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wanghan-iapcm merged 1 commit into from
May 6, 2022
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doc: add information abotu supported versions of dependencies #1683

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28 changes: 16 additions & 12 deletions doc/install/install-from-source.md
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Expand Up @@ -22,7 +22,7 @@ First, check the python version on your machine
python --version
```

We follow the virtual environment approach to install TensorFlow's Python interface. The full instruction can be found on the official [TensorFlow website](https://www.tensorflow.org/install/pip). Now we assume that the Python interface will be installed to virtual environment directory `$tensorflow_venv`
We follow the virtual environment approach to install TensorFlow's Python interface. The full instruction can be found on the official [TensorFlow website](https://www.tensorflow.org/install/pip). TensorFlow 1.8 or later is supported. Now we assume that the Python interface will be installed to virtual environment directory `$tensorflow_venv`
```bash
virtualenv -p python3 $tensorflow_venv
source $tensorflow_venv/bin/activate
Expand Down Expand Up @@ -51,8 +51,18 @@ python -c "import tensorflow as tf;print(tf.reduce_sum(tf.random.normal([1000, 1
```
One should remember to activate the virtual environment every time he/she uses deepmd-kit.

One can also [build TensorFlow Python interface from source](https://www.tensorflow.org/install/source) for custom hardward optimization, such as CUDA, ROCM, or OneDNN support.

### Install the DeePMD-kit's python interface

Check the compiler version on your machine

```
gcc --version
```

The compiler gcc 4.8 or later is supported in the DeePMD-kit. Note that TensorFlow may have specific requirement of the compiler version. It is recommended to use the same compiler version as TensorFlow, which can be printed by `python -c "import tensorflow;print(tensorflow.version.COMPILER_VERSION)"`.

Execute
```bash
cd $deepmd_source_dir
Expand All @@ -64,7 +74,7 @@ One may set the following environment variables before executing `pip`:
| Environment variables | Allowed value | Default value | Usage |
| --------------------- | ---------------------- | ------------- | -------------------------- |
| DP_VARIANT | `cpu`, `cuda`, `rocm` | `cpu` | Build CPU variant or GPU variant with CUDA or ROCM support. |
| CUDA_TOOLKIT_ROOT_DIR | Path | Detected automatically | The path to the CUDA toolkit directory. |
| CUDA_TOOLKIT_ROOT_DIR | Path | Detected automatically | The path to the CUDA toolkit directory. CUDA 7.0 or later is supported. NVCC is required. |
| ROCM_ROOT | Path | Detected automatically | The path to the ROCM toolkit directory. |

To test the installation, one should firstly jump out of the source directory
Expand Down Expand Up @@ -140,13 +150,7 @@ If one does not need to use DeePMD-kit with Lammps or I-Pi, then the python inte

### Install the Tensorflow's C++ interface

Check the compiler version on your machine

```
gcc --version
```

The C++ interface of DeePMD-kit was tested with compiler gcc >= 4.8. It is noticed that the I-Pi support is only compiled with gcc >= 4.8.
The C++ interface of DeePMD-kit was tested with compiler gcc >= 4.8. It is noticed that the I-Pi support is only compiled with gcc >= 4.8. Note that TensorFlow may have specific requirement of the compiler version.

First the C++ interface of Tensorflow should be installed. It is noted that the version of Tensorflow should be consistent with the python interface. You may follow [the instruction](install-tf.2.8.md) to install the corresponding C++ interface.

Expand All @@ -171,11 +175,11 @@ One may add the following arguments to `cmake`:
| -DTENSORFLOW_ROOT=<value> | Path | - | The Path to TensorFlow's C++ interface. |
| -DCMAKE_INSTALL_PREFIX=<value> | Path | - | The Path where DeePMD-kit will be installed. |
| -DUSE_CUDA_TOOLKIT=<value> | `TRUE` or `FALSE` | `FALSE` | If `TRUE`, Build GPU support with CUDA toolkit. |
| -DCUDA_TOOLKIT_ROOT_DIR=<value> | Path | Detected automatically | The path to the CUDA toolkit directory. |
| -DCUDA_TOOLKIT_ROOT_DIR=<value> | Path | Detected automatically | The path to the CUDA toolkit directory. CUDA 7.0 or later is supported. NVCC is required. |
| -DUSE_ROCM_TOOLKIT=<value> | `TRUE` or `FALSE` | `FALSE` | If `TRUE`, Build GPU support with ROCM toolkit. |
| -DROCM_ROOT=<value> | Path | Detected automatically | The path to the ROCM toolkit directory. |
| -DLAMMPS_VERSION_NUMBER=<value> | Number | `20210929` | Only neccessary for LAMMPS built-in mode. The version number of LAMMPS (yyyymmdd). |
| -DLAMMPS_SOURCE_ROOT=<value> | Path | - | Only neccessary for LAMMPS plugin mode. The path to the LAMMPS source code (later than 8Apr2021). If not assigned, the plugin mode will not be enabled. |
| -DLAMMPS_VERSION_NUMBER=<value> | Number | `20210929` | Only neccessary for LAMMPS built-in mode. The version number of LAMMPS (yyyymmdd). LAMMPS 29Oct2020 (20201029) or later is supported. |
| -DLAMMPS_SOURCE_ROOT=<value> | Path | - | Only neccessary for LAMMPS plugin mode. The path to the [LAMMPS source code](install-lammps.md). LAMMPS 8Apr2021 or later is supported. If not assigned, the plugin mode will not be enabled. |

If the cmake has been executed successfully, then run the following make commands to build the package:
```bash
Expand Down
3 changes: 3 additions & 0 deletions doc/install/install-gromacs.md
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@@ -1,4 +1,7 @@
# Install GROMACS with DeepMD

Before following this section, [DeePMD-kit C++ interface](install-from-source.md) should have be installed.

## Patch source code of GROMACS
Download source code of a supported gromacs version (2020.2) from https://manual.gromacs.org/2020.2/download.html. Run the following command:
```bash
Expand Down
12 changes: 7 additions & 5 deletions doc/install/install-lammps.md
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Expand Up @@ -3,13 +3,15 @@
There are two ways to install LAMMPS: the built-in mode and the plugin mode. The built-in mode builds LAMMPS along with the DeePMD-kit and DeePMD-kit will be loaded automatically when running LAMMPS. The plugin mode builds LAMMPS and a plugin separately, so one needs to use `plugin load` command to load the DeePMD-kit's LAMMPS plugin library.

## Install LAMMPS's DeePMD-kit module (built-in mode)
Before following this section, [DeePMD-kit C++ interface](install-from-source.md) should have be installed.

DeePMD-kit provides a module for running MD simulation with LAMMPS. Now make the DeePMD-kit module for LAMMPS.

```bash
cd $deepmd_source_dir/source/build
make lammps
```
DeePMD-kit will generate a module called `USER-DEEPMD` in the `build` directory. If you need the low precision version, move `env_low.sh` to `env.sh` in the directory. Now download the LAMMPS code (`29Oct2020` or later), and uncompress it:
DeePMD-kit will generate a module called `USER-DEEPMD` in the `build` directory. If you need the low precision version, move `env_low.sh` to `env.sh` in the directory. Now download the LAMMPS code, and uncompress it. The LAMMPS version should be the same as what is specified as the CMAKE argument `LAMMPS_VERSION_NUMBER`.
```bash
cd /some/workspace
wget https://github.com/lammps/lammps/archive/stable_29Sep2021_update3.tar.gz
Expand All @@ -19,11 +21,11 @@ The source code of LAMMPS is stored in directory `lammps-stable_29Sep2021_update
```bash
cd lammps-stable_29Sep2021_update3/src/
cp -r $deepmd_source_dir/source/build/USER-DEEPMD .
```
Now build LAMMPS
```bash
make yes-kspace
make yes-user-deepmd
```
You can enable any other package you want. Now build LAMMPS
```bash
make mpi -j4
```

Expand All @@ -47,7 +49,7 @@ wget https://github.com/lammps/lammps/archive/stable_29Sep2021_update3.tar.gz
tar xf stable_29Sep2021_update3.tar.gz
```

The source code of LAMMPS is stored in directory `lammps-stable_29Sep2021_update3`. Now go into the LAMMPS directory and create a directory called `build`
The source code of LAMMPS is stored in directory `lammps-stable_29Sep2021_update3`. The directory of the source code should be specified as the CMAKE argument `LAMMPS_SOURCE_ROOT` during installation of the DeePMD-kit C++ interface. Now go into the LAMMPS directory and create a directory called `build`

```bash
mkdir -p lammps-stable_29Sep2021_update3/build/
Expand Down