fftw-3.3.8-nompi_h7f3a6c3_1110
  fftw3f             omnia/linux-64::fftw3f-3.3.4-2
  fontconfig         conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001
  freetype           conda-forge/linux-64::freetype-2.10.1-he06d7ca_0
  gettext            conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002
  glib               conda-forge/linux-64::glib-2.58.3-py37he00f558_1004
  hdf4               conda-forge/linux-64::hdf4-4.2.13-hf30be14_1003
  hdf5               conda-forge/linux-64::hdf5-1.10.5-nompi_h3c11f04_1104
  icu                conda-forge/linux-64::icu-64.2-he1b5a44_1
  idna               conda-forge/noarch::idna-2.9-py_1
  importlib-metadata conda-forge/linux-64::importlib-metadata-1.6.0-py37hc8dfbb8_0
  importlib_metadata conda-forge/noarch::importlib_metadata-1.6.0-0
  ipykernel          conda-forge/linux-64::ipykernel-5.2.0-py37h43977f1_1
  ipython            conda-forge/linux-64::ipython-7.13.0-py37hc8dfbb8_2
  ipython_genutils   conda-forge/noarch::ipython_genutils-0.2.0-py_1
  jedi               conda-forge/linux-64::jedi-0.16.0-py37hc8dfbb8_1
  jinja2             conda-forge/noarch::jinja2-2.11.1-py_0
  jpeg               conda-forge/linux-64::jpeg-9c-h14c3975_1001
  jsonschema         conda-forge/linux-64::jsonschema-3.2.0-py37hc8dfbb8_1
  jupyter_client     conda-forge/noarch::jupyter_client-6.1.2-py_0
  jupyter_core       conda-forge/linux-64::jupyter_core-4.6.3-py37hc8dfbb8_1
  kiwisolver         conda-forge/linux-64::kiwisolver-1.2.0-py37h99015e2_0
  krb5               conda-forge/linux-64::krb5-1.17.1-h2fd8d38_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_0
  libblas            conda-forge/linux-64::libblas-3.8.0-16_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-16_openblas
  libcurl            conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0
  libedit            conda-forge/linux-64::libedit-3.1.20170329-hf8c457e_1001
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.3.0-hdf63c60_5
  libgomp            conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2
  libiconv           conda-forge/linux-64::libiconv-1.15-h516909a_1006
  liblapack          conda-forge/linux-64::liblapack-3.8.0-16_openblas
  libnetcdf          conda-forge/linux-64::libnetcdf-4.7.4-nompi_h9f9fd6a_101
  libopenblas        conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0
  libpng             conda-forge/linux-64::libpng-1.6.37-hed695b0_1
  libsodium          conda-forge/linux-64::libsodium-1.0.17-h516909a_0
  libssh2            conda-forge/linux-64::libssh2-1.8.2-h22169c7_2
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2
  libtiff            conda-forge/linux-64::libtiff-4.1.0-hc7e4089_6
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
  libwebp-base       conda-forge/linux-64::libwebp-base-1.1.0-h516909a_3
  libxcb             conda-forge/linux-64::libxcb-1.13-h14c3975_1002
  libxml2            conda-forge/linux-64::libxml2-2.9.10-hee79883_0
  llvm-openmp        conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0
  lz4-c              conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_0
  markupsafe         conda-forge/linux-64::markupsafe-1.1.1-py37h8f50634_1
  matplotlib-base    conda-forge/linux-64::matplotlib-base-3.2.1-py37h30547a4_0
  mistune            conda-forge/linux-64::mistune-0.8.4-py37h8f50634_1001
  msgpack-python     conda-forge/linux-64::msgpack-python-1.0.0-py37h99015e2_1
  nbconvert          conda-forge/linux-64::nbconvert-5.6.1-py37hc8dfbb8_1
  nbformat           conda-forge/noarch::nbformat-5.0.4-py_0
  ncurses            conda-forge/linux-64::ncurses-6.1-hf484d3e_1002
  netcdf-fortran     conda-forge/linux-64::netcdf-fortran-4.5.2-nompi_h45d7149_104
  networkx           conda-forge/noarch::networkx-2.4-py_1
  notebook           conda-forge/linux-64::notebook-6.0.3-py37_0
  numpy              conda-forge/linux-64::numpy-1.18.1-py37h8960a57_1
  olefile            conda-forge/noarch::olefile-0.46-py_0
  openforcefield     omnia/linux-64::openforcefield-0.6.0-py37_1
  openforcefields    omnia/linux-64::openforcefields-1.1.0-py37_0
  openmm             omnia/linux-64::openmm-7.4.1-py37_cuda101_rc_1
  openssl            conda-forge/linux-64::openssl-1.1.1f-h516909a_0
  packaging          conda-forge/noarch::packaging-20.1-py_0
  pandas             conda-forge/linux-64::pandas-1.0.3-py37h0da4684_0
  pandoc             conda-forge/linux-64::pandoc-2.9.2-0
  pandocfilters      conda-forge/noarch::pandocfilters-1.4.2-py_1
  parso              conda-forge/noarch::parso-0.6.2-py_0
  pcre               conda-forge/linux-64::pcre-8.44-he1b5a44_0
  perl               conda-forge/linux-64::perl-5.26.2-h516909a_1006
  pexpect            conda-forge/linux-64::pexpect-4.8.0-py37hc8dfbb8_1
  pickleshare        conda-forge/linux-64::pickleshare-0.7.5-py37hc8dfbb8_1001
  pillow             conda-forge/linux-64::pillow-7.1.1-py37h718be6c_0
  pip                conda-forge/noarch::pip-20.0.2-py_2
  pixman             conda-forge/linux-64::pixman-0.38.0-h516909a_1003
  prometheus_client  conda-forge/noarch::prometheus_client-0.7.1-py_0
  prompt-toolkit     conda-forge/noarch::prompt-toolkit-3.0.5-py_0
  pthread-stubs      conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
  ptyprocess         conda-forge/noarch::ptyprocess-0.6.0-py_1001
  pycairo            conda-forge/linux-64::pycairo-1.19.1-py37h01af8b0_3
  pycparser          conda-forge/noarch::pycparser-2.20-py_0
  pygments           conda-forge/noarch::pygments-2.6.1-py_0
  pyopenssl          conda-forge/noarch::pyopenssl-19.1.0-py_1
  pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
  pyrsistent         conda-forge/linux-64::pyrsistent-0.16.0-py37h8f50634_0
  pysocks            conda-forge/linux-64::pysocks-1.7.1-py37hc8dfbb8_1
  python             conda-forge/linux-64::python-3.7.6-h8356626_5_cpython
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  pytz               conda-forge/noarch::pytz-2019.3-py_0
  pyyaml             conda-forge/linux-64::pyyaml-5.3.1-py37h8f50634_0
  pyzmq              conda-forge/linux-64::pyzmq-19.0.0-py37hac76be4_1
  rdkit              conda-forge/linux-64::rdkit-2020.03.1-py37hdd87690_1
  readline           conda-forge/linux-64::readline-8.0-hf8c457e_0
  requests           conda-forge/noarch::requests-2.23.0-pyh8c360ce_2
  scipy              conda-forge/linux-64::scipy-1.4.1-py37ha3d9a3c_3
  send2trash         conda-forge/noarch::send2trash-1.5.0-py_0
  setuptools         conda-forge/linux-64::setuptools-46.1.3-py37hc8dfbb8_0
  six                conda-forge/noarch::six-1.14.0-py_1
  smirnoff99frosst   omnia/linux-64::smirnoff99frosst-1.1.0-py37_1
  sqlite             conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0
  terminado          conda-forge/linux-64::terminado-0.8.3-py37hc8dfbb8_1
  testpath           conda-forge/noarch::testpath-0.4.4-py_0
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_0
  toml               conda-forge/noarch::toml-0.10.0-py_0
  tornado            conda-forge/linux-64::tornado-6.0.4-py37h8f50634_1
  traitlets          conda-forge/linux-64::traitlets-4.3.3-py37hc8dfbb8_1
  urllib3            conda-forge/linux-64::urllib3-1.25.8-py37hc8dfbb8_1
  wcwidth            conda-forge/noarch::wcwidth-0.1.9-pyh9f0ad1d_0
  webencodings       conda-forge/noarch::webencodings-0.5.1-py_1
  wheel              conda-forge/noarch::wheel-0.34.2-py_1
  xmltodict          conda-forge/noarch::xmltodict-0.12.0-py_0
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
  xorg-libice        conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0
  xorg-libxau        conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
  xorg-libxdmcp      conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002
  xorg-libxt         conda-forge/linux-64::xorg-libxt-1.2.0-h516909a_0
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002
  xorg-xproto        conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_0
  yaml               conda-forge/linux-64::yaml-0.2.3-h516909a_0
  zeromq             conda-forge/linux-64::zeromq-4.3.2-he1b5a44_2
  zipp               conda-forge/noarch::zipp-3.1.0-py_0
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1006
  zstd               conda-forge/linux-64::zstd-1.4.4-h6597ccf_3

jaimergp on 13 Apr 2020

How are your channels defined? Mine are:

$ conda config --show

[...]
channel_priority: flexible
channels:
  - conda-forge
  - defaults
  - omnia
[...]

jaimergp on 13 Apr 2020

channel_alias: https://conda.anaconda.org
channel_priority: flexible
channels:
  - conda-forge
  - omnia
  - defaults
client_ssl_cert: None
client_ssl_cert_key: None

Kael-the-Mad on 13 Apr 2020

Try putting omnia under defaults. You should see these contents in ~/.condarc.

jaimergp on 13 Apr 2020

No, it didn't work. Here is the conda config section after the reorder:

channel_alias: https://conda.anaconda.org
channel_priority: flexible
channels:
  - conda-forge
  - defaults
  - omnia
client_ssl_cert: None

here is the output of the conda install openforcefield:

Solving environment: - 
The environment is inconsistent, please check the package plan carefully
The following packages are causing the inconsistency:

  - <unknown>/linux-64::openforcefield==0.6.0=py37_1                                             done

## Package Plan ##

  environment location: /home/kael/anaconda3

  added / updated specs:
    - openforcefield


The following packages will be SUPERSEDED by a higher-priority channel:

  openforcefield     <unknown>::openforcefield-0.6.0-py37_1 --> omnia::openforcefield-0.0.4-py37_1

Kael-the-Mad on 13 Apr 2020

Can you try _creating a new environment_ instead of installing the package on the base one? That will make it easier for the dep solver:

conda create -n openforcefield openforcefield
conda activate openforcefield

jaimergp on 13 Apr 2020

Here is the output of conda create -n openforcefield openforcefield

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/kael/anaconda3/envs/openforcefield

  added / updated specs:
    - openforcefield


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _libgcc_mutex-0.1          |      conda_forge           3 KB  conda-forge
    _openmp_mutex-4.5          |           1_llvm           5 KB  conda-forge
    ambertools-19.11           |   py37h00db77c_5        74.5 MB  conda-forge
    backcall-0.1.0             |             py_0          13 KB  conda-forge
    bleach-3.1.4               |     pyh9f0ad1d_0         111 KB  conda-forge
    boost-1.72.0               |   py37h9de70de_0         316 KB  conda-forge
    boost-cpp-1.72.0           |       h8e57a91_0        21.8 MB  conda-forge
    bson-0.5.9                 |             py_0          14 KB  conda-forge
    bzip2-1.0.8                |       h516909a_2         396 KB  conda-forge
    ca-certificates-2020.4.5.1 |       hecc5488_0         146 KB  conda-forge
    cairo-1.16.0               |    hcf35c78_1003         1.5 MB  conda-forge
    certifi-2020.4.5.1         |   py37hc8dfbb8_0         151 KB  conda-forge
    cffi-1.14.0                |   py37hd463f26_0         221 KB  conda-forge
    chardet-3.0.4              |py37hc8dfbb8_1006         169 KB  conda-forge
    cryptography-2.8           |   py37hb09aad4_2         617 KB  conda-forge
    curl-7.69.1                |       h33f0ec9_0         137 KB  conda-forge
    cycler-0.10.0              |             py_2           9 KB  conda-forge
    cython-0.29.16             |   py37h3340039_0         2.2 MB  conda-forge
    decorator-4.4.2            |             py_0          11 KB  conda-forge
    entrypoints-0.3            |py37hc8dfbb8_1001          12 KB  conda-forge
    fftw-3.3.8                 |nompi_h7f3a6c3_1110         5.8 MB  conda-forge
    fontconfig-2.13.1          |    h86ecdb6_1001         340 KB  conda-forge
    freetype-2.10.1            |       he06d7ca_0         877 KB  conda-forge
    gettext-0.19.8.1           |    hc5be6a0_1002         3.6 MB  conda-forge
    glib-2.58.3                |py37he00f558_1004         3.3 MB  conda-forge
    hdf4-4.2.13                |    hf30be14_1003         964 KB  conda-forge
    hdf5-1.10.5                |nompi_h3c11f04_1104         3.1 MB  conda-forge
    icu-64.2                   |       he1b5a44_1        12.6 MB  conda-forge
    idna-2.9                   |             py_1          52 KB  conda-forge
    importlib-metadata-1.6.0   |   py37hc8dfbb8_0          43 KB  conda-forge
    importlib_metadata-1.6.0   |                0           3 KB  conda-forge
    ipykernel-5.2.0            |   py37h43977f1_1         161 KB  conda-forge
    ipython-7.13.0             |   py37hc8dfbb8_2         1.1 MB  conda-forge
    ipython_genutils-0.2.0     |             py_1          21 KB  conda-forge
    jedi-0.16.0                |   py37hc8dfbb8_1         778 KB  conda-forge
    jpeg-9c                    |    h14c3975_1001         251 KB  conda-forge
    jsonschema-3.2.0           |   py37hc8dfbb8_1          89 KB  conda-forge
    jupyter_client-6.1.2       |             py_0          74 KB  conda-forge
    jupyter_core-4.6.3         |   py37hc8dfbb8_1          71 KB  conda-forge
    kiwisolver-1.2.0           |   py37h99015e2_0          87 KB  conda-forge
    krb5-1.17.1                |       h2fd8d38_0         1.5 MB  conda-forge
    ld_impl_linux-64-2.34      |       h53a641e_0         616 KB  conda-forge
    libblas-3.8.0              |      16_openblas          10 KB  conda-forge
    libcblas-3.8.0             |      16_openblas          10 KB  conda-forge
    libcurl-7.69.1             |       hf7181ac_0         573 KB  conda-forge
    libedit-3.1.20170329       |    hf8c457e_1001         172 KB  conda-forge
    libffi-3.2.1               |    he1b5a44_1007          47 KB  conda-forge
    libgcc-ng-9.2.0            |       h24d8f2e_2         8.2 MB  conda-forge
    libgfortran-ng-7.3.0       |       hdf63c60_5         1.7 MB  conda-forge
    libgomp-9.2.0              |       h24d8f2e_2         816 KB  conda-forge
    libiconv-1.15              |    h516909a_1006         2.0 MB  conda-forge
    liblapack-3.8.0            |      16_openblas          10 KB  conda-forge
    libnetcdf-4.7.4            |nompi_h9f9fd6a_101         1.3 MB  conda-forge
    libopenblas-0.3.9          |       h5ec1e0e_0         7.8 MB  conda-forge
    libpng-1.6.37              |       hed695b0_1         308 KB  conda-forge
    libsodium-1.0.17           |       h516909a_0         330 KB  conda-forge
    libssh2-1.8.2              |       h22169c7_2         257 KB  conda-forge
    libstdcxx-ng-9.2.0         |       hdf63c60_2         4.5 MB  conda-forge
    libtiff-4.1.0              |       hc7e4089_6         668 KB  conda-forge
    libuuid-2.32.1             |    h14c3975_1000          26 KB  conda-forge
    libwebp-base-1.1.0         |       h516909a_3         845 KB  conda-forge
    libxcb-1.13                |    h14c3975_1002         396 KB  conda-forge
    libxml2-2.9.10             |       hee79883_0         1.3 MB  conda-forge
    llvm-openmp-10.0.0         |       hc9558a2_0         2.8 MB  conda-forge
    lz4-c-1.9.2                |       he1b5a44_0         223 KB  conda-forge
    markupsafe-1.1.1           |   py37h8f50634_1          26 KB  conda-forge
    matplotlib-base-3.2.1      |   py37h30547a4_0         7.1 MB  conda-forge
    mistune-0.8.4              |py37h8f50634_1001          53 KB  conda-forge
    msgpack-python-1.0.0       |   py37h99015e2_1          90 KB  conda-forge
    nbconvert-5.6.1            |   py37hc8dfbb8_1         487 KB  conda-forge
    ncurses-6.1                |    hf484d3e_1002         1.3 MB  conda-forge
    netcdf-fortran-4.5.2       |nompi_h45d7149_104         1.2 MB  conda-forge
    networkx-2.4               |             py_1         1.2 MB  conda-forge
    numpy-1.18.1               |   py37h8960a57_1         5.2 MB  conda-forge
    olefile-0.46               |             py_0          31 KB  conda-forge
    openforcefield-0.6.0       |           py37_1        29.7 MB  omnia
    openssl-1.1.1f             |       h516909a_0         2.1 MB  conda-forge
    pandas-1.0.3               |   py37h0da4684_0        11.1 MB  conda-forge
    pandoc-2.9.2               |                0        16.8 MB  conda-forge
    pandocfilters-1.4.2        |             py_1           9 KB  conda-forge
    parso-0.6.2                |             py_0          66 KB  conda-forge
    pcre-8.44                  |       he1b5a44_0         261 KB  conda-forge
    perl-5.26.2                |    h516909a_1006        15.4 MB  conda-forge
    pexpect-4.8.0              |   py37hc8dfbb8_1          79 KB  conda-forge
    pickleshare-0.7.5          |py37hc8dfbb8_1001          13 KB  conda-forge
    pillow-7.1.1               |   py37h718be6c_0         654 KB  conda-forge
    pip-20.0.2                 |             py_2         1.0 MB  conda-forge
    pixman-0.38.0              |    h516909a_1003         594 KB  conda-forge
    prompt-toolkit-3.0.5       |             py_0         232 KB  conda-forge
    pthread-stubs-0.4          |    h14c3975_1001           5 KB  conda-forge
    ptyprocess-0.6.0           |          py_1001          15 KB  conda-forge
    pycairo-1.19.1             |   py37h01af8b0_3          77 KB  conda-forge
    pycparser-2.20             |             py_0          89 KB  conda-forge
    pygments-2.6.1             |             py_0         683 KB  conda-forge
    pyopenssl-19.1.0           |             py_1          47 KB  conda-forge
    pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  conda-forge
    pyrsistent-0.16.0          |   py37h8f50634_0          89 KB  conda-forge
    pysocks-1.7.1              |   py37hc8dfbb8_1          27 KB  conda-forge
    python-3.7.6               |h8356626_5_cpython        52.9 MB  conda-forge
    pyyaml-5.3.1               |   py37h8f50634_0         185 KB  conda-forge
    pyzmq-19.0.0               |   py37hac76be4_1         503 KB  conda-forge
    rdkit-2020.03.1            |   py37hdd87690_1        24.7 MB  conda-forge
    readline-8.0               |       hf8c457e_0         441 KB  conda-forge
    requests-2.23.0            |     pyh8c360ce_2          47 KB  conda-forge
    scipy-1.4.1                |   py37ha3d9a3c_3        18.8 MB  conda-forge
    send2trash-1.5.0           |             py_0          12 KB  conda-forge
    setuptools-46.1.3          |   py37hc8dfbb8_0         634 KB  conda-forge
    six-1.14.0                 |             py_1          13 KB  conda-forge
    smirnoff99frosst-1.1.0     |           py37_1          72 KB  omnia
    sqlite-3.30.1              |       hcee41ef_0         2.0 MB  conda-forge
    terminado-0.8.3            |   py37hc8dfbb8_1          23 KB  conda-forge
    tk-8.6.10                  |       hed695b0_0         3.2 MB  conda-forge
    toml-0.10.0                |             py_0          16 KB  conda-forge
    tornado-6.0.4              |   py37h8f50634_1         639 KB  conda-forge
    traitlets-4.3.3            |   py37hc8dfbb8_1         133 KB  conda-forge
    urllib3-1.25.8             |   py37hc8dfbb8_1         160 KB  conda-forge
    wcwidth-0.1.9              |     pyh9f0ad1d_0          20 KB  conda-forge
    webencodings-0.5.1         |             py_1          12 KB  conda-forge
    wheel-0.34.2               |             py_1          24 KB  conda-forge
    xorg-kbproto-1.0.7         |    h14c3975_1002          26 KB  conda-forge
    xorg-libice-1.0.10         |       h516909a_0          57 KB  conda-forge
    xorg-libsm-1.2.3           |    h84519dc_1000          25 KB  conda-forge
    xorg-libx11-1.6.9          |       h516909a_0         918 KB  conda-forge
    xorg-libxau-1.0.9          |       h14c3975_0          13 KB  conda-forge
    xorg-libxdmcp-1.1.3        |       h516909a_0          18 KB  conda-forge
    xorg-libxext-1.3.4         |       h516909a_0          51 KB  conda-forge
    xorg-libxrender-0.9.10     |    h516909a_1002          31 KB  conda-forge
    xorg-libxt-1.2.0           |       h516909a_0         374 KB  conda-forge
    xorg-renderproto-0.11.1    |    h14c3975_1002           8 KB  conda-forge
    xorg-xextproto-7.3.0       |    h14c3975_1002          27 KB  conda-forge
    xorg-xproto-7.0.31         |    h14c3975_1007          72 KB  conda-forge
    xz-5.2.5                   |       h516909a_0         430 KB  conda-forge
    yaml-0.2.3                 |       h516909a_0          82 KB  conda-forge
    zeromq-4.3.2               |       he1b5a44_2         668 KB  conda-forge
    zipp-3.1.0                 |             py_0          10 KB  conda-forge
    zlib-1.2.11                |    h516909a_1006         105 KB  conda-forge
    zstd-1.4.4                 |       h6597ccf_3         991 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       375.8 MB

The following NEW packages will be INSTALLED:

It seems that the pkgs are correctly solved.
Do I need to continue to download the pkgs for your further diagnosis?
(It does not trouble much ...)

Kael-the-Mad on 13 Apr 2020

Never mind, The pkgs are being downloaded. I will test the case after the new environment is completed.
#
Though, it seems that the major difference here, is my ambertools pkg.
my ambertools is from the source of ambermd, with size of about 150M, much larger than that on the above list.

Kael-the-Mad on 13 Apr 2020

ambermd's ambertools might have a different build process than the one in conda-forge. It bundles several libraries instead of adding them as conda dependencies, for example. That might explain the file size difference.

jaimergp on 13 Apr 2020

CondaError: Downloaded bytes did not match Content-Length
  url: https://conda.anaconda.org/conda-forge/linux-64/python-3.7.6-h8356626_5_cpython.tar.bz2
  target_path: /home/kael/anaconda3/pkgs/python-3.7.6-h8356626_5_cpython.tar.bz2
  Content-Length: 55424091
  downloaded bytes: 24127919

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/linux-64/rdkit-2020.03.1-py37hdd87690_1.tar.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/omnia/linux-64/openforcefield-0.6.0-py37_1.tar.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.10-hed695b0_0.tar.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.


(base) [kael@ecs-s6-large-2-linux-20200412093116 ~]$ 
Socket error Event: 32 Error: 10053.
Connection closing...Socket close.

Connection closed by foreign host.

Kael-the-Mad on 14 Apr 2020

That's very odd, @Kael-the-Mad. I also had some weird behavior from some conda channels earlier today, but it seems to have cleared up now. Are you still getting that error?

j-wags on 14 Apr 2020

I've seen the solver try to "upgrade" to 0.0.4 before -- It's a much earlier version of the toolkit, so it had far fewer dependencies. Usually it means that dependencies from conda-forge and omnia can't be found, so the only OpenFF Toolkit version that can have its dependencies satisfied is 0.0.4.

j-wags on 14 Apr 2020

After that failure, I have tried conda install -c omnia openforcefield on a totally different CentOS server.
Yet, the output is even worse:

$ conda install -c omnia openforcefield
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: | 
Found conflicts! Looking for incompatible packages.                                                            failed                                                                                                             

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

Output in format: Requested package -> Available versions

It seems that the only successful try to install openforcefield into the 'base' env is to manually install the *v0.6.0 tar.gz locally.
Creating new environment seems to require too much downloading to the (commercial) cloud servers: once get stuck by several pkgs, the full process could be ruined somehow. (Or I should try my luck later ...)

Kael-the-Mad on 14 Apr 2020

Maybe the openforcefield pkg is being maintained. Even creating new environment $ conda create -n openforcefield openforcefield failed...

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - openforcefield

Current channels:

  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

The openforcefield project really makes the simulation involving small molecules much more convenient.
Hopefully this could be fixed soon!

Kael-the-Mad on 14 Apr 2020

In this last attempt you are missing the needed channels. Correct command if those channels are not part of your permanent configuration (~/.condarc) is:

conda create -n openforcefield -c conda-forge -c omnia openforcefield

jaimergp on 14 Apr 2020

Thanks for the reminder. You are right.
I will try to create a new env on a third server node one more time.
nohup conda create -n openforcefield -c conda-forge -c omnia -y openforcefield &
I will check it and report in time.

Kael-the-Mad on 14 Apr 2020

👍3

...
pandoc-2.9.2.1       | 18.7 MB   | ########## | 100% 

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.2
  latest version: 4.8.3

Please update conda by running

    $ conda update -n base -c defaults conda



CondaError: Downloaded bytes did not match Content-Length
  url: https://conda.anaconda.org/conda-forge/linux-64/rdkit-2020.03.1-py37hdd87690_1.tar.bz2
  target_path: /home/kael/anaconda3/pkgs/rdkit-2020.03.1-py37hdd87690_1.tar.bz2
  Content-Length: 25866956
  downloaded bytes: 20781501

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/omnia/linux-64/openforcefield-0.6.0-py37_1.tar.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

There is no new env called 'openforcefield'.
Is there a way to 'continue' the download, to only download the previously unavailable pkgs?
By simply running again the nohup conda create -n openforcefield -c conda-forge -c omnia -y openforcefield &, could conda 'remember' that it has downloaded almost all the pkgs, but a few exceptions?

Kael-the-Mad on 15 Apr 2020

could conda 'remember' that it has downloaded almost all the pkgs, but a few exceptions?

That has been my experience -- I have several packages automatically cached on my computer, so new installs only need to download a few others. And you're using an up-to-date version of conda (4.8) so I'd expect it to have that behavior for you as well.

Thanks so much for digging into this. If you're free to continue, I'd love to figure out if there's a way to make these installations work reliably. However my best guess is that the internet is really saturated right now, and you are far from the package server.

In case you're unable to get the OFF Toolkit installed on a computer where you need it, an alternative is that we provide stable offline installers (which include all dependencies) with each release. For example you can get a "miniconda"-style installer for our latest release in the Assets section of the 0.6.0 GitHub release.

j-wags on 15 Apr 2020

Inspired by your experience, I continued the conda create -n openforcefield -c conda-forge -c omnia openforcefield. As you expected, the installation has been interrupted by bad internet several times. But the trials got normal conda responses. Finally, the installation is finished (as shown below.)

Proceed ([y]/n)? y


Downloading and Extracting Packages
openforcefield-0.6.0 | 29.7 MB   | ################################################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate openforcefield
#
# To deactivate an active environment, use
#
#     $ conda deactivate

I will test the examples (with the *.xml replaced), and report later.
I think this has proved that at least the conda create -n env ... would work.

Besides, the commercial cloud servers are located in Beijing, China, and owned by Huawei and Tencent companies. Linux release is CentOS Linux release 7.6.1810 (Core). Downloaded Anaconda installer is 'Anaconda3-2020.02-Linux-x86_64.sh'.

plus
All I need to pay is a little patience for the internet, then I could use an open-source and free of charge tool. Thank you!

I am learning to pack the newly created environment, then transfer it to the other servers.
If you want to add some new tests, please leave a message here.

Kael-the-Mad on 15 Apr 2020

👍2

I'm very happy to see that this works. I'll close this issue for now, since it seems to have been due to internet connectivity, but please feel free to re-open it if you have additional questions.

I am learning to pack the newly created environment, then transfer it to the other servers.

If you are looking for an installation that you can easily transfer to other servers, you should consider using our single-file installers. They work like Miniconda (so they "just install" on basically any system), and once installed, you can add/update conda packages and environments. Full instructions for using these builds are here.

j-wags on 15 Apr 2020

Openff-toolkit: Conda install (@ 2020, Apr. 13) automatically install version 0.04 (the oldest version)

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packages in environment at /home/kael/anaconda3:

Name Version Build Channel

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