Installation#
The page has information for installing openfe, installing software
packages that integrate with openfe, and testing that your openfe
installation is working.
openfe currently only works on POSIX system (macOS and UNIX/Linux). It
is tested against Python 3.9, 3.10, and 3.11.
When you install openfe through any of the methods described below, you
will install both the core library and the command line interface (CLI).
If you already have a Mamba installation, you can install openfe with:
mamba create -c conda-forge -n openfe_env openfe=0.14.0 mamba activate openfe_env
Note that you must run the latter line in each shell session where you want to use openfe. OpenFE recommends the Mamba package manager for most users as it is orders of magnitude faster than the default Conda package manager. Mamba is a drop in replacement for Conda.
Installation with mambaforge (recommended)#
We recommend installing openfe with MambaForge because it provides easy
installation of other software that openfe needs, such as OpenMM and
AmberTools. We recommend mambaforge because it is faster than conda and
comes preconfigured to use conda-forge.
To install and configure mambaforge, you need to know your operating
system, your machine architecture (output of uname -m), and your shell
(in most cases, can be determined from echo $SHELL). Select
your operating system and architecture from the tool below, and run the
commands it suggests.
You should then close your current session and open a fresh login to ensure that everything is properly registered.
Next we will create an environment called openfe_env with the openfe package and all required dependencies:
mamba create -n openfe_env openfe=0.14.0
Now we need to activate our new environment
mamba activate openfe_env
Warning
Installing on Macs with Apple Silicon requires a creating an x86_64 environment, as one of our requirements is not yet available for Apple Silicon. Run the following modified commands
CONDA_SUBDIR=osx-64 mamba create -n openfe_env openfe=0.14.0 mamba activate openfe_env mamba env config vars set CONDA_SUBDIR=osx-64
To make sure everything is working, run the tests
openfe test --long
The test suite contains several hundred individual tests. This may take up to
an hour, and all tests should complete with status either passed,
skipped, or xfailed (expected fail). The very first time you run this, the
initial check that you can import openfe will take a while, because some
code is compiled the first time it is encountered. That compilation only
happens once per installation.
With that, you should be ready to use openfe!
Single file installer#
Single file installers are available for x86_64 Linux and MacOS.
They are attached to our releases on GitHub and can be downloaded with a browser or curl (or similar tool).
For example, the Linux installer can be downloaded with
$ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/latest/download/OpenFEforge-Linux-x86_64.sh
And the MacOS installer
$ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/latest/download/OpenFEforge-MacOSX-x86_64.sh
The single file installer contains all of the dependencies required for openfe and does not require internet access to use.
Both conda and mamba are also available in the environment created by the single file installer and can be used to install additional packages.
The installer can be installed in batch mode or interactively
$ chmod +x ./OpenFEforge-Linux-x86_64.sh # Make installer executable
$ ./OpenFEforge-Linux-x86_64.sh # Run the installer
Example installer output is shown below (click to expand “Installer Output”)
Installer Output
Welcome to OpenFEforge 0.7.4
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
MIT License
Copyright (c) 2022 OpenFreeEnergy
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Do you accept the license terms? [yes|no]
[no] >>> yes
Note
The install location will be different when you run the installer.
OpenFEforge will now be installed into this location:
/home/mmh/openfeforge
- Press ENTER to confirm the location
- Press CTRL-C to abort the installation
- Or specify a different location below
[/home/mmh/openfeforge] >>>
PREFIX=/home/mmh/openfeforge
Unpacking payload ...
Installing base environment...
Downloading and Extracting Packages
Downloading and Extracting Packages
Preparing transaction: done
Executing transaction: \ By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html
| Enabling notebook extension jupyter-js-widgets/extension...
- Validating: OK
done
installation finished.
Do you wish the installer to initialize OpenFEforge
by running conda init? [yes|no]
[no] >>> yes
no change /home/mmh/openfeforge/condabin/conda
no change /home/mmh/openfeforge/bin/conda
no change /home/mmh/openfeforge/bin/conda-env
no change /home/mmh/openfeforge/bin/activate
no change /home/mmh/openfeforge/bin/deactivate
no change /home/mmh/openfeforge/etc/profile.d/conda.sh
no change /home/mmh/openfeforge/etc/fish/conf.d/conda.fish
no change /home/mmh/openfeforge/shell/condabin/Conda.psm1
no change /home/mmh/openfeforge/shell/condabin/conda-hook.ps1
no change /home/mmh/openfeforge/lib/python3.9/site-packages/xontrib/conda.xsh
no change /home/mmh/openfeforge/etc/profile.d/conda.csh
modified /home/mmh/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
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/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
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╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.4.2) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
no change /home/mmh/openfeforge/condabin/conda
no change /home/mmh/openfeforge/bin/conda
no change /home/mmh/openfeforge/bin/conda-env
no change /home/mmh/openfeforge/bin/activate
no change /home/mmh/openfeforge/bin/deactivate
no change /home/mmh/openfeforge/etc/profile.d/conda.sh
no change /home/mmh/openfeforge/etc/fish/conf.d/conda.fish
no change /home/mmh/openfeforge/shell/condabin/Conda.psm1
no change /home/mmh/openfeforge/shell/condabin/conda-hook.ps1
no change /home/mmh/openfeforge/lib/python3.9/site-packages/xontrib/conda.xsh
no change /home/mmh/openfeforge/etc/profile.d/conda.csh
no change /home/mmh/.bashrc
No action taken.
Added mamba to /home/mmh/.bashrc
==> For changes to take effect, close and re-open your current shell. <==
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing OpenFEforge!
After the installer completes, close and reopen your shell.
To check if your path is setup correctly, run which python your output should look something like this
(base) $ which python
/home/mmh/openfeforge/bin/python
Note
Your path will be different, but the important part is openfeforge/bin/python
Now the CLI tool should work as well
(base) $ openfe --help
Usage: openfe [OPTIONS] COMMAND [ARGS]...
This is the command line tool to provide easy access to functionality from
the OpenFE Python library.
Options:
--version Show the version and exit.
--log PATH logging configuration file
-h, --help Show this message and exit.
Setup Commands:
atommapping Check the atom mapping of a given pair of ligands
plan-rhfe-network Plan a relative hydration free energy network, saved in a
dir with multiple JSON files
plan-rbfe-network Plan a relative binding free energy network, saved in a
dir with multiple JSON files.
Simulation Commands:
gather Gather DAG result jsons for network of RFE results into single TSV
file
quickrun Run a given transformation, saved as a JSON file
To make sure everything is working, run the tests
$ pytest --pyargs openfe openfecli
The test suite contains several hundred individual tests. This will take a few minutes, and all tests should complete with status either passed, skipped, or xfailed (expected fail).
With that, you should be ready to use openfe!
Containers#
We provide an official docker and Apptainer (formerly Singularity) image.
The docker image is tagged with the version of openfe on the image and can be pulled with
$ docker pull ghcr.io/openfreeenergy/openfe:latest
The Apptainer image is pre-built and can be pulled with
$ singularity pull oras://ghcr.io/openfreeenergy/openfe:latest-apptainer
Warning
For production use, we recommend using version tags to prevent disruptions in workflows e.g.
$ docker pull ghcr.io/openfreeenergy/openfe:0.14.0 $ singularity pull oras://ghcr.io/openfreeenergy/openfe:0.14.0-apptainer
We recommend testing the container to ensure that it can access a GPU (if desired). This can be done with the following command
$ singularity run --nv openfe_latest-apptainer.sif python -m openmm.testInstallation
OpenMM Version: 8.0
Git Revision: a7800059645f4471f4b91c21e742fe5aa4513cda
There are 3 Platforms available:
1 Reference - Successfully computed forces
2 CPU - Successfully computed forces
3 CUDA - Successfully computed forces
Median difference in forces between platforms:
Reference vs. CPU: 6.29328e-06
Reference vs. CUDA: 6.7337e-06
CPU vs. CUDA: 7.44698e-07
All differences are within tolerance.
The --nv flag is required for the Apptainer image to access the GPU on the host.
Your output may produce different values for the forces, but should list the CUDA platform if everything is working properly.
You can access the openfe CLI from the Singularity image with
$ singularity run --nv openfe_latest-apptainer.sif openfe --help
To make sure everything is working, run the tests
$ singularity run --nv openfe_latest-apptainer.sif pytest --pyargs openfe openfecli
The test suite contains several hundred individual tests. This will take a few minutes, and all tests should complete with status either passed, skipped, or xfailed (expected fail).
With that, you should be ready to use openfe!
Developer install#
If you’re going to be developing for openfe, you will want an
installation where your changes to the code are immediately reflected in the
functionality. This is called a “developer” or “editable” installation.
Getting a developer installation for openfe first installing the
requirements, and then creating the editable installation. We recommend
doing that with mamba using the following procedure:
First, clone the openfe repository, and switch into its root directory:
$ git clone https://github.com/OpenFreeEnergy/openfe.git
$ cd openfe
Next create a conda environment containing the requirements from the
specification in that directory:
$ mamba create -f environment.yml
Then activate the openfe environment with:
$ mamba activate openfe_env
Finally, create the editable installation:
$ python -m pip install --no-deps -e .
Note the . at the end of that command, which indicates the current
directory.
Optional dependencies#
Certain functionalities are only available if you also install other, optional packages.
perses tools: To use perses, you need to install perses and OpenEye, and you need a valid OpenEye license. To install both packages, use:
$ mamba install -c openeye perses openeye-toolkits
HPC Environments#
When using High Performance Computing resources, jobs are typically submitted to a queue from a “login node” and then run at a later time, often on different hardware and in a different software environment.
This can complicate installation as getting something working on the login node does not guarantee it will work in the job.
We recommend using Apptainer (formerly Singularity) when running openfe workflows in HPC environments.
This images provide a software environment that is isolated from the host which can make workflow execution easier to setup and more reproducible.
See our guide on containers for how to get started using Apptainer/Singularity.
mamba in HPC Environments#
We recommend using a container to install openfe in HPC environments.
Nonetheless, openfe can be installed via Conda Forge on these environments also.
Conda Forge distributes its own CUDA binaries for interfacing with the GPU, rather than use the host drivers.
conda, mamba and micromamba all use virtual packages to detect and specify which version of CUDA should be installed.
This is a common point of difference in hardware between the login and job nodes in an HPC environment.
For example, on a login node where there likely is not a GPU or a CUDA environment, mamba info may produce output that looks like this
$ mamba info
mamba version : 1.5.1
active environment : base
active env location : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0
shell level : 1
user config file : /home/henrym3/.condarc
populated config files : /lila/home/henrym3/.condarc
conda version : 23.7.4
conda-build version : not installed
python version : 3.11.5.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.17=0
__linux=3.10.0=0
__unix=0=0
base environment : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0 (writable)
conda av data dir : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0/pkgs
/home/henrym3/.conda/pkgs
envs directories : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0/envs
/home/henrym3/.conda/envs
platform : linux-64
user-agent : conda/23.7.4 requests/2.31.0 CPython/3.11.5 Linux/3.10.0-957.12.2.el7.x86_64 centos/7.6.1810 glibc/2.17
UID:GID : 1987:3008
netrc file : None
offline mode : False
Now if we run the same command on a HPC node that has a GPU
$ mamba info
mamba version : 1.5.1
active environment : base
active env location : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0
shell level : 1
user config file : /home/henrym3/.condarc
populated config files : /lila/home/henrym3/.condarc
conda version : 23.7.4
conda-build version : not installed
python version : 3.11.5.final.0
virtual packages : __archspec=1=x86_64
__cuda=11.7=0
__glibc=2.17=0
__linux=3.10.0=0
__unix=0=0
base environment : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0 (writable)
conda av data dir : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0/pkgs
/home/henrym3/.conda/pkgs
envs directories : /lila/home/henrym3/mamba/envs/QA-openfe-0.14.0/envs
/home/henrym3/.conda/envs
platform : linux-64
user-agent : conda/23.7.4 requests/2.31.0 CPython/3.11.5 Linux/3.10.0-1160.45.1.el7.x86_64 centos/7.9.2009 glibc/2.17
UID:GID : 1987:3008
netrc file : None
offline mode : False
We can see that there is a virtual package __cuda=11.7=0.
This means that if we run a mamba install command on a node with a GPU, the solver will install the correct version of the cudatoolkit.
However, if we ran the same command on the login node, the solver may install the wrong version of the cudatoolkit, or depending on how the Conda packages are setup, a CPU only version of the package.
We can control the virtual package with the environmental variable CONDA_OVERRIDE_CUDA.
In order to determine the correct cudatoolkit version, we recommend connecting to the node where the simulation will be executed and run nvidia-smi.
For example
$ nvidia-smi
Tue Jun 13 17:47:11 2023
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 515.43.04 Driver Version: 515.43.04 CUDA Version: 11.7 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|===============================+======================+======================|
| 0 NVIDIA A40 On | 00000000:65:00.0 Off | 0 |
| 0% 30C P8 32W / 300W | 0MiB / 46068MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| No running processes found |
+-----------------------------------------------------------------------------+
in this output of nvidia-smi we can see in the upper right of the output CUDA Version: 11.7 which means the installed driver will support a cudatoolkit version up to 11.7
So on the login node, we can run CONDA_OVERRIDE_CUDA=11.7 mamba info and see that the “correct” virtual CUDA is listed.
For example, to install a version of openfe which is compatible with cudatoolkit 11.7, run:
$ CONDA_OVERRIDE_CUDA=11.7 mamba create -n openfe_env openfe=0.14.0
Common Errors#
- openmm.OpenMMException: Error loading CUDA module: CUDA_ERROR_UNSUPPORTED_PTX_VERSION (222)
This error likely means that the CUDA version that
openmmwas built with is incompatible with the CUDA driver. Try re-making the environment while specifying the correct CUDA toolkit version for your hardware and driver. See mamba in HPC Environments for more details.