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amcadmus merged 2 commits into from
Jan 23, 2020
Merged

update pip installation method; remove useless troubleshooting #157

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1a81455
update pip installation method; remove useless troubleshooting
njzjz Jan 21, 2020
d3f7cde
add document for cpu-only tensorflow
njzjz Jan 23, 2020
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62 changes: 29 additions & 33 deletions README.md
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Expand Up @@ -111,18 +111,17 @@ Both CPU and GPU version offline package are avaiable in [the Releases page](htt

## Install the python interface
### Install the Tensorflow's python interface
First, check the python version and compiler version on your machine
First, check the python version on your machine
```bash
python --version; gcc --version
python --version
```
If your python version is 3.7.x, it is highly recommended that the GNU C/C++ compiler is higher than or equal to 5.0.

We follow the virtual environment approach to install the tensorflow's Python interface. The full instruction can be found on [the tensorflow's official website](https://www.tensorflow.org/install/pip). 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
pip install --upgrade pip
pip install --upgrade tensorflow==1.14.0
pip install --upgrade tensorflow==2.1.0
```
It is notice that everytime a new shell is started and one wants to use `DeePMD-kit`, the virtual environment should be activated by
```bash
Expand All @@ -136,31 +135,21 @@ If one has multiple python interpreters named like python3.x, it can be specifie
```bash
virtualenv -p python3.7 $tensorflow_venv
```
If one needs the GPU support of deepmd-kit, the GPU version of tensorflow should be installed by
```bash
pip install --upgrade tensorflow-gpu==1.14.0
If one does not need the GPU support of deepmd-kit and is concerned about package size, the CPU-only version of tensorflow should be installed by
```bash
pip install --upgrade tensorflow-cpu==2.1.0
```
To verify the installation, run
```bash
python -c "import tensorflow as tf; sess=tf.Session(); print(sess.run(tf.reduce_sum(tf.random_normal([1000, 1000]))))"
python -c "import tensorflow as tf;print(tf.reduce_sum(tf.random.normal([1000, 1000])))"
```
One should remember to activate the virtual environment every time he/she uses deepmd-kit.

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

Clone the DeePMD-kit source code
```bash
cd /some/workspace
git clone --recursive https://github.com/deepmodeling/deepmd-kit.git deepmd-kit -b devel
```
If one downloads the .zip file from the github, then the default folder of source code would be `deepmd-kit-master` rather than `deepmd-kit`. For convenience, you may want to record the location of source to a variable, saying `deepmd_source_dir` by
Execute
```bash
cd deepmd-kit
deepmd_source_dir=`pwd`
```
Then execute
```bash
pip install .
pip install deepmd-kit
```
To test the installation, one may execute
```bash
Expand Down Expand Up @@ -189,11 +178,30 @@ If one does not need to use DeePMD-kit with Lammps or I-Pi, then the python inte

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

It is highly recommended that one keeps the same C/C++ compiler as the python interface. 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 >= 4.9.
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 >= 4.9.

First the C++ interface of Tensorflow should be installed. It is noted that the version of Tensorflow should be in consistent with the python interface. We assume that you have followed our instruction and installed tensorflow python interface 1.14.0 with, then you may follow [the instruction for CPU](doc/install-tf.1.14.md) to install the corresponding C++ interface (CPU only). If one wants GPU supports, he/she should follow [the instruction for GPU](doc/install-tf.1.14-gpu.md) to install the C++ interface.

### Install the DeePMD-kit's C++ interface

Clone the DeePMD-kit source code
```bash
cd /some/workspace
git clone --recursive https://github.com/deepmodeling/deepmd-kit.git deepmd-kit
```

For convenience, you may want to record the location of source to a variable, saying `deepmd_source_dir` by
```bash
cd deepmd-kit
deepmd_source_dir=`pwd`
```

Now goto the source code directory of DeePMD-kit and make a build place.
```bash
cd $deepmd_source_dir/source
Expand Down Expand Up @@ -606,18 +614,6 @@ rm -r *
```
and redo the `cmake` process.

## Training: TensorFlow abi binary cannot be found when doing training
If you confront such kind of error:

```
$deepmd_root/lib/deepmd/libop_abi.so: undefined symbol:
_ZN10tensorflow8internal21CheckOpMessageBuilder9NewStringB5cxx11Ev
```

This may happen if you are using a gcc >= 5.0, and tensorflow was compiled with gcc < 5.0. You may set `-DOP_CXX_ABI=0` in the process of `cmake`.

Another possible reason might be the large gap between the python version of TensorFlow and the TensorFlow c++ interface.

## MD: cannot run LAMMPS after installing a new version of DeePMD-kit
This typically happens when you install a new version of DeePMD-kit and copy directly the generated `USER-DEEPMD` to a LAMMPS source code folder and re-install LAMMPS.

Expand Down